From e2be23795d8d57bb697299ce3fbdf991b0bc3e86 Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Wed, 13 Sep 2023 17:04:18 -0400
Subject: [PATCH 01/24] Multitumor and Nested Dichotomous (#264)

* troubleshooting

* format

* trusted host all the things

* update documentation

* future flag change, rm background, testfix

* lint

* rm more background, testfix

* unused import

* testfix

rm used for testing

* docs

* review fixes

* formatting

* formatting

* to remove

* remove testing

* rm fake failing data

* mt breadcrumbs

* enable nested dichotomous

* run all permutations of lsc/ilc

* updates

* build basic excel/word reports

* ui stubs

* litter data & bootstrap

* enable nested dichotomous on frontend

* sr, ll, chi^2

* model params, misc values matched

* combined pvalue, -9999 -> ???

* excel exports

* update UI for multitumor degree settings

* MT excel exports

* sketch placeholders

* col headings, isSummary modal jank

* more plug n play, formatting

* rm t specific, reuse individual

* tweak incompatibility, chasing loose ends

* summary & parameter settings

* add !isSummary

* slightly less clonky?

* misc cleanup

* latest updates

* updates from review

* checkout `next`; tests will still fail

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 .github/workflows/main.yml                    |   8 +-
 bmds_server/analysis/executor.py              | 128 ++++++++-------
 bmds_server/analysis/models.py                | 102 ++++++++----
 bmds_server/analysis/reporting/excel.py       |  72 ++++++---
 bmds_server/analysis/schema.py                |  14 +-
 bmds_server/analysis/transforms.py            |  24 ++-
 bmds_server/analysis/utils.py                 |   2 +-
 bmds_server/analysis/validators/datasets.py   |   4 +-
 bmds_server/analysis/validators/models.py     |   4 +-
 bmds_server/analysis/validators/options.py    |  14 +-
 bmds_server/common/task_cache.py              |   1 +
 bmds_server/main/settings/testing.py          |   1 +
 .../IndividualModel/ModelDetailModal.js       |  35 ++--
 frontend/src/components/Logic/RuleRow.js      |   8 +-
 .../Main/AnalysisForm/AnalysisForm.js         |  17 +-
 .../DatasetModelOption.js                     |  10 +-
 .../DatasetModelOptionList.js                 |   7 +-
 .../Main/OptionsForm/OptionsReadOnly.js       |   4 +-
 frontend/src/components/Navigation.js         |  15 +-
 .../Output/Multitumor/AnalysisOfDeviance.js   |  57 +++++++
 .../Output/Multitumor/DatasetTable.js         |  80 ++++++++++
 .../src/components/Output/Multitumor/Doses.js |  42 +++++
 .../Output/Multitumor/GoodnessFit.js          |  98 ++++++++++++
 .../components/Output/Multitumor/InfoTable.js |  42 +++++
 .../components/Output/Multitumor/ModalBody.js |  69 ++++++++
 .../Output/Multitumor/ModelOptions.js         |  45 ++++++
 .../Output/Multitumor/ParameterSettings.js    |  44 +++++
 .../Output/Multitumor/ResultTable.js          | 103 ++++++++++++
 .../components/Output/Multitumor/Summary.js   |  67 ++++++++
 .../NestedDichotomous/BootstrapResults.js     |  12 +-
 .../Output/NestedDichotomous/BootstrapRuns.js |  28 +++-
 .../Output/NestedDichotomous/LitterData.js    |  26 +--
 .../Output/NestedDichotomous/ModalBody.js     |   4 +
 .../NestedDichotomous/ModelParameters.js      |  39 +++++
 .../Output/NestedDichotomous/ResultTable.js   |  16 +-
 .../NestedDichotomous/ScaledResidual.js       |  12 +-
 .../src/components/Output/OptionSetTable.js   |   9 ++
 frontend/src/components/Output/Output.js      |  54 ++++---
 frontend/src/constants/dataConstants.js       |  15 +-
 .../src/stores/DatasetModelOptionStore.js     |   5 +-
 frontend/src/stores/MainStore.js              |  14 +-
 frontend/src/stores/OutputStore.js            |  65 +++++++-
 manage.py                                     |   2 +-
 tests/analysis/test_models.py                 | 103 ++++++++++--
 tests/conftest.py                             | 150 ++++++++++++++++++
 tests/integration/test_integration.py         |   4 +-
 tests/test_env.py                             |  15 ++
 47 files changed, 1421 insertions(+), 269 deletions(-)
 create mode 100644 frontend/src/components/Output/Multitumor/AnalysisOfDeviance.js
 create mode 100644 frontend/src/components/Output/Multitumor/DatasetTable.js
 create mode 100644 frontend/src/components/Output/Multitumor/Doses.js
 create mode 100644 frontend/src/components/Output/Multitumor/GoodnessFit.js
 create mode 100644 frontend/src/components/Output/Multitumor/InfoTable.js
 create mode 100644 frontend/src/components/Output/Multitumor/ModalBody.js
 create mode 100644 frontend/src/components/Output/Multitumor/ModelOptions.js
 create mode 100644 frontend/src/components/Output/Multitumor/ParameterSettings.js
 create mode 100644 frontend/src/components/Output/Multitumor/ResultTable.js
 create mode 100644 frontend/src/components/Output/Multitumor/Summary.js
 create mode 100644 frontend/src/components/Output/NestedDichotomous/ModelParameters.js
 create mode 100644 tests/test_env.py

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0abe1c8f..2eb237e0 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -21,12 +21,12 @@ jobs:
     steps:
     - name: Checkout bmds-server
       uses: actions/checkout@v3
-    - name: Checkout bmds@main
+    - name: Checkout bmds@next
       uses: actions/checkout@v3
       with:
         repository: shapiromatron/bmds
         path: venv
-        ref: main
+        ref: next
         lfs: true
     - uses: actions/setup-python@v4
       with:
@@ -142,12 +142,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Checkout bmds@main
+    - name: Checkout bmds@next
       uses: actions/checkout@v3
       with:
         repository: shapiromatron/bmds
         path: venv
-        ref: main
+        ref: next
         lfs: true
     - uses: actions/setup-python@v4
       with:
diff --git a/bmds_server/analysis/executor.py b/bmds_server/analysis/executor.py
index 2de4df1d..d3b22a2a 100644
--- a/bmds_server/analysis/executor.py
+++ b/bmds_server/analysis/executor.py
@@ -3,9 +3,11 @@
 from typing import NamedTuple, Self
 
 import bmds
-import numpy as np
 from bmds.bmds3.constants import DistType
+from bmds.bmds3.models.multi_tumor import Multitumor, MultitumorBase
 from bmds.bmds3.sessions import BmdsSession
+from bmds.bmds3.types.nested_dichotomous import IntralitterCorrelation, LitterSpecificCovariate
+from bmds.constants import ModelClass
 
 from .schema import AnalysisSessionSchema
 from .transforms import (
@@ -31,7 +33,6 @@ def build_frequentist_session(dataset, inputs, options, dataset_options) -> Bmds
     bmds_version = inputs["bmds_version"]
     dataset_type = inputs["dataset_type"]
     recommendation_settings = inputs.get("recommender", None)
-
     session = bmds.BMDS.version(bmds_version)(
         dataset=dataset, recommendation_settings=recommendation_settings
     )
@@ -44,12 +45,7 @@ def build_frequentist_session(dataset, inputs, options, dataset_options) -> Bmds
             model_names = [model for model in model_names if model in lognormal_enabled]
 
         for model_name in model_names:
-            model_options = build_model_settings(
-                dataset_type,
-                prior_type,
-                options,
-                dataset_options,
-            )
+            model_options = build_model_settings(dataset_type, prior_type, options, dataset_options)
             if model_name in bmds.constants.VARIABLE_POLYNOMIAL:
                 min_degree = 2 if model_name in bmds.constants.M_Polynomial else 1
                 max_degree = (
@@ -62,6 +58,13 @@ def build_frequentist_session(dataset, inputs, options, dataset_options) -> Bmds
                     model_options = model_options.copy()
                     model_options.degree = degree
                     session.add_model(model_name, settings=model_options)
+            elif dataset_type == ModelClass.NESTED_DICHOTOMOUS:
+                # run all permutations of intralitter correlation and litter specific covariate
+                for ilc, lsc in itertools.product(IntralitterCorrelation, LitterSpecificCovariate):
+                    settings = model_options.copy()
+                    settings.intralitter_correlation = ilc
+                    settings.litter_specific_covariate = lsc
+                    session.add_model(model_name, settings=settings)
             else:
                 if model_name == bmds.constants.M_Linear:
                     # a linear model must have a degree of 1
@@ -111,7 +114,7 @@ class AnalysisSession(NamedTuple):
 
     All database state is decoupled from the execution engine, along with serialization and
     de-serialization methods.  Note that this is a custom BmdsSession implementation; the UI of
-    the bmds software allows you to effectively run multiple "indpendent" sessions at once;
+    the bmds software allows you to effectively run multiple "independent" sessions at once;
     for example, a frequentist model session with a bayesian model averaging session. This
     Session allows construction of these individual bmds sessions into a single analysis
     for presentation in the UI.
@@ -124,12 +127,6 @@ class AnalysisSession(NamedTuple):
 
     @classmethod
     def run(cls, inputs: dict, dataset_index: int, option_index: int) -> AnalysisSessionSchema:
-        # TODO - replace in BMDS 3.4
-        if inputs["dataset_type"] == bmds.constants.NESTED_DICHOTOMOUS:
-            return _mock_nested_dichotomous(inputs, dataset_index, option_index)
-        elif inputs["dataset_type"] == bmds.constants.MULTI_TUMOR:
-            return _mock_multitumor(inputs, dataset_index, option_index)
-
         session = cls.create(inputs, dataset_index, option_index)
         session.execute()
         return session.to_schema()
@@ -179,47 +176,64 @@ def to_dict(self) -> dict:
         return self.to_schema().dict()
 
 
-def _mock_results(inputs: dict, dataset_index: int, option_index: int) -> dict:
-    # TODO - replace in BMDS 3.4
-    models = []
-    for model_name in itertools.chain(inputs["models"]["frequentist_restricted"]):
-        doses = np.array(inputs["datasets"][dataset_index]["doses"])
-        median = np.percentile(doses, 50)
-        models.append(
-            {
-                "name": model_name,
-                "results": {
-                    "bmd": median,
-                    "bmdl": 0.9 * median,
-                    "bmdu": 1.1 * median,
-                    "plotting": {"dr_x": [0, 10, 20], "dr_y": [0, 0.5, 1]},
-                },
-                "settings": {},
-                "model_class": {},
-            }
+class MultiTumorSession(NamedTuple):
+    """
+    This is the execution engine for running Multitumor modeling in BMDS.
+    """
+
+    option_index: int
+    session: MultitumorBase | None
+
+    @classmethod
+    def run(cls, inputs: dict, option_index: int) -> AnalysisSessionSchema:
+        session = cls.create(inputs, option_index)
+        session.execute()
+        return session.to_schema()
+
+    @classmethod
+    def create(cls, inputs: dict, option_index: int) -> Self:
+        datasets = [
+            build_dataset(ds)
+            for i, ds in enumerate(inputs["datasets"])
+            if inputs["dataset_options"][i]["enabled"] is True
+        ]
+        degrees = [
+            option["degree"] for option in inputs["dataset_options"] if option["enabled"] is True
+        ]
+        dataset_type = inputs["dataset_type"]
+        options = inputs["options"][option_index]
+        model_settings = build_model_settings(
+            dataset_type, PriorEnum.frequentist_restricted, options, {}
         )
 
-    return {
-        "metadata": {"dataset_index": dataset_index, "option_index": option_index},
-        "bayesian": None,
-        "frequentist": {
-            "models": models,
-            "dataset": inputs["datasets"][dataset_index],
-            "version": {},
-            "selected": {"notes": "", "model_index": None},
-            "recommender": None,
-            "model_average": None,
-        },
-    }
-
-
-def _mock_nested_dichotomous(inputs: dict, dataset_index: int, option_index: int) -> dict:
-    # TODO - replace in BMDS 3.4
-    return _mock_results(inputs, dataset_index, option_index)
-
-
-def _mock_multitumor(inputs: dict, dataset_index: int, option_index: int) -> dict:
-    # TODO - replace in BMDS 3.4
-    results = _mock_results(inputs, dataset_index, option_index)
-    results["frequentist"]["combined"] = deepcopy(results["frequentist"]["models"][0]["results"])
-    return results
+        bmds_version = inputs["bmds_version"]
+        Multitumor = bmds.BMDS.multitumor(bmds_version)
+        session = Multitumor(datasets, degrees=degrees, model_settings=model_settings)
+        return cls(option_index=option_index, session=session)
+
+    def execute(self):
+        self.session.execute()
+
+    @classmethod
+    def deserialize(cls, data: dict) -> Self:
+        obj = AnalysisSessionSchema.parse_obj(data)
+        return cls(
+            option_index=obj.option_index,
+            session=Multitumor.from_serialized(obj.frequentist),
+        )
+
+    def to_schema(self) -> AnalysisSessionSchema:
+        return AnalysisSessionSchema(
+            dataset_index=-1, option_index=self.option_index, frequentist=self.session.to_dict()
+        )
+
+    def to_dict(self) -> dict:
+        return self.to_schema().dict()
+
+
+Session = AnalysisSession | MultiTumorSession
+
+
+def deserialize(model_class: ModelClass, data: dict) -> Session:
+    Runner = MultiTumorSession if model_class is ModelClass.MULTI_TUMOR else AnalysisSession
+    return Runner.deserialize(data)
diff --git a/bmds_server/analysis/models.py b/bmds_server/analysis/models.py
index 72ec9d63..bbc93624 100644
--- a/bmds_server/analysis/models.py
+++ b/bmds_server/analysis/models.py
@@ -8,10 +8,10 @@
 import bmds
 import pandas as pd
 import reversion
-from bmds.bmds3.batch import BmdsSessionBatch
+from bmds.bmds3.batch import BatchBase, BmdsSessionBatch, MultitumorBatch
 from bmds.bmds3.recommender.recommender import RecommenderSettings
 from bmds.bmds3.types.sessions import VersionSchema
-from bmds.constants import Dtype
+from bmds.constants import ModelClass
 from django.conf import settings
 from django.core.cache import cache
 from django.core.exceptions import ValidationError
@@ -21,9 +21,10 @@
 from django.utils.timezone import now
 
 from ..common.utils import random_string
-from . import executor, tasks, validators
+from . import tasks, validators
+from .executor import AnalysisSession, MultiTumorSession, Session, deserialize
+from .reporting import excel
 from .reporting.cache import DocxReportCache, ExcelReportCache
-from .reporting.excel import dataset_df, params_df, summary_df
 from .schema import AnalysisOutput, AnalysisSessionSchema
 
 logger = logging.getLogger(__name__)
@@ -139,23 +140,31 @@ def maybe_hanging(cls, queryset):
         """
         return queryset.filter(started__lt=now() - timedelta(hours=1), ended__isnull=True)
 
-    def get_session(self, index: int) -> executor.AnalysisSession:
+    @property
+    def model_class(self) -> ModelClass:
+        return ModelClass(self.inputs["dataset_type"])
+
+    def get_session(self, index: int) -> Session:
         if not self.is_finished or self.has_errors:
             raise ValueError("Session cannot be returned")
-        return executor.AnalysisSession.deserialize(deepcopy(self.outputs["outputs"][index]))
+        return deserialize(self.model_class, deepcopy(self.outputs["outputs"][index]))
 
-    def get_sessions(self) -> list[executor.AnalysisSession]:
+    def get_sessions(self) -> list[Session]:
         if not self.is_finished or self.has_errors:
             raise ValueError("Session cannot be returned")
         return [
-            executor.AnalysisSession.deserialize(output)
-            for output in deepcopy(self.outputs["outputs"])
+            deserialize(self.model_class, output) for output in deepcopy(self.outputs["outputs"])
         ]
 
-    def to_batch(self) -> BmdsSessionBatch:
-        # convert list[executor.AnalysisSession] to list[bmds.BmdsSession]
+    def to_batch(self) -> BatchBase:
+        # convert list[AnalysisSession] to list[bmds.BmdsSession]
         items = []
-        for session in self.get_sessions():
+        sessions = self.get_sessions()
+
+        if self.model_class == ModelClass.MULTI_TUMOR:
+            return MultitumorBatch(session.session for session in sessions)
+
+        for session in sessions:
             if session.frequentist:
                 items.append(session.frequentist)
             if session.bayesian:
@@ -171,10 +180,20 @@ def to_df(self) -> dict[str, pd.DataFrame]:
                     name="Status",
                 ).to_frame(),
             }
+
+        sessions = self.get_sessions()
+
+        if self.model_class == ModelClass.MULTI_TUMOR:
+            return {
+                "summary": excel.multitumor_summary_df(sessions),
+                "datasets": excel.multitumor_dataset_df(sessions),
+                "parameters": excel.multitumor_params_df(sessions),
+            }
+
         return {
-            "summary": summary_df(self),
-            "datasets": dataset_df(self),
-            "parameters": params_df(self),
+            "summary": excel.summary_df(sessions),
+            "datasets": excel.dataset_df(sessions),
+            "parameters": excel.params_df(sessions),
         }
 
     def to_excel(self) -> BytesIO:
@@ -213,13 +232,23 @@ def try_run_session(
         self, inputs: dict, dataset_index: int, option_index: int
     ) -> AnalysisSessionSchema:
         try:
-            return executor.AnalysisSession.run(inputs, dataset_index, option_index)
+            return AnalysisSession.run(inputs, dataset_index, option_index)
         except Exception:
-            exception = AnalysisSessionSchema(
+            response = AnalysisSessionSchema(
                 dataset_index=dataset_index, option_index=option_index, error=traceback.format_exc()
             )
-            logger.error(f"{self.id}: {exception}")
-            return exception
+            logger.error(f"{self.id}: {response}")
+            return response
+
+    def try_run_multitumor(self, inputs: dict, option_index: int) -> AnalysisSessionSchema:
+        try:
+            return MultiTumorSession.run(inputs, option_index)
+        except Exception:
+            response = AnalysisSessionSchema(
+                dataset_index=-1, option_index=option_index, error=traceback.format_exc()
+            )
+            logger.error(f"{self.id}: {response}")
+            return response
 
     def start_execute(self):
         # update model to indicate execution scheduled
@@ -230,10 +259,7 @@ def start_execute(self):
         # add to analysis queue...
         tasks.try_execute.delay(str(self.id))
 
-    def execute(self):
-        # update start time to actual time started
-        self.started = now()
-
+    def _execute_session(self) -> list[AnalysisSessionSchema]:
         # build combinations based on enabled datasets
         combinations = []
         for dataset_index in range(len(self.inputs["datasets"])):
@@ -241,11 +267,28 @@ def execute(self):
                 if self.inputs["dataset_options"][dataset_index]["enabled"]:
                     combinations.append((dataset_index, option_index))
 
-        outputs: list[AnalysisSessionSchema] = [
+        return [
             self.try_run_session(self.inputs, dataset_index, option_index)
             for dataset_index, option_index in combinations
         ]
 
+    def _execute_multitumor(self) -> list[AnalysisSessionSchema]:
+        n_options = len(self.inputs["options"])
+        return [
+            self.try_run_multitumor(self.inputs, option_index) for option_index in range(n_options)
+        ]
+
+    def _execute(self) -> list[AnalysisSessionSchema]:
+        is_multitumor = self.inputs.get("dataset_type") == bmds.constants.ModelClass.MULTI_TUMOR
+        if is_multitumor:
+            return self._execute_multitumor()
+        return self._execute_session()
+
+    def execute(self):
+        # update start time to actual time started
+        self.started = now()
+        outputs = self._execute()
+        # get bmds version
         bmds_python_version = None
         for output in outputs:
             if output.frequentist is not None:
@@ -254,15 +297,14 @@ def execute(self):
             if output.bayesian is not None:
                 bmds_python_version = output.bayesian["version"]
                 break
-
-        obj = AnalysisOutput(
+        # get prepare complete output object
+        analysis_output = AnalysisOutput(
             analysis_id=str(self.id),
-            analysis_schema_version="1.0",
             bmds_server_version=settings.COMMIT.sha,
             bmds_python_version=bmds_python_version,
             outputs=[output.dict() for output in outputs],
         )
-        self.outputs = obj.dict()
+        self.outputs = analysis_output.dict()
         self.errors = [output.error for output in outputs if output.error]
         self.ended = now()
         self.deletion_date = get_deletion_date()
@@ -286,8 +328,8 @@ def handle_execution_error(self, err):
 
     def default_input(self) -> dict:
         return {
-            "bmds_version": bmds.constants.BMDS330,
-            "dataset_type": Dtype.DICHOTOMOUS,
+            "bmds_version": bmds.constants.BMDS330,  # TODO - change?
+            "dataset_type": ModelClass.DICHOTOMOUS,
             "datasets": [],
             "models": {},
             "dataset_options": [],
diff --git a/bmds_server/analysis/reporting/excel.py b/bmds_server/analysis/reporting/excel.py
index 5e0f7b96..cf2f893b 100644
--- a/bmds_server/analysis/reporting/excel.py
+++ b/bmds_server/analysis/reporting/excel.py
@@ -1,12 +1,12 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any
+from typing import Any
 
 import pandas as pd
 from bmds.bmds3.sessions import BmdsSession
+from bmds.constants import Dtype
 
-if TYPE_CHECKING:
-    from ..models import Analysis
+from ..executor import AnalysisSession, MultiTumorSession
 
 
 def add_session(
@@ -47,11 +47,11 @@ def add_session(
         models.append(d)
 
 
-def summary_df(analysis: Analysis) -> pd.DataFrame:
+def summary_df(sessions: list[AnalysisSession]) -> pd.DataFrame:
     dataset_data: dict[int, dict] = {}
     model_data = []
 
-    for session in analysis.get_sessions():
+    for session in sessions:
         if session.dataset_index not in dataset_data:
             dataset = session.frequentist.dataset if session.frequentist else session.bayesian
             d = dict(dataset_index=session.dataset_index)
@@ -81,23 +81,35 @@ def summary_df(analysis: Analysis) -> pd.DataFrame:
     return df3
 
 
-def params_df(analysis: Analysis) -> pd.DataFrame:
+def params_df(sessions: list[AnalysisSession]) -> pd.DataFrame:
     data = []
-    for session in analysis.get_sessions():
+    for session in sessions:
         if session.frequentist:
             for model_index, model in enumerate(session.frequentist.models):
                 if model.has_results:
-                    data.extend(
-                        model.results.parameters.rows(
-                            extras=dict(
-                                dataset_index=session.dataset_index,
-                                option_index=session.option_index,
-                                analysis_type="frequentist",
-                                model_index=model_index,
-                                model_name=model.name(),
+                    if session.frequentist.dataset.dtype == Dtype.NESTED_DICHOTOMOUS:
+                        data.extend(
+                            model.results.parameter_rows(
+                                extras=dict(
+                                    dataset_index=session.dataset_index,
+                                    option_index=session.option_index,
+                                    model_index=model_index,
+                                    model_name=model.name(),
+                                )
+                            )
+                        )
+                    else:
+                        data.extend(
+                            model.results.parameters.rows(
+                                extras=dict(
+                                    dataset_index=session.dataset_index,
+                                    option_index=session.option_index,
+                                    analysis_type="frequentist",
+                                    model_index=model_index,
+                                    model_name=model.name(),
+                                )
                             )
                         )
-                    )
 
         if session.bayesian:
             for model_index, model in enumerate(session.bayesian.models):
@@ -116,12 +128,36 @@ def params_df(analysis: Analysis) -> pd.DataFrame:
     return pd.DataFrame(data=data)
 
 
-def dataset_df(analysis: Analysis) -> pd.DataFrame:
+def dataset_df(sessions: list[AnalysisSession]) -> pd.DataFrame:
     data: list[dict] = []
     datasets: set = set()
-    for session in analysis.get_sessions():
+    for session in sessions:
         if session.dataset_index not in datasets:
             dataset = session.frequentist.dataset if session.frequentist else session.bayesian
             datasets.add(session.dataset_index)
             data.extend(dataset.rows(extras=dict(dataset_index=session.dataset_index)))
     return pd.DataFrame(data=data)
+
+
+def multitumor_summary_df(sessions: list[MultiTumorSession]) -> pd.DataFrame:
+    return pd.concat(
+        [
+            session.session.to_df(extras=dict(option_index=session.option_index))
+            for session in sessions
+        ]
+    )
+
+
+def multitumor_params_df(sessions: list[MultiTumorSession]) -> pd.DataFrame:
+    return pd.concat(
+        [
+            session.session.params_df(extras=dict(option_index=session.option_index))
+            for session in sessions
+        ]
+    )
+
+
+def multitumor_dataset_df(sessions: list[MultiTumorSession]) -> pd.DataFrame:
+    # if users run multiple option-sets, only print datasets first time
+    first = sessions[0].session
+    return first.datasets_df()
diff --git a/bmds_server/analysis/schema.py b/bmds_server/analysis/schema.py
index 4327770d..e50079b3 100644
--- a/bmds_server/analysis/schema.py
+++ b/bmds_server/analysis/schema.py
@@ -4,7 +4,7 @@
 import pandas as pd
 from bmds.bmds3.types.sessions import VersionSchema
 from bmds.datasets.transforms.polyk import calculate
-from pydantic import BaseModel, confloat, validator
+from pydantic import BaseModel, Field, validator
 from pydantic.schema import schema as pyschema
 from rest_framework.schemas.openapi import SchemaGenerator
 
@@ -23,14 +23,14 @@ class WrappedAnalysisSelectedSchema(BaseModel):
 class AnalysisSessionSchema(BaseModel):
     dataset_index: int
     option_index: int
-    frequentist: dict | None
-    bayesian: dict | None
-    error: str | None
+    frequentist: dict | None = None
+    bayesian: dict | None = None
+    error: str | None = None
 
 
 class AnalysisOutput(BaseModel):
     analysis_id: str
-    analysis_schema_version: str = "1.0"
+    analysis_schema_version: str = "1.1"
     bmds_server_version: str
     bmds_python_version: VersionSchema | None
     outputs: list[AnalysisSessionSchema]
@@ -39,8 +39,8 @@ class AnalysisOutput(BaseModel):
 class PolyKInput(BaseModel):
     dataset: str
     dose_units: str
-    power: confloat(ge=0, le=5) = 3
-    duration: confloat(ge=0, le=10000) | None = None
+    power: float = Field(default=3, ge=0, le=5)
+    duration: float | None = Field(default=None, gt=0, le=10000)
 
     @validator("dataset")
     def check_dataset(cls, value):
diff --git a/bmds_server/analysis/transforms.py b/bmds_server/analysis/transforms.py
index ccd0d351..b016238a 100644
--- a/bmds_server/analysis/transforms.py
+++ b/bmds_server/analysis/transforms.py
@@ -34,12 +34,12 @@ def build_model_settings(
     prior_class: str,
     options: dict,
     dataset_options: dict,
-) -> DichotomousModelSettings | ContinuousModelSettings:
+) -> DichotomousModelSettings | ContinuousModelSettings | NestedDichotomousModelSettings:
     prior_class = bmd3_prior_map[prior_class]
     if dataset_type in bmds.constants.DICHOTOMOUS_DTYPES:
         return DichotomousModelSettings(
             bmr=options["bmr_value"],
-            alpha=1.0 - options["confidence_level"],
+            alpha=round(1.0 - options["confidence_level"], 3),
             bmr_type=options["bmr_type"],
             degree=dataset_options["degree"],
             priors=prior_class,
@@ -47,7 +47,7 @@ def build_model_settings(
     elif dataset_type in bmds.constants.CONTINUOUS_DTYPES:
         return ContinuousModelSettings(
             bmr=options["bmr_value"],
-            alpha=1.0 - options["confidence_level"],
+            alpha=round(1.0 - options["confidence_level"], 3),
             tailProb=options["tail_probability"],
             bmr_type=options["bmr_type"],
             disttype=options["dist_type"],
@@ -56,14 +56,24 @@ def build_model_settings(
             priors=prior_class,
         )
     elif dataset_type == bmds.constants.NESTED_DICHOTOMOUS:
+        is_restricted = prior_class == PriorClass.frequentist_restricted
         return NestedDichotomousModelSettings(
-            bmr=options["bmr_value"],
-            alpha=1.0 - options["confidence_level"],
-            bmr_type=options["bmr_type"],
+            bmr_type=options["bmr_value"],
+            bmr=options["bmr_type"],
+            alpha=round(1.0 - options["confidence_level"], 3),
             litter_specific_covariate=options["litter_specific_covariate"],
+            restricted=is_restricted,
             bootstrap_iterations=options["bootstrap_iterations"],
             bootstrap_seed=options["bootstrap_seed"],
         )
+    elif dataset_type == bmds.constants.MULTI_TUMOR:
+        return DichotomousModelSettings(
+            bmr_type=options["bmr_type"],
+            bmr=options["bmr_value"],
+            alpha=round(1.0 - options["confidence_level"], 3),
+            degree=2,
+            priors=PriorClass.frequentist_restricted,
+        )
     else:
         raise ValueError(f"Unknown dataset_type: {dataset_type}")
 
@@ -96,7 +106,7 @@ def remap_bayesian_exponential(models: list[dict]) -> list[dict]:
     for i, model in enumerate(models):
         if model["model"] == bmds.constants.M_Exponential:
             models = deepcopy(models)
-            weight = model["prior_weight"] / 2  # TODO - replace in BMDS 3.4
+            weight = model["prior_weight"] / 2  # TODO - replace in BMDS 23.3
             models[i : i + 1] = (
                 dict(model=bmds.constants.M_ExponentialM3, prior_weight=weight),
                 dict(model=bmds.constants.M_ExponentialM5, prior_weight=weight),
diff --git a/bmds_server/analysis/utils.py b/bmds_server/analysis/utils.py
index 427129fa..89b63d6b 100644
--- a/bmds_server/analysis/utils.py
+++ b/bmds_server/analysis/utils.py
@@ -15,7 +15,7 @@ def get_citation() -> str:
     try:
         bmds_version = get_latest_dll_version()
     except FileNotFoundError:
-        bmds_version = "<ADD>"  # TODO: remove try/catch when DLL released
+        bmds_version = "<ADD>"  # TODO: remove in BMDS 23.3
     uri = settings.WEBSITE_URI
     return dedent(
         f"""\
diff --git a/bmds_server/analysis/validators/datasets.py b/bmds_server/analysis/validators/datasets.py
index ad1b79cc..16007b9d 100644
--- a/bmds_server/analysis/validators/datasets.py
+++ b/bmds_server/analysis/validators/datasets.py
@@ -99,8 +99,8 @@ class NestedDichotomousDataset(DatasetValidator):
 
 
 class MultiTumorDatasets(DatasetValidator):
-    dataset_options: conlist(DichotomousModelOptions, min_items=2, max_items=10)
-    datasets: conlist(DichotomousDatasetSchema, min_items=2, max_items=10)
+    dataset_options: conlist(DichotomousModelOptions, min_items=1, max_items=10)
+    datasets: conlist(DichotomousDatasetSchema, min_items=1, max_items=10)
 
 
 def validate_datasets(dataset_type: str, datasets: Any, datasetOptions: Any):
diff --git a/bmds_server/analysis/validators/models.py b/bmds_server/analysis/validators/models.py
index 6c136684..ac6129ca 100644
--- a/bmds_server/analysis/validators/models.py
+++ b/bmds_server/analysis/validators/models.py
@@ -3,7 +3,7 @@
 import bmds
 import numpy as np
 from django.core.exceptions import ValidationError
-from pydantic import BaseModel, confloat, root_validator, validator
+from pydantic import BaseModel, Field, root_validator, validator
 
 from ...common.validation import pydantic_validate
 
@@ -42,7 +42,7 @@ class ModelTypeSchema(BaseModel):
 
 class BayesianModelSchema(BaseModel):
     model: str
-    prior_weight: confloat(ge=0, le=1)
+    prior_weight: float = Field(ge=0, le=1)
 
 
 class ModelListSchema(BaseModel):
diff --git a/bmds_server/analysis/validators/options.py b/bmds_server/analysis/validators/options.py
index ae43d5cd..a4b4ae0c 100644
--- a/bmds_server/analysis/validators/options.py
+++ b/bmds_server/analysis/validators/options.py
@@ -4,9 +4,9 @@
 from bmds.bmds3.constants import DistType
 from bmds.bmds3.types.continuous import ContinuousRiskType
 from bmds.bmds3.types.dichotomous import DichotomousRiskType
-from bmds.bmds3.types.nested_dichotomous import NestedDichotomousLSCType
+from bmds.bmds3.types.nested_dichotomous import LitterSpecificCovariate
 from django.core.exceptions import ValidationError
-from pydantic import BaseModel, confloat, conlist
+from pydantic import BaseModel, Field, conlist
 
 from ...common.validation import pydantic_validate
 
@@ -14,22 +14,22 @@
 class DichotomousOption(BaseModel):
     bmr_type: DichotomousRiskType
     bmr_value: float
-    confidence_level: confloat(ge=0.5, le=1)
+    confidence_level: float = Field(gt=0.5, lt=1)
 
 
 class ContinuousOption(BaseModel):
     bmr_type: ContinuousRiskType
     bmr_value: float
-    tail_probability: confloat(ge=0, le=1)
-    confidence_level: confloat(ge=0.5, le=1)
+    tail_probability: float = Field(gt=0, lt=1)
+    confidence_level: float = Field(gt=0.5, lt=1)
     dist_type: DistType
 
 
 class NestedDichotomousOption(BaseModel):
     bmr_type: DichotomousRiskType
     bmr_value: float
-    confidence_level: confloat(ge=0.5, le=1)
-    litter_specific_covariate: NestedDichotomousLSCType
+    confidence_level: float = Field(gt=0.5, lt=1)
+    litter_specific_covariate: LitterSpecificCovariate
     bootstrap_iterations: int
     bootstrap_seed: int
 
diff --git a/bmds_server/common/task_cache.py b/bmds_server/common/task_cache.py
index 441207d4..b33b4c63 100644
--- a/bmds_server/common/task_cache.py
+++ b/bmds_server/common/task_cache.py
@@ -18,6 +18,7 @@ class ReportResponse(BaseModel):
     message: str | None
 
 
+# TODO - remove this stuff; it doesn't work with our current workflow
 class ReportCache(abc.ABC):
     """
     A cache designed for long-running report tasks.  The cache is designed for polling requests;
diff --git a/bmds_server/main/settings/testing.py b/bmds_server/main/settings/testing.py
index 3cb61f86..7d3ba6b1 100644
--- a/bmds_server/main/settings/testing.py
+++ b/bmds_server/main/settings/testing.py
@@ -15,3 +15,4 @@
 PASSWORD_HASHERS = ("django.contrib.auth.hashers.MD5PasswordHasher",)
 
 AUTH_PROVIDERS = {AuthProvider.django, AuthProvider.external}
+ALWAYS_SHOW_FUTURE = False
diff --git a/frontend/src/components/IndividualModel/ModelDetailModal.js b/frontend/src/components/IndividualModel/ModelDetailModal.js
index f478d77d..529404d9 100644
--- a/frontend/src/components/IndividualModel/ModelDetailModal.js
+++ b/frontend/src/components/IndividualModel/ModelDetailModal.js
@@ -4,10 +4,10 @@ import React, {Component} from "react";
 import {Col, Modal, Row} from "react-bootstrap";
 
 import * as dc from "@/constants/dataConstants";
-import {MODEL_NESTED_DICHOTOMOUS} from "@/constants/mainConstants";
 
 import Button from "../common/Button";
 import DoseResponsePlot from "../common/DoseResponsePlot";
+import MultitumorModalBody from "../Output/Multitumor/ModalBody";
 import NestedDichotomousModalBody from "../Output/NestedDichotomous/ModalBody";
 import CDFPlot from "./CDFPlot";
 import CDFTable from "./CDFTable";
@@ -148,22 +148,37 @@ ModelAverageBody.propTypes = {
 @inject("outputStore")
 @observer
 class ModelDetailModal extends Component {
+    getTitle() {
+        const {outputStore} = this.props,
+            model = outputStore.modalModel;
+        if (outputStore.isMultiTumor) {
+            return outputStore.drModelModalIsMA ? "MS Combo" : "TODO";
+        } else {
+            return outputStore.drModelModalIsMA ? "Model Average" : model.name;
+        }
+    }
+    getBody() {
+        const {outputStore} = this.props;
+        if (outputStore.isMultiTumor) {
+            return MultitumorModalBody;
+        } else if (outputStore.drModelModalIsMA) {
+            return ModelAverageBody;
+        } else if (outputStore.isNestedDichotomous) {
+            return NestedDichotomousModalBody;
+        } else {
+            return ModelBody;
+        }
+    }
     render() {
         const {outputStore} = this.props,
-            model = outputStore.modalModel,
-            isMA = outputStore.drModelModalIsMA;
+            model = outputStore.modalModel;
 
         if (!model) {
             return null;
         }
 
-        const name = isMA ? "Model Average" : model.name,
-            modelType = outputStore.getModelType,
-            Body = isMA
-                ? ModelAverageBody
-                : modelType === MODEL_NESTED_DICHOTOMOUS
-                ? NestedDichotomousModalBody
-                : ModelBody;
+        const name = this.getTitle(),
+            Body = this.getBody();
 
         return (
             <Modal
diff --git a/frontend/src/components/Logic/RuleRow.js b/frontend/src/components/Logic/RuleRow.js
index 1163d179..110b344c 100644
--- a/frontend/src/components/Logic/RuleRow.js
+++ b/frontend/src/components/Logic/RuleRow.js
@@ -5,7 +5,11 @@ import React, {Component} from "react";
 
 import {checkOrEmpty} from "@/common";
 import {BIN_NAMES, logicBinOptions, ruleLookups} from "@/constants/logicConstants";
-import {MODEL_CONTINUOUS, MODEL_DICHOTOMOUS} from "@/constants/mainConstants";
+import {
+    MODEL_CONTINUOUS,
+    MODEL_DICHOTOMOUS,
+    MODEL_NESTED_DICHOTOMOUS,
+} from "@/constants/mainConstants";
 
 import CheckboxInput from "../common/CheckboxInput";
 import FloatInput from "../common/FloatInput";
@@ -14,10 +18,12 @@ import SelectInput from "../common/SelectInput";
 const fieldMap = {
         [MODEL_CONTINUOUS]: "enabled_continuous",
         [MODEL_DICHOTOMOUS]: "enabled_dichotomous",
+        [MODEL_NESTED_DICHOTOMOUS]: "enabled_nested",
     },
     lookupMap = {
         [MODEL_CONTINUOUS]: "enabledContinuous",
         [MODEL_DICHOTOMOUS]: "enabledDichotomous",
+        [MODEL_NESTED_DICHOTOMOUS]: "enabledNested",
     };
 
 @observer
diff --git a/frontend/src/components/Main/AnalysisForm/AnalysisForm.js b/frontend/src/components/Main/AnalysisForm/AnalysisForm.js
index 336b45cd..ef06fec1 100644
--- a/frontend/src/components/Main/AnalysisForm/AnalysisForm.js
+++ b/frontend/src/components/Main/AnalysisForm/AnalysisForm.js
@@ -2,8 +2,6 @@ import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
-import * as mc from "@/constants/mainConstants";
-
 import Button from "../../common/Button";
 import Icon from "../../common/Icon";
 import SelectInput from "../../common/SelectInput";
@@ -86,17 +84,10 @@ class AnalysisForm extends Component {
                                     complete={mainStore.hasAtLeastOneModelSelected}
                                     message="At least one model is selected"
                                 />
-                                {mainStore.model_type === mc.MODEL_MULTI_TUMOR ? (
-                                    <RunChecklist
-                                        complete={mainStore.hasAtLeastTwoDatasetsSelected}
-                                        message="At least two datasets are selected"
-                                    />
-                                ) : (
-                                    <RunChecklist
-                                        complete={mainStore.hasAtLeastOneDatasetSelected}
-                                        message="At least one dataset is selected"
-                                    />
-                                )}
+                                <RunChecklist
+                                    complete={mainStore.hasAtLeastOneDatasetSelected}
+                                    message="At least one dataset is selected"
+                                />
                                 <RunChecklist
                                     complete={mainStore.hasAtLeastOneOptionSelected}
                                     message="At least one option is selected"
diff --git a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js
index ef03bcbc..a7c1284a 100644
--- a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js
+++ b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js
@@ -3,6 +3,7 @@ import PropTypes from "prop-types";
 import React, {Component} from "react";
 
 import {checkOrEmpty, getLabel} from "@/common";
+import {Dtype} from "@/constants/dataConstants";
 import {
     adverseDirectionOptions,
     allDegreeOptions,
@@ -12,6 +13,10 @@ import {
 import CheckboxInput from "../../common/CheckboxInput";
 import SelectInput from "../../common/SelectInput";
 
+const getDegreeText = (dtype, degree) => {
+    return degree === 0 && dtype == Dtype.MULTI_TUMOR ? "auto" : getLabel(degree, allDegreeOptions);
+};
+
 @observer
 class DatasetModelOption extends Component {
     render() {
@@ -19,6 +24,7 @@ class DatasetModelOption extends Component {
             option = store.options[datasetId],
             dataset = store.getDataset(option),
             {canEdit, updateOption} = store,
+            dtype = store.getModelType,
             hasDegree = option.degree !== undefined,
             hasAdverseDirection = option.adverse_direction !== undefined;
 
@@ -34,7 +40,7 @@ class DatasetModelOption extends Component {
                 {hasDegree ? (
                     <td>
                         <SelectInput
-                            choices={getDegreeOptions(dataset).map(option => {
+                            choices={getDegreeOptions(dtype, dataset).map(option => {
                                 return {value: option.value, text: option.label};
                             })}
                             onChange={value => updateOption(datasetId, "degree", parseInt(value))}
@@ -60,7 +66,7 @@ class DatasetModelOption extends Component {
             <tr>
                 <td className="text-center">{checkOrEmpty(option.enabled)}</td>
                 <td>{dataset.metadata.name}</td>
-                <td>{getLabel(option.degree, allDegreeOptions)}</td>
+                <td>{getDegreeText(dtype, option.degree)}</td>
                 {hasAdverseDirection ? (
                     <td>{getLabel(option.adverse_direction, adverseDirectionOptions)}</td>
                 ) : null}
diff --git a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOptionList.js b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOptionList.js
index bc47c86e..3016802e 100644
--- a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOptionList.js
+++ b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOptionList.js
@@ -10,7 +10,8 @@ import DatasetModelOption from "./DatasetModelOption";
 const maxDegreeText = `Studies have indicated that higher degree polynomial models are not
     warranted in that they generally do not sufficiently improve fit over simpler models
     (Nitcheva et al., 2007; PMC2040324).  Complex models also increase computer processing time
-    and the chance of model failure.`;
+    and the chance of model failure.`,
+    multiTumorDegreeText = `Degree used for each dataset. If set to auto (default), all degrees to N-1 are executed and the best-fitting is used. If a numeric value, only that degree will be modeled.`;
 
 @inject("dataOptionStore")
 @observer
@@ -42,6 +43,10 @@ class DatasetModelOptionList extends Component {
                         <tr className="bg-custom">
                             <th>Enabled</th>
                             <th>Dataset</th>
+                            <th>
+                                Degree
+                                <HelpTextPopover content={multiTumorDegreeText} />
+                            </th>
                         </tr>
                     ) : null}
                     {dtype == Dtype.DICHOTOMOUS ? (
diff --git a/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js b/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js
index bb217c6e..bc359baf 100644
--- a/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js
+++ b/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js
@@ -2,7 +2,7 @@ import PropTypes from "prop-types";
 import React from "react";
 
 import {getLabel} from "@/common";
-import {MODEL_CONTINUOUS, MODEL_DICHOTOMOUS} from "@/constants/mainConstants";
+import {MODEL_CONTINUOUS, MODEL_DICHOTOMOUS, MODEL_MULTI_TUMOR} from "@/constants/mainConstants";
 import {
     continuousBmrOptions,
     dichotomousBmrOptions,
@@ -24,7 +24,7 @@ const OptionsReadOnly = props => {
                     <td>{getLabel(options.dist_type, distTypeOptions)}</td>
                 </>
             ) : null}
-            {modelType === MODEL_DICHOTOMOUS ? (
+            {modelType === MODEL_DICHOTOMOUS || modelType === MODEL_MULTI_TUMOR ? (
                 <>
                     <td>{getLabel(options.bmr_type, dichotomousBmrOptions)}</td>
                     <td>{ff(options.bmr_value)}</td>
diff --git a/frontend/src/components/Navigation.js b/frontend/src/components/Navigation.js
index 8e21953f..f732bbc9 100644
--- a/frontend/src/components/Navigation.js
+++ b/frontend/src/components/Navigation.js
@@ -16,7 +16,8 @@ import Output from "./Output/Output";
 @observer
 class Navigation extends Component {
     render() {
-        const {mainStore} = this.props;
+        const {mainStore} = this.props,
+            {isMultitumor} = mainStore;
         return (
             <>
                 <ul className="nav nav-tabs d-flex mt-3">
@@ -35,11 +36,13 @@ class Navigation extends Component {
                             Output
                         </NavLink>
                     </li>
-                    <li className="nav-item">
-                        <NavLink className="nav-link" to="/logic">
-                            Logic
-                        </NavLink>
-                    </li>
+                    {isMultitumor ? null : (
+                        <li className="nav-item">
+                            <NavLink className="nav-link" to="/logic">
+                                Logic
+                            </NavLink>
+                        </li>
+                    )}
                     {mainStore.canEdit ? (
                         <li className="nav-item ml-auto mr-1">
                             <ShareActions />
diff --git a/frontend/src/components/Output/Multitumor/AnalysisOfDeviance.js b/frontend/src/components/Output/Multitumor/AnalysisOfDeviance.js
new file mode 100644
index 00000000..4209aad4
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/AnalysisOfDeviance.js
@@ -0,0 +1,57 @@
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+import {ff, fractionalFormatter} from "@/utils/formatters";
+
+@observer
+class AnalysisOfDeviance extends Component {
+    render() {
+        const deviances = this.props.model.deviance;
+        return (
+            <table className="table table-sm table-bordered text-right col-l-1">
+                <colgroup>
+                    <col width="20%" />
+                    <col width="16%" />
+                    <col width="16%" />
+                    <col width="16%" />
+                    <col width="16%" />
+                    <col width="16%" />
+                </colgroup>
+                <thead>
+                    <tr className="bg-custom">
+                        <th colSpan="9">Analysis of Deviance</th>
+                    </tr>
+                    <tr>
+                        <th>Model</th>
+                        <th>Log Likelihood</th>
+                        <th># Parameters</th>
+                        <th>Deviance</th>
+                        <th>Test DOF</th>
+                        <th>
+                            <i>P</i>-Value
+                        </th>
+                    </tr>
+                </thead>
+                <tbody>
+                    {deviances.names.map((name, i) => {
+                        return (
+                            <tr key={i}>
+                                <td>{name}</td>
+                                <td>{ff(deviances.ll[i])}</td>
+                                <td>{deviances.params[i]}</td>
+                                <td>{ff(deviances.deviance[i])}</td>
+                                <td>{ff(deviances.df[i])}</td>
+                                <td>{fractionalFormatter(deviances.p_value[i])} </td>
+                            </tr>
+                        );
+                    })}
+                </tbody>
+            </table>
+        );
+    }
+}
+AnalysisOfDeviance.propTypes = {
+    model: PropTypes.object,
+};
+export default AnalysisOfDeviance;
diff --git a/frontend/src/components/Output/Multitumor/DatasetTable.js b/frontend/src/components/Output/Multitumor/DatasetTable.js
new file mode 100644
index 00000000..d6da764e
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/DatasetTable.js
@@ -0,0 +1,80 @@
+import _ from "lodash";
+import {inject, observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+const getData = datasets => {
+    const headers = ["Dose"],
+        rows = [],
+        doses = new Set();
+
+    datasets.forEach(dataset => {
+        headers.push(dataset.metadata.name);
+        dataset.doses.forEach(dose => doses.add(dose));
+    });
+
+    const doseArr = [...doses].sort((a, b) => a - b);
+    doseArr.forEach(dose => {
+        const thisRow = [dose];
+        rows.push(thisRow);
+        datasets.forEach(dataset => {
+            const idx = _.findIndex(dataset.doses, d => d == dose);
+            if (idx >= 0) {
+                thisRow.push(`${dataset.incidences[idx]}/${dataset.ns[idx]}`);
+            } else {
+                thisRow.push("-");
+            }
+        });
+    });
+    return {
+        headers,
+        colWidths: _.fill(Array(headers.length), `${Math.round(100 / headers.length)}%`),
+        rows,
+    };
+};
+
+@inject("outputStore")
+@observer
+class DatasetTable extends Component {
+    render() {
+        const store = this.props.outputStore,
+            {selectedFrequentist} = store;
+
+        if (!selectedFrequentist) {
+            return null;
+        }
+        const {multitumorDatasets} = store,
+            data = getData(multitumorDatasets);
+
+        return (
+            <table className="table table-sm">
+                <colgroup>
+                    {_.map(data.colWidths).map((value, idx) => (
+                        <col key={idx} width={value}></col>
+                    ))}
+                </colgroup>
+                <thead className="table-bordered">
+                    <tr className="bg-custom">
+                        {data.headers.map((text, idx) => (
+                            <th key={idx}>{text}</th>
+                        ))}
+                    </tr>
+                </thead>
+                <tbody className="table-bordered">
+                    {data.rows.map((rows, idx) => (
+                        <tr key={idx}>
+                            {rows.map((text, idx) => (
+                                <td key={idx}>{text}</td>
+                            ))}
+                        </tr>
+                    ))}
+                </tbody>
+            </table>
+        );
+    }
+}
+DatasetTable.propTypes = {
+    outputStore: PropTypes.object,
+};
+
+export default DatasetTable;
diff --git a/frontend/src/components/Output/Multitumor/Doses.js b/frontend/src/components/Output/Multitumor/Doses.js
new file mode 100644
index 00000000..c0989160
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/Doses.js
@@ -0,0 +1,42 @@
+import _ from "lodash";
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+@observer
+class Doses extends Component {
+    render() {
+        const dataset = this.props.model,
+            temp_rslt_len = _.size(dataset.doses);
+        return (
+            <table className="table table-sm table-bordered">
+                <thead>
+                    <tr className="bg-custom">
+                        <th colSpan="3">Doses</th>
+                    </tr>
+                    <tr>
+                        <th>Dose</th>
+                        <th>Incidence</th>
+                        <th>N</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    {_.range(temp_rslt_len).map(i => {
+                        return (
+                            <tr key={i}>
+                                <td>{dataset.doses[i]}</td>
+                                <td>{dataset.incidences[i]}</td>
+                                <td>{dataset.ns[i]}</td>
+                            </tr>
+                        );
+                    })}
+                </tbody>
+            </table>
+        );
+    }
+}
+Doses.propTypes = {
+    model: PropTypes.object,
+};
+
+export default Doses;
diff --git a/frontend/src/components/Output/Multitumor/GoodnessFit.js b/frontend/src/components/Output/Multitumor/GoodnessFit.js
new file mode 100644
index 00000000..d896efcb
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/GoodnessFit.js
@@ -0,0 +1,98 @@
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+import {Dtype} from "@/constants/dataConstants";
+import {isLognormal} from "@/constants/modelConstants";
+import {ff} from "@/utils/formatters";
+
+/* eslint-disable */
+const hdr_c_normal = [
+        "Dose", "Size", "Observed Mean", "Calculated Mean", "Estimated Mean",
+        "Observed SD", "Calculated SD", "Estimated SD", "Scaled Residual",
+    ],
+    hdr_c_lognormal = [
+        "Dose", "Size", "Observed Mean", "Calculated Median", "Estimated Median",
+        "Observed SD", "Calculated GSD", "Estimated GSD", "Scaled Residual",
+    ],
+    hdr_d = [ "Dose", "Size", "Observed", "Expected", "Estimated Probability", "Scaled Residual"];
+/* eslint-enable */
+
+@observer
+class GoodnessFit extends Component {
+    getHeaders(dtype, settings) {
+        if (dtype == Dtype.CONTINUOUS || dtype == Dtype.CONTINUOUS_INDIVIDUAL) {
+            const headers = isLognormal(settings.disttype) ? hdr_c_lognormal : hdr_c_normal;
+            return [headers, [10, 10, 10, 12, 12, 12, 10, 12, 12]];
+        }
+        if (dtype == Dtype.DICHOTOMOUS) {
+            return [hdr_d, [17, 16, 16, 17, 17, 17]];
+        }
+        throw Error("Unknown dtype");
+    }
+    render() {
+        const {store} = this.props,
+            settings = store.modalModel.settings,
+            gof = store.modalModel.gof,
+            dataset = store.modalDataset,
+            {dtype} = dataset,
+            headers = this.getHeaders(dtype, settings);
+        return (
+            <table className="table table-sm table-bordered text-right">
+                <colgroup>
+                    {headers[1].map((d, i) => (
+                        <col key={i} width={`${d}%`} />
+                    ))}
+                </colgroup>
+                <thead>
+                    <tr className="bg-custom text-left">
+                        <th colSpan={headers[0].length}>Goodness of Fit</th>
+                    </tr>
+                    <tr>
+                        {headers[0].map((d, i) => (
+                            <th key={i}>{d}</th>
+                        ))}
+                    </tr>
+                </thead>
+                <tbody>
+                    {dtype == Dtype.CONTINUOUS || dtype == Dtype.CONTINUOUS_INDIVIDUAL
+                        ? gof.dose.map((item, i) => {
+                              const useFF = dtype === Dtype.CONTINUOUS_INDIVIDUAL;
+                              return (
+                                  <tr key={i}>
+                                      <td>{item}</td>
+                                      <td>{gof.size[i]}</td>
+                                      <td>{useFF ? ff(gof.obs_mean[i]) : gof.obs_mean[i]}</td>
+                                      <td>{ff(gof.calc_mean[i])}</td>
+                                      <td>{ff(gof.est_mean[i])}</td>
+                                      <td>{useFF ? ff(gof.obs_sd[i]) : gof.obs_sd[i]}</td>
+                                      <td>{ff(gof.calc_sd[i])}</td>
+                                      <td>{ff(gof.est_sd[i])}</td>
+                                      <td>{ff(gof.residual[i])}</td>
+                                  </tr>
+                              );
+                          })
+                        : null}
+                    {dtype == Dtype.DICHOTOMOUS
+                        ? dataset.doses.map((dose, i) => {
+                              return (
+                                  <tr key={i}>
+                                      <td>{dose}</td>
+                                      <td>{dataset.ns[i]}</td>
+                                      <td>{dataset.incidences[i]}</td>
+                                      <td>{ff(gof.expected[i])}</td>
+                                      <td>{ff(gof.expected[i] / dataset.ns[i])}</td>
+                                      <td>{ff(gof.residual[i])}</td>
+                                  </tr>
+                              );
+                          })
+                        : null}
+                </tbody>
+            </table>
+        );
+    }
+}
+GoodnessFit.propTypes = {
+    store: PropTypes.object,
+};
+export default GoodnessFit;
diff --git a/frontend/src/components/Output/Multitumor/InfoTable.js b/frontend/src/components/Output/Multitumor/InfoTable.js
new file mode 100644
index 00000000..def6cbe4
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/InfoTable.js
@@ -0,0 +1,42 @@
+import {inject, observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+@inject("outputStore")
+@observer
+class InfoTable extends Component {
+    render() {
+        const {outputStore} = this.props,
+            model = outputStore.modalModel,
+            isSummary = outputStore.drModelModalIsMA,
+            dataset = outputStore.modalDataset;
+
+        return (
+            <table id="info-table" className="table table-sm table-bordered">
+                <thead>
+                    <tr className="bg-custom">
+                        <th colSpan="2">Info</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    <tr>
+                        <td>Dataset</td>
+                        {isSummary ? <td>Summary</td> : <td>{dataset.metadata.name}</td>}
+                    </tr>
+                    <tr>
+                        <td>Model</td>
+                        <td>{model.name}</td>
+                    </tr>
+                    <tr>
+                        <td>Equation</td>
+                        <td></td>
+                    </tr>
+                </tbody>
+            </table>
+        );
+    }
+}
+InfoTable.propTypes = {
+    outputStore: PropTypes.object,
+};
+export default InfoTable;
diff --git a/frontend/src/components/Output/Multitumor/ModalBody.js b/frontend/src/components/Output/Multitumor/ModalBody.js
new file mode 100644
index 00000000..4376f9fd
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/ModalBody.js
@@ -0,0 +1,69 @@
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+import {Col, Modal, Row} from "react-bootstrap";
+
+import ModelParameters from "../../IndividualModel/ModelParameters";
+import AnalysisOfDeviance from "./AnalysisOfDeviance";
+import Doses from "./Doses";
+import GoodnessFit from "./GoodnessFit";
+import InfoTable from "./InfoTable";
+import ModelOptions from "./ModelOptions";
+import ParameterSettings from "./ParameterSettings";
+import Summary from "./Summary";
+
+@observer
+class ModalBody extends Component {
+    render() {
+        const {outputStore} = this.props,
+            model = outputStore.modalModel,
+            isSummary = outputStore.drModelModalIsMA,
+            dataset = outputStore.modalDataset;
+        return (
+            <Modal.Body>
+                <Row>
+                    <Col xl={3}>
+                        <InfoTable />
+                    </Col>
+                    <Col xl={3}>{!isSummary && <ModelOptions model={model} />}</Col>
+                    <Col xl={3}>{!isSummary && <Doses model={dataset} />}</Col>
+                </Row>
+                {!isSummary && (
+                    <Row>
+                        <Col xl={4}>
+                            <Summary model={model} />
+                        </Col>
+                        <Col xl={5}>
+                            <ParameterSettings model={model} />
+                        </Col>
+                    </Row>
+                )}
+                {!isSummary && (
+                    <Row>
+                        <Col xl={9}>
+                            <ModelParameters parameters={model.parameters} />
+                        </Col>
+                    </Row>
+                )}
+                {!isSummary && (
+                    <Row>
+                        <Col xl={9}>
+                            <GoodnessFit store={outputStore} />
+                        </Col>
+                    </Row>
+                )}
+                {!isSummary && (
+                    <Row>
+                        <Col xl={9}>
+                            <AnalysisOfDeviance model={model} />
+                        </Col>
+                    </Row>
+                )}
+            </Modal.Body>
+        );
+    }
+}
+ModalBody.propTypes = {
+    outputStore: PropTypes.object,
+};
+export default ModalBody;
diff --git a/frontend/src/components/Output/Multitumor/ModelOptions.js b/frontend/src/components/Output/Multitumor/ModelOptions.js
new file mode 100644
index 00000000..b5b44e55
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/ModelOptions.js
@@ -0,0 +1,45 @@
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+@observer
+class ModelOptions extends Component {
+    render() {
+        // const {model} = this.props;
+        let data = [];
+
+        data = [
+            ["BMR Type", "BMR Type"],
+            ["BMR", "BMR"],
+            ["Confidence Level", "confidence level"],
+            ["Degree", "degree"],
+        ];
+
+        return (
+            <table className="table table-sm table-bordered col-r-2">
+                <thead>
+                    <tr className="bg-custom">
+                        <th colSpan="2">Model Options</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    {data.map((d, i) => {
+                        if (!d) {
+                            return null;
+                        }
+                        return (
+                            <tr key={i}>
+                                <td>{d[0]}</td>
+                                <td>{d[1]}</td>
+                            </tr>
+                        );
+                    })}
+                </tbody>
+            </table>
+        );
+    }
+}
+ModelOptions.propTypes = {
+    model: PropTypes.object.isRequired,
+};
+export default ModelOptions;
diff --git a/frontend/src/components/Output/Multitumor/ParameterSettings.js b/frontend/src/components/Output/Multitumor/ParameterSettings.js
new file mode 100644
index 00000000..8082ab2c
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/ParameterSettings.js
@@ -0,0 +1,44 @@
+import _ from "lodash";
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+@observer
+class ParameterSettings extends Component {
+    render() {
+        const model = this.props.model.parameters,
+            temp_rslt_len = _.size(model.names);
+        return (
+            <table className="table table-sm table-bordered">
+                <thead>
+                    <tr className="bg-custom">
+                        <th colSpan="4">Parameter Settings</th>
+                    </tr>
+                    <tr>
+                        <th>Parameter</th>
+                        <th>Initial</th>
+                        <th>Min</th>
+                        <th>Max</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    {_.range(temp_rslt_len).map(i => {
+                        return (
+                            <tr key={i}>
+                                <td>{model.names[i]}</td>
+                                <td>{model.prior_initial_value[i]}</td>
+                                <td>{model.prior_min_value[i]}</td>
+                                <td>{model.prior_max_value[i]}</td>
+                            </tr>
+                        );
+                    })}
+                </tbody>
+            </table>
+        );
+    }
+}
+ParameterSettings.propTypes = {
+    model: PropTypes.object,
+};
+
+export default ParameterSettings;
diff --git a/frontend/src/components/Output/Multitumor/ResultTable.js b/frontend/src/components/Output/Multitumor/ResultTable.js
new file mode 100644
index 00000000..cd85a288
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/ResultTable.js
@@ -0,0 +1,103 @@
+import _ from "lodash";
+import {inject, observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+import {ff} from "@/utils/formatters";
+
+@inject("outputStore")
+@observer
+class ResultTable extends Component {
+    render() {
+        const store = this.props.outputStore,
+            {selectedFrequentist} = store;
+
+        if (!selectedFrequentist) {
+            return null;
+        }
+        const colWidths = [11, 11, 11, 11, 11, 11, 11, 11, 11],
+            {results} = selectedFrequentist,
+            {selectedMultitumorModels} = store,
+            indexes = results.selected_model_indexes;
+
+        return (
+            <table className="table table-sm">
+                <colgroup>
+                    {_.map(colWidths).map((value, idx) => (
+                        <col key={idx} width={`${value}%`}></col>
+                    ))}
+                </colgroup>
+                <thead className="table-bordered">
+                    <tr className="bg-custom">
+                        <th>Model</th>
+                        <th>BMDL</th>
+                        <th>BMD</th>
+                        <th>BMDU</th>
+                        <th>
+                            <i>P</i>-Value
+                        </th>
+                        <th>AIC</th>
+                        <th>Unnormalized Log Posterior Probability</th>
+                        <th>Scaled Residual for Dose Group near BMD</th>
+                        <th>Scaled Residual for Control Dose Group</th>
+                    </tr>
+                </thead>
+                <tbody className="table-bordered">
+                    <tr key={-1}>
+                        <td>
+                            <a
+                                id={`freq-result-${-1}`}
+                                href="#"
+                                onClick={e => {
+                                    e.preventDefault();
+                                    store.showModalDetailMultitumor(-1, -1);
+                                }}>
+                                Multi-tumor (MS Combo)
+                            </a>
+                        </td>
+                        <td>{ff(results.bmdl)}</td>
+                        <td>{ff(results.bmd)}</td>
+                        <td>{ff(results.bmdu)}</td>
+                        <td>-9999</td>
+                        <td>-9999</td>
+                        <td>???</td>
+                        <td>???</td>
+                        <td>???</td>
+                    </tr>
+                    {selectedMultitumorModels.map((model, index) => {
+                        const degree = model.parameters.names.length - 1,
+                            name = `Multistage ${degree}°`;
+                        return (
+                            <tr key={index}>
+                                <td>
+                                    <a
+                                        id={`freq-result-${index}`}
+                                        href="#"
+                                        onClick={e => {
+                                            e.preventDefault();
+                                            store.showModalDetailMultitumor(index, indexes[index]);
+                                        }}>
+                                        {name}
+                                    </a>
+                                </td>
+                                <td>{ff(model.bmdl)}</td>
+                                <td>{ff(model.bmd)}</td>
+                                <td>{ff(model.bmdu)}</td>
+                                <td>-9999</td>
+                                <td>-9999</td>
+                                <td>???</td>
+                                <td>???</td>
+                                <td>???</td>
+                            </tr>
+                        );
+                    })}
+                </tbody>
+            </table>
+        );
+    }
+}
+ResultTable.propTypes = {
+    outputStore: PropTypes.object,
+};
+
+export default ResultTable;
diff --git a/frontend/src/components/Output/Multitumor/Summary.js b/frontend/src/components/Output/Multitumor/Summary.js
new file mode 100644
index 00000000..12ce8934
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/Summary.js
@@ -0,0 +1,67 @@
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+import {ff, fourDecimalFormatter} from "@/utils/formatters";
+
+@observer
+class Summary extends Component {
+    render() {
+        const dataset = this.props.model;
+        return (
+            <table className="table table-sm table-bordered col-r-2">
+                <colgroup>
+                    <col width="60%" />
+                    <col width="40%" />
+                </colgroup>
+                <thead>
+                    <tr className="bg-custom">
+                        <th colSpan="2">Summary</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    <tr>
+                        <td>BMD</td>
+                        <td>{ff(dataset.bmd)}</td>
+                    </tr>
+                    <tr>
+                        <td>BMDL</td>
+                        <td>{ff(dataset.bmdl)}</td>
+                    </tr>
+                    <tr>
+                        <td>BMDU</td>
+                        <td>{ff(dataset.bmdu)}</td>
+                    </tr>
+                    <tr>
+                        <td>AIC</td>
+                        <td>{ff(dataset.fit.aic)}</td>
+                    </tr>
+                    <tr>
+                        <td>Log Likelihood</td>
+                        <td>{ff(dataset.fit.loglikelihood)}</td>
+                    </tr>
+                    <tr>
+                        <td>
+                            <i>P</i>-Value
+                        </td>
+                        <td>{fourDecimalFormatter(dataset.gof.p_value)}</td>
+                    </tr>
+                    <tr>
+                        <td>Overall DOF</td>
+                        <td>{ff(dataset.gof.df)}</td>
+                    </tr>
+                    <tr>
+                        <td>Chi²</td>
+                        <td>{ff(dataset.fit.chisq)}</td>
+                    </tr>
+                </tbody>
+            </table>
+        );
+    }
+}
+
+Summary.propTypes = {
+    model: PropTypes.object,
+};
+
+export default Summary;
diff --git a/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js b/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js
index a739cf61..86d5f487 100644
--- a/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js
+++ b/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js
@@ -2,6 +2,8 @@ import {observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import {ff} from "@/utils/formatters";
+
 @observer
 class BootstrapResult extends Component {
     render() {
@@ -15,25 +17,25 @@ class BootstrapResult extends Component {
                 <tbody>
                     <tr>
                         <th># Iterations</th>
-                        <td>{1}</td>
+                        <td>{this.props.model.settings.bootstrap_iterations}</td>
                     </tr>
                     <tr>
                         <th>Bootstrap Seed</th>
-                        <td>{1}</td>
+                        <td>{ff(this.props.model.settings.bootstrap_seed)}</td>
                     </tr>
                     <tr>
                         <th>Log-likelihood</th>
-                        <td>{1}</td>
+                        <td>{ff(this.props.model.results.ll)}</td>
                     </tr>
                     <tr>
                         <th>Observed Chi-square</th>
-                        <td>{1}</td>
+                        <td>{ff(this.props.model.results.obs_chi_sq)}</td>
                     </tr>
                     <tr>
                         <th>
                             Combined <i>P</i>-Value
                         </th>
-                        <td>{1}</td>
+                        <td>{ff(this.props.model.results.combined_pvalue)}</td>
                     </tr>
                 </tbody>
             </table>
diff --git a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
index 66ced0c2..807a2c14 100644
--- a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
+++ b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
@@ -1,10 +1,14 @@
+import _ from "lodash";
 import {observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import {ff} from "@/utils/formatters";
+
 @observer
 class BootstrapRuns extends Component {
     render() {
+        const results = this.props.model.results.bootstrap;
         return (
             <table className="table table-sm table-bordered">
                 <thead className="bg-custom">
@@ -23,13 +27,25 @@ class BootstrapRuns extends Component {
                     </tr>
                 </thead>
                 <tbody>
+                    {_.range(results.n_runs).map(run => {
+                        return (
+                            <tr key={run}>
+                                <td>{run + 1}</td>
+                                <td>{results.p_value[run]}</td>
+                                <td>{ff(results.p50[run])}</td>
+                                <td>{ff(results.p90[run])}</td>
+                                <td>{ff(results.p95[run])}</td>
+                                <td>{ff(results.p99[run])}</td>
+                            </tr>
+                        );
+                    })}
                     <tr>
-                        <td>{1}</td>
-                        <td>{1}</td>
-                        <td>{1}</td>
-                        <td>{1}</td>
-                        <td>{1}</td>
-                        <td>{1}</td>
+                        <td>Combined</td>
+                        <td>{results.p_value[3]}</td>
+                        <td>{ff(results.p50[3])}</td>
+                        <td>{ff(results.p90[3])}</td>
+                        <td>{ff(results.p95[3])}</td>
+                        <td>{ff(results.p99[3])}</td>
                     </tr>
                 </tbody>
             </table>
diff --git a/frontend/src/components/Output/NestedDichotomous/LitterData.js b/frontend/src/components/Output/NestedDichotomous/LitterData.js
index f37c1c9a..0c425fe4 100644
--- a/frontend/src/components/Output/NestedDichotomous/LitterData.js
+++ b/frontend/src/components/Output/NestedDichotomous/LitterData.js
@@ -3,19 +3,22 @@ import {observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import {ff} from "@/utils/formatters";
+
 @observer
 class LitterData extends Component {
     render() {
+        const litter = this.props.model.results.litter,
+            temp_rslt_len = _.size(litter.lsc);
         return (
             <table className="table table-sm table-bordered">
                 <thead>
                     <tr className="bg-custom">
-                        <th colSpan="8">Litter Data</th>
+                        <th colSpan="7">Litter Data</th>
                     </tr>
                     <tr>
                         <th>Dose</th>
                         <th>Lit. Spec. Cov.</th>
-                        <th>Lit. Spec. Cov.</th>
                         <th>Est. Prob.</th>
                         <th>Liter Size</th>
                         <th>Expected</th>
@@ -24,17 +27,16 @@ class LitterData extends Component {
                     </tr>
                 </thead>
                 <tbody>
-                    {_.range(10).map(d => {
+                    {_.range(temp_rslt_len).map(i => {
                         return (
-                            <tr key={d}>
-                                <td>1</td>
-                                <td>2</td>
-                                <td>3</td>
-                                <td>4</td>
-                                <td>5</td>
-                                <td>6</td>
-                                <td>7</td>
-                                <td>8</td>
+                            <tr key={i}>
+                                <td>{litter.dose[i]}</td>
+                                <td>{litter.lsc[i]}</td>
+                                <td>{ff(litter.estimated_probabilities[i])}</td>
+                                <td>{litter.litter_size[i]}</td>
+                                <td>{ff(litter.expected[i])}</td>
+                                <td>{litter.observed[i]}</td>
+                                <td>{ff(litter.sr[i])}</td>
                             </tr>
                         );
                     })}
diff --git a/frontend/src/components/Output/NestedDichotomous/ModalBody.js b/frontend/src/components/Output/NestedDichotomous/ModalBody.js
index e9eb4f5d..b8a9a0a4 100644
--- a/frontend/src/components/Output/NestedDichotomous/ModalBody.js
+++ b/frontend/src/components/Output/NestedDichotomous/ModalBody.js
@@ -6,6 +6,7 @@ import {Col, Modal, Row} from "react-bootstrap";
 import BootstrapResults from "./BootstrapResults";
 import BootstrapRuns from "./BootstrapRuns";
 import LitterData from "./LitterData";
+import ModelParameters from "./ModelParameters";
 import ScaledResidual from "./ScaledResidual";
 
 @observer
@@ -23,6 +24,9 @@ class ModalBody extends Component {
                         <p>Borrow benchmark dose, model parameters, from other model</p>
                     </Col>
                 </Row>
+                <Col xs={6}>
+                    <ModelParameters model={model} />
+                </Col>
                 <Row>
                     <Col xs={6}>
                         <BootstrapResults model={model} />
diff --git a/frontend/src/components/Output/NestedDichotomous/ModelParameters.js b/frontend/src/components/Output/NestedDichotomous/ModelParameters.js
new file mode 100644
index 00000000..81e40eb0
--- /dev/null
+++ b/frontend/src/components/Output/NestedDichotomous/ModelParameters.js
@@ -0,0 +1,39 @@
+import _ from "lodash";
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+@observer
+class ModelParameters extends Component {
+    render() {
+        const names = this.props.model.results.parameter_names,
+            values = this.props.model.results.parameters;
+
+        return (
+            <table id="info-table" className="table table-sm table-bordered">
+                <thead>
+                    <tr className="bg-custom">
+                        <th colSpan="2" className="text-center">
+                            Model Parameters
+                        </th>
+                    </tr>
+                </thead>
+                <tbody>
+                    {_.range(_.size(names)).map(i => {
+                        return (
+                            <tr key={i}>
+                                <td>{names[i]}</td>
+                                <td>{values[i]}</td>
+                            </tr>
+                        );
+                    })}
+                </tbody>
+            </table>
+        );
+    }
+}
+ModelParameters.propTypes = {
+    model: PropTypes.object,
+};
+
+export default ModelParameters;
diff --git a/frontend/src/components/Output/NestedDichotomous/ResultTable.js b/frontend/src/components/Output/NestedDichotomous/ResultTable.js
index 6cb6052d..c8c8bdc1 100644
--- a/frontend/src/components/Output/NestedDichotomous/ResultTable.js
+++ b/frontend/src/components/Output/NestedDichotomous/ResultTable.js
@@ -56,14 +56,14 @@ class ResultTable extends Component {
                                     {model.name}
                                 </a>
                             </td>
-                            <td>{ff(model.results.bmdl)}</td>
-                            <td>{ff(model.results.bmd)}</td>
-                            <td>{ff(model.results.bmdu)}</td>
-                            <td>-9999</td>
-                            <td>-9999</td>
-                            <td>-9999</td>
-                            <td>-9999</td>
-                            <td>-9999</td>
+                            <td>{ff(model.results.summary.bmdl)}</td>
+                            <td>{ff(model.results.summary.bmd)}</td>
+                            <td>{model.results.summary.bmdu}</td>
+                            <td>{ff(model.results.combined_pvalue)}</td>
+                            <td>{ff(model.results.summary.aic)}</td>
+                            <td>???</td>
+                            <td>???</td>
+                            <td>???</td>
                         </tr>
                     ))}
                 </tbody>
diff --git a/frontend/src/components/Output/NestedDichotomous/ScaledResidual.js b/frontend/src/components/Output/NestedDichotomous/ScaledResidual.js
index 95529822..d4a671aa 100644
--- a/frontend/src/components/Output/NestedDichotomous/ScaledResidual.js
+++ b/frontend/src/components/Output/NestedDichotomous/ScaledResidual.js
@@ -17,27 +17,27 @@ class ScaledResidual extends Component {
                 <tbody>
                     <tr>
                         <td>Minimum scaled residual for dose group nearest the BMD</td>
-                        <td>{1}</td>
+                        <td>{this.props.model.results.scaled_residuals[0]}</td>
                     </tr>
                     <tr>
                         <td>Minimum ABS(scaled residual) for dose group nearest the BMD</td>
-                        <td>{1}</td>
+                        <td>{this.props.model.results.scaled_residuals[1]}</td>
                     </tr>
                     <tr>
                         <td>Average Scaled residual for dose group nearest the BMD</td>
-                        <td>{1}</td>
+                        <td>{this.props.model.results.scaled_residuals[2]}</td>
                     </tr>
                     <tr>
                         <td>Average ABS(scaled residual) for dose group nearest the BMD</td>
-                        <td>{1}</td>
+                        <td>{this.props.model.results.scaled_residuals[3]}</td>
                     </tr>
                     <tr>
                         <td>Maximum scaled residual for dose group nearest the BMD</td>
-                        <td>{1}</td>
+                        <td>{this.props.model.results.scaled_residuals[4]}</td>
                     </tr>
                     <tr>
                         <td>Maximum ABS(scaled residual) for dose group nearest the BMD</td>
-                        <td>{1}</td>
+                        <td>{this.props.model.results.scaled_residuals[5]}</td>
                     </tr>
                 </tbody>
             </table>
diff --git a/frontend/src/components/Output/OptionSetTable.js b/frontend/src/components/Output/OptionSetTable.js
index 79427dc1..0a21e220 100644
--- a/frontend/src/components/Output/OptionSetTable.js
+++ b/frontend/src/components/Output/OptionSetTable.js
@@ -46,6 +46,15 @@ class OptionSetTable extends Component {
                     getLabel(selectedDatasetOptions.degree, allDegreeOptions),
                 ],
             ];
+        } else if (outputStore.isNestedDichotomous) {
+            rows = [["TODO", "ADD"]];
+        } else if (outputStore.isMultiTumor) {
+            rows = [
+                ["BMR Type", getLabel(selectedModelOptions.bmr_type, dichotomousBmrOptions)],
+                ["BMR", ff(selectedModelOptions.bmr_value)],
+                ["Confidence Level", ff(selectedModelOptions.confidence_level)],
+                ["Degree Setting", outputStore.multitumorDegreeInputSettings.join(", ")],
+            ];
         } else {
             throw `Unknown model type: ${getModelType}`;
         }
diff --git a/frontend/src/components/Output/Output.js b/frontend/src/components/Output/Output.js
index e60ae17d..320a2fe1 100644
--- a/frontend/src/components/Output/Output.js
+++ b/frontend/src/components/Output/Output.js
@@ -4,8 +4,6 @@ import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
-import {MODEL_NESTED_DICHOTOMOUS} from "@/constants/mainConstants";
-
 import DoseResponsePlot from "../common/DoseResponsePlot";
 import Icon from "../common/Icon";
 import SelectInput from "../common/SelectInput";
@@ -13,6 +11,8 @@ import DatasetTable from "../Data/DatasetTable";
 import ModelDetailModal from "../IndividualModel/ModelDetailModal";
 import BayesianResultTable from "./BayesianResultTable";
 import FrequentistResultTable from "./FrequentistResultTable";
+import MultitumorDatasetTable from "./Multitumor/DatasetTable";
+import MultitumorResultTable from "./Multitumor/ResultTable";
 import NestedDichotomousResultTable from "./NestedDichotomous/ResultTable";
 import OptionSetTable from "./OptionSetTable";
 import SelectModel from "./SelectModel";
@@ -46,7 +46,6 @@ class Output extends Component {
                 selectedFrequentist,
                 selectedBayesian,
             } = outputStore,
-            modelType = outputStore.getModelType,
             {isFuture, analysisSavedAndValidated} = outputStore.rootStore.mainStore;
 
         if (hasAnyError) {
@@ -98,31 +97,44 @@ class Output extends Component {
                         </div>
                     ) : null}
                     <div className="col-lg-5">
-                        <DatasetTable dataset={outputStore.selectedDataset} />
+                        {outputStore.isMultiTumor ? (
+                            <MultitumorDatasetTable />
+                        ) : (
+                            <DatasetTable dataset={outputStore.selectedDataset} />
+                        )}
                     </div>
                     <div className="col-lg-5">
                         <OptionSetTable />
                     </div>
                 </div>
                 {selectedFrequentist ? (
-                    <div className="row">
-                        <div className="col-lg-8">
-                            <h4>Frequentist Model Results</h4>
-                            {modelType === MODEL_NESTED_DICHOTOMOUS ? (
-                                <NestedDichotomousResultTable />
-                            ) : (
-                                <FrequentistResultTable />
-                            )}
-                            {canEdit ? <SelectModel /> : null}
+                    outputStore.isMultiTumor ? (
+                        <div className="row">
+                            <div className="col-lg-12">
+                                <h4>Model Results</h4>
+                                <MultitumorResultTable />
+                            </div>
                         </div>
-                        <div className="align-items-center d-flex col-lg-4">
-                            <DoseResponsePlot
-                                onRelayout={outputStore.updateUserPlotSettings}
-                                layout={outputStore.drFrequentistPlotLayout}
-                                data={outputStore.drFrequentistPlotData}
-                            />
+                    ) : (
+                        <div className="row">
+                            <div className="col-lg-8">
+                                <h4>Frequentist Model Results</h4>
+                                {outputStore.isNestedDichotomous ? (
+                                    <NestedDichotomousResultTable />
+                                ) : (
+                                    <FrequentistResultTable />
+                                )}
+                                {canEdit ? <SelectModel /> : null}
+                            </div>
+                            <div className="align-items-center d-flex col-lg-4">
+                                <DoseResponsePlot
+                                    onRelayout={outputStore.updateUserPlotSettings}
+                                    layout={outputStore.drFrequentistPlotLayout}
+                                    data={outputStore.drFrequentistPlotData}
+                                />
+                            </div>
                         </div>
-                    </div>
+                    )
                 ) : null}
                 {selectedBayesian ? (
                     <div className="row">
@@ -140,7 +152,7 @@ class Output extends Component {
                     </div>
                 ) : null}
 
-                {isFuture ? (
+                {isFuture && !outputStore.isMultiTumor ? (
                     <div className="row">
                         {selectedFrequentist ? (
                             <div className="col col-lg-6">
diff --git a/frontend/src/constants/dataConstants.js b/frontend/src/constants/dataConstants.js
index 7003975e..5685ff49 100644
--- a/frontend/src/constants/dataConstants.js
+++ b/frontend/src/constants/dataConstants.js
@@ -241,11 +241,18 @@ export const DATA_CONTINUOUS_SUMMARY = "CS",
     getNumDoseGroups = function(dataset) {
         return _.uniq(dataset.doses).length;
     },
-    getDefaultDegree = function(dataset) {
+    getDefaultDegree = function(dtype, dataset) {
+        if (dtype === Dtype.MULTI_TUMOR) {
+            return 0; // auto
+        }
         const n = getNumDoseGroups(dataset) - 1;
         return _.clamp(n, 1, 3);
     },
-    getDegreeOptions = function(dataset) {
-        const maxDegree = Math.max(Math.min(8, getNumDoseGroups(dataset) - 1), 1);
-        return allDegreeOptions.filter(d => d.value <= maxDegree);
+    getDegreeOptions = function(dtype, dataset) {
+        const maxDegree = Math.max(Math.min(8, getNumDoseGroups(dataset) - 1), 1),
+            options = _.cloneDeep(allDegreeOptions).filter(d => d.value <= maxDegree);
+        if (dtype === Dtype.MULTI_TUMOR) {
+            options[0].label = "auto";
+        }
+        return options;
     };
diff --git a/frontend/src/stores/DatasetModelOptionStore.js b/frontend/src/stores/DatasetModelOptionStore.js
index 01281975..801e1c9b 100644
--- a/frontend/src/stores/DatasetModelOptionStore.js
+++ b/frontend/src/stores/DatasetModelOptionStore.js
@@ -36,9 +36,10 @@ class DatasetModelOptionStore {
         this.options.push(option);
     }
     @action.bound updateDefaultDegree(dataset) {
-        const index = _.findIndex(this.options, d => d.dataset_id === dataset.metadata.id);
+        const index = _.findIndex(this.options, d => d.dataset_id === dataset.metadata.id),
+            dtype = this.getModelType;
         if (this.options[index].degree !== undefined) {
-            this.options[index].degree = getDefaultDegree(dataset);
+            this.options[index].degree = getDefaultDegree(dtype, dataset);
         }
     }
     @action.bound getDataset(option) {
diff --git a/frontend/src/stores/MainStore.js b/frontend/src/stores/MainStore.js
index 66509e3a..e9599e87 100644
--- a/frontend/src/stores/MainStore.js
+++ b/frontend/src/stores/MainStore.js
@@ -71,6 +71,9 @@ class MainStore {
             },
         };
     }
+    @computed get isMultitumor() {
+        return this.model_type === mc.MODEL_MULTI_TUMOR;
+    }
 
     @action.bound
     async saveAnalysis() {
@@ -322,22 +325,11 @@ class MainStore {
         return !_.isEmpty(this.getEnabledDatasets);
     }
 
-    @computed get hasAtLeastTwoDatasetsSelected() {
-        return this.getEnabledDatasets.length >= 2;
-    }
-
     @computed get hasAtLeastOneOptionSelected() {
         return !_.isEmpty(this.getOptions);
     }
 
     @computed get isValid() {
-        if (this.model_type === mc.MODEL_MULTI_TUMOR) {
-            return (
-                this.hasAtLeastOneModelSelected &&
-                this.hasAtLeastTwoDatasetsSelected &&
-                this.hasAtLeastOneOptionSelected
-            );
-        }
         return (
             this.hasAtLeastOneModelSelected &&
             this.hasAtLeastOneDatasetSelected &&
diff --git a/frontend/src/stores/OutputStore.js b/frontend/src/stores/OutputStore.js
index 718e3db8..10f79376 100644
--- a/frontend/src/stores/OutputStore.js
+++ b/frontend/src/stores/OutputStore.js
@@ -2,6 +2,7 @@ import _ from "lodash";
 import {action, computed, observable, toJS} from "mobx";
 
 import {getHeaders} from "@/common";
+import {MODEL_MULTI_TUMOR, MODEL_NESTED_DICHOTOMOUS} from "@/constants/mainConstants";
 import {maIndex, modelClasses} from "@/constants/outputConstants";
 import {
     bmaColor,
@@ -49,6 +50,14 @@ class OutputStore {
         return this.rootStore.mainStore.model_type;
     }
 
+    @computed get isMultiTumor() {
+        return this.getModelType === MODEL_MULTI_TUMOR;
+    }
+
+    @computed get isNestedDichotomous() {
+        return this.getModelType === MODEL_NESTED_DICHOTOMOUS;
+    }
+
     @computed get globalErrorMessage() {
         return this.rootStore.mainStore.errorMessage;
     }
@@ -81,8 +90,8 @@ class OutputStore {
 
     @computed get selectedFrequentist() {
         const output = this.selectedOutput;
-        if (output && output.frequentist) {
-            return output.frequentist;
+        if (output) {
+            return output.frequentist || output.session || null;
         }
         return null;
     }
@@ -110,9 +119,16 @@ class OutputStore {
         return this.rootStore.dataOptionStore.options[index];
     }
 
+    @computed get multitumorDegreeInputSettings() {
+        return this.rootStore.dataOptionStore.options
+            .filter(d => d.enabled)
+            .map(d => (d.degree === 0 ? "auto" : d.degree));
+    }
+
     @computed get recommendationEnabled() {
         return (
             this.selectedOutput.frequentist &&
+            this.selectedOutput.frequentist.recommender &&
             this.selectedOutput.frequentist.recommender.settings.enabled
         );
     }
@@ -146,6 +162,30 @@ class OutputStore {
         return null;
     }
 
+    @computed get selectedMultitumorModels() {
+        const results = this.selectedOutput.frequentist.results;
+        return results.selected_model_indexes.map((idx, i) => results.models[i][idx]);
+    }
+
+    @computed get multitumorActiveDatasetIndexes() {
+        // some datasets entered may not have been enabled during execution; this gives the adjusted
+        // indexes for the datasets which enabled during modeling
+        const idx = _.cloneDeep(this.rootStore.dataOptionStore.options)
+            .map((d, i) => {
+                d._idx = i;
+                return d;
+            })
+            .filter(d => d.enabled)
+            .map(d => d._idx);
+        return idx;
+    }
+
+    @computed get multitumorDatasets() {
+        return this.multitumorActiveDatasetIndexes.map(
+            idx => this.rootStore.dataStore.datasets[idx]
+        );
+    }
+
     // start modal methods
     getModel(index) {
         if (this.modalModelClass === modelClasses.frequentist) {
@@ -174,6 +214,18 @@ class OutputStore {
         this.showModelModal = true;
     }
 
+    @action.bound showModalDetailMultitumor(i, j) {
+        const isMa = i === -1,
+            datasetIndexes = this.multitumorActiveDatasetIndexes;
+        this.modalModelClass = null;
+        this.modalModel = isMa
+            ? this.selectedFrequentist.results
+            : this.selectedFrequentist.results.models[i][j];
+        this.modalDataset = isMa ? null : this.rootStore.dataStore.datasets[datasetIndexes[i]];
+        this.drModelModalIsMA = isMa;
+        this.showModelModal = true;
+    }
+
     @action.bound closeModal() {
         this.modalModel = null;
         this.drModelModal = null;
@@ -226,7 +278,6 @@ class OutputStore {
         }
         return data;
     }
-
     @computed get drFrequentistPlotLayout() {
         // the main frequentist plot shown on the output page
         let layout = getDrLayout(
@@ -390,9 +441,13 @@ class OutputStore {
         Not @computed because it has a parameter, this is still observable; prevents caching;
         source: https://mobx.js.org/computeds-with-args.html
         */
-        const output = this.outputs[idx],
-            dataset = this.rootStore.dataStore.datasets[output.dataset_index];
+        const output = this.outputs[idx];
+
+        if (this.isMultiTumor) {
+            return `Option Set ${output.option_index + 1}`;
+        }
 
+        const dataset = this.rootStore.dataStore.datasets[output.dataset_index];
         if (this.rootStore.optionsStore.optionsList.length > 1) {
             return `${dataset.metadata.name}: Option Set ${output.option_index + 1}`;
         } else {
diff --git a/manage.py b/manage.py
index 36b4426f..c80a8616 100644
--- a/manage.py
+++ b/manage.py
@@ -2,7 +2,7 @@
 TODO - remove this file
 
 This file should be removed when we can. Using a console_script named `manage` worked fine with
-Django 3.2 However, when upgrading to Django 4.0, we now get an error:
+Django 3.2 However, when upgrading to Django 4.2, we now get an error:
 
 $ manage runserver
 > Error while finding module specification for '__main__' (ValueError: __main__.__spec__ is None)
diff --git a/tests/analysis/test_models.py b/tests/analysis/test_models.py
index 20793b1f..888dc177 100644
--- a/tests/analysis/test_models.py
+++ b/tests/analysis/test_models.py
@@ -1,13 +1,21 @@
+from pathlib import Path
+
+import pandas as pd
 import pytest
 
 from bmds_server.analysis.models import Analysis
 from bmds_server.analysis.reporting.docx import build_docx
-from bmds_server.analysis.reporting.excel import dataset_df, params_df, summary_df
+
+
+def write_excel(data: dict, path: Path):
+    with pd.ExcelWriter(path) as writer:
+        for name, df in data.items():
+            df.to_excel(writer, sheet_name=name, index=False)
 
 
 @pytest.mark.django_db()
 class TestBmds3Execution:
-    def test_c(self, bmds3_complete_continuous):
+    def test_continuous(self, bmds3_complete_continuous, data_path, rewrite_data_files):
         analysis = Analysis.objects.create(inputs=bmds3_complete_continuous)
 
         assert analysis.is_finished is False
@@ -25,12 +33,17 @@ def test_c(self, bmds3_complete_continuous):
         assert analysis.errors == []
 
         # test reporting (for completion)
-        build_docx(analysis, "http://bmds-python.com")
-        summary_df(analysis)
-        dataset_df(analysis)
-        params_df(analysis)
+        docx = build_docx(analysis, "http://bmds-python.com")
+        df = analysis.to_df()
+        assert len(df) == 3
 
-    def test_ci(self, bmds3_complete_continuous_individual):
+        if rewrite_data_files:
+            write_excel(df, data_path / "continuous.xlsx")
+            (data_path / "continuous.docx").write_bytes(docx.getvalue())
+
+    def test_continuous_individual(
+        self, bmds3_complete_continuous_individual, data_path, rewrite_data_files
+    ):
         analysis = Analysis.objects.create(inputs=bmds3_complete_continuous_individual)
 
         assert analysis.is_finished is False
@@ -48,12 +61,15 @@ def test_ci(self, bmds3_complete_continuous_individual):
         assert analysis.errors == []
 
         # test reporting (for completion)
-        build_docx(analysis, "http://bmds-python.com")
-        summary_df(analysis)
-        dataset_df(analysis)
-        params_df(analysis)
+        docx = build_docx(analysis, "http://bmds-python.com")
+        df = analysis.to_df()
+        assert len(df) == 3
+
+        if rewrite_data_files:
+            write_excel(df, data_path / "continuous_individual.xlsx")
+            (data_path / "continuous_individual.docx").write_bytes(docx.getvalue())
 
-    def test_d(self, bmds3_complete_dichotomous):
+    def test_dichotomous(self, bmds3_complete_dichotomous, data_path, rewrite_data_files):
         analysis = Analysis.objects.create(inputs=bmds3_complete_dichotomous)
 
         assert analysis.is_finished is False
@@ -71,7 +87,62 @@ def test_d(self, bmds3_complete_dichotomous):
         assert analysis.errors == []
 
         # test reporting (for completion)
-        build_docx(analysis, "http://bmds-python.com")
-        summary_df(analysis)
-        dataset_df(analysis)
-        params_df(analysis)
+        docx = build_docx(analysis, "http://bmds-python.com")
+        df = analysis.to_df()
+        assert len(df) == 3
+
+        if rewrite_data_files:
+            write_excel(df, data_path / "dichotomous.xlsx")
+            (data_path / "dichotomous.docx").write_bytes(docx.getvalue())
+
+    def test_nested_dichotomous(self, bmds_complete_nd, data_path, rewrite_data_files):
+        analysis = Analysis.objects.create(inputs=bmds_complete_nd)
+
+        assert analysis.is_finished is False
+        assert analysis.has_errors is False
+
+        analysis.execute()
+
+        assert analysis.is_finished is True
+        assert analysis.has_errors is False
+        assert analysis.outputs["outputs"][0]["dataset_index"] == 0
+        assert analysis.outputs["outputs"][0]["option_index"] == 0
+        assert len(analysis.outputs["outputs"]) == 1
+        assert len(analysis.outputs["outputs"][0]["frequentist"]["models"]) == 4
+        assert analysis.outputs["outputs"][0]["bayesian"] is None
+        assert analysis.errors == []
+
+        # test reporting (for completion)
+        docx = build_docx(analysis, "http://bmds-python.com")
+        df = analysis.to_df()
+        assert len(df) == 3
+
+        if rewrite_data_files:
+            write_excel(df, data_path / "nested_dichotomous.xlsx")
+            (data_path / "nested_dichotomous.docx").write_bytes(docx.getvalue())
+
+    def test_multitumor(self, bmds_complete_mt, data_path, rewrite_data_files):
+        analysis = Analysis.objects.create(inputs=bmds_complete_mt)
+
+        assert analysis.is_finished is False
+        assert analysis.has_errors is False
+
+        analysis.execute()
+
+        assert analysis.is_finished is True
+        assert analysis.has_errors is False
+        assert len(analysis.outputs["outputs"]) == 1
+        assert len(analysis.outputs["outputs"][0]["frequentist"]["results"]["models"]) == 3
+        assert len(analysis.outputs["outputs"][0]["frequentist"]["results"]["models"][0]) == 1
+        assert len(analysis.outputs["outputs"][0]["frequentist"]["results"]["models"][1]) == 4
+        assert analysis.outputs["outputs"][0]["bayesian"] is None
+        assert analysis.errors == []
+
+        # test reporting (for completion)
+        docx = build_docx(analysis, "http://bmds-python.com")
+        df = analysis.to_df()
+        assert len(df) == 3
+
+        if rewrite_data_files:
+            write_excel(df, data_path / "multitumor.xlsx")
+            (data_path / "multitumor.docx").write_bytes(docx.getvalue())
diff --git a/tests/conftest.py b/tests/conftest.py
index 9d382b7d..2841eb59 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -5,6 +5,24 @@
 from django.core.management import call_command
 
 
+@pytest.fixture(scope="session")
+def data_path():
+    return Path(__file__).parent.absolute() / "data"
+
+
+@pytest.fixture(scope="session")
+def rewrite_data_files():
+    """
+    If you're making changes to datasets and it's expected that previously saved data will need to
+    be written, then you can set this flag to True and then all saved data will be rewritten.
+
+    Please review changes to ensure they're expected after modifying this flag.
+
+    A test exists in CI to ensure that this flag is set to False on commit.
+    """
+    return False
+
+
 @pytest.fixture(scope="session", autouse=True)
 def test_db(django_db_setup, django_db_blocker):
     with django_db_blocker.unblock():
@@ -166,6 +184,138 @@ def nested_dichotomous_datasets():
     # fmt: on
 
 
+# fmt:off
+@pytest.fixture
+def bmds_complete_nd():
+    return {
+        "bmds_version": "BMDS330",
+        "dataset_type": "ND",
+        "models": {
+            "frequentist_restricted": ["Nested Logistic"],
+            "frequentist_unrestricted": []
+        },
+        "options": [
+            {
+                "bmr_type": 1,
+                "bmr_value": 0.1,
+                "bootstrap_seed": 0,
+                "confidence_level": 0.95,
+                "bootstrap_iterations": 1000,
+                "litter_specific_covariate": 1
+            }
+        ],
+        "datasets": [
+            {
+                "doses": [
+                    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+                    25, 25, 25, 25, 25, 25, 25, 25, 25,
+                    50, 50, 50, 50, 50, 50, 50, 50, 50
+                ],
+                "dtype": "ND",
+                "metadata": {
+                    "id": 0,
+                    "name": "Dataset #1",
+                    "dose_name": "Dose",
+                    "dose_units": "",
+                    "response_name": "Incidence",
+                    "response_units": ""
+                },
+                "litter_ns": [
+                    16, 9, 15, 14, 13, 9, 10, 14, 10, 11, 14,
+                    9, 14, 9, 13, 12, 10, 10, 11, 14,
+                    11, 11, 14, 11, 10, 11, 10, 15, 7,
+                ],
+                "incidences": [
+                    1, 1, 2, 3, 3, 0, 2, 2, 1, 2, 4,
+                    5, 6, 2, 6, 3, 1, 2, 4, 3,
+                    4, 5, 5, 4, 5, 4, 5, 6, 2,
+                ],
+                "litter_covariates": [
+                    16, 9, 15, 14, 13, 9, 10, 14, 10, 11, 14,
+                    9, 14, 9, 13, 12, 10, 10, 11, 14,
+                    11, 11, 14, 11, 10, 11, 10, 15, 7,
+                ]
+            }
+        ],
+        "dataset_options": [
+            {"enabled": True, "dataset_id": 0},
+        ],
+        "recommender": RecommenderSettings.build_default().dict(),
+    }
+    #fmt: on
+
+
+# fmt:off
+@pytest.fixture
+def bmds_complete_mt():
+    return {
+        "bmds_version": "BMDS330",
+        "dataset_type": "MT",
+        "models": {
+            "frequentist_restricted": ["Multistage"],
+            "frequentist_unrestricted": []
+        },
+        "options": [
+            {
+                "bmr_type": 1,
+                "bmr_value": 0.1,
+                "confidence_level": 0.95
+            }
+        ],
+        "datasets": [
+            {
+                "dtype": "D",
+                "doses": [0, 50, 100, 200, 400],
+                "ns": [20, 20, 20, 20, 20],
+                "incidences": [0, 1, 2, 10, 19],
+                "metadata": {
+                    "id": 0,
+                    "name": "Dataset #1",
+                    "dose_name": "Dose",
+                    "dose_units": "",
+                    "response_name": "Incidence",
+                    "response_units": ""
+                },
+            },
+            {
+                "dtype": "D",
+                "doses": [0, 50, 100, 200, 400],
+                "ns": [20, 20, 20, 20, 20],
+                "incidences": [0, 1, 2, 4, 11],
+                "metadata": {
+                    "id": 1,
+                    "name": "Dataset #2",
+                    "dose_name": "Dose",
+                    "dose_units": "",
+                    "response_name": "Incidence",
+                    "response_units": ""
+                },
+            },
+            {
+                "dtype": "D",
+                "doses": [0, 50, 100, 200, 400],
+                "ns": [20, 20, 20, 20, 20],
+                "incidences": [0, 2, 2, 6, 9],
+                "metadata": {
+                    "id": 2,
+                    "name": "Dataset #3",
+                    "dose_name": "Dose",
+                    "dose_units": "",
+                    "response_name": "Incidence",
+                    "response_units": ""
+                },
+            },
+        ],
+        "dataset_options": [
+            {"enabled": True, "dataset_id": 0, "degree": 3},
+            {"enabled": True, "dataset_id": 1, "degree": 0},
+            {"enabled": True, "dataset_id": 2, "degree": 0},
+        ],
+        "recommender": RecommenderSettings.build_default().dict(),
+    }
+    #fmt: on
+
+
 @pytest.fixture
 def polyk_dataset() -> dict:
     return {
diff --git a/tests/integration/test_integration.py b/tests/integration/test_integration.py
index 6eb1176f..a71fa2a9 100644
--- a/tests/integration/test_integration.py
+++ b/tests/integration/test_integration.py
@@ -54,7 +54,7 @@ def test_continuous(self):
         expect(page.locator("#decision-logic tbody tr")).to_have_count(4)
         expect(page.locator("#rule-table tbody tr")).to_have_count(20)
 
-        # TODO - add read-only views
+        # TODO - add read-only views in BMDS 23.3
 
     def test_dichotomous(self):
         page = self.page
@@ -117,4 +117,4 @@ def test_dichotomous(self):
         expect(page.locator("#decision-logic tbody tr")).to_have_count(4)
         expect(page.locator("#rule-table tbody tr")).to_have_count(18)
 
-        # TODO - add read-only views
+        # TODO - add read-only views in BMDS 23.3
diff --git a/tests/test_env.py b/tests/test_env.py
new file mode 100644
index 00000000..ab063c7e
--- /dev/null
+++ b/tests/test_env.py
@@ -0,0 +1,15 @@
+import os
+
+import pytest
+
+in_ci = os.environ.get("GITHUB_RUN_ID") is not None
+
+
+@pytest.mark.skipif(not in_ci, reason="only run in CI")
+def test_rewrite_flag(rewrite_data_files):
+    """
+    safety check- rewrite datafiles must be False in CI; otherwise we'd just rewrite
+    data every-time and our tests would always pass
+    """
+    if rewrite_data_files is True:
+        raise ValueError("Fixture `rewrite_data_files` must be `False`.")

From c2a00c7eb47bdb5aad0bf27b74a1f495c8a09a67 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Wed, 20 Sep 2023 22:54:40 -0400
Subject: [PATCH 02/24] BMDS Desktop settings flag (#261)

* sketch is_desktop

* notes, add to config test

* add further restrictions, override item limit, ui fix

* pin pydantic to version 1.10.* series

* updates

* revise

* wrap up desktop

* final review

---------

Co-authored-by: hausman-gdit <karen.hausman@gdit.com>
---
 bmds_server/analysis/models.py                  |  6 ++++--
 bmds_server/analysis/validators/session.py      |  8 ++++++--
 bmds_server/analysis/views.py                   |  1 +
 bmds_server/main/context_processors.py          |  1 +
 bmds_server/main/settings/base.py               |  1 +
 bmds_server/main/settings/testing.py            |  2 ++
 frontend/src/components/Main/Actions/Actions.js | 11 +++++++----
 frontend/src/components/Navigation.js           |  6 ++++--
 frontend/src/stores/DataStore.js                |  3 ++-
 frontend/src/stores/MainStore.js                |  3 +++
 frontend/src/stores/OptionsStore.js             |  3 ++-
 requirements/base.txt                           |  2 +-
 tests/analysis/test_views.py                    |  2 ++
 13 files changed, 36 insertions(+), 13 deletions(-)

diff --git a/bmds_server/analysis/models.py b/bmds_server/analysis/models.py
index bbc93624..a83cb087 100644
--- a/bmds_server/analysis/models.py
+++ b/bmds_server/analysis/models.py
@@ -2,7 +2,7 @@
 import traceback
 import uuid
 from copy import deepcopy
-from datetime import timedelta
+from datetime import datetime, timedelta
 from io import BytesIO
 
 import bmds
@@ -30,7 +30,9 @@
 logger = logging.getLogger(__name__)
 
 
-def get_deletion_date(current_deletion_date=None):
+def get_deletion_date(current_deletion_date: datetime | None = None) -> datetime | None:
+    if settings.IS_DESKTOP:
+        return None
     date = now() + timedelta(days=settings.DAYS_TO_KEEP_ANALYSES)
     if current_deletion_date:
         return max(current_deletion_date, date)
diff --git a/bmds_server/analysis/validators/session.py b/bmds_server/analysis/validators/session.py
index 8055bbeb..b925f7d2 100644
--- a/bmds_server/analysis/validators/session.py
+++ b/bmds_server/analysis/validators/session.py
@@ -1,6 +1,7 @@
 from typing import Any, Literal
 
 import bmds
+from django.conf import settings
 from pydantic import BaseModel, conlist
 
 from ...common.validation import pydantic_validate
@@ -15,10 +16,13 @@ class BaseSession(BaseModel):
     dataset_type: bmds.constants.ModelClass
 
 
+max_items = 1000 if settings.IS_DESKTOP else 10
+
+
 class BaseSessionComplete(BaseSession):
-    datasets: conlist(Any, min_items=1, max_items=10)
+    datasets: conlist(Any, min_items=1, max_items=max_items)
     models: dict
-    options: conlist(Any, min_items=1, max_items=10)
+    options: conlist(Any, min_items=1, max_items=max_items)
 
 
 def validate_session(data: dict, partial: bool = False):
diff --git a/bmds_server/analysis/views.py b/bmds_server/analysis/views.py
index df30b827..b5a35892 100644
--- a/bmds_server/analysis/views.py
+++ b/bmds_server/analysis/views.py
@@ -83,6 +83,7 @@ def get_context_data(self, **kwargs):
             "wordUrl": self.object.get_word_url(),
             "future": settings.ALWAYS_SHOW_FUTURE
             or (self.request.user.is_staff and bool(self.request.GET.get("future"))),
+            "is_desktop": settings.IS_DESKTOP,
         }
         if self.can_edit:
             context["config"]["editSettings"] = {
diff --git a/bmds_server/main/context_processors.py b/bmds_server/main/context_processors.py
index 1f021312..93e6553b 100644
--- a/bmds_server/main/context_processors.py
+++ b/bmds_server/main/context_processors.py
@@ -13,4 +13,5 @@ def from_settings(request):
         CONTACT_US_EMAIL=settings.CONTACT_US_LINK,
         commit=settings.COMMIT,
         GTM_ID=settings.GTM_ID,
+        IS_DESKTOP=settings.IS_DESKTOP,
     )
diff --git a/bmds_server/main/settings/base.py b/bmds_server/main/settings/base.py
index ac161bec..b34f7f35 100644
--- a/bmds_server/main/settings/base.py
+++ b/bmds_server/main/settings/base.py
@@ -234,3 +234,4 @@ def get_git_commit() -> Commit:
 INCLUDE_ADMIN = bool(os.environ.get("INCLUDE_ADMIN", "True") == "True")
 
 INCLUDE_BETA_FEATURES = bool(os.environ.get("INCLUDE_BETA", "False") == "True")
+IS_DESKTOP = False
diff --git a/bmds_server/main/settings/testing.py b/bmds_server/main/settings/testing.py
index 7d3ba6b1..0b3e946c 100644
--- a/bmds_server/main/settings/testing.py
+++ b/bmds_server/main/settings/testing.py
@@ -15,4 +15,6 @@
 PASSWORD_HASHERS = ("django.contrib.auth.hashers.MD5PasswordHasher",)
 
 AUTH_PROVIDERS = {AuthProvider.django, AuthProvider.external}
+
 ALWAYS_SHOW_FUTURE = False
+IS_DESKTOP = False
diff --git a/frontend/src/components/Main/Actions/Actions.js b/frontend/src/components/Main/Actions/Actions.js
index 37640300..b4b8d9b7 100644
--- a/frontend/src/components/Main/Actions/Actions.js
+++ b/frontend/src/components/Main/Actions/Actions.js
@@ -56,7 +56,8 @@ class Actions extends Component {
                                     }}
                                 />
                             </div>
-                            {_.isNumber(config.editSettings.deletionDaysUntilDeletion) ? (
+                            {_.isNumber(config.editSettings.deletionDaysUntilDeletion) &&
+                            !mainStore.isDesktop ? (
                                 <>
                                     <a
                                         className="dropdown-item"
@@ -69,9 +70,11 @@ class Actions extends Component {
                                     </p>
                                 </>
                             ) : null}
-                            <a className="dropdown-item" href={config.editSettings.deleteUrl}>
-                                <Icon name="trash3-fill" text="Delete analysis" />
-                            </a>
+                            {!mainStore.isDesktop ? (
+                                <a className="dropdown-item" href={config.editSettings.deleteUrl}>
+                                    <Icon name="trash3-fill" text="Delete analysis" />
+                                </a>
+                            ) : null}
                             <div className="dropdown-divider"></div>
                         </>
                     ) : null}
diff --git a/frontend/src/components/Navigation.js b/frontend/src/components/Navigation.js
index f732bbc9..52556f27 100644
--- a/frontend/src/components/Navigation.js
+++ b/frontend/src/components/Navigation.js
@@ -43,11 +43,13 @@ class Navigation extends Component {
                             </NavLink>
                         </li>
                     )}
-                    {mainStore.canEdit ? (
+                    {mainStore.canEdit && !mainStore.isDesktop ? (
                         <li className="nav-item ml-auto mr-1">
                             <ShareActions />
                         </li>
-                    ) : null}
+                    ) : (
+                        <span className="ml-auto"></span>
+                    )}
                     <li
                         className={mainStore.canEdit ? "nav-item" : "nav-item ml-auto"}
                         style={{position: "relative"}}>
diff --git a/frontend/src/stores/DataStore.js b/frontend/src/stores/DataStore.js
index ad8da210..296f823a 100644
--- a/frontend/src/stores/DataStore.js
+++ b/frontend/src/stores/DataStore.js
@@ -268,7 +268,8 @@ class DataStore {
     }
 
     @computed get canAddNewDataset() {
-        return this.datasets.length < 6;
+        const maxItems = this.rootStore.mainStore.isDesktop ? 1000 : 6;
+        return this.datasets.length < maxItems;
     }
 
     @computed get hasSelectedDataset() {
diff --git a/frontend/src/stores/MainStore.js b/frontend/src/stores/MainStore.js
index e9599e87..f59f0e94 100644
--- a/frontend/src/stores/MainStore.js
+++ b/frontend/src/stores/MainStore.js
@@ -284,6 +284,9 @@ class MainStore {
     @computed get isFuture() {
         return this.config.future;
     }
+    @computed get isDesktop() {
+        return this.config.is_desktop;
+    }
     @computed get getExecutionOutputs() {
         return this.executionOutputs;
     }
diff --git a/frontend/src/stores/OptionsStore.js b/frontend/src/stores/OptionsStore.js
index 94e94cad..0a039e98 100644
--- a/frontend/src/stores/OptionsStore.js
+++ b/frontend/src/stores/OptionsStore.js
@@ -50,7 +50,8 @@ class OptionsStore {
     }
 
     @computed get canAddNewOption() {
-        return this.optionsList.length < 6;
+        const maxItems = this.rootStore.mainStore.isDesktop ? 1000 : 6;
+        return this.optionsList.length < maxItems;
     }
 }
 
diff --git a/requirements/base.txt b/requirements/base.txt
index 94d689f5..ea5a9f84 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -1,5 +1,5 @@
 # website
-Django~=4.2.1
+Django~=4.2.5
 django-anymail==9.1
 django-redis==5.2.0
 django-webpack-loader==1.8.0
diff --git a/tests/analysis/test_views.py b/tests/analysis/test_views.py
index 22227008..b62fe27b 100644
--- a/tests/analysis/test_views.py
+++ b/tests/analysis/test_views.py
@@ -42,6 +42,7 @@ def test_context(self):
             "excelUrl": f"/api/v1/analysis/{pk}/excel/",
             "wordUrl": f"/api/v1/analysis/{pk}/word/",
             "future": False,
+            "is_desktop": False,
         }
 
         # write view should have edit context
@@ -55,6 +56,7 @@ def test_context(self):
             "excelUrl": f"/api/v1/analysis/{pk}/excel/",
             "wordUrl": f"/api/v1/analysis/{pk}/word/",
             "future": False,
+            "is_desktop": False,
             "editSettings": {
                 "editKey": pw,
                 "viewUrl": f"http://testserver/analysis/{pk}/",

From 35ca68b5f9655f4eaa3b55e999826b0145e11df1 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Wed, 27 Sep 2023 10:18:37 -0400
Subject: [PATCH 03/24] UI updates for nested dichotomous and multitumor (#265)

* set max height for dataset tables

* fix layout issues with ND

* add ND hover

* make dataset y-size resizable

* ND model options

* ND read only options

* add modal outputs

* deployment updates

* nested logistic UI updaets

* complete nested dichotomous modal

* fix resizing of dataset table

* a few summary table/option updates

* dont show multitumor model selection since there's only one

* add ms combo summary tables

* add CSF to summary table

* multitumor updates

* individual plot

* show all models in result table; highlight selected

* add multitumor plot

* 4 dose groups

* add bottom margin

* simplify legend

* expand use of TwoColumnTable
---
 bmds_server/analysis/executor.py              |   8 +-
 bmds_server/main/settings/base.py             |   2 +-
 compose/app/Dockerfile                        |   4 +-
 compose/example.env                           |   1 +
 compose/postgres/Dockerfile                   |   2 +-
 frontend/src/components/Data/DatasetTable.js  |  47 ++++---
 .../components/IndividualModel/InfoTable.js   |  33 ++---
 .../IndividualModel/MaBenchmarkDose.js        |  37 ++---
 .../IndividualModel/ModelDetailModal.js       |   9 +-
 .../IndividualModel/ModelOptionsTable.js      |  53 +++----
 .../DatasetModelOption.js                     |   4 +-
 frontend/src/components/Main/Main.js          |   8 --
 .../Main/ModelsForm/ModelsCheckBox.js         |  18 +--
 .../Main/ModelsForm/ModelsCheckBoxList.js     |  37 +++--
 .../Main/OptionsForm/OptionsForm.js           |   8 +-
 .../Main/OptionsForm/OptionsReadOnly.js       |  23 ++-
 .../src/components/Output/Multitumor/Doses.js |  42 ------
 .../components/Output/Multitumor/InfoTable.js |  36 ++---
 .../components/Output/Multitumor/ModalBody.js |  84 ++++++-----
 .../Output/Multitumor/ModelOptions.js         |  53 +++----
 .../components/Output/Multitumor/MsCombo.js   |  48 +++++++
 .../Output/Multitumor/MultitumorPlot.js       |  97 +++++++++++++
 .../Output/Multitumor/ResultTable.js          | 133 +++++++++++-------
 .../components/Output/Multitumor/Summary.js   |  68 +++------
 .../NestedDichotomous/BootstrapResults.js     |  48 ++-----
 .../Output/NestedDichotomous/LitterData.js    |  19 ++-
 .../Output/NestedDichotomous/ModalBody.js     |  38 +++--
 .../NestedDichotomous/ModelParameters.js      |   4 +-
 .../Output/NestedDichotomous/ResultTable.js   |  17 ++-
 .../NestedDichotomous/ScaledResidual.js       |  49 ++-----
 .../Output/NestedDichotomous/Summary.js       |  39 +++++
 .../src/components/Output/OptionSetTable.js   |  16 ++-
 frontend/src/components/Output/Output.js      |   8 +-
 .../src/components/common/TwoColumnTable.js   |  42 ++++++
 frontend/src/constants/modelConstants.js      |  12 +-
 frontend/src/constants/optionsConstants.js    |   9 +-
 frontend/src/constants/plotting.js            |  30 ++--
 frontend/src/stores/MainStore.js              |   8 +-
 frontend/src/stores/OutputStore.js            |  34 +++++
 tests/conftest.py                             |  12 +-
 40 files changed, 715 insertions(+), 525 deletions(-)
 delete mode 100644 frontend/src/components/Output/Multitumor/Doses.js
 create mode 100644 frontend/src/components/Output/Multitumor/MsCombo.js
 create mode 100644 frontend/src/components/Output/Multitumor/MultitumorPlot.js
 create mode 100644 frontend/src/components/Output/NestedDichotomous/Summary.js
 create mode 100644 frontend/src/components/common/TwoColumnTable.js

diff --git a/bmds_server/analysis/executor.py b/bmds_server/analysis/executor.py
index d3b22a2a..345e67e1 100644
--- a/bmds_server/analysis/executor.py
+++ b/bmds_server/analysis/executor.py
@@ -60,10 +60,14 @@ def build_frequentist_session(dataset, inputs, options, dataset_options) -> Bmds
                     session.add_model(model_name, settings=model_options)
             elif dataset_type == ModelClass.NESTED_DICHOTOMOUS:
                 # run all permutations of intralitter correlation and litter specific covariate
-                for ilc, lsc in itertools.product(IntralitterCorrelation, LitterSpecificCovariate):
+                for ilc, lsc_on in itertools.product(IntralitterCorrelation, [True, False]):
                     settings = model_options.copy()
                     settings.intralitter_correlation = ilc
-                    settings.litter_specific_covariate = lsc
+                    settings.litter_specific_covariate = (
+                        settings.litter_specific_covariate
+                        if lsc_on
+                        else LitterSpecificCovariate.Unused
+                    )
                     session.add_model(model_name, settings=settings)
             else:
                 if model_name == bmds.constants.M_Linear:
diff --git a/bmds_server/main/settings/base.py b/bmds_server/main/settings/base.py
index b34f7f35..38ba8a61 100644
--- a/bmds_server/main/settings/base.py
+++ b/bmds_server/main/settings/base.py
@@ -110,7 +110,7 @@
 TIME_ZONE = os.getenv("TIME_ZONE", "US/Eastern")
 USE_TZ = True
 
-ALWAYS_SHOW_FUTURE = False
+ALWAYS_SHOW_FUTURE = bool(os.environ.get("ALWAYS_SHOW_FUTURE_MODE", "False") == "True")
 
 EMAIL_SUBJECT_PREFIX = f"[{PROJECT_NAME}] "
 DEFAULT_FROM_EMAIL = f"admin@{PROJECT_NAME}.com"
diff --git a/compose/app/Dockerfile b/compose/app/Dockerfile
index 94c42855..b44fd73c 100644
--- a/compose/app/Dockerfile
+++ b/compose/app/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.11-slim
+FROM python:3.11-slim-bullseye
 
 RUN groupadd -g 555 -r app && \
     useradd -u 555 -r -g app app
@@ -42,5 +42,5 @@ USER app
 
 ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
-RUN ldd /usr/local/lib/python3.11/site-packages/bmds/bin/BMDS330/libDRBMD.so && \
+RUN ldd /usr/local/lib/python3.11/site-packages/bmds/bmdscore.cpython-311-x86_64-linux-gnu.so && \
     python /app/test.py
diff --git a/compose/example.env b/compose/example.env
index fe5c8a46..af69dac9 100644
--- a/compose/example.env
+++ b/compose/example.env
@@ -40,3 +40,4 @@ REDIS_PASSWORD=ZhMycQumkiiQRwLCSO9LaNKdRvXv8-I67dNaXRJ2vqA
 BMDS_REQUEST_URL=http://bmds-python.com/api/dfile/
 BMDS_TOKEN=e8348f40f62e00b8acbcfb6a22dacb2f834c5bfd47af6d74dc3d3290d180de37
 INCLUDE_BETA=False
+ALWAYS_SHOW_FUTURE_MODE=False
diff --git a/compose/postgres/Dockerfile b/compose/postgres/Dockerfile
index db1ee643..5607b40a 100644
--- a/compose/postgres/Dockerfile
+++ b/compose/postgres/Dockerfile
@@ -1,4 +1,4 @@
-FROM postgres:12.5-alpine
+FROM postgres:12-alpine
 
 # add backup scripts
 ADD backup.sh /usr/local/bin/backup
diff --git a/frontend/src/components/Data/DatasetTable.js b/frontend/src/components/Data/DatasetTable.js
index ad0e1c5d..c94395de 100644
--- a/frontend/src/components/Data/DatasetTable.js
+++ b/frontend/src/components/Data/DatasetTable.js
@@ -46,7 +46,13 @@ class DatasetTable extends Component {
     render() {
         const {dataset} = this.props,
             columnNames = columns[dataset.dtype],
-            width = `${100 / columnNames.length}%`;
+            width = `${100 / columnNames.length}%`,
+            isIndividual = dataset.dtype === Dtype.CONTINUOUS_INDIVIDUAL,
+            nRows = dataset.doses.length,
+            divStyle =
+                !isIndividual && nRows > 10
+                    ? {height: "50vh", overflowY: "auto", resize: "vertical"}
+                    : {};
 
         return (
             <>
@@ -54,26 +60,27 @@ class DatasetTable extends Component {
                     <label>Dataset Name:&nbsp;</label>
                     {dataset.metadata.name}
                 </div>
-
-                <table className="table table-sm table-bordered text-right">
-                    <colgroup>
-                        {columnNames.map((d, i) => (
-                            <col key={i} width={width} />
-                        ))}
-                    </colgroup>
-                    <thead className="bg-custom">
-                        <tr>
-                            {columnNames.map((column, i) => (
-                                <th key={i}>{columnHeaders[column]}</th>
+                <div style={divStyle}>
+                    <table className="table table-sm table-bordered text-right">
+                        <colgroup>
+                            {columnNames.map((d, i) => (
+                                <col key={i} width={width} />
                             ))}
-                        </tr>
-                    </thead>
-                    <tbody>
-                        {dataset.dtype === Dtype.CONTINUOUS_INDIVIDUAL
-                            ? individualDataRows(dataset)
-                            : dataRows(dataset, columnNames)}
-                    </tbody>
-                </table>
+                        </colgroup>
+                        <thead className="bg-custom">
+                            <tr>
+                                {columnNames.map((column, i) => (
+                                    <th key={i}>{columnHeaders[column]}</th>
+                                ))}
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {isIndividual
+                                ? individualDataRows(dataset)
+                                : dataRows(dataset, columnNames)}
+                        </tbody>
+                    </table>
+                </div>
             </>
         );
     }
diff --git a/frontend/src/components/IndividualModel/InfoTable.js b/frontend/src/components/IndividualModel/InfoTable.js
index a575266f..5b3582b1 100644
--- a/frontend/src/components/IndividualModel/InfoTable.js
+++ b/frontend/src/components/IndividualModel/InfoTable.js
@@ -2,36 +2,21 @@ import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import TwoColumnTable from "@/components/common/TwoColumnTable";
+
 @inject("outputStore")
 @observer
 class InfoTable extends Component {
     render() {
         const {outputStore} = this.props,
             model = outputStore.modalModel,
-            dataset = outputStore.selectedDataset;
-        return (
-            <table id="info-table" className="table table-sm table-bordered">
-                <thead>
-                    <tr className="bg-custom">
-                        <th colSpan="2">Info</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    <tr>
-                        <td>Dataset</td>
-                        <td>{dataset.metadata.name}</td>
-                    </tr>
-                    <tr>
-                        <td>Model</td>
-                        <td>{model.name}</td>
-                    </tr>
-                    <tr>
-                        <td>Equation</td>
-                        <td>{model.model_class.model_form_str}</td>
-                    </tr>
-                </tbody>
-            </table>
-        );
+            dataset = outputStore.selectedDataset,
+            data = [
+                ["Dataset", dataset.metadata.name],
+                ["Model", model.name],
+                ["Equation", model.model_class.model_form_str],
+            ];
+        return <TwoColumnTable data={data} label="Info" />;
     }
 }
 InfoTable.propTypes = {
diff --git a/frontend/src/components/IndividualModel/MaBenchmarkDose.js b/frontend/src/components/IndividualModel/MaBenchmarkDose.js
index 8c8802dc..bb0e91c2 100644
--- a/frontend/src/components/IndividualModel/MaBenchmarkDose.js
+++ b/frontend/src/components/IndividualModel/MaBenchmarkDose.js
@@ -4,37 +4,18 @@ import React, {Component} from "react";
 
 import {ff} from "@/utils/formatters";
 
+import TwoColumnTable from "../common/TwoColumnTable";
+
 @observer
 class MaBenchmarkDose extends Component {
     render() {
-        const {results} = this.props;
-        return (
-            <table id="ma-result-summary" className="table table-sm table-bordered col-r-2">
-                <colgroup>
-                    <col width="60%" />
-                    <col width="40%" />
-                </colgroup>
-                <thead>
-                    <tr className="bg-custom">
-                        <th colSpan="2">Summary</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    <tr>
-                        <td>BMD</td>
-                        <td>{ff(results.bmd)}</td>
-                    </tr>
-                    <tr>
-                        <td>BMDL</td>
-                        <td>{ff(results.bmdl)}</td>
-                    </tr>
-                    <tr>
-                        <td>BMDU</td>
-                        <td>{ff(results.bmdu)}</td>
-                    </tr>
-                </tbody>
-            </table>
-        );
+        const {results} = this.props,
+            data = [
+                ["BMD", ff(results.bmd)],
+                ["BMDL", ff(results.bmdl)],
+                ["BMDU", ff(results.bmdu)],
+            ];
+        return <TwoColumnTable id="ma-result-summary" label="Summary" data={data} />;
     }
 }
 MaBenchmarkDose.propTypes = {
diff --git a/frontend/src/components/IndividualModel/ModelDetailModal.js b/frontend/src/components/IndividualModel/ModelDetailModal.js
index 529404d9..85f985bc 100644
--- a/frontend/src/components/IndividualModel/ModelDetailModal.js
+++ b/frontend/src/components/IndividualModel/ModelDetailModal.js
@@ -149,13 +149,8 @@ ModelAverageBody.propTypes = {
 @observer
 class ModelDetailModal extends Component {
     getTitle() {
-        const {outputStore} = this.props,
-            model = outputStore.modalModel;
-        if (outputStore.isMultiTumor) {
-            return outputStore.drModelModalIsMA ? "MS Combo" : "TODO";
-        } else {
-            return outputStore.drModelModalIsMA ? "Model Average" : model.name;
-        }
+        const {outputStore} = this.props;
+        return outputStore.modalName;
     }
     getBody() {
         const {outputStore} = this.props;
diff --git a/frontend/src/components/IndividualModel/ModelOptionsTable.js b/frontend/src/components/IndividualModel/ModelOptionsTable.js
index 2e0bdf3f..690a7fe4 100644
--- a/frontend/src/components/IndividualModel/ModelOptionsTable.js
+++ b/frontend/src/components/IndividualModel/ModelOptionsTable.js
@@ -3,12 +3,15 @@ import PropTypes from "prop-types";
 import React, {Component} from "react";
 
 import {getLabel} from "@/common";
+import TwoColumnTable from "@/components/common/TwoColumnTable";
 import {Dtype} from "@/constants/dataConstants";
 import {hasDegrees} from "@/constants/modelConstants";
 import {
     continuousBmrOptions,
     dichotomousBmrOptions,
     distTypeOptions,
+    intralitterCorrelation,
+    litterSpecificCovariateOptions,
 } from "@/constants/optionsConstants";
 import {priorClassLabels} from "@/constants/outputConstants";
 import {ff} from "@/utils/formatters";
@@ -23,8 +26,12 @@ const restrictionMapping = {
 class ModelOptionsTable extends Component {
     render() {
         const {dtype, model} = this.props,
-            priorLabels = restrictionMapping[model.settings.priors.prior_class],
-            priorClass = getLabel(model.settings.priors.prior_class, priorClassLabels),
+            priorLabels = model.settings.priors
+                ? restrictionMapping[model.settings.priors.prior_class]
+                : null,
+            priorClass = model.settings.priors
+                ? getLabel(model.settings.priors.prior_class, priorClassLabels)
+                : null,
             isBayesian = priorClass === "Bayesian";
         let data = [];
 
@@ -55,32 +62,30 @@ class ModelOptionsTable extends Component {
                 isBayesian ? ["Samples", model.settings.samples] : null,
                 isBayesian ? ["Burn In", model.settings.burnin] : null,
             ];
+        } else if (dtype == Dtype.NESTED_DICHOTOMOUS) {
+            data = [
+                ["BMR Type", getLabel(model.settings.bmr_type, dichotomousBmrOptions)],
+                ["BMR", ff(model.settings.bmr)],
+                ["Confidence Level", ff(1 - model.settings.alpha)],
+                ["Bootstrap Seed", model.settings.bootstrap_seed],
+                ["Bootstrap Iterations", model.settings.bootstrap_iterations],
+                [
+                    "Intralitter Correlation",
+                    getLabel(model.settings.intralitter_correlation, intralitterCorrelation),
+                ],
+                [
+                    "Litter Specific Covariate",
+                    getLabel(
+                        model.settings.litter_specific_covariate,
+                        litterSpecificCovariateOptions
+                    ),
+                ],
+            ];
         } else {
             throw "Unknown dtype";
         }
 
-        return (
-            <table className="table table-sm table-bordered col-r-2">
-                <thead>
-                    <tr className="bg-custom">
-                        <th colSpan="2">Model Options</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    {data.map((d, i) => {
-                        if (!d) {
-                            return null;
-                        }
-                        return (
-                            <tr key={i}>
-                                <td>{d[0]}</td>
-                                <td>{d[1]}</td>
-                            </tr>
-                        );
-                    })}
-                </tbody>
-            </table>
-        );
+        return <TwoColumnTable data={data} label="Model Options" />;
     }
 }
 ModelOptionsTable.propTypes = {
diff --git a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js
index a7c1284a..1215faa2 100644
--- a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js
+++ b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js
@@ -66,7 +66,9 @@ class DatasetModelOption extends Component {
             <tr>
                 <td className="text-center">{checkOrEmpty(option.enabled)}</td>
                 <td>{dataset.metadata.name}</td>
-                <td>{getDegreeText(dtype, option.degree)}</td>
+                {option.degree !== undefined ? (
+                    <td>{getDegreeText(dtype, option.degree)}</td>
+                ) : null}
                 {hasAdverseDirection ? (
                     <td>{getLabel(option.adverse_direction, adverseDirectionOptions)}</td>
                 ) : null}
diff --git a/frontend/src/components/Main/Main.js b/frontend/src/components/Main/Main.js
index e62fcf95..4ca3987e 100644
--- a/frontend/src/components/Main/Main.js
+++ b/frontend/src/components/Main/Main.js
@@ -2,7 +2,6 @@ import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
-import Button from "../common/Button";
 import AnalysisForm from "./AnalysisForm/AnalysisForm";
 import AnalysisFormReadOnly from "./AnalysisForm/AnalysisFormReadOnly";
 import DatasetModelOptionList from "./DatasetModelOptionList/DatasetModelOptionList";
@@ -24,13 +23,6 @@ class Main extends Component {
                     <div>{mainStore.getDatasetLength ? <DatasetModelOptionList /> : null}</div>
                 </div>
                 <div className="col-lg-8">
-                    {mainStore.canEdit ? (
-                        <Button
-                            className="btn btn-sm btn-warning"
-                            onClick={mainStore.resetModelSelection}
-                            text="Reset Model Selection"
-                        />
-                    ) : null}
                     <ModelsCheckBoxList />
                     <OptionsFormList />
                 </div>
diff --git a/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js b/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
index 188c6d33..ef93aded 100644
--- a/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
+++ b/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
@@ -193,22 +193,8 @@ const ModelsCheckBox = observer(props => {
                 </tr>
                 <tr>
                     <td className="text-left align-middle">NCTR</td>
-                    <CheckBoxTd store={store} type={fr} model={"NCTR"} />
-                    <CheckBoxTd store={store} type={fu} model={"NCTR"} />
-                </tr>
-            </tbody>
-        );
-    }
-    if (store.getModelType === mc.MODEL_MULTI_TUMOR) {
-        return (
-            <tbody>
-                <tr>
-                    <td className="text-left align-middle">
-                        Multistage
-                        {writeMode ? <HelpTextPopover content={multistageHelpText} /> : null}
-                    </td>
-                    <CheckBoxTd store={store} type={fr} model={"Multistage"} />
-                    <CheckBoxTd store={store} type={fu} model={"Multistage"} disabled={true} />
+                    <CheckBoxTd store={store} type={fr} model={"NCTR"} disabled={true} />
+                    <CheckBoxTd store={store} type={fu} model={"NCTR"} disabled={true} />
                 </tr>
             </tbody>
         );
diff --git a/frontend/src/components/Main/ModelsForm/ModelsCheckBoxList.js b/frontend/src/components/Main/ModelsForm/ModelsCheckBoxList.js
index d20dc448..eedc0d2d 100644
--- a/frontend/src/components/Main/ModelsForm/ModelsCheckBoxList.js
+++ b/frontend/src/components/Main/ModelsForm/ModelsCheckBoxList.js
@@ -2,6 +2,9 @@ import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import {MODEL_MULTI_TUMOR} from "@/constants/mainConstants";
+
+import Button from "../../common/Button";
 import ModelsCheckBox from "./ModelsCheckBox";
 import ModelsCheckBoxHeader from "./ModelsCheckBoxHeader";
 
@@ -9,16 +12,34 @@ import ModelsCheckBoxHeader from "./ModelsCheckBoxHeader";
 @observer
 class ModelsCheckBoxList extends Component {
     render() {
-        const {modelsStore} = this.props;
-        let models = modelsStore.models;
+        const {modelsStore} = this.props,
+            mainStore = modelsStore.rootStore.mainStore;
+        if (modelsStore.getModelType === MODEL_MULTI_TUMOR) {
+            return (
+                <div className="alert alert-info my-3">
+                    If multiple tumor datasets are evaluated, this tool will output individual and
+                    combined tumor risk estimates.
+                    <br />
+                    <br />
+                    The combined tumor risk estimates will only be relevant for tumors from the same
+                    study and the model assumes that tumors develop independently, eg., one tumor
+                    does not progress to or influence the development of another
+                </div>
+            );
+        }
         return (
-            <div className="mt-2 text-center">
-                {!(typeof models === "undefined") ? (
-                    <table className="table table-sm table-bordered">
-                        <ModelsCheckBoxHeader store={modelsStore} />
-                        <ModelsCheckBox store={modelsStore} />
-                    </table>
+            <div className="mt-2">
+                {mainStore.canEdit ? (
+                    <Button
+                        className="btn btn-sm btn-warning"
+                        onClick={mainStore.resetModelSelection}
+                        text="Reset Model Selection"
+                    />
                 ) : null}
+                <table className="table table-sm table-bordered">
+                    <ModelsCheckBoxHeader store={modelsStore} />
+                    <ModelsCheckBox store={modelsStore} />
+                </table>
             </div>
         );
     }
diff --git a/frontend/src/components/Main/OptionsForm/OptionsForm.js b/frontend/src/components/Main/OptionsForm/OptionsForm.js
index fa442ef0..87a36113 100644
--- a/frontend/src/components/Main/OptionsForm/OptionsForm.js
+++ b/frontend/src/components/Main/OptionsForm/OptionsForm.js
@@ -92,9 +92,11 @@ const OptionsForm = props => {
                                     props.idx
                                 )
                             }
-                            choices={litterSpecificCovariateOptions.map(option => {
-                                return {value: option.value, text: option.label};
-                            })}
+                            choices={litterSpecificCovariateOptions
+                                .filter(d => d.value > 0)
+                                .map(option => {
+                                    return {value: option.value, text: option.label};
+                                })}
                         />
                     </td>
                     <td>
diff --git a/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js b/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js
index bc359baf..c213996c 100644
--- a/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js
+++ b/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js
@@ -2,11 +2,17 @@ import PropTypes from "prop-types";
 import React from "react";
 
 import {getLabel} from "@/common";
-import {MODEL_CONTINUOUS, MODEL_DICHOTOMOUS, MODEL_MULTI_TUMOR} from "@/constants/mainConstants";
+import {
+    MODEL_CONTINUOUS,
+    MODEL_DICHOTOMOUS,
+    MODEL_MULTI_TUMOR,
+    MODEL_NESTED_DICHOTOMOUS,
+} from "@/constants/mainConstants";
 import {
     continuousBmrOptions,
     dichotomousBmrOptions,
     distTypeOptions,
+    litterSpecificCovariateOptions,
 } from "@/constants/optionsConstants";
 import {ff} from "@/utils/formatters";
 
@@ -31,6 +37,21 @@ const OptionsReadOnly = props => {
                     <td>{ff(options.confidence_level * 100)}%</td>
                 </>
             ) : null}
+            {modelType === MODEL_NESTED_DICHOTOMOUS ? (
+                <>
+                    <td>{getLabel(options.bmr_type, dichotomousBmrOptions)}</td>
+                    <td>{ff(options.bmr_value)}</td>
+                    <td>{ff(options.confidence_level * 100)}%</td>
+                    <td>
+                        {getLabel(
+                            options.litter_specific_covariate,
+                            litterSpecificCovariateOptions
+                        )}
+                    </td>
+                    <td>{options.bootstrap_iterations}</td>
+                    <td>{options.bootstrap_seed}</td>
+                </>
+            ) : null}
         </tr>
     );
 };
diff --git a/frontend/src/components/Output/Multitumor/Doses.js b/frontend/src/components/Output/Multitumor/Doses.js
deleted file mode 100644
index c0989160..00000000
--- a/frontend/src/components/Output/Multitumor/Doses.js
+++ /dev/null
@@ -1,42 +0,0 @@
-import _ from "lodash";
-import {observer} from "mobx-react";
-import PropTypes from "prop-types";
-import React, {Component} from "react";
-
-@observer
-class Doses extends Component {
-    render() {
-        const dataset = this.props.model,
-            temp_rslt_len = _.size(dataset.doses);
-        return (
-            <table className="table table-sm table-bordered">
-                <thead>
-                    <tr className="bg-custom">
-                        <th colSpan="3">Doses</th>
-                    </tr>
-                    <tr>
-                        <th>Dose</th>
-                        <th>Incidence</th>
-                        <th>N</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    {_.range(temp_rslt_len).map(i => {
-                        return (
-                            <tr key={i}>
-                                <td>{dataset.doses[i]}</td>
-                                <td>{dataset.incidences[i]}</td>
-                                <td>{dataset.ns[i]}</td>
-                            </tr>
-                        );
-                    })}
-                </tbody>
-            </table>
-        );
-    }
-}
-Doses.propTypes = {
-    model: PropTypes.object,
-};
-
-export default Doses;
diff --git a/frontend/src/components/Output/Multitumor/InfoTable.js b/frontend/src/components/Output/Multitumor/InfoTable.js
index def6cbe4..2e205aad 100644
--- a/frontend/src/components/Output/Multitumor/InfoTable.js
+++ b/frontend/src/components/Output/Multitumor/InfoTable.js
@@ -2,38 +2,22 @@ import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import TwoColumnTable from "@/components/common/TwoColumnTable";
+import {getNameFromDegrees} from "@/constants/modelConstants";
+
 @inject("outputStore")
 @observer
 class InfoTable extends Component {
     render() {
         const {outputStore} = this.props,
             model = outputStore.modalModel,
-            isSummary = outputStore.drModelModalIsMA,
-            dataset = outputStore.modalDataset;
-
-        return (
-            <table id="info-table" className="table table-sm table-bordered">
-                <thead>
-                    <tr className="bg-custom">
-                        <th colSpan="2">Info</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    <tr>
-                        <td>Dataset</td>
-                        {isSummary ? <td>Summary</td> : <td>{dataset.metadata.name}</td>}
-                    </tr>
-                    <tr>
-                        <td>Model</td>
-                        <td>{model.name}</td>
-                    </tr>
-                    <tr>
-                        <td>Equation</td>
-                        <td></td>
-                    </tr>
-                </tbody>
-            </table>
-        );
+            dataset = outputStore.modalDataset,
+            data = [
+                ["Dataset", dataset.metadata.name],
+                ["Model", getNameFromDegrees(model)],
+                ["Equation", "P[dose] = g + (1 - g) * (1 - exp(-b1 * dose^1 - b2 * dose^2 - ...))"],
+            ];
+        return <TwoColumnTable data={data} label="Info" />;
     }
 }
 InfoTable.propTypes = {
diff --git a/frontend/src/components/Output/Multitumor/ModalBody.js b/frontend/src/components/Output/Multitumor/ModalBody.js
index 4376f9fd..50dd9484 100644
--- a/frontend/src/components/Output/Multitumor/ModalBody.js
+++ b/frontend/src/components/Output/Multitumor/ModalBody.js
@@ -3,12 +3,14 @@ import PropTypes from "prop-types";
 import React, {Component} from "react";
 import {Col, Modal, Row} from "react-bootstrap";
 
+import DoseResponsePlot from "../../common/DoseResponsePlot";
 import ModelParameters from "../../IndividualModel/ModelParameters";
 import AnalysisOfDeviance from "./AnalysisOfDeviance";
-import Doses from "./Doses";
 import GoodnessFit from "./GoodnessFit";
 import InfoTable from "./InfoTable";
 import ModelOptions from "./ModelOptions";
+import {MsComboInfo, MsComboSummary} from "./MsCombo";
+import MultitumorPlot from "./MultitumorPlot";
 import ParameterSettings from "./ParameterSettings";
 import Summary from "./Summary";
 
@@ -17,48 +19,56 @@ class ModalBody extends Component {
     render() {
         const {outputStore} = this.props,
             model = outputStore.modalModel,
-            isSummary = outputStore.drModelModalIsMA,
-            dataset = outputStore.modalDataset;
+            isSummary = outputStore.drModelModalIsMA;
+
+        if (isSummary) {
+            return (
+                <Modal.Body>
+                    <Row>
+                        <Col xl={6}>
+                            <MsComboInfo options={outputStore.selectedModelOptions} />
+                        </Col>
+                        <Col xl={6}>
+                            <MsComboSummary results={model} />
+                        </Col>
+                        <Col xl={12}>
+                            <MultitumorPlot />
+                        </Col>
+                    </Row>
+                </Modal.Body>
+            );
+        }
         return (
             <Modal.Body>
                 <Row>
-                    <Col xl={3}>
+                    <Col xl={4}>
                         <InfoTable />
                     </Col>
-                    <Col xl={3}>{!isSummary && <ModelOptions model={model} />}</Col>
-                    <Col xl={3}>{!isSummary && <Doses model={dataset} />}</Col>
+                    <Col xl={4}>
+                        <ModelOptions />
+                    </Col>
+                    <Col xl={4}>
+                        <ParameterSettings model={model} />
+                    </Col>
+                    <Col xl={6}>
+                        <Summary model={model} />
+                    </Col>
+                    <Col xs={6}>
+                        <DoseResponsePlot
+                            layout={outputStore.drIndividualMultitumorPlotLayout}
+                            data={outputStore.drIndividualMultitumorPlotData}
+                        />
+                    </Col>
+                    <Col xl={6}>
+                        <ModelParameters parameters={model.parameters} />
+                    </Col>
+                    <Col xl={6}>
+                        <GoodnessFit store={outputStore} />
+                    </Col>
+                    <Col xl={6}>
+                        <AnalysisOfDeviance model={model} />
+                    </Col>
                 </Row>
-                {!isSummary && (
-                    <Row>
-                        <Col xl={4}>
-                            <Summary model={model} />
-                        </Col>
-                        <Col xl={5}>
-                            <ParameterSettings model={model} />
-                        </Col>
-                    </Row>
-                )}
-                {!isSummary && (
-                    <Row>
-                        <Col xl={9}>
-                            <ModelParameters parameters={model.parameters} />
-                        </Col>
-                    </Row>
-                )}
-                {!isSummary && (
-                    <Row>
-                        <Col xl={9}>
-                            <GoodnessFit store={outputStore} />
-                        </Col>
-                    </Row>
-                )}
-                {!isSummary && (
-                    <Row>
-                        <Col xl={9}>
-                            <AnalysisOfDeviance model={model} />
-                        </Col>
-                    </Row>
-                )}
             </Modal.Body>
         );
     }
diff --git a/frontend/src/components/Output/Multitumor/ModelOptions.js b/frontend/src/components/Output/Multitumor/ModelOptions.js
index b5b44e55..b073ac4b 100644
--- a/frontend/src/components/Output/Multitumor/ModelOptions.js
+++ b/frontend/src/components/Output/Multitumor/ModelOptions.js
@@ -1,45 +1,30 @@
-import {observer} from "mobx-react";
+import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import {getLabel} from "@/common";
+import TwoColumnTable from "@/components/common/TwoColumnTable";
+import {dichotomousBmrOptions} from "@/constants/optionsConstants";
+import {ff} from "@/utils/formatters";
+
+@inject("outputStore")
 @observer
 class ModelOptions extends Component {
     render() {
-        // const {model} = this.props;
-        let data = [];
-
-        data = [
-            ["BMR Type", "BMR Type"],
-            ["BMR", "BMR"],
-            ["Confidence Level", "confidence level"],
-            ["Degree", "degree"],
-        ];
-
-        return (
-            <table className="table table-sm table-bordered col-r-2">
-                <thead>
-                    <tr className="bg-custom">
-                        <th colSpan="2">Model Options</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    {data.map((d, i) => {
-                        if (!d) {
-                            return null;
-                        }
-                        return (
-                            <tr key={i}>
-                                <td>{d[0]}</td>
-                                <td>{d[1]}</td>
-                            </tr>
-                        );
-                    })}
-                </tbody>
-            </table>
-        );
+        const {outputStore} = this.props,
+            options = outputStore.selectedModelOptions,
+            {modalOptionSet} = outputStore,
+            degree = modalOptionSet.degree == 0 ? "auto" : modalOptionSet.degree,
+            data = [
+                ["Risk Type", getLabel(options.bmr_type, dichotomousBmrOptions)],
+                ["BMR", ff(options.bmr_value)],
+                ["Confidence Level", ff(options.confidence_level)],
+                ["Degree", degree],
+            ];
+        return <TwoColumnTable data={data} label="Model Options" />;
     }
 }
 ModelOptions.propTypes = {
-    model: PropTypes.object.isRequired,
+    outputStore: PropTypes.object,
 };
 export default ModelOptions;
diff --git a/frontend/src/components/Output/Multitumor/MsCombo.js b/frontend/src/components/Output/Multitumor/MsCombo.js
new file mode 100644
index 00000000..5038617d
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/MsCombo.js
@@ -0,0 +1,48 @@
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+import {getLabel} from "@/common";
+import TwoColumnTable from "@/components/common/TwoColumnTable";
+import {dichotomousBmrOptions} from "@/constants/optionsConstants";
+import {ff} from "@/utils/formatters";
+
+@observer
+class MsComboInfo extends Component {
+    render() {
+        const {options} = this.props,
+            label = "Settings",
+            data = [
+                ["Model", "Multitumor"],
+                ["Risk Type", getLabel(options.bmr_type, dichotomousBmrOptions)],
+                ["BMR", ff(options.bmr_value)],
+                ["Confidence Level", ff(options.confidence_level)],
+            ];
+        return <TwoColumnTable data={data} label={label} />;
+    }
+}
+MsComboInfo.propTypes = {
+    options: PropTypes.object.isRequired,
+};
+
+@observer
+class MsComboSummary extends Component {
+    render() {
+        const {results} = this.props,
+            label = "Summary",
+            data = [
+                ["BMD", ff(results.bmd)],
+                ["BMDL", ff(results.bmdl)],
+                ["BMDU", ff(results.bmdu)],
+                ["Slope Factor", ff(results.slope_factor)],
+                ["Combined Log-Likelihood", ff(results.ll)],
+                ["Combined Log-Likelihood Constant", ff(results.ll_constant)],
+            ];
+        return <TwoColumnTable data={data} label={label} />;
+    }
+}
+MsComboSummary.propTypes = {
+    results: PropTypes.object.isRequired,
+};
+
+export {MsComboInfo, MsComboSummary};
diff --git a/frontend/src/components/Output/Multitumor/MultitumorPlot.js b/frontend/src/components/Output/Multitumor/MultitumorPlot.js
new file mode 100644
index 00000000..ad23b5a4
--- /dev/null
+++ b/frontend/src/components/Output/Multitumor/MultitumorPlot.js
@@ -0,0 +1,97 @@
+import {inject, observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+import DoseResponsePlot from "@/components/common/DoseResponsePlot";
+import {getNameFromDegrees} from "@/constants/modelConstants";
+import {colorCodes, getDrLayout, getResponse} from "@/constants/plotting";
+
+const getLayout = function(datasets) {
+    let layout;
+    datasets.forEach(dataset => {
+        if (layout === undefined) {
+            layout = getDrLayout(dataset);
+            layout.title.text = "Multitumor (MS Combo)";
+            layout.yaxis.range = [0, 1];
+        } else {
+            const revised = getDrLayout(dataset);
+            if (revised.xaxis.range[0] < layout.xaxis.range[0]) {
+                layout.xaxis.range[0] = revised.xaxis.range[0];
+            }
+            if (revised.xaxis.range[1] > layout.xaxis.range[1]) {
+                layout.xaxis.range[1] = revised.xaxis.range[1];
+            }
+        }
+    });
+    return layout;
+};
+
+const getData = function(ma, datasets, models) {
+    let data = [];
+
+    // add individual datasets
+    datasets.forEach((dataset, index) => {
+        data.push({
+            x: dataset.doses.slice(),
+            y: getResponse(dataset).slice(),
+            mode: "markers",
+            type: "scatter",
+            marker: {
+                size: 12,
+                color: "rgba(0,0,0,0)",
+                line: {color: colorCodes[index], width: 2},
+            },
+            legendgroup: index,
+            showlegend: false,
+        });
+    });
+
+    // add selected models
+    models.forEach((model, index) => {
+        let dataset = datasets[index];
+        data.push({
+            x: model.plotting.dr_x,
+            y: model.plotting.dr_y,
+            line: {
+                width: 3,
+                color: colorCodes[index],
+            },
+            legendgroup: index,
+            name: `${dataset.metadata.name} ${getNameFromDegrees(model)}`,
+        });
+    });
+
+    // add slope factor
+    data.push({
+        x: [0, ma.bmd],
+        y: [0, ma.bmd * ma.slope_factor],
+        name: "Cancer Slope Factor",
+        line: {
+            width: 5,
+            color: "black",
+            dash: "dot",
+        },
+    });
+
+    return data;
+};
+
+@inject("outputStore")
+@observer
+class MultitumorPlot extends Component {
+    render() {
+        const store = this.props.outputStore,
+            layout = getLayout(store.multitumorDatasets),
+            data = getData(
+                store.selectedFrequentist.results,
+                store.multitumorDatasets,
+                store.selectedMultitumorModels
+            );
+
+        return <DoseResponsePlot data={data} layout={layout} />;
+    }
+}
+MultitumorPlot.propTypes = {
+    outputStore: PropTypes.object,
+};
+export default MultitumorPlot;
diff --git a/frontend/src/components/Output/Multitumor/ResultTable.js b/frontend/src/components/Output/Multitumor/ResultTable.js
index cd85a288..ec0eeadd 100644
--- a/frontend/src/components/Output/Multitumor/ResultTable.js
+++ b/frontend/src/components/Output/Multitumor/ResultTable.js
@@ -3,6 +3,7 @@ import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import {getNameFromDegrees} from "@/constants/modelConstants";
 import {ff} from "@/utils/formatters";
 
 @inject("outputStore")
@@ -15,10 +16,11 @@ class ResultTable extends Component {
         if (!selectedFrequentist) {
             return null;
         }
-        const colWidths = [11, 11, 11, 11, 11, 11, 11, 11, 11],
+        const colWidths = [15, 15, 10, 10, 10, 10, 10, 10],
             {results} = selectedFrequentist,
-            {selectedMultitumorModels} = store,
-            indexes = results.selected_model_indexes;
+            {multitumorDatasets} = store,
+            indexes = results.selected_model_indexes,
+            showMultitumor = store.multitumorDatasets.length > 1;
 
         return (
             <table className="table table-sm">
@@ -30,68 +32,93 @@ class ResultTable extends Component {
                 <thead className="table-bordered">
                     <tr className="bg-custom">
                         <th>Model</th>
+                        <th>Dataset</th>
                         <th>BMDL</th>
                         <th>BMD</th>
                         <th>BMDU</th>
+                        <th>CSF</th>
                         <th>
                             <i>P</i>-Value
                         </th>
                         <th>AIC</th>
-                        <th>Unnormalized Log Posterior Probability</th>
-                        <th>Scaled Residual for Dose Group near BMD</th>
-                        <th>Scaled Residual for Control Dose Group</th>
                     </tr>
                 </thead>
                 <tbody className="table-bordered">
-                    <tr key={-1}>
-                        <td>
-                            <a
-                                id={`freq-result-${-1}`}
-                                href="#"
-                                onClick={e => {
-                                    e.preventDefault();
-                                    store.showModalDetailMultitumor(-1, -1);
-                                }}>
-                                Multi-tumor (MS Combo)
-                            </a>
-                        </td>
-                        <td>{ff(results.bmdl)}</td>
-                        <td>{ff(results.bmd)}</td>
-                        <td>{ff(results.bmdu)}</td>
-                        <td>-9999</td>
-                        <td>-9999</td>
-                        <td>???</td>
-                        <td>???</td>
-                        <td>???</td>
-                    </tr>
-                    {selectedMultitumorModels.map((model, index) => {
-                        const degree = model.parameters.names.length - 1,
-                            name = `Multistage ${degree}°`;
-                        return (
-                            <tr key={index}>
-                                <td>
-                                    <a
-                                        id={`freq-result-${index}`}
-                                        href="#"
-                                        onClick={e => {
-                                            e.preventDefault();
-                                            store.showModalDetailMultitumor(index, indexes[index]);
-                                        }}>
-                                        {name}
-                                    </a>
-                                </td>
-                                <td>{ff(model.bmdl)}</td>
-                                <td>{ff(model.bmd)}</td>
-                                <td>{ff(model.bmdu)}</td>
-                                <td>-9999</td>
-                                <td>-9999</td>
-                                <td>???</td>
-                                <td>???</td>
-                                <td>???</td>
-                            </tr>
-                        );
+                    {showMultitumor ? (
+                        <tr key={-1}>
+                            <td>
+                                <a
+                                    id={`freq-result-${-1}`}
+                                    href="#"
+                                    onClick={e => {
+                                        e.preventDefault();
+                                        store.showModalDetailMultitumor(-1, -1);
+                                    }}>
+                                    Multi-tumor (MS Combo)
+                                </a>
+                            </td>
+                            <td>-</td>
+                            <td>{ff(results.bmdl)}</td>
+                            <td>{ff(results.bmd)}</td>
+                            <td>{ff(results.bmdu)}</td>
+                            <td>{ff(results.slope_factor)}</td>
+                            <td>-</td>
+                            <td>-</td>
+                        </tr>
+                    ) : null}
+                    {results.models.map((dataset_models, dataset_index) => {
+                        const dataset = multitumorDatasets[dataset_index],
+                            rows = _.flatten(
+                                dataset_models.map((model, model_index) => {
+                                    const key = `${dataset_index}-${model_index}`,
+                                        name = getNameFromDegrees(model),
+                                        selected = indexes[dataset_index] === model_index;
+                                    return (
+                                        <tr key={key} className={selected ? "table-info" : ""}>
+                                            <td>
+                                                <a
+                                                    id={key}
+                                                    href="#"
+                                                    onClick={e => {
+                                                        e.preventDefault();
+                                                        store.showModalDetailMultitumor(
+                                                            dataset_index,
+                                                            model_index
+                                                        );
+                                                    }}>
+                                                    {name}
+                                                    {selected ? "*" : ""}
+                                                </a>
+                                            </td>
+                                            <td>{dataset.metadata.name}</td>
+                                            <td>{ff(model.bmdl)}</td>
+                                            <td>{ff(model.bmd)}</td>
+                                            <td>{ff(model.bmdu)}</td>
+                                            <td>TODO</td>
+                                            <td>{ff(model.gof.p_value)}</td>
+                                            <td>{ff(model.fit.aic)}</td>
+                                        </tr>
+                                    );
+                                })
+                            );
+                        return rows;
                     })}
                 </tbody>
+                <tfoot>
+                    <tr>
+                        <td colSpan={8} className="text-muted">
+                            {
+                                <ul className="list-unstyled text-muted mb-0">
+                                    <li>
+                                        {showMultitumor
+                                            ? "* Selected model is included in MS Combo model."
+                                            : "* Recommended best fitting model."}
+                                    </li>
+                                </ul>
+                            }
+                        </td>
+                    </tr>
+                </tfoot>
             </table>
         );
     }
diff --git a/frontend/src/components/Output/Multitumor/Summary.js b/frontend/src/components/Output/Multitumor/Summary.js
index 12ce8934..33057485 100644
--- a/frontend/src/components/Output/Multitumor/Summary.js
+++ b/frontend/src/components/Output/Multitumor/Summary.js
@@ -2,61 +2,29 @@ import {observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import TwoColumnTable from "@/components/common/TwoColumnTable";
 import {ff, fourDecimalFormatter} from "@/utils/formatters";
 
 @observer
 class Summary extends Component {
     render() {
-        const dataset = this.props.model;
-        return (
-            <table className="table table-sm table-bordered col-r-2">
-                <colgroup>
-                    <col width="60%" />
-                    <col width="40%" />
-                </colgroup>
-                <thead>
-                    <tr className="bg-custom">
-                        <th colSpan="2">Summary</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    <tr>
-                        <td>BMD</td>
-                        <td>{ff(dataset.bmd)}</td>
-                    </tr>
-                    <tr>
-                        <td>BMDL</td>
-                        <td>{ff(dataset.bmdl)}</td>
-                    </tr>
-                    <tr>
-                        <td>BMDU</td>
-                        <td>{ff(dataset.bmdu)}</td>
-                    </tr>
-                    <tr>
-                        <td>AIC</td>
-                        <td>{ff(dataset.fit.aic)}</td>
-                    </tr>
-                    <tr>
-                        <td>Log Likelihood</td>
-                        <td>{ff(dataset.fit.loglikelihood)}</td>
-                    </tr>
-                    <tr>
-                        <td>
-                            <i>P</i>-Value
-                        </td>
-                        <td>{fourDecimalFormatter(dataset.gof.p_value)}</td>
-                    </tr>
-                    <tr>
-                        <td>Overall DOF</td>
-                        <td>{ff(dataset.gof.df)}</td>
-                    </tr>
-                    <tr>
-                        <td>Chi²</td>
-                        <td>{ff(dataset.fit.chisq)}</td>
-                    </tr>
-                </tbody>
-            </table>
-        );
+        const {model} = this.props,
+            data = [
+                ["BMD", ff(model.bmd)],
+                ["BMDL", ff(model.bmdl)],
+                ["BMDU", ff(model.bmdu)],
+                ["AIC", ff(model.fit.aic)],
+                [
+                    <span key="0">
+                        <i>P</i>-Value
+                    </span>,
+                    fourDecimalFormatter(model.gof.p_value),
+                ],
+                ["Overall DOF", ff(model.gof.df)],
+                ["Chi²", ff(model.fit.chisq)][("Log Likelihood", ff(model.fit.loglikelihood))],
+                ["Slope Factor", "TODO"],
+            ];
+        return <TwoColumnTable data={data} label="Summary" />;
     }
 }
 
diff --git a/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js b/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js
index 86d5f487..0b396ac2 100644
--- a/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js
+++ b/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js
@@ -2,44 +2,26 @@ import {observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import TwoColumnTable from "@/components/common/TwoColumnTable";
 import {ff} from "@/utils/formatters";
 
 @observer
 class BootstrapResult extends Component {
     render() {
-        return (
-            <table className="table table-sm table-bordered">
-                <thead className="bg-custom">
-                    <tr>
-                        <th colSpan="2">Bootstrap Results</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    <tr>
-                        <th># Iterations</th>
-                        <td>{this.props.model.settings.bootstrap_iterations}</td>
-                    </tr>
-                    <tr>
-                        <th>Bootstrap Seed</th>
-                        <td>{ff(this.props.model.settings.bootstrap_seed)}</td>
-                    </tr>
-                    <tr>
-                        <th>Log-likelihood</th>
-                        <td>{ff(this.props.model.results.ll)}</td>
-                    </tr>
-                    <tr>
-                        <th>Observed Chi-square</th>
-                        <td>{ff(this.props.model.results.obs_chi_sq)}</td>
-                    </tr>
-                    <tr>
-                        <th>
-                            Combined <i>P</i>-Value
-                        </th>
-                        <td>{ff(this.props.model.results.combined_pvalue)}</td>
-                    </tr>
-                </tbody>
-            </table>
-        );
+        const {settings, results} = this.props.model,
+            data = [
+                ["# Iterations", settings.bootstrap_iterations],
+                ["Bootstrap Seed", ff(settings.bootstrap_seed)],
+                ["Log-likelihood", ff(results.ll)],
+                ["Observed Chi-square", ff(results.obs_chi_sq)],
+                [
+                    <span key={0}>
+                        Combined <i>P</i>-Value
+                    </span>,
+                    ff(results.combined_pvalue),
+                ],
+            ];
+        return <TwoColumnTable data={data} label="Bootstrap Results" />;
     }
 }
 BootstrapResult.propTypes = {
diff --git a/frontend/src/components/Output/NestedDichotomous/LitterData.js b/frontend/src/components/Output/NestedDichotomous/LitterData.js
index 0c425fe4..fdc5ebc5 100644
--- a/frontend/src/components/Output/NestedDichotomous/LitterData.js
+++ b/frontend/src/components/Output/NestedDichotomous/LitterData.js
@@ -9,17 +9,26 @@ import {ff} from "@/utils/formatters";
 class LitterData extends Component {
     render() {
         const litter = this.props.model.results.litter,
-            temp_rslt_len = _.size(litter.lsc);
+            n = _.size(litter.lsc);
         return (
             <table className="table table-sm table-bordered">
+                <colgroup>
+                    <col width="14%" />
+                    <col width="15%" />
+                    <col width="14%" />
+                    <col width="14%" />
+                    <col width="14%" />
+                    <col width="14%" />
+                    <col width="15%" />
+                </colgroup>
                 <thead>
                     <tr className="bg-custom">
                         <th colSpan="7">Litter Data</th>
                     </tr>
                     <tr>
                         <th>Dose</th>
-                        <th>Lit. Spec. Cov.</th>
-                        <th>Est. Prob.</th>
+                        <th>Litter Specific Covariance</th>
+                        <th>Estimated Probability</th>
                         <th>Liter Size</th>
                         <th>Expected</th>
                         <th>Observed</th>
@@ -27,7 +36,7 @@ class LitterData extends Component {
                     </tr>
                 </thead>
                 <tbody>
-                    {_.range(temp_rslt_len).map(i => {
+                    {_.range(n).map(i => {
                         return (
                             <tr key={i}>
                                 <td>{litter.dose[i]}</td>
@@ -36,7 +45,7 @@ class LitterData extends Component {
                                 <td>{litter.litter_size[i]}</td>
                                 <td>{ff(litter.expected[i])}</td>
                                 <td>{litter.observed[i]}</td>
-                                <td>{ff(litter.sr[i])}</td>
+                                <td>{ff(litter.scaled_residuals[i])}</td>
                             </tr>
                         );
                     })}
diff --git a/frontend/src/components/Output/NestedDichotomous/ModalBody.js b/frontend/src/components/Output/NestedDichotomous/ModalBody.js
index b8a9a0a4..d778150b 100644
--- a/frontend/src/components/Output/NestedDichotomous/ModalBody.js
+++ b/frontend/src/components/Output/NestedDichotomous/ModalBody.js
@@ -3,45 +3,55 @@ import PropTypes from "prop-types";
 import React, {Component} from "react";
 import {Col, Modal, Row} from "react-bootstrap";
 
+import DoseResponsePlot from "../../common/DoseResponsePlot";
+import InfoTable from "../../IndividualModel/InfoTable";
+import ModelOptionsTable from "../../IndividualModel/ModelOptionsTable";
 import BootstrapResults from "./BootstrapResults";
 import BootstrapRuns from "./BootstrapRuns";
 import LitterData from "./LitterData";
 import ModelParameters from "./ModelParameters";
 import ScaledResidual from "./ScaledResidual";
+import Summary from "./Summary";
 
 @observer
 class ModalBody extends Component {
     render() {
         const {outputStore} = this.props,
+            dataset = outputStore.selectedDataset,
+            dtype = dataset.dtype,
             model = outputStore.modalModel;
 
         return (
             <Modal.Body>
                 <Row>
-                    <Col>
-                        <p>Once we have real data...</p>
-                        <p>Borrow user info (info, model options, model data) from other modal</p>
-                        <p>Borrow benchmark dose, model parameters, from other model</p>
+                    <Col xs={6}>
+                        <InfoTable />
+                    </Col>
+                    <Col xs={6}>
+                        <ModelOptionsTable dtype={dtype} model={model} />
+                    </Col>
+                    <Col xs={6}>
+                        <Summary results={model.results} />
+                    </Col>
+                    <Col xs={6}>
+                        <DoseResponsePlot
+                            layout={outputStore.drIndividualPlotLayout}
+                            data={outputStore.drIndividualPlotData}
+                        />
                     </Col>
-                </Row>
-                <Col xs={6}>
-                    <ModelParameters model={model} />
-                </Col>
-                <Row>
                     <Col xs={6}>
                         <BootstrapResults model={model} />
                     </Col>
                     <Col xs={6}>
                         <BootstrapRuns model={model} />
                     </Col>
-                </Row>
-                <Row>
+                    <Col xs={6}>
+                        <ModelParameters model={model} />
+                    </Col>
                     <Col xs={6}>
                         <ScaledResidual model={model} />
                     </Col>
-                </Row>
-                <Row>
-                    <Col>
+                    <Col xs={12}>
                         <LitterData model={model} />
                     </Col>
                 </Row>
diff --git a/frontend/src/components/Output/NestedDichotomous/ModelParameters.js b/frontend/src/components/Output/NestedDichotomous/ModelParameters.js
index 81e40eb0..c5c31a6a 100644
--- a/frontend/src/components/Output/NestedDichotomous/ModelParameters.js
+++ b/frontend/src/components/Output/NestedDichotomous/ModelParameters.js
@@ -13,9 +13,7 @@ class ModelParameters extends Component {
             <table id="info-table" className="table table-sm table-bordered">
                 <thead>
                     <tr className="bg-custom">
-                        <th colSpan="2" className="text-center">
-                            Model Parameters
-                        </th>
+                        <th colSpan="2">Model Parameters</th>
                     </tr>
                 </thead>
                 <tbody>
diff --git a/frontend/src/components/Output/NestedDichotomous/ResultTable.js b/frontend/src/components/Output/NestedDichotomous/ResultTable.js
index c8c8bdc1..641abe5b 100644
--- a/frontend/src/components/Output/NestedDichotomous/ResultTable.js
+++ b/frontend/src/components/Output/NestedDichotomous/ResultTable.js
@@ -17,7 +17,7 @@ class ResultTable extends Component {
             return null;
         }
 
-        const colWidths = [11, 11, 11, 11, 11, 11, 11, 11, 11],
+        const colWidths = [15, 11, 11, 11, 11, 11, 30],
             {models} = selectedFrequentist;
 
         return (
@@ -37,14 +37,15 @@ class ResultTable extends Component {
                             <i>P</i>-Value
                         </th>
                         <th>AIC</th>
-                        <th>Unnormalized Log Posterior Probability</th>
-                        <th>Scaled Residual for Dose Group near BMD</th>
-                        <th>Scaled Residual for Control Dose Group</th>
+                        <th>Recommendation and Notes</th>
                     </tr>
                 </thead>
                 <tbody className="table-bordered">
                     {models.map((model, index) => (
-                        <tr key={index}>
+                        <tr
+                            key={index}
+                            onMouseEnter={() => store.drPlotAddHover(model)}
+                            onMouseLeave={store.drPlotRemoveHover}>
                             <td>
                                 <a
                                     id={`freq-result-${index}`}
@@ -58,12 +59,10 @@ class ResultTable extends Component {
                             </td>
                             <td>{ff(model.results.summary.bmdl)}</td>
                             <td>{ff(model.results.summary.bmd)}</td>
-                            <td>{model.results.summary.bmdu}</td>
+                            <td>{ff(model.results.summary.bmdu)}</td>
                             <td>{ff(model.results.combined_pvalue)}</td>
                             <td>{ff(model.results.summary.aic)}</td>
-                            <td>???</td>
-                            <td>???</td>
-                            <td>???</td>
+                            <td>TODO</td>
                         </tr>
                     ))}
                 </tbody>
diff --git a/frontend/src/components/Output/NestedDichotomous/ScaledResidual.js b/frontend/src/components/Output/NestedDichotomous/ScaledResidual.js
index d4a671aa..0a4534d4 100644
--- a/frontend/src/components/Output/NestedDichotomous/ScaledResidual.js
+++ b/frontend/src/components/Output/NestedDichotomous/ScaledResidual.js
@@ -2,46 +2,21 @@ import {observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import TwoColumnTable from "@/components/common/TwoColumnTable";
+
 @observer
 class ScaledResidual extends Component {
     render() {
-        return (
-            <table id="info-table" className="table table-sm table-bordered">
-                <thead>
-                    <tr className="bg-custom">
-                        <th colSpan="2" className="text-center">
-                            Scaled Residuals
-                        </th>
-                    </tr>
-                </thead>
-                <tbody>
-                    <tr>
-                        <td>Minimum scaled residual for dose group nearest the BMD</td>
-                        <td>{this.props.model.results.scaled_residuals[0]}</td>
-                    </tr>
-                    <tr>
-                        <td>Minimum ABS(scaled residual) for dose group nearest the BMD</td>
-                        <td>{this.props.model.results.scaled_residuals[1]}</td>
-                    </tr>
-                    <tr>
-                        <td>Average Scaled residual for dose group nearest the BMD</td>
-                        <td>{this.props.model.results.scaled_residuals[2]}</td>
-                    </tr>
-                    <tr>
-                        <td>Average ABS(scaled residual) for dose group nearest the BMD</td>
-                        <td>{this.props.model.results.scaled_residuals[3]}</td>
-                    </tr>
-                    <tr>
-                        <td>Maximum scaled residual for dose group nearest the BMD</td>
-                        <td>{this.props.model.results.scaled_residuals[4]}</td>
-                    </tr>
-                    <tr>
-                        <td>Maximum ABS(scaled residual) for dose group nearest the BMD</td>
-                        <td>{this.props.model.results.scaled_residuals[5]}</td>
-                    </tr>
-                </tbody>
-            </table>
-        );
+        const residuals = this.props.model.results.scaled_residuals,
+            data = [
+                ["Minimum scaled residual for dose group nearest the BMD", residuals[0]],
+                ["Minimum ABS(scaled residual) for dose group nearest the BMD", residuals[1]],
+                ["Average Scaled residual for dose group nearest the BMD", residuals[2]],
+                ["Average ABS(scaled residual) for dose group nearest the BMD", residuals[3]],
+                ["Maximum scaled residual for dose group nearest the BMD", residuals[4]],
+                ["Maximum ABS(scaled residual) for dose group nearest the BMD", residuals[5]],
+            ];
+        return <TwoColumnTable label="Scaled Residuals" data={data} colwidths={[70, 30]} />;
     }
 }
 ScaledResidual.propTypes = {
diff --git a/frontend/src/components/Output/NestedDichotomous/Summary.js b/frontend/src/components/Output/NestedDichotomous/Summary.js
new file mode 100644
index 00000000..9589f6f1
--- /dev/null
+++ b/frontend/src/components/Output/NestedDichotomous/Summary.js
@@ -0,0 +1,39 @@
+import {observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+import TwoColumnTable from "@/components/common/TwoColumnTable";
+import {ff} from "@/utils/formatters";
+
+@observer
+class Summary extends Component {
+    render() {
+        const {results} = this.props,
+            data = [
+                ["BMD", ff(results.summary.bmd)],
+                ["BMDL", ff(results.summary.bmdl)],
+                ["BMDU", ff(results.summary.bmdu)],
+                ["AIC", ff(results.summary.aic)],
+                [
+                    <span key={0}>
+                        <i>P</i>-value
+                    </span>,
+                    ff(results.combined_pvalue),
+                ],
+                ["D.O.F.", ff(results.dof)],
+                [
+                    <span key={1}>
+                        Chi<sup>2</sup>
+                    </span>,
+                    ff(results.summary.chi_squared),
+                ],
+            ];
+        return <TwoColumnTable label="Summary" data={data} />;
+    }
+}
+Summary.propTypes = {
+    model: PropTypes.object,
+    results: PropTypes.object.isRequired,
+};
+
+export default Summary;
diff --git a/frontend/src/components/Output/OptionSetTable.js b/frontend/src/components/Output/OptionSetTable.js
index 0a21e220..5f9f9275 100644
--- a/frontend/src/components/Output/OptionSetTable.js
+++ b/frontend/src/components/Output/OptionSetTable.js
@@ -9,6 +9,7 @@ import {
     continuousBmrOptions,
     dichotomousBmrOptions,
     distTypeOptions,
+    litterSpecificCovariateOptions,
 } from "@/constants/optionsConstants";
 import {ff} from "@/utils/formatters";
 
@@ -47,7 +48,20 @@ class OptionSetTable extends Component {
                 ],
             ];
         } else if (outputStore.isNestedDichotomous) {
-            rows = [["TODO", "ADD"]];
+            rows = [
+                ["BMR Type", getLabel(selectedModelOptions.bmr_type, dichotomousBmrOptions)],
+                ["BMR", ff(selectedModelOptions.bmr_value)],
+                ["Confidence Level", ff(selectedModelOptions.confidence_level)],
+                ["Bootstrap Seed", selectedModelOptions.bootstrap_seed],
+                ["Bootstrap Iterations", selectedModelOptions.bootstrap_iterations],
+                [
+                    "Litter Specific Covariate",
+                    getLabel(
+                        selectedModelOptions.litter_specific_covariate,
+                        litterSpecificCovariateOptions
+                    ),
+                ],
+            ];
         } else if (outputStore.isMultiTumor) {
             rows = [
                 ["BMR Type", getLabel(selectedModelOptions.bmr_type, dichotomousBmrOptions)],
diff --git a/frontend/src/components/Output/Output.js b/frontend/src/components/Output/Output.js
index 320a2fe1..b20a77a4 100644
--- a/frontend/src/components/Output/Output.js
+++ b/frontend/src/components/Output/Output.js
@@ -12,6 +12,7 @@ import ModelDetailModal from "../IndividualModel/ModelDetailModal";
 import BayesianResultTable from "./BayesianResultTable";
 import FrequentistResultTable from "./FrequentistResultTable";
 import MultitumorDatasetTable from "./Multitumor/DatasetTable";
+import MultitumorPlot from "./Multitumor/MultitumorPlot";
 import MultitumorResultTable from "./Multitumor/ResultTable";
 import NestedDichotomousResultTable from "./NestedDichotomous/ResultTable";
 import OptionSetTable from "./OptionSetTable";
@@ -80,7 +81,7 @@ class Output extends Component {
         }
 
         return (
-            <div className="container-fluid">
+            <div className="container-fluid mb-3">
                 <div className="row">
                     {outputStore.outputs.length > 1 ? (
                         <div className="col-lg-2">
@@ -96,14 +97,14 @@ class Output extends Component {
                             />
                         </div>
                     ) : null}
-                    <div className="col-lg-5">
+                    <div className="col-lg-6">
                         {outputStore.isMultiTumor ? (
                             <MultitumorDatasetTable />
                         ) : (
                             <DatasetTable dataset={outputStore.selectedDataset} />
                         )}
                     </div>
-                    <div className="col-lg-5">
+                    <div className="col-lg-4">
                         <OptionSetTable />
                     </div>
                 </div>
@@ -113,6 +114,7 @@ class Output extends Component {
                             <div className="col-lg-12">
                                 <h4>Model Results</h4>
                                 <MultitumorResultTable />
+                                <MultitumorPlot />
                             </div>
                         </div>
                     ) : (
diff --git a/frontend/src/components/common/TwoColumnTable.js b/frontend/src/components/common/TwoColumnTable.js
new file mode 100644
index 00000000..b660f084
--- /dev/null
+++ b/frontend/src/components/common/TwoColumnTable.js
@@ -0,0 +1,42 @@
+import _ from "lodash";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+class TwoColumnTable extends Component {
+    render() {
+        const {id, data, label, colwidths} = this.props,
+            widths = colwidths.map(d => `${d}%`);
+        return (
+            <table id={id} className="table table-sm table-bordered">
+                <colgroup>
+                    <col width={widths[0]} />
+                    <col width={widths[1]} />
+                </colgroup>
+                <thead>
+                    <tr className="bg-custom">
+                        <th colSpan="2">{label}</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    {data.filter(_.isArrayLike).map((item, i) => (
+                        <tr key={i}>
+                            <td>{item[0]}</td>
+                            <td>{item[1]}</td>
+                        </tr>
+                    ))}
+                </tbody>
+            </table>
+        );
+    }
+}
+TwoColumnTable.propTypes = {
+    id: PropTypes.string,
+    data: PropTypes.array.isRequired,
+    label: PropTypes.string.isRequired,
+    colwidths: PropTypes.array,
+};
+TwoColumnTable.defaultProps = {
+    colwidths: [30, 70],
+};
+
+export default TwoColumnTable;
diff --git a/frontend/src/constants/modelConstants.js b/frontend/src/constants/modelConstants.js
index 3401b129..35dfcc18 100644
--- a/frontend/src/constants/modelConstants.js
+++ b/frontend/src/constants/modelConstants.js
@@ -63,8 +63,8 @@ const modelsList = {
             bayesian: modelsList.D,
         },
         [MODEL_NESTED_DICHOTOMOUS]: {
-            frequentist_restricted: ["Nested Logistic", "NCTR"],
-            frequentist_unrestricted: ["Nested Logistic", "NCTR"],
+            frequentist_restricted: ["Nested Logistic"],
+            frequentist_unrestricted: ["Nested Logistic"],
         },
 
         [MODEL_MULTI_TUMOR]: {
@@ -75,6 +75,10 @@ const modelsList = {
     isLognormal = function(disttype) {
         return disttype == 3;
     },
-    hasDegrees = new Set(["Multistage", "Polynomial"]);
+    hasDegrees = new Set(["Multistage", "Polynomial"]),
+    getNameFromDegrees = function(model) {
+        const degree = model.parameters.names.length - 1;
+        return `Multistage ${degree}°`;
+    };
 
-export {allModelOptions, hasDegrees, isLognormal, models, modelsList};
+export {allModelOptions, getNameFromDegrees, hasDegrees, isLognormal, models, modelsList};
diff --git a/frontend/src/constants/optionsConstants.js b/frontend/src/constants/optionsConstants.js
index f816104c..e79cf094 100644
--- a/frontend/src/constants/optionsConstants.js
+++ b/frontend/src/constants/optionsConstants.js
@@ -50,8 +50,13 @@ export const options = {
         {value: 3, label: "Lognormal"},
     ],
     litterSpecificCovariateOptions = [
-        {value: 0, label: "Overall Mean"},
-        {value: 1, label: "Control Group Mean"},
+        {value: 0, label: "Unused"},
+        {value: 1, label: "Overall Mean"},
+        {value: 2, label: "Control Group Mean"},
+    ],
+    intralitterCorrelation = [
+        {value: 0, label: "Zero"},
+        {value: 1, label: "Estimate"},
     ],
     backgroundOptions = [
         {value: 0, label: "Zero"},
diff --git a/frontend/src/constants/plotting.js b/frontend/src/constants/plotting.js
index 83f8207e..ae358555 100644
--- a/frontend/src/constants/plotting.js
+++ b/frontend/src/constants/plotting.js
@@ -24,7 +24,20 @@ const doseResponseLayout = {
             },
         },
     },
-    getResponse = dataset => {
+    hexToRgbA = (hex, alpha) => {
+        var c;
+        if (/^#([A-Fa-f0-9]{3}){1,2}$/.test(hex)) {
+            c = hex.substring(1).split("");
+            if (c.length == 3) {
+                c = [c[0], c[0], c[1], c[1], c[2], c[2]];
+            }
+            c = "0x" + c.join("");
+            return "rgba(" + [(c >> 16) & 255, (c >> 8) & 255, c & 255].join(",") + `,${alpha})`;
+        }
+        throw new Error("Bad Hex");
+    };
+
+export const getResponse = dataset => {
         let incidences, ns;
 
         switch (dataset.dtype) {
@@ -44,20 +57,7 @@ const doseResponseLayout = {
                 throw `Unknown dtype: ${dataset.dtype}`;
         }
     },
-    hexToRgbA = (hex, alpha) => {
-        var c;
-        if (/^#([A-Fa-f0-9]{3}){1,2}$/.test(hex)) {
-            c = hex.substring(1).split("");
-            if (c.length == 3) {
-                c = [c[0], c[0], c[1], c[1], c[2], c[2]];
-            }
-            c = "0x" + c.join("");
-            return "rgba(" + [(c >> 16) & 255, (c >> 8) & 255, c & 255].join(",") + `,${alpha})`;
-        }
-        throw new Error("Bad Hex");
-    };
-
-export const getDoseLabel = function(dataset) {
+    getDoseLabel = function(dataset) {
         let label = dataset.metadata.dose_name;
         if (dataset.metadata.dose_units) {
             label = `${label} (${dataset.metadata.dose_units})`;
diff --git a/frontend/src/stores/MainStore.js b/frontend/src/stores/MainStore.js
index f59f0e94..6a08d8b0 100644
--- a/frontend/src/stores/MainStore.js
+++ b/frontend/src/stores/MainStore.js
@@ -300,15 +300,9 @@ class MainStore {
         return _.find(mc.modelTypes, {value: this.model_type}).name;
     }
     @computed get getModelTypeChoices() {
-        let choices = mc.modelTypes.map((item, i) => {
+        return mc.modelTypes.map((item, i) => {
             return {value: item.value, text: item.name};
         });
-        if (!this.isFuture) {
-            return choices.filter(
-                d => d.value != mc.MODEL_NESTED_DICHOTOMOUS && d.value != mc.MODEL_MULTI_TUMOR
-            );
-        }
-        return choices;
     }
 
     @computed get getModels() {
diff --git a/frontend/src/stores/OutputStore.js b/frontend/src/stores/OutputStore.js
index 10f79376..303cb9e7 100644
--- a/frontend/src/stores/OutputStore.js
+++ b/frontend/src/stores/OutputStore.js
@@ -3,6 +3,7 @@ import {action, computed, observable, toJS} from "mobx";
 
 import {getHeaders} from "@/common";
 import {MODEL_MULTI_TUMOR, MODEL_NESTED_DICHOTOMOUS} from "@/constants/mainConstants";
+import {getNameFromDegrees} from "@/constants/modelConstants";
 import {maIndex, modelClasses} from "@/constants/outputConstants";
 import {
     bmaColor,
@@ -186,6 +187,20 @@ class OutputStore {
         );
     }
 
+    @computed get modalName() {
+        const model = this.modalModel;
+        if (this.isMultiTumor) {
+            if (this.drModelModalIsMA) {
+                return "MS Combo";
+            } else {
+                const dataset = this.modalDataset;
+                return `${dataset.metadata.name} - ${getNameFromDegrees(model)}`;
+            }
+        } else {
+            return this.drModelModalIsMA ? "Model Average" : model.name;
+        }
+    }
+
     // start modal methods
     getModel(index) {
         if (this.modalModelClass === modelClasses.frequentist) {
@@ -222,6 +237,9 @@ class OutputStore {
             ? this.selectedFrequentist.results
             : this.selectedFrequentist.results.models[i][j];
         this.modalDataset = isMa ? null : this.rootStore.dataStore.datasets[datasetIndexes[i]];
+        this.modalOptionSet = isMa
+            ? null
+            : this.rootStore.dataOptionStore.options[datasetIndexes[i]];
         this.drModelModalIsMA = isMa;
         this.showModelModal = true;
     }
@@ -335,6 +353,22 @@ class OutputStore {
         return data;
     }
 
+    @computed get drIndividualMultitumorPlotLayout() {
+        // a single model, shown in the modal
+        return getDrLayout(this.modalDataset, this.modalModel, null, null);
+    }
+
+    @computed get drIndividualMultitumorPlotData() {
+        // a single model, shown in the modal
+        const model = this.modalModel,
+            modelMock = {name: getNameFromDegrees(model), results: _.cloneDeep(model)},
+            data = [
+                getDrDatasetPlotData(this.modalDataset),
+                ...getDrBmdLine(modelMock, hoverColor),
+            ];
+        return data;
+    }
+
     @action.bound drPlotAddHover(model) {
         if (this.drModelSelected && this.drModelSelected[0].name === model.name) {
             return;
diff --git a/tests/conftest.py b/tests/conftest.py
index 2841eb59..b5a217ce 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -209,7 +209,8 @@ def bmds_complete_nd():
                 "doses": [
                     0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
                     25, 25, 25, 25, 25, 25, 25, 25, 25,
-                    50, 50, 50, 50, 50, 50, 50, 50, 50
+                    50, 50, 50, 50, 50, 50,
+                    75, 75, 75,
                 ],
                 "dtype": "ND",
                 "metadata": {
@@ -223,17 +224,20 @@ def bmds_complete_nd():
                 "litter_ns": [
                     16, 9, 15, 14, 13, 9, 10, 14, 10, 11, 14,
                     9, 14, 9, 13, 12, 10, 10, 11, 14,
-                    11, 11, 14, 11, 10, 11, 10, 15, 7,
+                    11, 11, 14, 11, 10, 11,
+                    10, 15, 7,
                 ],
                 "incidences": [
                     1, 1, 2, 3, 3, 0, 2, 2, 1, 2, 4,
                     5, 6, 2, 6, 3, 1, 2, 4, 3,
-                    4, 5, 5, 4, 5, 4, 5, 6, 2,
+                    4, 5, 5, 4, 5, 4,
+                    5, 6, 2,
                 ],
                 "litter_covariates": [
                     16, 9, 15, 14, 13, 9, 10, 14, 10, 11, 14,
                     9, 14, 9, 13, 12, 10, 10, 11, 14,
-                    11, 11, 14, 11, 10, 11, 10, 15, 7,
+                    11, 11, 14, 11, 10, 11,
+                    10, 15, 7,
                 ]
             }
         ],

From 013c784555aa5e8689758ed740e775ef73394631 Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Wed, 4 Oct 2023 10:37:14 -0400
Subject: [PATCH 04/24] 293 mt min max datasets (#266)

* increase MT datasets to 10

* decrease MT option set

* move logic to store

* update contraints on server to relax for desktop

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 bmds_server/analysis/validators/datasets.py   | 24 ++++++++++---------
 bmds_server/analysis/validators/options.py    | 11 +++++----
 bmds_server/analysis/validators/session.py    |  6 ++---
 .../src/components/Data/SelectModelType.js    |  5 ++--
 .../Main/OptionsForm/OptionsFormList.js       |  5 ++--
 frontend/src/stores/DataStore.js              | 10 ++++++--
 frontend/src/stores/OptionsStore.js           | 11 ++++++---
 7 files changed, 45 insertions(+), 27 deletions(-)

diff --git a/bmds_server/analysis/validators/datasets.py b/bmds_server/analysis/validators/datasets.py
index 16007b9d..cfca9765 100644
--- a/bmds_server/analysis/validators/datasets.py
+++ b/bmds_server/analysis/validators/datasets.py
@@ -8,11 +8,14 @@
     DichotomousDatasetSchema,
     NestedDichotomousDatasetSchema,
 )
+from django.conf import settings
 from django.core.exceptions import ValidationError
-from pydantic import BaseModel, conlist, root_validator
+from pydantic import BaseModel, Field, root_validator
 
 from ...common.validation import pydantic_validate
 
+max_items = 1000 if settings.IS_DESKTOP else 10
+
 
 class MaxDegree(IntEnum):
     N_MINUS_ONE = 0
@@ -80,27 +83,26 @@ class MaxNestedDichotomousDatasetSchema(NestedDichotomousDatasetSchema):
 
 
 class DichotomousDatasets(DatasetValidator):
-    dataset_options: conlist(DichotomousModelOptions, min_items=1, max_items=10)
-    datasets: conlist(MaxDichotomousDatasetSchema, min_items=1, max_items=10)
+    dataset_options: list[DichotomousModelOptions] = Field(min_items=1, max_items=max_items)
+    datasets: list[MaxDichotomousDatasetSchema] = Field(min_items=1, max_items=max_items)
 
 
 class ContinuousDatasets(DatasetValidator):
-    dataset_options: conlist(ContinuousModelOptions, min_items=1, max_items=10)
-    datasets: conlist(
-        MaxContinuousDatasetSchema | MaxContinuousIndividualDatasetSchema,
+    dataset_options: list[ContinuousModelOptions] = Field(min_items=1, max_items=max_items)
+    datasets: list[MaxContinuousDatasetSchema | MaxContinuousIndividualDatasetSchema] = Field(
         min_items=1,
-        max_items=10,
+        max_items=max_items,
     )
 
 
 class NestedDichotomousDataset(DatasetValidator):
-    dataset_options: conlist(NestedDichotomousModelOptions, min_items=1, max_items=10)
-    datasets: conlist(MaxNestedDichotomousDatasetSchema, min_items=1, max_items=10)
+    dataset_options: list[NestedDichotomousModelOptions] = Field(min_items=1, max_items=max_items)
+    datasets: list[MaxNestedDichotomousDatasetSchema] = Field(min_items=1, max_items=max_items)
 
 
 class MultiTumorDatasets(DatasetValidator):
-    dataset_options: conlist(DichotomousModelOptions, min_items=1, max_items=10)
-    datasets: conlist(DichotomousDatasetSchema, min_items=1, max_items=10)
+    dataset_options: list[DichotomousModelOptions] = Field(min_items=1, max_items=max_items)
+    datasets: list[DichotomousDatasetSchema] = Field(min_items=1, max_items=max_items)
 
 
 def validate_datasets(dataset_type: str, datasets: Any, datasetOptions: Any):
diff --git a/bmds_server/analysis/validators/options.py b/bmds_server/analysis/validators/options.py
index a4b4ae0c..7cd1e211 100644
--- a/bmds_server/analysis/validators/options.py
+++ b/bmds_server/analysis/validators/options.py
@@ -5,11 +5,14 @@
 from bmds.bmds3.types.continuous import ContinuousRiskType
 from bmds.bmds3.types.dichotomous import DichotomousRiskType
 from bmds.bmds3.types.nested_dichotomous import LitterSpecificCovariate
+from django.conf import settings
 from django.core.exceptions import ValidationError
-from pydantic import BaseModel, Field, conlist
+from pydantic import BaseModel, Field
 
 from ...common.validation import pydantic_validate
 
+max_items = 1000 if settings.IS_DESKTOP else 6
+
 
 class DichotomousOption(BaseModel):
     bmr_type: DichotomousRiskType
@@ -35,15 +38,15 @@ class NestedDichotomousOption(BaseModel):
 
 
 class DichotomousOptions(BaseModel):
-    options: conlist(DichotomousOption, min_items=1, max_items=10)
+    options: list[DichotomousOption] = Field(min_items=1, max_items=max_items)
 
 
 class ContinuousOptions(BaseModel):
-    options: conlist(ContinuousOption, min_items=1, max_items=10)
+    options: list[ContinuousOption] = Field(min_items=1, max_items=max_items)
 
 
 class NestedDichotomousOptions(BaseModel):
-    options: conlist(NestedDichotomousOption, min_items=1, max_items=3)
+    options: list[NestedDichotomousOption] = Field(min_items=1, max_items=max_items)
 
 
 def validate_options(dataset_type: str, data: Any):
diff --git a/bmds_server/analysis/validators/session.py b/bmds_server/analysis/validators/session.py
index b925f7d2..fdf99ab8 100644
--- a/bmds_server/analysis/validators/session.py
+++ b/bmds_server/analysis/validators/session.py
@@ -2,7 +2,7 @@
 
 import bmds
 from django.conf import settings
-from pydantic import BaseModel, conlist
+from pydantic import BaseModel, Field
 
 from ...common.validation import pydantic_validate
 
@@ -20,9 +20,9 @@ class BaseSession(BaseModel):
 
 
 class BaseSessionComplete(BaseSession):
-    datasets: conlist(Any, min_items=1, max_items=max_items)
+    datasets: list[Any] = Field(min_items=1, max_items=max_items)
     models: dict
-    options: conlist(Any, min_items=1, max_items=max_items)
+    options: list[Any] = Field(min_items=1, max_items=max_items)
 
 
 def validate_session(data: dict, partial: bool = False):
diff --git a/frontend/src/components/Data/SelectModelType.js b/frontend/src/components/Data/SelectModelType.js
index a10b2e3f..be92bf46 100644
--- a/frontend/src/components/Data/SelectModelType.js
+++ b/frontend/src/components/Data/SelectModelType.js
@@ -15,7 +15,6 @@ class SelectModelType extends Component {
             <div className="model-type mb-2">
                 <Button
                     className="btn btn-primary btn-sm float-right"
-                    title="Can add up to 6 datasets"
                     disabled={!dataStore.canAddNewDataset}
                     icon="plus-circle"
                     text="New"
@@ -31,7 +30,9 @@ class SelectModelType extends Component {
                     })}
                 />
                 {dataStore.canAddNewDataset ? null : (
-                    <p className="text-danger">Can have a maximum of 6 datasets per analysis.</p>
+                    <p className="text-danger">
+                        Can have a maximum of {dataStore.maxItems} datasets per analysis.
+                    </p>
                 )}
             </div>
         );
diff --git a/frontend/src/components/Main/OptionsForm/OptionsFormList.js b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
index c7411403..9477b652 100644
--- a/frontend/src/components/Main/OptionsForm/OptionsFormList.js
+++ b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
@@ -74,7 +74,7 @@ class OptionsFormList extends Component {
                                     {optionsStore.canEdit ? (
                                         <th>
                                             <Button
-                                                title="Can add up to 6 option sets"
+                                                title="Maximum number of option sets reached."
                                                 className="btn btn-primary"
                                                 disabled={!optionsStore.canAddNewOption}
                                                 onClick={optionsStore.addOptions}
@@ -112,7 +112,8 @@ class OptionsFormList extends Component {
                         </table>
                         {optionsStore.canAddNewOption ? null : (
                             <p className="text-danger">
-                                Can have a maximum of 6 option sets per analysis.
+                                Can have a maximum of {optionsStore.maxItems} option sets per
+                                analysis.
                             </p>
                         )}
                     </form>
diff --git a/frontend/src/stores/DataStore.js b/frontend/src/stores/DataStore.js
index 296f823a..413f45f0 100644
--- a/frontend/src/stores/DataStore.js
+++ b/frontend/src/stores/DataStore.js
@@ -267,9 +267,15 @@ class DataStore {
             .map(d => d.dataset);
     }
 
+    @computed get maxItems() {
+        return this.rootStore.mainStore.isDesktop
+            ? 1000
+            : this.rootStore.mainStore.isMultitumor
+            ? 10
+            : 6;
+    }
     @computed get canAddNewDataset() {
-        const maxItems = this.rootStore.mainStore.isDesktop ? 1000 : 6;
-        return this.datasets.length < maxItems;
+        return this.datasets.length < this.maxItems;
     }
 
     @computed get hasSelectedDataset() {
diff --git a/frontend/src/stores/OptionsStore.js b/frontend/src/stores/OptionsStore.js
index 0a039e98..ff72798a 100644
--- a/frontend/src/stores/OptionsStore.js
+++ b/frontend/src/stores/OptionsStore.js
@@ -48,10 +48,15 @@ class OptionsStore {
     @computed get getModelType() {
         return this.rootStore.mainStore.model_type;
     }
-
+    @computed get maxItems() {
+        return this.rootStore.mainStore.isDesktop
+            ? 1000
+            : this.rootStore.mainStore.isMultitumor
+            ? 3
+            : 6;
+    }
     @computed get canAddNewOption() {
-        const maxItems = this.rootStore.mainStore.isDesktop ? 1000 : 6;
-        return this.optionsList.length < maxItems;
+        return this.optionsList.length < this.maxItems;
     }
 }
 

From 1ef00b74c792d93c6478cb79a505d59f3925ce8a Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Wed, 4 Oct 2023 11:11:45 -0400
Subject: [PATCH 05/24] Complete nested dichotomous summary table (#267)

* wip

* improve nested dichotomous table!
---
 .../Output/FrequentistResultTable.js          | 164 ++++++++++++------
 .../Output/NestedDichotomous/ResultTable.js   |  77 --------
 frontend/src/components/Output/Output.js      |   7 +-
 3 files changed, 116 insertions(+), 132 deletions(-)
 delete mode 100644 frontend/src/components/Output/NestedDichotomous/ResultTable.js

diff --git a/frontend/src/components/Output/FrequentistResultTable.js b/frontend/src/components/Output/FrequentistResultTable.js
index 10b1a6af..ae3a8bdc 100644
--- a/frontend/src/components/Output/FrequentistResultTable.js
+++ b/frontend/src/components/Output/FrequentistResultTable.js
@@ -5,7 +5,6 @@ import PropTypes from "prop-types";
 import React, {Component} from "react";
 
 import {BIN_LABELS} from "@/constants/logicConstants";
-import {MODEL_MULTI_TUMOR} from "@/constants/mainConstants";
 import {getPValue, modelClasses, priorClass} from "@/constants/outputConstants";
 import {fractionalFormatter} from "@/utils/formatters";
 import {ff} from "@/utils/formatters";
@@ -128,62 +127,128 @@ FrequentistRowSet.propTypes = {
     colSpan: PropTypes.number.isRequired,
 };
 
+class ModelNameTd extends Component {
+    render() {
+        const {store, data, rowIcon, modelClasses} = this.props;
+        return (
+            <td>
+                <a
+                    id={`freq-result-${data.index}`}
+                    href="#"
+                    onClick={e => {
+                        e.preventDefault();
+                        store.showModalDetail(modelClasses.frequentist, data.index);
+                    }}>
+                    {data.model.name}
+                    {rowIcon}
+                </a>
+            </td>
+        );
+    }
+}
+ModelNameTd.propTypes = {
+    store: PropTypes.object.isRequired,
+    data: PropTypes.object.isRequired,
+    rowIcon: PropTypes.string.isRequired,
+    modelClasses: PropTypes.object.isRequired,
+};
+
+class RecommendationTd extends Component {
+    render() {
+        const {store, data, selectedFrequentist} = this.props;
+
+        if (!store.recommendationEnabled) {
+            return null;
+        }
+
+        const {name} = data.model,
+            popoverTitle = `${name}: ${getModelBinLabel(selectedFrequentist, data.index)}`,
+            popoverContent =
+                getModelBinText(selectedFrequentist, data.index)
+                    .toString()
+                    .split(",")
+                    .join("<br/>") || "<i>No notes.</i>";
+
+        return store.showInlineNotes ? (
+            <td>
+                <u>{getModelBinLabel(selectedFrequentist, data.index)}</u>
+                <br />
+                {getRecommenderText(selectedFrequentist, data.index)}
+            </td>
+        ) : (
+            <Popover element="td" title={popoverTitle} content={popoverContent}>
+                <u>{getModelBinLabel(selectedFrequentist, data.index)}</u>
+            </Popover>
+        );
+    }
+}
+RecommendationTd.propTypes = {
+    store: PropTypes.object.isRequired,
+    data: PropTypes.object.isRequired,
+    selectedFrequentist: PropTypes.object.isRequired,
+};
+
 @observer
 class FrequentistRow extends Component {
     render() {
         const {store, data, dataset, selectedFrequentist, footnotes} = this.props,
-            {name} = data.model,
             fns = footnotes.filter(d => d.index == data.index),
             rowClass = fns.length > 0 ? fns[fns.length - 1].class : "",
             rowIcon = fns.map(d => d.icon).join(""),
-            popoverTitle = store.recommendationEnabled
-                ? `${name}: ${getModelBinLabel(selectedFrequentist, data.index)}`
-                : null,
-            popoverContent = store.recommendationEnabled
-                ? getModelBinText(selectedFrequentist, data.index)
-                      .toString()
-                      .split(",")
-                      .join("<br/>") || "<i>No notes.</i>"
-                : null;
+            {results} = data.model;
 
+        if (store.isNestedDichotomous) {
+            return (
+                <tr
+                    key={data.index}
+                    onMouseEnter={() => store.drPlotAddHover(data.model)}
+                    onMouseLeave={store.drPlotRemoveHover}
+                    className={rowClass}>
+                    <ModelNameTd
+                        store={store}
+                        data={data}
+                        rowIcon={rowIcon}
+                        modelClasses={modelClasses}
+                    />
+                    <td>{ff(results.summary.bmdl)}</td>
+                    <td>{ff(results.summary.bmd)}</td>
+                    <td>{ff(results.summary.bmdu)}</td>
+                    <td>{ff(results.combined_pvalue)}</td>
+                    <td>{ff(results.summary.aic)}</td>
+                    <td>-</td>
+                    <td>-</td>
+                    <RecommendationTd
+                        store={store}
+                        data={data}
+                        selectedFrequentist={selectedFrequentist}
+                    />
+                </tr>
+            );
+        }
         return (
             <tr
                 key={data.index}
                 onMouseEnter={() => store.drPlotAddHover(data.model)}
                 onMouseLeave={store.drPlotRemoveHover}
                 className={rowClass}>
-                <td>
-                    <a
-                        id={`freq-result-${data.index}`}
-                        href="#"
-                        onClick={e => {
-                            e.preventDefault();
-                            store.showModalDetail(modelClasses.frequentist, data.index);
-                        }}>
-                        {data.model.name}
-                        {rowIcon}
-                    </a>
-                </td>
-                <td>{ff(data.model.results.bmdl)}</td>
-                <td>{ff(data.model.results.bmd)}</td>
-                <td>{ff(data.model.results.bmdu)}</td>
-                <td>{fractionalFormatter(getPValue(dataset.dtype, data.model.results))}</td>
-                <td>{ff(data.model.results.fit.aic)}</td>
-                <td>{ff(data.model.results.gof.roi)}</td>
-                <td>{ff(data.model.results.gof.residual[0])}</td>
-                {store.recommendationEnabled ? (
-                    store.showInlineNotes ? (
-                        <td>
-                            <u>{getModelBinLabel(selectedFrequentist, data.index)}</u>
-                            <br />
-                            {getRecommenderText(selectedFrequentist, data.index)}
-                        </td>
-                    ) : (
-                        <Popover element="td" title={popoverTitle} content={popoverContent}>
-                            <u>{getModelBinLabel(selectedFrequentist, data.index)}</u>
-                        </Popover>
-                    )
-                ) : null}
+                <ModelNameTd
+                    store={store}
+                    data={data}
+                    rowIcon={rowIcon}
+                    modelClasses={modelClasses}
+                />
+                <td>{ff(results.bmdl)}</td>
+                <td>{ff(results.bmd)}</td>
+                <td>{ff(results.bmdu)}</td>
+                <td>{fractionalFormatter(getPValue(dataset.dtype, results))}</td>
+                <td>{ff(results.fit.aic)}</td>
+                <td>{ff(results.gof.roi)}</td>
+                <td>{ff(results.gof.residual[0])}</td>
+                <RecommendationTd
+                    store={store}
+                    data={data}
+                    selectedFrequentist={selectedFrequentist}
+                />
             </tr>
         );
     }
@@ -202,20 +267,18 @@ class FrequentistResultTable extends Component {
     render() {
         const store = this.props.outputStore,
             dataset = store.selectedDataset,
-            {selectedFrequentist} = store,
-            modelType = store.getModelType;
+            {selectedFrequentist, isNestedDichotomous} = store;
 
         if (!selectedFrequentist) {
             return null;
         }
 
-        if (modelType === MODEL_MULTI_TUMOR) {
-            return <p>Add multi tumor results table here ...</p>;
-        }
-
         const {models} = selectedFrequentist,
             restrictedModels = _.chain(models)
                 .map((model, index) => {
+                    if (isNestedDichotomous) {
+                        return model.settings.restricted ? {model, index} : null;
+                    }
                     if (model.settings.priors.prior_class === priorClass.frequentist_restricted) {
                         return {model, index};
                     }
@@ -225,6 +288,9 @@ class FrequentistResultTable extends Component {
                 .value(),
             unrestrictedModels = _.chain(models)
                 .map((model, index) => {
+                    if (isNestedDichotomous) {
+                        return !model.settings.restricted ? {model, index} : null;
+                    }
                     if (model.settings.priors.prior_class === priorClass.frequentist_unrestricted) {
                         return {model, index};
                     }
diff --git a/frontend/src/components/Output/NestedDichotomous/ResultTable.js b/frontend/src/components/Output/NestedDichotomous/ResultTable.js
deleted file mode 100644
index 641abe5b..00000000
--- a/frontend/src/components/Output/NestedDichotomous/ResultTable.js
+++ /dev/null
@@ -1,77 +0,0 @@
-import _ from "lodash";
-import {inject, observer} from "mobx-react";
-import PropTypes from "prop-types";
-import React, {Component} from "react";
-
-import {modelClasses} from "@/constants/outputConstants";
-import {ff} from "@/utils/formatters";
-
-@inject("outputStore")
-@observer
-class ResultTable extends Component {
-    render() {
-        const store = this.props.outputStore,
-            {selectedFrequentist} = store;
-
-        if (!selectedFrequentist) {
-            return null;
-        }
-
-        const colWidths = [15, 11, 11, 11, 11, 11, 30],
-            {models} = selectedFrequentist;
-
-        return (
-            <table className="table table-sm">
-                <colgroup>
-                    {_.map(colWidths).map((value, idx) => (
-                        <col key={idx} width={`${value}%`}></col>
-                    ))}
-                </colgroup>
-                <thead className="table-bordered">
-                    <tr className="bg-custom">
-                        <th>Model</th>
-                        <th>BMDL</th>
-                        <th>BMD</th>
-                        <th>BMDU</th>
-                        <th>
-                            <i>P</i>-Value
-                        </th>
-                        <th>AIC</th>
-                        <th>Recommendation and Notes</th>
-                    </tr>
-                </thead>
-                <tbody className="table-bordered">
-                    {models.map((model, index) => (
-                        <tr
-                            key={index}
-                            onMouseEnter={() => store.drPlotAddHover(model)}
-                            onMouseLeave={store.drPlotRemoveHover}>
-                            <td>
-                                <a
-                                    id={`freq-result-${index}`}
-                                    href="#"
-                                    onClick={e => {
-                                        e.preventDefault();
-                                        store.showModalDetail(modelClasses.frequentist, index);
-                                    }}>
-                                    {model.name}
-                                </a>
-                            </td>
-                            <td>{ff(model.results.summary.bmdl)}</td>
-                            <td>{ff(model.results.summary.bmd)}</td>
-                            <td>{ff(model.results.summary.bmdu)}</td>
-                            <td>{ff(model.results.combined_pvalue)}</td>
-                            <td>{ff(model.results.summary.aic)}</td>
-                            <td>TODO</td>
-                        </tr>
-                    ))}
-                </tbody>
-            </table>
-        );
-    }
-}
-ResultTable.propTypes = {
-    outputStore: PropTypes.object,
-};
-
-export default ResultTable;
diff --git a/frontend/src/components/Output/Output.js b/frontend/src/components/Output/Output.js
index b20a77a4..f3aea0b9 100644
--- a/frontend/src/components/Output/Output.js
+++ b/frontend/src/components/Output/Output.js
@@ -14,7 +14,6 @@ import FrequentistResultTable from "./FrequentistResultTable";
 import MultitumorDatasetTable from "./Multitumor/DatasetTable";
 import MultitumorPlot from "./Multitumor/MultitumorPlot";
 import MultitumorResultTable from "./Multitumor/ResultTable";
-import NestedDichotomousResultTable from "./NestedDichotomous/ResultTable";
 import OptionSetTable from "./OptionSetTable";
 import SelectModel from "./SelectModel";
 
@@ -121,11 +120,7 @@ class Output extends Component {
                         <div className="row">
                             <div className="col-lg-8">
                                 <h4>Frequentist Model Results</h4>
-                                {outputStore.isNestedDichotomous ? (
-                                    <NestedDichotomousResultTable />
-                                ) : (
-                                    <FrequentistResultTable />
-                                )}
+                                <FrequentistResultTable />
                                 {canEdit ? <SelectModel /> : null}
                             </div>
                             <div className="align-items-center d-flex col-lg-4">

From 0f839628e022bbca7086c5f3568b18b92c1cc445 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Tue, 31 Oct 2023 10:20:25 -0400
Subject: [PATCH 06/24] switch to ruff format (#271)

---
 Makefile                  | 4 ++--
 bmds_server/common/git.py | 4 ++--
 make.bat                  | 8 ++++----
 pyproject.toml            | 7 +------
 requirements/dev.txt      | 3 +--
 5 files changed, 10 insertions(+), 16 deletions(-)

diff --git a/Makefile b/Makefile
index 88541297..73821d28 100644
--- a/Makefile
+++ b/Makefile
@@ -75,10 +75,10 @@ lint: lint-py lint-js  ## Check formatting issues
 format: format-py format-js  ## Fix formatting issues where possible
 
 lint-py:  ## Check python formatting issues
-	@black . --check && ruff .
+	@ruff format . --check && ruff .
 
 format-py:  ## Fix python formatting issues where possible
-	@black . && ruff . --fix --show-fixes
+	@ruff format . && ruff . --fix --show-fixes
 
 lint-js:  ## Check javascript formatting issues
 	@npm --prefix ./frontend run lint
diff --git a/bmds_server/common/git.py b/bmds_server/common/git.py
index b0f42038..c2469183 100644
--- a/bmds_server/common/git.py
+++ b/bmds_server/common/git.py
@@ -17,10 +17,10 @@ def current(cls, cwd: str = ".") -> Self:
             A Commit instance
         """
         cmd = "git log -1 --format=%H"
-        sha = subprocess.check_output(cmd.split(), cwd=cwd).decode().strip()[:8]
+        sha = subprocess.check_output(cmd.split(), cwd=cwd).decode().strip()[:8]  # noqa: S603
         cmd = "git show -s --format=%ct"
         dt = datetime.fromtimestamp(
-            int(subprocess.check_output(cmd.split(), cwd=cwd).decode().strip())
+            int(subprocess.check_output(cmd.split(), cwd=cwd).decode().strip())  # noqa: S603
         )
         return cls(sha=sha, dt=dt)
 
diff --git a/make.bat b/make.bat
index d2e00188..d0565593 100644
--- a/make.bat
+++ b/make.bat
@@ -48,21 +48,21 @@ mkdocs serve -f docs/mkdocs.yml -a localhost:8050
 goto :eof
 
 :lint
-black . --check && ruff .
+ruff format . --check && ruff .
 npm --prefix .\frontend run lint
 goto :eof
 
 :format
-black . && ruff . --fix --show-fixes
+ruff format . && ruff . --fix --show-fixes
 npm --prefix .\frontend run format
 goto :eof
 
 :lint-py
-black . --check && ruff .
+ruff format . --check && ruff .
 goto :eof
 
 :format-py
-black . && ruff . --fix --show-fixes
+ruff format . && ruff . --fix --show-fixes
 goto :eof
 
 :lint-js
diff --git a/pyproject.toml b/pyproject.toml
index 315612ce..44fe2e9d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,3 @@
-[tool.black]
-line-length = 100
-target-version = ['py311']
-extend-exclude = '(frontend|public|scripts/private)'
-
 [tool.coverage.run]
 omit = [
     "./bmds_server/main/settings/*",
@@ -25,4 +20,4 @@ known-third-party = ["bmds"]
 "test_*.py" = ["S101", "S106"]
 "scripts/*.py" = ["T201"]
 "**/management/**.py" = ["T201"]
-"**/migrations/**.py" = ["T201"]
+"**/migrations/**.py" = ["T201", "RUF012"]
diff --git a/requirements/dev.txt b/requirements/dev.txt
index ff98a9c5..946bef4a 100644
--- a/requirements/dev.txt
+++ b/requirements/dev.txt
@@ -21,8 +21,7 @@ playwright==1.29.1
 pytest-playwright==0.3.0
 
 # lint and formatting tools
-black==23.3.0
-ruff==0.0.261
+ruff~=0.1.3
 
 # install in editable mode
 -e .

From ee2b6aa1103321006785babac8921e523327f1af Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Tue, 31 Oct 2023 11:42:07 -0400
Subject: [PATCH 07/24] update python package versions (#268)

* karen dev ev fix, package updates

* sync frontend packages too

* fix integration tests

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 bmds_server/analysis/reporting/analytics.py   |  2 +-
 bmds_server/common/figures.py                 |  2 +-
 frontend/package.json                         | 10 ++++----
 .../components/IndividualModel/InfoTable.js   |  2 +-
 frontend/webpack.config.js                    |  7 +++++-
 make.bat                                      |  2 +-
 requirements/base.txt                         | 24 +++++++++----------
 requirements/dev.txt                          | 22 ++++++++---------
 requirements/production.txt                   |  4 ++--
 9 files changed, 40 insertions(+), 35 deletions(-)

diff --git a/bmds_server/analysis/reporting/analytics.py b/bmds_server/analysis/reporting/analytics.py
index 10b74cec..6f2cb305 100644
--- a/bmds_server/analysis/reporting/analytics.py
+++ b/bmds_server/analysis/reporting/analytics.py
@@ -175,7 +175,7 @@ def datasets() -> dict:
             df.frequentist,
             columns=df.bayesian,
             values=df.counts,
-            aggfunc=sum,
+            aggfunc="sum",
             margins=True,
             margins_name="Total",
         )
diff --git a/bmds_server/common/figures.py b/bmds_server/common/figures.py
index 0c0d185f..d33d41f1 100644
--- a/bmds_server/common/figures.py
+++ b/bmds_server/common/figures.py
@@ -45,7 +45,7 @@ def punchcard(df: pd.DataFrame, color_scale: str = "viridis") -> Figure:
     df.loc[:, "y"] = df.day.dt.day_of_week  # Monday=0, Sunday=6
 
     piv = (
-        df.pivot_table(index="y", columns="xlabel", values="count", aggfunc=sum)
+        df.pivot_table(index="y", columns="xlabel", values="count", aggfunc="sum")
         .fillna(0)
         .astype(int)
     )
diff --git a/frontend/package.json b/frontend/package.json
index 71bb75c8..5869324f 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -45,10 +45,10 @@
     "prettier": "^1.19.1",
     "rimraf": "^2.4.3",
     "style-loader": "^0.19.0",
-    "webpack": "^5.74.0",
-    "webpack-bundle-tracker": "^1.8.0",
-    "webpack-cli": "^4.7.2",
-    "webpack-dev-middleware": "^5.0.0"
+    "webpack": "^5.88.1",
+    "webpack-bundle-tracker": "^2.0.1",
+    "webpack-cli": "^5.1.4",
+    "webpack-dev-middleware": "^6.1.1"
   },
   "dependencies": {
     "bootstrap": "^4.6.2",
@@ -58,7 +58,7 @@
     "lodash": "^4.17.21",
     "mobx": "^5.15.7",
     "mobx-react": "^6.3.1",
-    "plotly.js": "^1.58.4",
+    "plotly.js": "2.27.0",
     "popper.js": "^1.16.1",
     "prop-types": "^15.7.2",
     "react": "^17.0.2",
diff --git a/frontend/src/components/IndividualModel/InfoTable.js b/frontend/src/components/IndividualModel/InfoTable.js
index 5b3582b1..f6b12af4 100644
--- a/frontend/src/components/IndividualModel/InfoTable.js
+++ b/frontend/src/components/IndividualModel/InfoTable.js
@@ -16,7 +16,7 @@ class InfoTable extends Component {
                 ["Model", model.name],
                 ["Equation", model.model_class.model_form_str],
             ];
-        return <TwoColumnTable data={data} label="Info" />;
+        return <TwoColumnTable id="info-table" data={data} label="Info" />;
     }
 }
 InfoTable.propTypes = {
diff --git a/frontend/webpack.config.js b/frontend/webpack.config.js
index b3fd33de..dec8110b 100644
--- a/frontend/webpack.config.js
+++ b/frontend/webpack.config.js
@@ -42,7 +42,12 @@ module.exports = {
         publicPath: "/static/bundles/",
     },
 
-    plugins: [new BundleTracker({filename: "../bmds_server/webpack-stats.json"})],
+    plugins: [
+        new BundleTracker({
+            path: path.resolve(__dirname, "../bmds_server"),
+            filename: "webpack-stats.json",
+        }),
+    ],
 
     resolve: {
         roots: [path.join(__dirname, "src")],
diff --git a/make.bat b/make.bat
index d0565593..01c1c3e2 100644
--- a/make.bat
+++ b/make.bat
@@ -33,7 +33,7 @@ echo.  format-js    fix javascript formatting issues where possible
 goto :eof
 
 :sync-dev
-python -m pip install -U pip
+python -m pip install -U pip --trusted-host=pypi.org --trusted-host=files.pythonhosted.org
 pip install -r requirements/dev.txt --trusted-host=pypi.org --trusted-host=files.pythonhosted.org
 yarn --cwd frontend
 manage.py migrate
diff --git a/requirements/base.txt b/requirements/base.txt
index ea5a9f84..bd4598e3 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -1,20 +1,20 @@
 # website
-Django~=4.2.5
-django-anymail==9.1
-django-redis==5.2.0
-django-webpack-loader==1.8.0
+Django~=4.2.6
+django-anymail==10.2
+django-redis==5.4.0
+django-webpack-loader==2.0.1
 djangorestframework==3.14.0
   uritemplate==4.1.1  # schema dependencies
-  PyYAML==6.0
-django-reversion==5.0.4
+  PyYAML==6.0.1
+django-reversion==5.0.6
 
 # db
-psycopg2-binary==2.9.6
+psycopg2-binary==2.9.9
 
 # tasks
-celery==5.2.7
-  billiard==3.6.4.0
-  kombu==5.2.4
+celery==5.3.4
+  billiard==4.1.0
+  kombu==5.3.2
 
-plotly==5.13.0
-redis==4.5.4
+plotly==5.18.0
+redis==5.0.1
diff --git a/requirements/dev.txt b/requirements/dev.txt
index 946bef4a..b675f4fd 100644
--- a/requirements/dev.txt
+++ b/requirements/dev.txt
@@ -1,24 +1,24 @@
 -r base.txt
 
 # debug
-django-debug-toolbar==4.0.0
-django_extensions==3.2.1
-django-browser-reload==1.11.0
+django-debug-toolbar==4.2.0
+django_extensions==3.2.3
+django-browser-reload==1.12.0
 
 # docs
-mkdocs-material==9.0.6
+mkdocs-material==9.4.7
 
 # tests
-pytest==7.4.0
-pytest-django==4.5.2
-vcrpy==4.2.1
-  urllib3~=1.26.16
+pytest==7.4.3
+pytest-django==4.6.0
+vcrpy==5.1.0
+  urllib3==2.0.6
 pytest-vcr==1.0.2
-coverage==7.3.0
+coverage==7.3.2
 
 # integration tests
-playwright==1.29.1
-pytest-playwright==0.3.0
+playwright==1.39.0
+pytest-playwright==0.4.3
 
 # lint and formatting tools
 ruff~=0.1.3
diff --git a/requirements/production.txt b/requirements/production.txt
index 07073380..1fe58198 100644
--- a/requirements/production.txt
+++ b/requirements/production.txt
@@ -1,6 +1,6 @@
 -r base.txt
 
-gunicorn==20.1.0
-bmds==23.2
+gunicorn==21.2.0
+bmds==23.3
 
 ./dist/bmds_server-2023.3-py3-none-any.whl

From 26933371bd50b556b619ef6464aadcfdae3a4bf5 Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Tue, 31 Oct 2023 12:23:55 -0400
Subject: [PATCH 08/24] integration tests - nested dichotomous + multitumor
 (#269)

* basic ND MT test, tweak button language

* update test data, R-O sketch

* read-only update

* misc changes

* a few updates

* add back change

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 .../Main/OptionsForm/OptionsFormList.js       |   2 +-
 frontend/src/constants/dataConstants.js       |   2 +-
 tests/integration/common.py                   |   2 +-
 tests/integration/test_integration.py         | 173 ++++++++++++++++--
 4 files changed, 162 insertions(+), 17 deletions(-)

diff --git a/frontend/src/components/Main/OptionsForm/OptionsFormList.js b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
index 9477b652..075cafea 100644
--- a/frontend/src/components/Main/OptionsForm/OptionsFormList.js
+++ b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
@@ -74,7 +74,7 @@ class OptionsFormList extends Component {
                                     {optionsStore.canEdit ? (
                                         <th>
                                             <Button
-                                                title="Maximum number of option sets reached."
+                                                title="Add option set."
                                                 className="btn btn-primary"
                                                 disabled={!optionsStore.canAddNewOption}
                                                 onClick={optionsStore.addOptions}
diff --git a/frontend/src/constants/dataConstants.js b/frontend/src/constants/dataConstants.js
index 5685ff49..14b0f51d 100644
--- a/frontend/src/constants/dataConstants.js
+++ b/frontend/src/constants/dataConstants.js
@@ -181,7 +181,7 @@ export const DATA_CONTINUOUS_SUMMARY = "CS",
                     doses: [
                         0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
                         25, 25, 25, 25, 25, 25, 25, 25, 25,
-                        50, 50, 50, 50, 50, 50, 50, 50, 50,
+                        50, 50, 50, 50, 50, 50, 150, 150, 150,
                     ],
                     litter_ns: [
                         16, 9, 15, 14, 13, 9, 10, 14, 10, 11, 14,
diff --git a/tests/integration/common.py b/tests/integration/common.py
index fd9632eb..85235350 100644
--- a/tests/integration/common.py
+++ b/tests/integration/common.py
@@ -11,7 +11,7 @@
     os.environ["DJANGO_ALLOW_ASYNC_UNSAFE"] = "true"
 
 
-@pytest.mark.skipif(not RUN_INTEGRATION, reason="integration test")
+@pytest.mark.skipif(not RUN_INTEGRATION, reason=f"RUN_INTEGRATION is {RUN_INTEGRATION}")
 class PlaywrightTestCase(StaticLiveServerTestCase, TestCase):
     """
     We use a single class that inherits from both StaticLiveServerTestCase and TestCase
diff --git a/tests/integration/test_integration.py b/tests/integration/test_integration.py
index a71fa2a9..55da2b39 100644
--- a/tests/integration/test_integration.py
+++ b/tests/integration/test_integration.py
@@ -6,13 +6,10 @@
 class TestContinuousIntegration(PlaywrightTestCase):
     def test_continuous(self):
         page = self.page
-
         page.goto(self.url("/"))
-        page = self.page
 
-        page.goto(self.url("/"))
         with page.expect_navigation():
-            page.locator("text=Create a new BMDS analysis").click()
+            page.get_by_role("button", name="Create a new BMDS analysis").click()
 
         # set main input
         page.locator("#analysis_name").fill("abc")
@@ -23,9 +20,9 @@ def test_continuous(self):
         page.locator("#select_all_frequentist_restricted").click()
 
         # view data tab
-        page.locator('a:has-text("Data")').click()
-        page.locator('button:has-text("New")').click()
-        page.locator("text=Load an example dataset").click()
+        page.get_by_role("link", name="Data").click()
+        page.get_by_role("button", name="New").click()
+        page.get_by_role("button", name="Load an example dataset").click()
 
         # save current settings
         page.locator('a:has-text("Settings")').click()
@@ -54,14 +51,31 @@ def test_continuous(self):
         expect(page.locator("#decision-logic tbody tr")).to_have_count(4)
         expect(page.locator("#rule-table tbody tr")).to_have_count(20)
 
-        # TODO - add read-only views in BMDS 23.3
+        # Read-only
+        if self.can_execute:
+            page.get_by_role("button", name="Share").click()
+            with page.expect_popup() as page2_info:
+                page.get_by_role("link", name="Open").first.click()
+            page2 = page2_info.value
+
+            page2.get_by_role("link", name="Settings").click()
+            expect(page2.get_by_role("cell", name="abc")).to_be_visible()
+
+            page2.get_by_role("link", name="Data").click()
+            expect(page2.get_by_text("Dataset Name: Dataset #1")).to_be_visible()
+
+            page2.get_by_role("link", name="Output").click()
+            expect(page2.get_by_text("Dataset Name: Dataset #1")).to_be_visible()
+
+            page2.get_by_role("link", name="Logic").click()
+            expect(page2.get_by_role("cell", name="Decision Logic")).to_be_visible()
 
     def test_dichotomous(self):
         page = self.page
-
         page.goto(self.url("/"))
+
         with page.expect_navigation():
-            page.locator("text=Create a new BMDS analysis").click()
+            page.get_by_role("button", name="Create a new BMDS analysis").click()
 
         # set main input
         page.locator("#analysis_name").fill("abc")
@@ -75,9 +89,9 @@ def test_dichotomous(self):
         page.locator("#bayesian-Logistic").check()
 
         # view data tab
-        page.locator('a:has-text("Data")').click()
-        page.locator('button:has-text("New")').click()
-        page.locator("text=Load an example dataset").click()
+        page.get_by_role("link", name="Data").click()
+        page.get_by_role("button", name="New").click()
+        page.get_by_role("button", name="Load an example dataset").click()
 
         # save current settings
         page.locator('a:has-text("Settings")').click()
@@ -117,4 +131,135 @@ def test_dichotomous(self):
         expect(page.locator("#decision-logic tbody tr")).to_have_count(4)
         expect(page.locator("#rule-table tbody tr")).to_have_count(18)
 
-        # TODO - add read-only views in BMDS 23.3
+        # Read-only
+        if self.can_execute:
+            page.get_by_role("button", name="Share").click()
+            with page.expect_popup() as page2_info:
+                page.get_by_role("link", name="Open").first.click()
+            page2 = page2_info.value
+
+            page2.get_by_role("link", name="Settings").click()
+            expect(page2.get_by_role("cell", name="abc")).to_be_visible()
+
+            page2.get_by_role("link", name="Data").click()
+            expect(page2.get_by_text("Dataset Name: Dataset #1")).to_be_visible()
+
+            page2.get_by_role("link", name="Output").click()
+            expect(page2.get_by_text("Dataset Name: Dataset #1")).to_be_visible()
+
+            page2.get_by_role("link", name="Logic").click()
+            expect(page2.get_by_role("cell", name="Decision Logic")).to_be_visible()
+
+    def test_nested_dichotomous(self):
+        page = self.page
+        page.goto(self.url("/"))
+
+        with page.expect_navigation():
+            page.get_by_role("button", name="Create a new BMDS analysis").click()
+
+        # set main input
+        page.locator("#analysis_name").fill("abc")
+        page.locator("#analysis_description").fill("def")
+        page.locator("#analysis_model_type").select_option("ND")
+
+        # view data tab, add 2 datasets
+        page.get_by_role("link", name="Data").click()
+        page.get_by_role("button", name="New").click()
+        page.get_by_role("button", name="Load an example dataset").click()
+        page.get_by_role("button", name="New").click()
+        page.get_by_role("button", name="Load an example dataset").click()
+
+        # save current settings
+        page.locator('a:has-text("Settings")').click()
+        page.get_by_role("button", name="Save Analysis").click()
+
+        if self.can_execute:
+            # execute and wait until complete
+            page.locator("text=Run Analysis").click()
+            expect(page.locator("#controlPanel")).to_contain_text("Executing, please wait...")
+
+            # view output summary tables
+            page.locator('a:has-text("Output")').click()
+            # num rows in results table
+            expect(page.locator("#frequentist-model-result tbody tr")).to_have_count(5)
+
+            # check one result
+            page.get_by_role("link", name="Nested Logistic (lsc+ilc-)*").click()
+            expect(page.get_by_role("dialog")).to_contain_text("Nested Logistic (lsc+ilc-)")
+            page.locator("#close-modal").click()
+
+            # Read-only
+            page.get_by_role("button", name="Share").click()
+            with page.expect_popup() as page2_info:
+                page.get_by_role("link", name="Open").first.click()
+            page2 = page2_info.value
+
+            page2.get_by_role("link", name="Settings").click()
+            expect(page2.get_by_role("cell", name="abc")).to_be_visible()
+
+            page2.get_by_role("link", name="Data").click()
+            expect(page2.get_by_text("Dataset Name: Dataset #1")).to_be_visible()
+
+            page2.get_by_role("link", name="Output").click()
+            expect(page2.get_by_text("Dataset Name: Dataset #1")).to_be_visible()
+
+            page2.get_by_role("link", name="Logic").click()
+            expect(page2.get_by_role("cell", name="Decision Logic")).to_be_visible()
+
+    def test_multi_tumor(self):
+        page = self.page
+        page.goto(self.url("/"))
+
+        with page.expect_navigation():
+            page.get_by_role("button", name="Create a new BMDS analysis").click()
+
+        # set main input
+        page.locator("#analysis_name").fill("abc")
+        page.locator("#analysis_description").fill("def")
+        page.locator("#analysis_model_type").select_option("MT")
+
+        # view data tab, add 3 datasets
+        page.get_by_role("link", name="Data").click()
+        page.get_by_role("button", name="New").click()
+
+        page.get_by_role("button", name="Load an example dataset").click()
+
+        # 2nd dataset
+        page.get_by_role("button", name="New").click()
+        page.get_by_role("button", name="Load an example dataset").click()
+
+        # 3rd dataset
+        page.get_by_role("button", name="New").click()
+        page.get_by_role("button", name="Load an example dataset").click()
+
+        # save current settings
+        page.locator('a:has-text("Settings")').click()
+        page.locator("text=Save Analysis").click()
+
+        if self.can_execute:
+            # execute and wait until complete
+            page.locator("text=Run Analysis").click()
+            expect(page.locator("#controlPanel")).to_contain_text("Executing, please wait...")
+
+            # view output summary tables
+            page.locator('a:has-text("Output")').click()
+
+            # check one result
+            page.get_by_role("link", name="Multi-tumor (MS Combo)").click()
+            expect(page.get_by_role("dialog")).to_contain_text("MS Combo")
+            page.locator("#close-modal").click()
+
+            # Read-only
+            page.get_by_role("button", name="Share").click()
+            with page.expect_popup() as page2_info:
+                page.get_by_role("link", name="Open").first.click()
+            page2 = page2_info.value
+
+            page2.get_by_role("link", name="Settings").click()
+            expect(page2.get_by_role("cell", name="abc")).to_be_visible()
+
+            page2.get_by_role("link", name="Data").click()
+            expect(page2.get_by_text("Select existing")).to_be_visible()
+
+            page2.get_by_role("link", name="Output").click()
+            expect(page2.get_by_text("Model Results")).to_be_visible()

From ade134cadd9af141d3a47687c00e9c0498079023 Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Tue, 31 Oct 2023 13:51:06 -0400
Subject: [PATCH 09/24] 297 dynamic word export (#270)

* change default download options

* forgot this

* big T little t, set defaults but still wonky model_type reset

* oops

* a little better

* move logic to one location

* delete

* change default type to continuous

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 bmds_server/analysis/models.py                |  2 +-
 .../Main/Actions/WordReportOptionsModal.js    | 66 +++++++++++--------
 frontend/src/components/Navigation.js         |  4 +-
 frontend/src/stores/DataStore.js              |  2 +-
 frontend/src/stores/MainStore.js              | 22 ++++---
 frontend/src/stores/OptionsStore.js           |  2 +-
 6 files changed, 55 insertions(+), 43 deletions(-)

diff --git a/bmds_server/analysis/models.py b/bmds_server/analysis/models.py
index a83cb087..9685e015 100644
--- a/bmds_server/analysis/models.py
+++ b/bmds_server/analysis/models.py
@@ -331,7 +331,7 @@ def handle_execution_error(self, err):
     def default_input(self) -> dict:
         return {
             "bmds_version": bmds.constants.BMDS330,  # TODO - change?
-            "dataset_type": ModelClass.DICHOTOMOUS,
+            "dataset_type": ModelClass.CONTINUOUS,
             "datasets": [],
             "models": {},
             "dataset_options": [],
diff --git a/frontend/src/components/Main/Actions/WordReportOptionsModal.js b/frontend/src/components/Main/Actions/WordReportOptionsModal.js
index b91719bc..cf659246 100644
--- a/frontend/src/components/Main/Actions/WordReportOptionsModal.js
+++ b/frontend/src/components/Main/Actions/WordReportOptionsModal.js
@@ -18,6 +18,7 @@ class WordReportOptionsModal extends Component {
             submitWordReportRequest,
             closeWordReportOptionModal,
             wordReportOptions,
+            isMultiTumorOrNestedDichotomous,
         } = this.props.mainStore;
         return (
             <Modal
@@ -39,20 +40,25 @@ class WordReportOptionsModal extends Component {
                                 please be patient.
                             </p>
                         </div>
-                        <div className="col-md-4">
-                            <LabelInput label="Long dataset format" htmlFor="datasetFormatLong" />
-                            <br />
-                            <CheckboxInput
-                                id="datasetFormatLong"
-                                checked={wordReportOptions.datasetFormatLong}
-                                onChange={v => changeReportOptions("datasetFormatLong", v)}
-                            />
-                            <p className="text-muted">
-                                Print the dataset table in a long format (good for Excel or
-                                additional data analysis), or a narrow format, which is more concise
-                                for a narrative report.
-                            </p>
-                        </div>
+                        {isMultiTumorOrNestedDichotomous ? null : (
+                            <div className="col-md-4">
+                                <LabelInput
+                                    label="Long dataset format"
+                                    htmlFor="datasetFormatLong"
+                                />
+                                <br />
+                                <CheckboxInput
+                                    id="datasetFormatLong"
+                                    checked={wordReportOptions.datasetFormatLong}
+                                    onChange={v => changeReportOptions("datasetFormatLong", v)}
+                                />
+                                <p className="text-muted">
+                                    Print the dataset table in a long format (good for Excel or
+                                    additional data analysis), or a narrow format, which is more
+                                    concise for a narrative report.
+                                </p>
+                            </div>
+                        )}
                         <div className="col-md-4">
                             <LabelInput label="Include all models" htmlFor="allModels" />
                             <br />
@@ -68,21 +74,23 @@ class WordReportOptionsModal extends Component {
                                 models which were executed will be included.
                             </p>
                         </div>
-                        <div className="col-md-4">
-                            <LabelInput label="Include BMD CDF Table" htmlFor="bmdCdfTable" />
-                            <br />
-                            <CheckboxInput
-                                id="bmdCdfTable"
-                                checked={wordReportOptions.bmdCdfTable}
-                                onChange={v => changeReportOptions("bmdCdfTable", v)}
-                            />
-                            <p className="text-muted">
-                                Include the BMD cumulative distribution function (CDF) table for
-                                each model. This is a large table and makes the report considerably
-                                longer, but may be necessary for some downstream analysis of
-                                results.
-                            </p>
-                        </div>
+                        {isMultiTumorOrNestedDichotomous ? null : (
+                            <div className="col-md-4">
+                                <LabelInput label="Include BMD CDF Table" htmlFor="bmdCdfTable" />
+                                <br />
+                                <CheckboxInput
+                                    id="bmdCdfTable"
+                                    checked={wordReportOptions.bmdCdfTable}
+                                    onChange={v => changeReportOptions("bmdCdfTable", v)}
+                                />
+                                <p className="text-muted">
+                                    Include the BMD cumulative distribution function (CDF) table for
+                                    each model. This is a large table and makes the report
+                                    considerably longer, but may be necessary for some downstream
+                                    analysis of results.
+                                </p>
+                            </div>
+                        )}
                     </div>
                 </Modal.Body>
                 <Modal.Footer>
diff --git a/frontend/src/components/Navigation.js b/frontend/src/components/Navigation.js
index 52556f27..d5294b99 100644
--- a/frontend/src/components/Navigation.js
+++ b/frontend/src/components/Navigation.js
@@ -17,7 +17,7 @@ import Output from "./Output/Output";
 class Navigation extends Component {
     render() {
         const {mainStore} = this.props,
-            {isMultitumor} = mainStore;
+            {isMultiTumor} = mainStore;
         return (
             <>
                 <ul className="nav nav-tabs d-flex mt-3">
@@ -36,7 +36,7 @@ class Navigation extends Component {
                             Output
                         </NavLink>
                     </li>
-                    {isMultitumor ? null : (
+                    {isMultiTumor ? null : (
                         <li className="nav-item">
                             <NavLink className="nav-link" to="/logic">
                                 Logic
diff --git a/frontend/src/stores/DataStore.js b/frontend/src/stores/DataStore.js
index 413f45f0..7f8c791b 100644
--- a/frontend/src/stores/DataStore.js
+++ b/frontend/src/stores/DataStore.js
@@ -270,7 +270,7 @@ class DataStore {
     @computed get maxItems() {
         return this.rootStore.mainStore.isDesktop
             ? 1000
-            : this.rootStore.mainStore.isMultitumor
+            : this.rootStore.mainStore.isMultiTumor
             ? 10
             : 6;
     }
diff --git a/frontend/src/stores/MainStore.js b/frontend/src/stores/MainStore.js
index 6a08d8b0..dc3280a9 100644
--- a/frontend/src/stores/MainStore.js
+++ b/frontend/src/stores/MainStore.js
@@ -12,12 +12,11 @@ class MainStore {
     }
 
     @observable config = {};
-    @observable models = {};
 
     @observable analysis_name = "";
     @observable analysis_description = "";
-    @observable model_type = mc.MODEL_CONTINUOUS;
-    @observable errorMessage = "";
+    @observable model_type = null;
+    @observable errorMessage = null;
     @observable errorData = null;
     @observable hasEditSettings = false;
     @observable executionOutputs = null;
@@ -36,6 +35,11 @@ class MainStore {
     }
     @action.bound changeDatasetType(value) {
         this.model_type = value;
+        // word export options setting
+        if (this.isMultiTumorOrNestedDichotomous) {
+            this.changeReportOptions("datasetFormatLong", false);
+            this.changeReportOptions("allModels", true);
+        }
         this.rootStore.modelsStore.setDefaultsByDatasetType(true);
         this.rootStore.optionsStore.setDefaultsByDatasetType(true);
         this.rootStore.dataStore.setDefaultsByDatasetType();
@@ -71,10 +75,14 @@ class MainStore {
             },
         };
     }
-    @computed get isMultitumor() {
+    @computed get isMultiTumor() {
         return this.model_type === mc.MODEL_MULTI_TUMOR;
     }
 
+    @computed get isMultiTumorOrNestedDichotomous() {
+        return this.model_type === "ND" || this.model_type === "MT";
+    }
+
     @action.bound
     async saveAnalysis() {
         this.rootStore.dataStore.cleanRows();
@@ -337,10 +345,6 @@ class MainStore {
         return _.isArray(this.executionOutputs);
     }
 
-    @computed get isMultiTumor() {
-        return this.model_type === mc.MODEL_MULTI_TUMOR;
-    }
-
     // *** TOAST ***
     @observable toastVisible = false;
     @observable toastHeader = "";
@@ -388,7 +392,7 @@ class MainStore {
     }
     // *** END TOAST ***
 
-    // *** REPORT OPTIONS ***
+    // *** DEFAULT REPORT OPTIONS ***
     @observable wordReportOptions = {
         datasetFormatLong: true,
         allModels: false,
diff --git a/frontend/src/stores/OptionsStore.js b/frontend/src/stores/OptionsStore.js
index ff72798a..420a10ce 100644
--- a/frontend/src/stores/OptionsStore.js
+++ b/frontend/src/stores/OptionsStore.js
@@ -51,7 +51,7 @@ class OptionsStore {
     @computed get maxItems() {
         return this.rootStore.mainStore.isDesktop
             ? 1000
-            : this.rootStore.mainStore.isMultitumor
+            : this.rootStore.mainStore.isMultiTumor
             ? 3
             : 6;
     }

From df3f7b849693633086146cb0265179940ed3fa76 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Tue, 7 Nov 2023 10:59:37 -0500
Subject: [PATCH 10/24] update to pydantic v2 (#273)

* ran bump, tweaking

* err message change, mod deprecated

* future test tweak, forgot something, alias not working?

* deprecated

* more updates

* fix tests

* add key so that page updates

* revert changes

---------

Co-authored-by: hausman-gdit <karen.hausman@gdit.com>
---
 bmds_server/analysis/api.py                   |  4 +-
 bmds_server/analysis/executor.py              | 12 ++--
 bmds_server/analysis/models.py                |  8 +--
 bmds_server/analysis/schema.py                | 15 +++--
 bmds_server/analysis/transforms.py            |  6 +-
 bmds_server/analysis/validators/__init__.py   |  4 +-
 bmds_server/analysis/validators/datasets.py   | 34 +++++-----
 bmds_server/analysis/validators/models.py     | 48 +++++++-------
 bmds_server/analysis/validators/options.py    |  8 +--
 bmds_server/analysis/validators/session.py    |  8 +--
 bmds_server/common/task_cache.py              |  6 +-
 bmds_server/common/validation.py              |  2 +-
 bmds_server/main/settings/base.py             |  2 +-
 compose/app/test.py                           |  2 +-
 .../Main/ModelsForm/ModelsCheckBox.js         | 10 +--
 tests/analysis/test_api.py                    | 54 +++++++--------
 tests/analysis/test_schema.py                 | 16 ++---
 tests/analysis/test_validators.py             | 66 +++++++------------
 tests/conftest.py                             | 10 +--
 19 files changed, 145 insertions(+), 170 deletions(-)

diff --git a/bmds_server/analysis/api.py b/bmds_server/analysis/api.py
index 64824a16..74aca94a 100644
--- a/bmds_server/analysis/api.py
+++ b/bmds_server/analysis/api.py
@@ -133,7 +133,7 @@ def excel(self, request, *args, **kwargs):
             data = renderers.BinaryFile(data=response.content, filename=instance.slug)
             return Response(data)
 
-        return Response(response.dict(), content_type="application/json")
+        return Response(response.model_dump(), content_type="application/json")
 
     @action(detail=True, renderer_classes=(renderers.DocxRenderer,))
     def word(self, request, *args, **kwargs):
@@ -155,7 +155,7 @@ def word(self, request, *args, **kwargs):
             data = add_update_url(instance, response.content, uri) if edit else response.content
             return Response(renderers.BinaryFile(data=data, filename=instance.slug))
 
-        return Response(response.dict(), content_type="application/json")
+        return Response(response.model_dump(), content_type="application/json")
 
 
 @api_view(["POST"])
diff --git a/bmds_server/analysis/executor.py b/bmds_server/analysis/executor.py
index 345e67e1..5b1d24e6 100644
--- a/bmds_server/analysis/executor.py
+++ b/bmds_server/analysis/executor.py
@@ -55,13 +55,13 @@ def build_frequentist_session(dataset, inputs, options, dataset_options) -> Bmds
                 )
                 degrees = list(range(min_degree, max(min(max_degree, 9), 2)))
                 for degree in degrees:
-                    model_options = model_options.copy()
+                    model_options = model_options.model_copy()
                     model_options.degree = degree
                     session.add_model(model_name, settings=model_options)
             elif dataset_type == ModelClass.NESTED_DICHOTOMOUS:
                 # run all permutations of intralitter correlation and litter specific covariate
                 for ilc, lsc_on in itertools.product(IntralitterCorrelation, [True, False]):
-                    settings = model_options.copy()
+                    settings = model_options.model_copy()
                     settings.intralitter_correlation = ilc
                     settings.litter_specific_covariate = (
                         settings.litter_specific_covariate
@@ -149,7 +149,7 @@ def create(cls, inputs: dict, dataset_index: int, option_index: int) -> Self:
 
     @classmethod
     def deserialize(cls, data: dict) -> Self:
-        obj = AnalysisSessionSchema.parse_obj(data)
+        obj = AnalysisSessionSchema.model_validate(data)
         return cls(
             dataset_index=obj.dataset_index,
             option_index=obj.option_index,
@@ -177,7 +177,7 @@ def to_schema(self) -> AnalysisSessionSchema:
         )
 
     def to_dict(self) -> dict:
-        return self.to_schema().dict()
+        return self.to_schema().model_dump(by_alias=True)
 
 
 class MultiTumorSession(NamedTuple):
@@ -220,7 +220,7 @@ def execute(self):
 
     @classmethod
     def deserialize(cls, data: dict) -> Self:
-        obj = AnalysisSessionSchema.parse_obj(data)
+        obj = AnalysisSessionSchema.model_validate(data)
         return cls(
             option_index=obj.option_index,
             session=Multitumor.from_serialized(obj.frequentist),
@@ -232,7 +232,7 @@ def to_schema(self) -> AnalysisSessionSchema:
         )
 
     def to_dict(self) -> dict:
-        return self.to_schema().dict()
+        return self.to_schema().model_dump(by_alias=True)
 
 
 Session = AnalysisSession | MultiTumorSession
diff --git a/bmds_server/analysis/models.py b/bmds_server/analysis/models.py
index 9685e015..15616c60 100644
--- a/bmds_server/analysis/models.py
+++ b/bmds_server/analysis/models.py
@@ -304,9 +304,9 @@ def execute(self):
             analysis_id=str(self.id),
             bmds_server_version=settings.COMMIT.sha,
             bmds_python_version=bmds_python_version,
-            outputs=[output.dict() for output in outputs],
+            outputs=[output.model_dump(by_alias=True) for output in outputs],
         )
-        self.outputs = analysis_output.dict()
+        self.outputs = analysis_output.model_dump(by_alias=True)
         self.errors = [output.error for output in outputs if output.error]
         self.ended = now()
         self.deletion_date = get_deletion_date()
@@ -336,7 +336,7 @@ def default_input(self) -> dict:
             "models": {},
             "dataset_options": [],
             "options": [],
-            "recommender": RecommenderSettings.build_default().dict(),
+            "recommender": RecommenderSettings.build_default().model_dump(),
         }
 
     def renew(self):
@@ -345,7 +345,7 @@ def renew(self):
     def get_bmds_version(self) -> VersionSchema | None:
         if not self.is_finished or self.has_errors:
             return None
-        return AnalysisOutput.parse_obj(self.outputs).bmds_python_version
+        return AnalysisOutput.model_validate(self.outputs).bmds_python_version
 
     @property
     def deletion_date_str(self) -> str | None:
diff --git a/bmds_server/analysis/schema.py b/bmds_server/analysis/schema.py
index e50079b3..b407a2d7 100644
--- a/bmds_server/analysis/schema.py
+++ b/bmds_server/analysis/schema.py
@@ -4,8 +4,7 @@
 import pandas as pd
 from bmds.bmds3.types.sessions import VersionSchema
 from bmds.datasets.transforms.polyk import calculate
-from pydantic import BaseModel, Field, validator
-from pydantic.schema import schema as pyschema
+from pydantic import BaseModel, Field, field_validator
 from rest_framework.schemas.openapi import SchemaGenerator
 
 from .validators import AnalysisSelectedSchema
@@ -32,7 +31,7 @@ class AnalysisOutput(BaseModel):
     analysis_id: str
     analysis_schema_version: str = "1.1"
     bmds_server_version: str
-    bmds_python_version: VersionSchema | None
+    bmds_python_version: VersionSchema | None = None
     outputs: list[AnalysisSessionSchema]
 
 
@@ -42,7 +41,8 @@ class PolyKInput(BaseModel):
     power: float = Field(default=3, ge=0, le=5)
     duration: float | None = Field(default=None, gt=0, le=10000)
 
-    @validator("dataset")
+    @field_validator("dataset")
+    @classmethod
     def check_dataset(cls, value):
         if len(value) > 100_000:
             raise ValueError("Dataset too large")
@@ -81,9 +81,10 @@ def calculate(self) -> tuple[pd.DataFrame, pd.DataFrame]:
 
 
 def add_schemas(schema: dict, models: list):
-    additions = pyschema(models, ref_prefix="#/components/schemas/")
-    for key, value in additions["definitions"].items():
-        schema["components"]["schemas"][key] = value
+    for model in models:
+        schema["components"]["schemas"][model.__name__] = model.model_json_schema(
+            ref_template=f"#/components/schemas/{model}"
+        )
 
 
 def add_schema_to_path(schema: dict, path: str, verb: str, name: str):
diff --git a/bmds_server/analysis/transforms.py b/bmds_server/analysis/transforms.py
index b016238a..61383872 100644
--- a/bmds_server/analysis/transforms.py
+++ b/bmds_server/analysis/transforms.py
@@ -58,8 +58,8 @@ def build_model_settings(
     elif dataset_type == bmds.constants.NESTED_DICHOTOMOUS:
         is_restricted = prior_class == PriorClass.frequentist_restricted
         return NestedDichotomousModelSettings(
-            bmr_type=options["bmr_value"],
-            bmr=options["bmr_type"],
+            bmr_type=options["bmr_type"],
+            bmr=options["bmr_value"],
             alpha=round(1.0 - options["confidence_level"], 3),
             litter_specific_covariate=options["litter_specific_covariate"],
             restricted=is_restricted,
@@ -90,7 +90,7 @@ def build_dataset(dataset: dict[str, list[float]]) -> bmds.datasets.DatasetType:
         schema = bmds.datasets.NestedDichotomousDatasetSchema
     else:
         raise ValueError(f"Unknown dataset type: {dataset_type}")
-    return schema.parse_obj(dataset).deserialize()
+    return schema.model_validate(dataset).deserialize()
 
 
 def remap_exponential(models: list[str]) -> list[str]:
diff --git a/bmds_server/analysis/validators/__init__.py b/bmds_server/analysis/validators/__init__.py
index c1dbd272..3836a137 100644
--- a/bmds_server/analysis/validators/__init__.py
+++ b/bmds_server/analysis/validators/__init__.py
@@ -1,4 +1,3 @@
-import bmds
 from bmds.bmds3.recommender import RecommenderSettings
 
 from ...common.validation import pydantic_validate
@@ -22,7 +21,6 @@ def validate_input(data: dict, partial: bool = False) -> None:
     """
     # check session
     validate_session(data, partial=partial)
-    bmds_version = data["bmds_version"]
     dataset_type = data["dataset_type"]
 
     # check dataset schema
@@ -37,7 +35,7 @@ def validate_input(data: dict, partial: bool = False) -> None:
         validate_models(dataset_type, models)
 
     options = data.get("options")
-    if options or (partial is False and bmds_version in bmds.constants.BMDS_THREES):
+    if options or partial is False:
         validate_options(dataset_type, data.get("options"))
 
     recommender = data.get("recommender")
diff --git a/bmds_server/analysis/validators/datasets.py b/bmds_server/analysis/validators/datasets.py
index cfca9765..63d3c4aa 100644
--- a/bmds_server/analysis/validators/datasets.py
+++ b/bmds_server/analysis/validators/datasets.py
@@ -10,11 +10,11 @@
 )
 from django.conf import settings
 from django.core.exceptions import ValidationError
-from pydantic import BaseModel, Field, root_validator
+from pydantic import BaseModel, Field, model_validator
 
 from ...common.validation import pydantic_validate
 
-max_items = 1000 if settings.IS_DESKTOP else 10
+max_length = 1000 if settings.IS_DESKTOP else 10
 
 
 class MaxDegree(IntEnum):
@@ -54,15 +54,15 @@ class NestedDichotomousModelOptions(BaseModel):
 
 
 class DatasetValidator(BaseModel):
-    @root_validator(skip_on_failure=True)
-    def check_id_matches(cls, values):
-        dataset_ids = [dataset.metadata.id for dataset in values["datasets"]]
-        ds_option_ids = [opt.dataset_id for opt in values["dataset_options"]]
+    @model_validator(mode="after")
+    def check_id_matches(self):
+        dataset_ids = [dataset.metadata.id for dataset in self.datasets]
+        ds_option_ids = [opt.dataset_id for opt in self.dataset_options]
         if len(set(dataset_ids)) != len(dataset_ids):
             raise ValueError("Dataset IDs are not unique")
         if set(dataset_ids) != set(ds_option_ids):
             raise ValueError("Dataset IDs are not the same as dataset option IDs")
-        return values
+        return self
 
 
 class MaxDichotomousDatasetSchema(DichotomousDatasetSchema):
@@ -83,26 +83,28 @@ class MaxNestedDichotomousDatasetSchema(NestedDichotomousDatasetSchema):
 
 
 class DichotomousDatasets(DatasetValidator):
-    dataset_options: list[DichotomousModelOptions] = Field(min_items=1, max_items=max_items)
-    datasets: list[MaxDichotomousDatasetSchema] = Field(min_items=1, max_items=max_items)
+    dataset_options: list[DichotomousModelOptions] = Field(min_length=1, max_length=max_length)
+    datasets: list[MaxDichotomousDatasetSchema] = Field(min_length=1, max_length=max_length)
 
 
 class ContinuousDatasets(DatasetValidator):
-    dataset_options: list[ContinuousModelOptions] = Field(min_items=1, max_items=max_items)
+    dataset_options: list[ContinuousModelOptions] = Field(min_length=1, max_length=max_length)
     datasets: list[MaxContinuousDatasetSchema | MaxContinuousIndividualDatasetSchema] = Field(
-        min_items=1,
-        max_items=max_items,
+        min_length=1,
+        max_length=max_length,
     )
 
 
 class NestedDichotomousDataset(DatasetValidator):
-    dataset_options: list[NestedDichotomousModelOptions] = Field(min_items=1, max_items=max_items)
-    datasets: list[MaxNestedDichotomousDatasetSchema] = Field(min_items=1, max_items=max_items)
+    dataset_options: list[NestedDichotomousModelOptions] = Field(
+        min_length=1, max_length=max_length
+    )
+    datasets: list[MaxNestedDichotomousDatasetSchema] = Field(min_length=1, max_length=max_length)
 
 
 class MultiTumorDatasets(DatasetValidator):
-    dataset_options: list[DichotomousModelOptions] = Field(min_items=1, max_items=max_items)
-    datasets: list[DichotomousDatasetSchema] = Field(min_items=1, max_items=max_items)
+    dataset_options: list[DichotomousModelOptions] = Field(min_length=1, max_length=max_length)
+    datasets: list[DichotomousDatasetSchema] = Field(min_length=1, max_length=max_length)
 
 
 def validate_datasets(dataset_type: str, datasets: Any, datasetOptions: Any):
diff --git a/bmds_server/analysis/validators/models.py b/bmds_server/analysis/validators/models.py
index ac6129ca..ee318540 100644
--- a/bmds_server/analysis/validators/models.py
+++ b/bmds_server/analysis/validators/models.py
@@ -3,7 +3,7 @@
 import bmds
 import numpy as np
 from django.core.exceptions import ValidationError
-from pydantic import BaseModel, Field, root_validator, validator
+from pydantic import BaseModel, Field, model_validator
 
 from ...common.validation import pydantic_validate
 
@@ -49,25 +49,24 @@ class ModelListSchema(BaseModel):
     frequentist_restricted: list[str] = []
     frequentist_unrestricted: list[str] = []
     bayesian: list[BayesianModelSchema] = []
-    model_schema: ModelTypeSchema
+    bmds_model_schema: ModelTypeSchema = Field(alias="model_schema")
 
-    @validator("bayesian")
-    def bayesian_weights(cls, values):
-        if len(values) > 0:
-            weights = sum([value.prior_weight for value in values])
+    @model_validator(mode="after")
+    def bayesian_weights(self):
+        if len(self.bayesian) > 0:
+            weights = sum([b.prior_weight for b in self.bayesian])
             if not np.isclose(weights, 1.0, atol=0.005):
                 raise ValueError("Prior weight in bayesian does not sum to 1")
+        return self
 
-        return values
-
-    @root_validator()
-    def uniqueness(cls, values):
-        schema = values.get("model_schema")
+    @model_validator(mode="after")
+    def uniqueness(self):
+        schema = self.bmds_model_schema
         for field, valid_models in [
             ("frequentist_restricted", schema.restricted),
             ("frequentist_unrestricted", schema.unrestricted),
         ]:
-            models = values.get(field)
+            models = getattr(self, field)
             if len(models) != len(set(models)):
                 raise ValueError(f"Models in {field} are not unique")
             extras = list(set(models) - valid_models)
@@ -77,41 +76,40 @@ def uniqueness(cls, values):
         for field, valid_models in [
             ("bayesian", schema.bayesian),
         ]:
-            models = [model.model for model in values.get(field)]
+            models = [model.model for model in getattr(self, field)]
             if len(models) != len(set(models)):
                 raise ValueError(f"Models in {field} are not unique")
             extras = list(set(models) - valid_models)
             if len(extras) > 0:
                 raise ValueError(f"Invalid model(s) in {field}: {','.join(extras)}")
+        return self
 
-        return values
-
-    @root_validator()
-    def at_least_one(cls, values):
+    @model_validator(mode="after")
+    def at_least_one(self):
         num_models = (
-            len(values.get("frequentist_restricted"))
-            + len(values.get("frequentist_unrestricted"))
-            + len(values.get("bayesian"))
+            len(self.frequentist_restricted)
+            + len(self.frequentist_unrestricted)
+            + len(self.bayesian)
         )
         if num_models == 0:
             raise ValueError("At least one model must be selected")
-        return values
+        return self
 
 
 class DichotomousModelListSchema(ModelListSchema):
-    model_schema: ModelTypeSchema = DichotomousModelSchema
+    bmds_model_schema: ModelTypeSchema = DichotomousModelSchema
 
 
 class ContinuousModelListSchema(ModelListSchema):
-    model_schema: ModelTypeSchema = ContinuousModelSchema
+    bmds_model_schema: ModelTypeSchema = ContinuousModelSchema
 
 
 class NestedDichotomousModelListSchema(ModelListSchema):
-    model_schema: ModelTypeSchema = NestedDichotomousModelSchema
+    bmds_model_schema: ModelTypeSchema = NestedDichotomousModelSchema
 
 
 class MultiTumorModelListSchema(ModelListSchema):
-    model_schema: ModelTypeSchema = MultiTumorModelSchema
+    bmds_model_schema: ModelTypeSchema = MultiTumorModelSchema
 
 
 schema_map = {
diff --git a/bmds_server/analysis/validators/options.py b/bmds_server/analysis/validators/options.py
index 7cd1e211..33778f65 100644
--- a/bmds_server/analysis/validators/options.py
+++ b/bmds_server/analysis/validators/options.py
@@ -11,7 +11,7 @@
 
 from ...common.validation import pydantic_validate
 
-max_items = 1000 if settings.IS_DESKTOP else 6
+max_length = 1000 if settings.IS_DESKTOP else 6
 
 
 class DichotomousOption(BaseModel):
@@ -38,15 +38,15 @@ class NestedDichotomousOption(BaseModel):
 
 
 class DichotomousOptions(BaseModel):
-    options: list[DichotomousOption] = Field(min_items=1, max_items=max_items)
+    options: list[DichotomousOption] = Field(min_length=1, max_length=max_length)
 
 
 class ContinuousOptions(BaseModel):
-    options: list[ContinuousOption] = Field(min_items=1, max_items=max_items)
+    options: list[ContinuousOption] = Field(min_length=1, max_length=max_length)
 
 
 class NestedDichotomousOptions(BaseModel):
-    options: list[NestedDichotomousOption] = Field(min_items=1, max_items=max_items)
+    options: list[NestedDichotomousOption] = Field(min_length=1, max_length=max_length)
 
 
 def validate_options(dataset_type: str, data: Any):
diff --git a/bmds_server/analysis/validators/session.py b/bmds_server/analysis/validators/session.py
index fdf99ab8..66ce5d16 100644
--- a/bmds_server/analysis/validators/session.py
+++ b/bmds_server/analysis/validators/session.py
@@ -10,19 +10,19 @@
 
 
 class BaseSession(BaseModel):
-    id: int | str | None
+    id: int | str | None = None
     bmds_version: _versions
     description: str = ""
     dataset_type: bmds.constants.ModelClass
 
 
-max_items = 1000 if settings.IS_DESKTOP else 10
+max_length = 1000 if settings.IS_DESKTOP else 10
 
 
 class BaseSessionComplete(BaseSession):
-    datasets: list[Any] = Field(min_items=1, max_items=max_items)
+    datasets: list[Any] = Field(min_length=1, max_length=max_length)
     models: dict
-    options: list[Any] = Field(min_items=1, max_items=max_items)
+    options: list[Any] = Field(min_length=1, max_length=max_length)
 
 
 def validate_session(data: dict, partial: bool = False):
diff --git a/bmds_server/common/task_cache.py b/bmds_server/common/task_cache.py
index b33b4c63..90c52ab3 100644
--- a/bmds_server/common/task_cache.py
+++ b/bmds_server/common/task_cache.py
@@ -13,9 +13,9 @@ class ReportStatus(IntEnum):
 
 class ReportResponse(BaseModel):
     status: ReportStatus
-    content: Any | None
-    header: str | None
-    message: str | None
+    content: Any | None = None
+    header: str | None = None
+    message: str | None = None
 
 
 # TODO - remove this stuff; it doesn't work with our current workflow
diff --git a/bmds_server/common/validation.py b/bmds_server/common/validation.py
index 25232c40..ee34f8b7 100644
--- a/bmds_server/common/validation.py
+++ b/bmds_server/common/validation.py
@@ -21,6 +21,6 @@ def pydantic_validate(data: Any, model: type[T]) -> T:
         BaseModel: Instance of class, if successful.
     """
     try:
-        return model.parse_obj(data)
+        return model.model_validate(data)
     except PydanticValidationError as err:
         raise ValidationError(err.json())
diff --git a/bmds_server/main/settings/base.py b/bmds_server/main/settings/base.py
index 38ba8a61..a5a41b55 100644
--- a/bmds_server/main/settings/base.py
+++ b/bmds_server/main/settings/base.py
@@ -215,7 +215,7 @@
 # commit information
 def get_git_commit() -> Commit:
     if GIT_COMMIT_FILE.exists():
-        return Commit.parse_file(GIT_COMMIT_FILE)
+        return Commit.model_validate_json(GIT_COMMIT_FILE.read_text())
     try:
         return Commit.current(str(ROOT_DIR))
     except (CalledProcessError, FileNotFoundError):
diff --git a/compose/app/test.py b/compose/app/test.py
index 924f97dd..c326ec45 100644
--- a/compose/app/test.py
+++ b/compose/app/test.py
@@ -6,4 +6,4 @@
 )
 model = Logistic(dataset=dataset)
 result = model.execute()
-print(result.dict())  # noqa: T201
+print(result.model_dump())  # noqa: T201
diff --git a/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js b/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
index ef93aded..d78fdfe5 100644
--- a/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
+++ b/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
@@ -45,19 +45,19 @@ const isModelChecked = function(models, type, model) {
         );
     }),
     CheckBoxTd = observer(props => {
-        const {store, type, model, disabled} = props;
-
+        const {store, type, model, disabled} = props,
+            id = `${type}-${model}`;
         return store.canEdit ? (
-            <td>
+            <td key={id}>
                 <CheckboxInput
-                    id={type + "-" + model}
+                    id={id}
                     disabled={disabled}
                     onChange={value => store.setModelSelection(type, model, value)}
                     checked={isModelChecked(store.models, type, model)}
                 />
             </td>
         ) : (
-            <td>{checkOrEmpty(isModelChecked(store.models, type, model))}</td>
+            <td key={id}>{checkOrEmpty(isModelChecked(store.models, type, model))}</td>
         );
     }),
     multistageHelpText = `All Multistage model polynomial degrees will be run up to a maximum
diff --git a/tests/analysis/test_api.py b/tests/analysis/test_api.py
index 9e752c07..9c127b95 100644
--- a/tests/analysis/test_api.py
+++ b/tests/analysis/test_api.py
@@ -7,6 +7,12 @@
 from bmds_server.analysis.models import Analysis
 
 
+def check_error(response: dict, type: str, loc: list, msg: str):
+    assert response["type"] == type
+    assert response["loc"] == loc
+    assert response["msg"] == msg
+
+
 @pytest.mark.django_db
 class TestAnalysisViewSet:
     def test_auth(self, bmds3_complete_continuous):
@@ -89,28 +95,21 @@ def test_patch_partial(self):
             "editKey": analysis.password,
             "data": {"bmds_version": "BMDS330", "dataset_type": "C"},
         }
-        response = client.patch(
-            url,
-            payload,
-            format="json",
-        )
+        response = client.patch(url, payload, format="json")
         assert response.status_code == 400
-        assert json.loads(response.json()[0])[0] == {
-            "loc": ["datasets"],
-            "msg": "field required",
-            "type": "value_error.missing",
-        }
+        check_error(
+            json.loads(response.json()[0])[0],
+            type="missing",
+            loc=["datasets"],
+            msg="Field required",
+        )
 
         payload = {
             "editKey": analysis.password,
             "data": {"bmds_version": "BMDS330", "dataset_type": "C"},
             "partial": True,
         }
-        response = client.patch(
-            url,
-            payload,
-            format="json",
-        )
+        response = client.patch(url, payload, format="json")
         assert response.status_code == 200
         assert response.json()["inputs"] == payload["data"]
 
@@ -119,29 +118,22 @@ def test_patch_partial(self):
             "dataset_type": "C",
             "models": {"frequentist_restricted": ["ZZZ"]},
         }
-        response = client.patch(
-            url,
-            payload,
-            format="json",
-        )
+        response = client.patch(url, payload, format="json")
         assert response.status_code == 400
-        assert json.loads(response.json()[0])[0] == {
-            "loc": ["__root__"],
-            "msg": "Invalid model(s) in frequentist_restricted: ZZZ",
-            "type": "value_error",
-        }
+        check_error(
+            json.loads(response.json()[0])[0],
+            type="value_error",
+            loc=[],
+            msg="Value error, Invalid model(s) in frequentist_restricted: ZZZ",
+        )
 
         payload["data"] = {
             "bmds_version": "BMDS330",
             "dataset_type": "C",
             "models": {"frequentist_restricted": ["Power"]},
-            "recommender": RecommenderSettings.build_default().dict(),
+            "recommender": RecommenderSettings.build_default().model_dump(),
         }
-        response = client.patch(
-            url,
-            payload,
-            format="json",
-        )
+        response = client.patch(url, payload, format="json")
         assert response.status_code == 200
         assert response.json()["inputs"] == payload["data"]
 
diff --git a/tests/analysis/test_schema.py b/tests/analysis/test_schema.py
index 78847bec..967583fc 100644
--- a/tests/analysis/test_schema.py
+++ b/tests/analysis/test_schema.py
@@ -8,38 +8,38 @@
 
 class TestPolyKInput:
     def test_calculate(self, polyk_dataset):
-        analysis = PolyKInput.parse_obj(polyk_dataset)
+        analysis = PolyKInput.model_validate(polyk_dataset)
         df1, df2 = analysis.calculate()
         assert df1.shape == (200, 4)
         assert df2.shape == (4, 6)
 
     def test_validate_dataset(self, polyk_dataset):
         # confirm success
-        PolyKInput.parse_obj(polyk_dataset)
+        PolyKInput.model_validate(polyk_dataset)
 
         # no dataset
         settings = deepcopy(polyk_dataset)
         settings.pop("dataset")
-        with pytest.raises(ValidationError, match="field required"):
-            PolyKInput.parse_obj(settings)
+        with pytest.raises(ValidationError, match="Field required"):
+            PolyKInput.model_validate(settings)
 
         # columns
         settings = deepcopy(polyk_dataset)
         settings["dataset"] = settings["dataset"].replace("dose,day,has_tumor", "dose,day,BAD")
         with pytest.raises(ValidationError, match="Bad column names"):
-            PolyKInput.parse_obj(settings)
+            PolyKInput.model_validate(settings)
 
         # columns
         settings = deepcopy(polyk_dataset)
         settings["dataset"] = settings["dataset"].replace("0,452,0", "-1,452,0")
         with pytest.raises(ValidationError, match="`doses` must be ≥ 0"):
-            PolyKInput.parse_obj(settings)
+            PolyKInput.model_validate(settings)
 
         # columns
         settings = deepcopy(polyk_dataset)
         settings["dataset"] = settings["dataset"].replace("0,452,0", "0,-1,0")
         with pytest.raises(ValidationError, match="`day` must be ≥ 0"):
-            PolyKInput.parse_obj(settings)
+            PolyKInput.model_validate(settings)
 
         # columns
         settings = deepcopy(polyk_dataset)
@@ -47,4 +47,4 @@ def test_validate_dataset(self, polyk_dataset):
         with pytest.raises(
             ValidationError, match="`has_tumor` must include only the values {0, 1}"
         ):
-            PolyKInput.parse_obj(settings)
+            PolyKInput.model_validate(settings)
diff --git a/tests/analysis/test_validators.py b/tests/analysis/test_validators.py
index 3e61f07b..425e9aca 100644
--- a/tests/analysis/test_validators.py
+++ b/tests/analysis/test_validators.py
@@ -14,7 +14,7 @@
 def _missing_field(err, missing_field: str):
     data = json.loads(err.value.message)
     assert data[0]["loc"] == [missing_field]
-    assert data[0]["msg"] == "field required"
+    assert data[0]["msg"] == "Field required"
 
 
 class TestInputValidation:
@@ -198,63 +198,47 @@ def test_bmds3_dichotomous(self):
         logprobit = bmds.constants.M_LogProbit
 
         # test success
-        assert (
-            validators.validate_models(
-                dtype,
-                {"frequentist_restricted": [logprobit]},
-            )
-            is None
-        )
+        validators.validate_models(dtype, {"frequentist_restricted": [logprobit]})
 
         # assert wrong model type
+        data = {"frequentist_restricted": [bmds.constants.M_Power]}
         with pytest.raises(ValidationError) as err:
-            validators.validate_models(
-                dtype,
-                {"frequentist_restricted": [bmds.constants.M_Power]},
-            )
+            validators.validate_models(dtype, data)
         assert "Invalid model(s) in frequentist_restricted: Power" in str(err)
 
         # assert duplicates model type
+        data = {"frequentist_restricted": [logprobit, logprobit]}
         with pytest.raises(ValidationError) as err:
-            validators.validate_models(
-                dtype,
-                {"frequentist_restricted": [logprobit, logprobit]},
-            )
+            validators.validate_models(dtype, data)
         assert "Models in frequentist_restricted are not unique" in str(err)
 
         # assert empty
+        data = {"frequentist_restricted": []}
         with pytest.raises(ValidationError) as err:
-            validators.validate_models(
-                dtype,
-                {"frequentist_restricted": []},
-            )
+            validators.validate_models(dtype, data)
         assert "At least one model must be selected" in str(err)
 
         # assert bayesian duplicates
+        data = {
+            "bayesian": [
+                {"model": probit, "prior_weight": 0.3},
+                {"model": logprobit, "prior_weight": 0.4},
+                {"model": logprobit, "prior_weight": 0.3},
+            ]
+        }
         with pytest.raises(ValidationError) as err:
-            validators.validate_models(
-                dtype,
-                {
-                    "bayesian": [
-                        {"model": probit, "prior_weight": 0.3},
-                        {"model": logprobit, "prior_weight": 0.4},
-                        {"model": logprobit, "prior_weight": 0.3},
-                    ]
-                },
-            )
+            validators.validate_models(dtype, data)
         assert "Models in bayesian are not unique" in str(err)
 
         # assert bayesian prior_weight sum
+        data = {
+            "bayesian": [
+                {"model": probit, "prior_weight": 0.5},
+                {"model": logprobit, "prior_weight": 0.49},
+            ]
+        }
         with pytest.raises(ValidationError) as err:
-            validators.validate_models(
-                dtype,
-                {
-                    "bayesian": [
-                        {"model": probit, "prior_weight": 0.5},
-                        {"model": logprobit, "prior_weight": 0.49},
-                    ]
-                },
-            )
+            validators.validate_models(dtype, data)
         assert "Prior weight in bayesian does not sum to 1" in str(err.value)
 
     def test_bmds3_continuous(self):
@@ -333,7 +317,7 @@ def test_dichotomous(self):
         data = []
         with pytest.raises(ValidationError) as err:
             validators.validate_options(bmds.constants.DICHOTOMOUS, data)
-        assert "ensure this value has at least 1 items" in str(err)
+        assert "List should have at least 1 item" in str(err)
 
     def test_continuous(self):
         # test success
@@ -352,7 +336,7 @@ def test_continuous(self):
         data = []
         with pytest.raises(ValidationError) as err:
             validators.validate_options(bmds.constants.CONTINUOUS, data)
-        assert "ensure this value has at least 1 items" in str(err)
+        assert "List should have at least 1 item" in str(err)
 
 
 class TestDatasetValidation:
diff --git a/tests/conftest.py b/tests/conftest.py
index b5a217ce..87336b19 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -73,7 +73,7 @@ def bmds3_complete_continuous():
         "dataset_options": [
             {"dataset_id": 123, "enabled": True, "degree": 0, "adverse_direction": -1}
         ],
-        "recommender": RecommenderSettings.build_default().dict(),
+        "recommender": RecommenderSettings.build_default().model_dump(),
     }
 
 
@@ -123,7 +123,7 @@ def bmds3_complete_continuous_individual():
         "dataset_options": [
             {"dataset_id": 123, "enabled": True, "degree": 0, "adverse_direction": -1}
         ],
-        "recommender": RecommenderSettings.build_default().dict(),
+        "recommender": RecommenderSettings.build_default().model_dump(),
     }
     # fmt: on
 
@@ -148,7 +148,7 @@ def bmds3_complete_dichotomous():
         ],
         "options": [{"bmr_type": 1, "bmr_value": 0.1, "confidence_level": 0.95}],
         "dataset_options": [{"dataset_id": 123, "enabled": True, "degree": 0}],
-        "recommender": RecommenderSettings.build_default().dict(),
+        "recommender": RecommenderSettings.build_default().model_dump(),
     }
 
 
@@ -244,7 +244,7 @@ def bmds_complete_nd():
         "dataset_options": [
             {"enabled": True, "dataset_id": 0},
         ],
-        "recommender": RecommenderSettings.build_default().dict(),
+        "recommender": RecommenderSettings.build_default().model_dump(),
     }
     #fmt: on
 
@@ -315,7 +315,7 @@ def bmds_complete_mt():
             {"enabled": True, "dataset_id": 1, "degree": 0},
             {"enabled": True, "dataset_id": 2, "degree": 0},
         ],
-        "recommender": RecommenderSettings.build_default().dict(),
+        "recommender": RecommenderSettings.build_default().model_dump(by_alias=True),
     }
     #fmt: on
 

From fd5bccfb410248508fad51e42b4fd685378c9208 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Wed, 8 Nov 2023 15:00:18 -0500
Subject: [PATCH 11/24] multitumor display edits (#272)

* add residuals to summary table

* rename model name

* rename model average row

* add bmd diamonds to multitumor result

* lint

* draw csf to bmdl, not bmd

* (unrelated) update django version

* add slope factor for individual models; see bmds PR 123
---
 .../Output/Multitumor/MultitumorPlot.js       |  33 +++--
 .../Output/Multitumor/ResultTable.js          |  12 +-
 .../components/Output/Multitumor/Summary.js   |   2 +-
 frontend/src/constants/mainConstants.js       |   2 +-
 frontend/src/constants/plotting.js            | 137 ++++++++----------
 requirements/base.txt                         |   2 +-
 tests/integration/test_integration.py         |   2 +-
 7 files changed, 95 insertions(+), 95 deletions(-)

diff --git a/frontend/src/components/Output/Multitumor/MultitumorPlot.js b/frontend/src/components/Output/Multitumor/MultitumorPlot.js
index ad23b5a4..00533270 100644
--- a/frontend/src/components/Output/Multitumor/MultitumorPlot.js
+++ b/frontend/src/components/Output/Multitumor/MultitumorPlot.js
@@ -4,14 +4,14 @@ import React, {Component} from "react";
 
 import DoseResponsePlot from "@/components/common/DoseResponsePlot";
 import {getNameFromDegrees} from "@/constants/modelConstants";
-import {colorCodes, getDrLayout, getResponse} from "@/constants/plotting";
+import {colorCodes, getBmdDiamond, getDrLayout, getResponse} from "@/constants/plotting";
 
 const getLayout = function(datasets) {
     let layout;
     datasets.forEach(dataset => {
         if (layout === undefined) {
             layout = getDrLayout(dataset);
-            layout.title.text = "Multitumor (MS Combo)";
+            layout.title.text = "Multitumor";
             layout.yaxis.range = [0, 1];
         } else {
             const revised = getDrLayout(dataset);
@@ -27,7 +27,8 @@ const getLayout = function(datasets) {
 };
 
 const getData = function(ma, datasets, models) {
-    let data = [];
+    const data = [],
+        bmd_y = ma.bmdl * ma.slope_factor;
 
     // add individual datasets
     datasets.forEach((dataset, index) => {
@@ -61,17 +62,21 @@ const getData = function(ma, datasets, models) {
         });
     });
 
-    // add slope factor
-    data.push({
-        x: [0, ma.bmd],
-        y: [0, ma.bmd * ma.slope_factor],
-        name: "Cancer Slope Factor",
-        line: {
-            width: 5,
-            color: "black",
-            dash: "dot",
-        },
-    });
+    if (ma.bmdl) {
+        // add slope factor
+        data.push({
+            x: [0, ma.bmdl],
+            y: [0, bmd_y],
+            name: "Cancer Slope Factor",
+            legendgroup: "Cancer Slope Factor",
+            line: {
+                width: 5,
+                color: "#000000",
+                dash: "dot",
+            },
+        });
+        data.push(getBmdDiamond("Cancer Slope Factor", ma.bmd, ma.bmdl, ma.bmdu, bmd_y, "#000000"));
+    }
 
     return data;
 };
diff --git a/frontend/src/components/Output/Multitumor/ResultTable.js b/frontend/src/components/Output/Multitumor/ResultTable.js
index ec0eeadd..ce51c436 100644
--- a/frontend/src/components/Output/Multitumor/ResultTable.js
+++ b/frontend/src/components/Output/Multitumor/ResultTable.js
@@ -16,7 +16,7 @@ class ResultTable extends Component {
         if (!selectedFrequentist) {
             return null;
         }
-        const colWidths = [15, 15, 10, 10, 10, 10, 10, 10],
+        const colWidths = [15, 15, 8, 8, 8, 8, 8, 8, 11, 11],
             {results} = selectedFrequentist,
             {multitumorDatasets} = store,
             indexes = results.selected_model_indexes,
@@ -41,6 +41,8 @@ class ResultTable extends Component {
                             <i>P</i>-Value
                         </th>
                         <th>AIC</th>
+                        <th>Scaled Residual for Dose Group near BMD</th>
+                        <th>Scaled Residual for Control Dose Group</th>
                     </tr>
                 </thead>
                 <tbody className="table-bordered">
@@ -54,7 +56,7 @@ class ResultTable extends Component {
                                         e.preventDefault();
                                         store.showModalDetailMultitumor(-1, -1);
                                     }}>
-                                    Multi-tumor (MS Combo)
+                                    Multitumor
                                 </a>
                             </td>
                             <td>-</td>
@@ -64,6 +66,8 @@ class ResultTable extends Component {
                             <td>{ff(results.slope_factor)}</td>
                             <td>-</td>
                             <td>-</td>
+                            <td>-</td>
+                            <td>-</td>
                         </tr>
                     ) : null}
                     {results.models.map((dataset_models, dataset_index) => {
@@ -94,9 +98,11 @@ class ResultTable extends Component {
                                             <td>{ff(model.bmdl)}</td>
                                             <td>{ff(model.bmd)}</td>
                                             <td>{ff(model.bmdu)}</td>
-                                            <td>TODO</td>
+                                            <td>{ff(model.slope_factor)}</td>
                                             <td>{ff(model.gof.p_value)}</td>
                                             <td>{ff(model.fit.aic)}</td>
+                                            <td>{ff(model.gof.roi)}</td>
+                                            <td>{ff(model.gof.residual[0])}</td>
                                         </tr>
                                     );
                                 })
diff --git a/frontend/src/components/Output/Multitumor/Summary.js b/frontend/src/components/Output/Multitumor/Summary.js
index 33057485..244f2d09 100644
--- a/frontend/src/components/Output/Multitumor/Summary.js
+++ b/frontend/src/components/Output/Multitumor/Summary.js
@@ -13,6 +13,7 @@ class Summary extends Component {
                 ["BMD", ff(model.bmd)],
                 ["BMDL", ff(model.bmdl)],
                 ["BMDU", ff(model.bmdu)],
+                ["Slope Factor", ff(model.slope_factor)],
                 ["AIC", ff(model.fit.aic)],
                 [
                     <span key="0">
@@ -22,7 +23,6 @@ class Summary extends Component {
                 ],
                 ["Overall DOF", ff(model.gof.df)],
                 ["Chi²", ff(model.fit.chisq)][("Log Likelihood", ff(model.fit.loglikelihood))],
-                ["Slope Factor", "TODO"],
             ];
         return <TwoColumnTable data={data} label="Summary" />;
     }
diff --git a/frontend/src/constants/mainConstants.js b/frontend/src/constants/mainConstants.js
index 574bf24a..6c7119be 100644
--- a/frontend/src/constants/mainConstants.js
+++ b/frontend/src/constants/mainConstants.js
@@ -8,5 +8,5 @@ export const VERSION_330 = "BMDS330",
         {name: "Continuous", value: MODEL_CONTINUOUS},
         {name: "Dichotomous", value: MODEL_DICHOTOMOUS},
         {name: "Nested Dichotomous", value: MODEL_NESTED_DICHOTOMOUS},
-        {name: "Multi-tumor", value: MODEL_MULTI_TUMOR},
+        {name: "Multistage Cancer / Multitumor", value: MODEL_MULTI_TUMOR},
     ];
diff --git a/frontend/src/constants/plotting.js b/frontend/src/constants/plotting.js
index ae358555..2135a8ff 100644
--- a/frontend/src/constants/plotting.js
+++ b/frontend/src/constants/plotting.js
@@ -143,35 +143,16 @@ export const getResponse = dataset => {
             name: "Response",
         };
     },
-    getDrBmdLine = function(model, hexColor) {
-        // https://plotly.com/python/marker-style/
-        // https://plotly.com/javascript/reference/scatter/
-        const hasBmd = model.results.bmd > 0,
-            hasBmdl = model.results.bmdl > 0,
-            hasBmdu = model.results.bmdu > 0,
-            data = [
-                {
-                    x: model.results.plotting.dr_x,
-                    y: model.results.plotting.dr_y,
-                    mode: "lines",
-                    name: model.name,
-                    hoverinfo: "y",
-                    line: {
-                        color: hexToRgbA(hexColor, 0.8),
-                        width: 4,
-                        opacity: 0.5,
-                    },
-                    legendgroup: model.name,
-                },
-            ];
+    getBmdDiamond = function(name, bmd, bmdl, bmdu, bmd_y, hexColor) {
+        const hasBmd = bmd > 0;
 
-        if (hasBmd) {
-            // prettier-ignore
-            const template = `<b>${model.name}</b><br />BMD: ${ff(model.results.bmd)}<br />BMDL: ${ff(model.results.bmdl)}<br />BMDU: ${ff(model.results.bmdu)}<br />BMR: ${ff(model.results.plotting.bmd_y)}<extra></extra>`;
+        // prettier-ignore
+        const template = `<b>${name}</b><br />BMD: ${ff(bmd)}<br />BMDL: ${ff(bmdl)}<br />BMDU: ${ff(bmdu)}<br />BMR: ${ff(bmd_y)}<extra></extra>`;
 
-            data.push({
-                x: [model.results.bmd],
-                y: [model.results.plotting.bmd_y],
+        if (hasBmd) {
+            return {
+                x: [bmd],
+                y: [bmd_y],
                 mode: "markers",
                 type: "scatter",
                 hoverinfo: "x",
@@ -185,66 +166,74 @@ export const getResponse = dataset => {
                         width: 2,
                     },
                 },
-                legendgroup: model.name,
+                legendgroup: name,
                 showlegend: false,
                 error_x: {
-                    array: [hasBmdu ? model.results.bmdu - model.results.bmd : 0],
-                    arrayminus: [hasBmdl ? model.results.bmd - model.results.bmdl : 0],
+                    array: [bmdu > 0 ? bmdu - bmd : 0],
+                    arrayminus: [bmdl > 0 ? bmd - bmdl : 0],
                     color: hexToRgbA(hexColor, 0.6),
                     thickness: 12,
                     width: 0,
                 },
-            });
+            };
         }
+    },
+    getDrBmdLine = function(model, hexColor) {
+        // https://plotly.com/python/marker-style/
+        // https://plotly.com/javascript/reference/scatter/
+        const data = [
+            {
+                x: model.results.plotting.dr_x,
+                y: model.results.plotting.dr_y,
+                mode: "lines",
+                name: model.name,
+                hoverinfo: "y",
+                line: {
+                    color: hexToRgbA(hexColor, 0.8),
+                    width: 4,
+                    opacity: 0.5,
+                },
+                legendgroup: model.name,
+            },
+        ];
 
+        const diamond = getBmdDiamond(
+            model.name,
+            model.results.bmd,
+            model.results.bmdl,
+            model.results.bmdu,
+            model.results.plotting.bmd_y,
+            hexColor
+        );
+        if (diamond) {
+            data.push(diamond);
+        }
         return data;
     },
     getBayesianBMDLine = function(model, hexColor) {
-        const hasBmd = model.results.bmd > 0,
-            hasBmdl = model.results.bmdl > 0,
-            hasBmdu = model.results.bmdu > 0,
-            data = [
-                {
-                    x: model.results.dr_x,
-                    y: model.results.dr_y,
-                    name: "Model average",
-                    legendgroup: "BMA",
-                    line: {
-                        width: 6,
-                        color: hexColor,
-                    },
-                },
-            ];
-
-        if (hasBmd) {
-            // prettier-ignore
-            const template = `<b>Model Average</b><br />BMD: ${ff(model.results.bmd)}<br />BMDL: ${ff(model.results.bmdl)}<br />BMDU: ${ff(model.results.bmdu)}<br />BMR: ${ff(model.results.bmd_y)}<extra></extra>`;
-            data.push({
-                x: [model.results.bmd],
-                y: [model.results.bmd_y],
-                mode: "markers",
-                type: "scatter",
-                hoverinfo: "x",
-                hovertemplate: template,
-                marker: {
+        const data = [
+            {
+                x: model.results.dr_x,
+                y: model.results.dr_y,
+                name: "Model Average",
+                legendgroup: "Model Average",
+                line: {
+                    width: 6,
                     color: hexColor,
-                    size: 16,
-                    symbol: "diamond-tall",
-                    line: {
-                        color: "white",
-                        width: 2,
-                    },
-                },
-                legendgroup: "BMA",
-                showlegend: false,
-                error_x: {
-                    array: [hasBmdu ? model.results.bmdu - model.results.bmd : 0],
-                    arrayminus: [hasBmdl ? model.results.bmd - model.results.bmdl : 0],
-                    color: hexToRgbA(hexColor, 0.6),
-                    thickness: 12,
-                    width: 0,
                 },
-            });
+            },
+        ];
+
+        const diamond = getBmdDiamond(
+            "Model Average",
+            model.results.bmd,
+            model.results.bmdl,
+            model.results.bmdu,
+            model.results.bmd_y,
+            hexColor
+        );
+        if (diamond) {
+            data.push(diamond);
         }
 
         return data;
diff --git a/requirements/base.txt b/requirements/base.txt
index bd4598e3..1269f79e 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -1,5 +1,5 @@
 # website
-Django~=4.2.6
+Django~=4.2.7
 django-anymail==10.2
 django-redis==5.4.0
 django-webpack-loader==2.0.1
diff --git a/tests/integration/test_integration.py b/tests/integration/test_integration.py
index 55da2b39..dd490541 100644
--- a/tests/integration/test_integration.py
+++ b/tests/integration/test_integration.py
@@ -245,7 +245,7 @@ def test_multi_tumor(self):
             page.locator('a:has-text("Output")').click()
 
             # check one result
-            page.get_by_role("link", name="Multi-tumor (MS Combo)").click()
+            page.get_by_role("link", name="Multistage Cancer / Multitumor").click()
             expect(page.get_by_role("dialog")).to_contain_text("MS Combo")
             page.locator("#close-modal").click()
 

From fed530ad6ac3f6a82693ef5c13a830be232cfed3 Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Wed, 8 Nov 2023 20:31:31 -0500
Subject: [PATCH 12/24] add years context (#274)

---
 frontend/src/components/transforms/polyk/AboutModal.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend/src/components/transforms/polyk/AboutModal.js b/frontend/src/components/transforms/polyk/AboutModal.js
index 1c5cb012..859ade69 100644
--- a/frontend/src/components/transforms/polyk/AboutModal.js
+++ b/frontend/src/components/transforms/polyk/AboutModal.js
@@ -164,7 +164,7 @@ class AboutModal extends Component {
                                 "Kissling et al. (2008)"
                             )}
                             , the authors note that the poly-3 adjustment has not been validated for
-                            carcinogenicity studies longer than years, consistent with the
+                            carcinogenicity studies longer than two years, consistent with the
                             conclusion of the Portier et al. (1986) analysis that acknowledges that
                             “animals used in historical control data base were generally sacrificed
                             if they lived to 109 weeks…. Thus, the application of these models

From d52466ba0d1db0f889313eeae92757cfb13a8f48 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Thu, 7 Dec 2023 16:33:57 -0500
Subject: [PATCH 13/24] remove zenodo.org badge (#278)

---
 README.rst | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/README.rst b/README.rst
index ec5a6327..f8a13f41 100644
--- a/README.rst
+++ b/README.rst
@@ -5,9 +5,6 @@ BMDS webserver
         :target: https://bmds-server.readthedocs.io/en/master/
         :alt: Documentation Status
 
-.. image:: https://zenodo.org/badge/73124145.svg
-   :target: https://zenodo.org/badge/latestdoi/73124145
-
 Run a webserver that will batch process dose-response data using the US EPA's
 benchmark dose modeling software (`BMDS`_).  Under the hood, this web application
 uses the `BMDS Python interface`_.

From d6bb7c0983d2ce3b66ef8dababadfdda68b28f0e Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Thu, 7 Dec 2023 16:52:40 -0500
Subject: [PATCH 14/24] 283 polyk data link (#275)

* try gitattribute fix before reset

* add button for polyk

* better

* </> --> null

* use flex layout for icons; update icon

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 frontend/src/components/Data/DatasetForm.js | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/frontend/src/components/Data/DatasetForm.js b/frontend/src/components/Data/DatasetForm.js
index 5e72d860..f73eb7a8 100644
--- a/frontend/src/components/Data/DatasetForm.js
+++ b/frontend/src/components/Data/DatasetForm.js
@@ -3,10 +3,12 @@ import PropTypes from "prop-types";
 import React, {Component} from "react";
 
 import {columnHeaders, columns} from "@/constants/dataConstants";
+import {MODEL_MULTI_TUMOR} from "@/constants/mainConstants";
 
 import Button from "../common/Button";
 import ErrorMessage from "../common/ErrorMessage";
 import FloatInput from "../common/FloatInput";
+import Icon from "../common/Icon";
 import TextInput from "../common/TextInput";
 import TabularDatasetModal from "./TabularDatasetModal";
 
@@ -72,7 +74,6 @@ class DatasetForm extends Component {
                         </div>
                     </div>
                 </div>
-
                 <div className="form-group row mx-0">
                     <label htmlFor="doseName" className="col-md-2 px-0">
                         Dose name
@@ -93,7 +94,6 @@ class DatasetForm extends Component {
                         />
                     </div>
                 </div>
-
                 <div className="form-group row mx-0">
                     <label htmlFor="doseUnits" className="col-md-2 px-0">
                         Dose units
@@ -156,14 +156,23 @@ class DatasetForm extends Component {
                         })}
                     </tbody>
                 </table>
-                <p>
+                <div className="d-flex ">
                     <Button
                         className="btn btn-link"
                         onClick={dataStore.loadExampleData}
                         icon="layer-forward"
                         text="Load an example dataset"
                     />
-                </p>
+                    {dataStore.rootStore.mainStore.model_type == MODEL_MULTI_TUMOR ? (
+                        <a
+                            className="ml-auto"
+                            href="/transforms/polyk/"
+                            target="_blank"
+                            rel="noopener noreferrer">
+                            <Icon name="calculator" text="Poly K Adjustment" />
+                        </a>
+                    ) : null}
+                </div>
                 <TabularDatasetModal />
             </div>
         );

From 155da51512d10ba23f92904b6548f464f409790f Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Thu, 7 Dec 2023 17:28:07 -0500
Subject: [PATCH 15/24] polyk - copy dataset to clipboard for bmds modeling
 (#276)

* add copy to clipboard

* basic copied alert

* clean up

* missed one

* missed another one

* use ClipobardButton; add on optional click handler

* removed store info

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 .../src/components/common/ClipboardButton.js   |  6 +++++-
 .../components/transforms/polyk/OutputTabs.js  | 18 +++++++++++++++++-
 2 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/frontend/src/components/common/ClipboardButton.js b/frontend/src/components/common/ClipboardButton.js
index ac036d41..5f684775 100644
--- a/frontend/src/components/common/ClipboardButton.js
+++ b/frontend/src/components/common/ClipboardButton.js
@@ -11,8 +11,11 @@ class ClipboardButton extends Component {
         this.ref = React.createRef();
     }
     componentDidMount() {
-        const {textToCopy} = this.props;
+        const {textToCopy, onCopy} = this.props;
         this.clipboardEvent = new Clipboard(this.ref.current, {text: () => textToCopy});
+        if (onCopy) {
+            this.clipboardEvent.on("success", onCopy);
+        }
     }
     componentWillUnmount() {
         this.clipboardEvent.destroy();
@@ -35,6 +38,7 @@ ClipboardButton.propTypes = {
     text: PropTypes.string.isRequired,
     textToCopy: PropTypes.string.isRequired,
     className: PropTypes.string.isRequired,
+    onCopy: PropTypes.func,
 };
 ClipboardButton.defaultProps = {
     text: "",
diff --git a/frontend/src/components/transforms/polyk/OutputTabs.js b/frontend/src/components/transforms/polyk/OutputTabs.js
index f030c31f..39e233b4 100644
--- a/frontend/src/components/transforms/polyk/OutputTabs.js
+++ b/frontend/src/components/transforms/polyk/OutputTabs.js
@@ -6,6 +6,7 @@ import Tab from "react-bootstrap/Tab";
 import Tabs from "react-bootstrap/Tabs";
 import Plot from "react-plotly.js";
 
+import ClipboardButton from "@/components/common/ClipboardButton";
 import DataFrameTable from "@/components/common/DataFrameTable";
 
 @inject("store")
@@ -132,7 +133,10 @@ RawDataPlot.propTypes = {
 @observer
 class OutputTabs extends Component {
     render() {
-        const {df, df2} = this.props.store.outputs;
+        const {df, df2} = this.props.store.outputs,
+            copyText = _.zip(df2.dose, df2.adj_n, df2.incidence)
+                .map(d => `${d[0]}\t${d[1].toFixed(4)}\t${d[2]}`)
+                .join("\n");
         df["weight"] = df["adj_n"];
         return (
             <Tabs
@@ -158,6 +162,18 @@ class OutputTabs extends Component {
                             adj_proportion: v => v.toFixed(4),
                         }}
                     />
+                    <div className="d-flex flex-row-reverse">
+                        <ClipboardButton
+                            text="Copy Data for BMDS Modeling"
+                            textToCopy={copyText}
+                            onCopy={e => {
+                                alert(
+                                    'Data copied to your clipboard! You can paste into Excel, or paste into an a BMDS analysis creating a new dataset and pressing the "Load dataset from Excel" button.'
+                                );
+                            }}
+                            className="btn btn-link my-1"
+                        />
+                    </div>
                     <SummaryPlot />
                 </Tab>
                 <Tab eventKey="plots" title="Plots">

From 84633d17a5443c1707db252b69da71b8183571c5 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Sun, 10 Dec 2023 19:11:35 -0500
Subject: [PATCH 16/24] Add Word and Excel reports to Poly K adjustments (#277)

* add download buttons and apis for polyk reports

* wip

* resketch

* update integration with new polyk adjustment type

* add tests for all api views

* sync w/ latest bmds branch

* pass dose_units

---------

Co-authored-by: hausman-gdit <karen.hausman@gdit.com>
---
 bmds_server/analysis/api.py                   | 47 +++++++++++++++----
 bmds_server/analysis/reporting/docx.py        | 32 +++++++++----
 bmds_server/analysis/schema.py                |  8 ++--
 bmds_server/common/serializers.py             | 10 ++++
 bmds_server/main/urls.py                      |  5 +-
 .../src/components/transforms/polyk/App.js    | 39 ++++++++++++++-
 .../src/components/transforms/polyk/store.js  | 39 ++++++++++++---
 tests/analysis/test_api.py                    | 33 +++++++++++++
 tests/analysis/test_schema.py                 |  6 +--
 9 files changed, 182 insertions(+), 37 deletions(-)
 create mode 100644 bmds_server/common/serializers.py

diff --git a/bmds_server/analysis/api.py b/bmds_server/analysis/api.py
index 74aca94a..334e9e74 100644
--- a/bmds_server/analysis/api.py
+++ b/bmds_server/analysis/api.py
@@ -1,15 +1,18 @@
+from bmds.datasets.transforms.polyk import PolyKAdjustment
 from django.core.exceptions import ValidationError
 from rest_framework import exceptions, mixins, viewsets
-from rest_framework.decorators import action, api_view
+from rest_framework.decorators import action
 from rest_framework.response import Response
 
 from ..common import renderers
+from ..common.renderers import BinaryFile
+from ..common.serializers import UnusedSerializer
 from ..common.task_cache import ReportStatus
 from ..common.utils import get_bool
 from ..common.validation import pydantic_validate
 from . import models, schema, serializers, validators
 from .reporting.cache import DocxReportCache, ExcelReportCache
-from .reporting.docx import add_update_url
+from .reporting.docx import add_update_url, build_polyk_docx
 
 
 class AnalysisViewset(mixins.RetrieveModelMixin, viewsets.GenericViewSet):
@@ -158,11 +161,35 @@ def word(self, request, *args, **kwargs):
         return Response(response.model_dump(), content_type="application/json")
 
 
-@api_view(["POST"])
-def polyk_transform(request):
-    try:
-        settings = pydantic_validate(request.data, schema.PolyKInput)
-    except ValidationError as err:
-        raise exceptions.ValidationError(err.message)
-    (df, df2) = settings.calculate()
-    return Response({"df": df.to_dict(orient="list"), "df2": df2.to_dict(orient="list")})
+class PolyKViewset(viewsets.GenericViewSet):
+    queryset = models.Analysis.objects.none()
+    serializer_class = UnusedSerializer
+
+    def _run_analysis(self, request) -> PolyKAdjustment:
+        try:
+            settings = pydantic_validate(request.data, schema.PolyKInput)
+        except ValidationError as err:
+            raise exceptions.ValidationError(err.message)
+        return settings.calculate()
+
+    def create(self, request, *args, **kwargs):
+        analysis = self._run_analysis(request)
+        return Response(
+            {
+                "df": analysis.adjusted_data.to_dict(orient="list"),
+                "df2": analysis.summary.to_dict(orient="list"),
+            }
+        )
+
+    @action(detail=False, methods=["POST"], renderer_classes=(renderers.XlsxRenderer,))
+    def excel(self, request, *args, **kwargs):
+        analysis = self._run_analysis(request)
+        data = BinaryFile(analysis.to_excel(), "polyk-adjustment")
+        return Response(data)
+
+    @action(detail=False, methods=["POST"], renderer_classes=(renderers.DocxRenderer,))
+    def word(self, request, *args, **kwargs):
+        analysis = self._run_analysis(request)
+        f = build_polyk_docx(analysis)
+        data = BinaryFile(f, "polyk-adjustment")
+        return Response(data)
diff --git a/bmds_server/analysis/reporting/docx.py b/bmds_server/analysis/reporting/docx.py
index df04f616..15c8bb48 100644
--- a/bmds_server/analysis/reporting/docx.py
+++ b/bmds_server/analysis/reporting/docx.py
@@ -4,6 +4,9 @@
 from typing import TYPE_CHECKING
 
 import docx
+from bmds import __version__
+from bmds.bmds3.reporting import write_setting_p
+from bmds.datasets.transforms.polyk import PolyKAdjustment
 from bmds.reporting.styling import Report
 from django.conf import settings
 from django.utils.timezone import now
@@ -46,9 +49,7 @@ def build_docx(
     if description:
         report.document.add_paragraph(description)
 
-    p = report.document.add_paragraph()
-    p.add_run("Report generated: ").bold = True
-    p.add_run(to_timestamp(now()))
+    write_setting_p(report, "Report generated: ", to_timestamp(now()))
 
     p = report.document.add_paragraph()
     p.add_run(ANALYSIS_URL).bold = True
@@ -57,13 +58,9 @@ def build_docx(
 
     bmds_version = analysis.get_bmds_version()
     if bmds_version:
-        p = report.document.add_paragraph()
-        p.add_run("BMDS version: ").bold = True
-        p.add_run(f"{bmds_version.pretty} ({bmds_version.dll})")
+        write_setting_p(report, "BMDS version: ", f"{bmds_version.pretty} ({bmds_version.dll})")
 
-    p = report.document.add_paragraph()
-    p.add_run("BMDS online version: ").bold = True
-    p.add_run(str(settings.COMMIT))
+    write_setting_p(report, "BMDS Online version: ", str(settings.COMMIT))
 
     if not analysis.is_finished:
         report.document.add_paragraph("Execution is incomplete; no report could be generated")
@@ -120,3 +117,20 @@ def add_update_url(analysis: Analysis, data: BytesIO, uri: str) -> BytesIO:
     f = BytesIO()
     document.save(f)
     return f
+
+
+def build_polyk_docx(analysis: PolyKAdjustment) -> BytesIO:
+    report = Report.build_default()
+
+    # build custom title section
+    report.document.add_heading("Poly K Adjustment", 1)
+    write_setting_p(report, "Report generated: ", to_timestamp(now()))
+    write_setting_p(report, "BMDS version: ", __version__)
+    write_setting_p(report, "BMDS online version: ", str(settings.COMMIT))
+
+    # return generic report
+    document = analysis.to_docx(report=report, show_title=False)
+
+    f = BytesIO()
+    document.save(f)
+    return f
diff --git a/bmds_server/analysis/schema.py b/bmds_server/analysis/schema.py
index b407a2d7..4ca46f1c 100644
--- a/bmds_server/analysis/schema.py
+++ b/bmds_server/analysis/schema.py
@@ -3,7 +3,7 @@
 
 import pandas as pd
 from bmds.bmds3.types.sessions import VersionSchema
-from bmds.datasets.transforms.polyk import calculate
+from bmds.datasets.transforms.polyk import PolyKAdjustment
 from pydantic import BaseModel, Field, field_validator
 from rest_framework.schemas.openapi import SchemaGenerator
 
@@ -68,16 +68,16 @@ def check_dataset(cls, value):
 
         return value
 
-    def calculate(self) -> tuple[pd.DataFrame, pd.DataFrame]:
+    def calculate(self) -> PolyKAdjustment:
         input_df = pd.read_csv(StringIO(self.dataset)).sort_values(["dose", "day"])
-        (df1, df2) = calculate(
+        return PolyKAdjustment(
             doses=input_df.dose.tolist(),
             day=input_df.day.tolist(),
             has_tumor=input_df.has_tumor.tolist(),
             k=self.power,
             max_day=self.duration,
+            dose_units=self.dose_units,
         )
-        return (df1, df2)
 
 
 def add_schemas(schema: dict, models: list):
diff --git a/bmds_server/common/serializers.py b/bmds_server/common/serializers.py
new file mode 100644
index 00000000..4ad556af
--- /dev/null
+++ b/bmds_server/common/serializers.py
@@ -0,0 +1,10 @@
+from rest_framework import serializers
+
+
+class UnusedSerializer(serializers.Serializer):
+    """
+    Nondescript serializer. Used in instances where a view does not use a serializer
+    but one needs to be set, such as for OpenAPI generation.
+    """
+
+    pass
diff --git a/bmds_server/main/urls.py b/bmds_server/main/urls.py
index 69350322..d117aa8b 100644
--- a/bmds_server/main/urls.py
+++ b/bmds_server/main/urls.py
@@ -7,7 +7,7 @@
 from rest_framework.schemas import get_schema_view
 
 from ..analysis import schema, views
-from ..analysis.api import AnalysisViewset, polyk_transform
+from ..analysis.api import AnalysisViewset, PolyKViewset
 from ..common import views as common_views
 from ..common.api import HealthcheckViewset
 from .constants import AuthProvider
@@ -18,6 +18,8 @@
 
 router = SimpleRouter()
 router.register("analysis", AnalysisViewset, basename="analysis")
+if settings.INCLUDE_BETA_FEATURES:
+    router.register("polyk", PolyKViewset, basename="polyk")
 router.register(healthcheck_url, HealthcheckViewset, basename="healthcheck")
 
 edit_pattern = "analysis/<uuid:pk>/<str:password>/"
@@ -46,7 +48,6 @@
 
 if settings.INCLUDE_BETA_FEATURES:
     urlpatterns += [
-        path("api/v1/polyk/", polyk_transform, name="polyk"),
         path("transforms/polyk/", views.PolyKAdjustment.as_view(), name="polyk"),
     ]
 
diff --git a/frontend/src/components/transforms/polyk/App.js b/frontend/src/components/transforms/polyk/App.js
index 60f47f42..b643d30d 100644
--- a/frontend/src/components/transforms/polyk/App.js
+++ b/frontend/src/components/transforms/polyk/App.js
@@ -2,6 +2,8 @@ import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
+import Button from "@/components/common/Button";
+
 import AboutModal from "./AboutModal";
 import InputForm from "./InputForm";
 import OutputTabs from "./OutputTabs";
@@ -10,7 +12,13 @@ import OutputTabs from "./OutputTabs";
 @observer
 class App extends Component {
     render() {
-        const {outputs, showAboutModal, setAboutModal} = this.props.store;
+        const {
+            outputs,
+            showAboutModal,
+            setAboutModal,
+            downloadExcel,
+            downloadWord,
+        } = this.props.store;
         return (
             <div className="container py-3">
                 <div className="d-flex justify-content-between">
@@ -35,7 +43,34 @@ class App extends Component {
                 <InputForm />
                 {outputs ? (
                     <>
-                        <h3 className="pt-3">Results</h3>
+                        <div className="d-flex">
+                            <h3 className="pt-3">Results</h3>
+                            <div className="dropdown ml-auto align-self-start">
+                                <Button
+                                    text="Actions&nbsp;"
+                                    className="btn btn-primary dropdown-toggle"
+                                    type="button"
+                                    id="bmdSessionActions"
+                                    dataToggle="dropdown"
+                                    hasPopup={true}
+                                />
+                                <div className="dropdown-menu dropdown-menu-right">
+                                    <span className="dropdown-header">Reporting</span>
+                                    <Button
+                                        className="dropdown-item"
+                                        onClick={() => downloadExcel()}
+                                        icon="file-excel"
+                                        text="Download data"
+                                    />
+                                    <Button
+                                        className="dropdown-item"
+                                        onClick={() => downloadWord()}
+                                        icon="file-word"
+                                        text="Download report"
+                                    />
+                                </div>
+                            </div>
+                        </div>
                         <OutputTabs />
                     </>
                 ) : null}
diff --git a/frontend/src/components/transforms/polyk/store.js b/frontend/src/components/transforms/polyk/store.js
index c0ae701e..f1e05f50 100644
--- a/frontend/src/components/transforms/polyk/store.js
+++ b/frontend/src/components/transforms/polyk/store.js
@@ -1,9 +1,16 @@
 import {saveAs} from "file-saver";
-import {action, observable} from "mobx";
+import {action, computed, observable} from "mobx";
 
 import {getHeaders} from "../../../common";
 import {exampleData} from "./data";
 
+const getBlob = function(response, defaultName) {
+    const header = response.headers.get("Content-Disposition"),
+        match = header.match(/filename="(.*)"/),
+        filename = match ? match[1] : defaultName;
+    return response.blob().then(blob => ({blob, filename}));
+};
+
 class Store {
     constructor(token) {
         this.token = token;
@@ -34,12 +41,7 @@ class Store {
     async submit() {
         const url = "/api/v1/polyk/";
         this.error = null;
-        await fetch(url, {
-            method: "POST",
-            mode: "cors",
-            headers: getHeaders(this.token),
-            body: JSON.stringify(this.settings),
-        })
+        await fetch(url, this.submissionRequest)
             .then(response => {
                 if (response.ok) {
                     response.json().then(data => {
@@ -69,6 +71,29 @@ class Store {
             });
     }
 
+    @computed get submissionRequest() {
+        return {
+            method: "POST",
+            mode: "cors",
+            headers: getHeaders(this.token),
+            body: JSON.stringify(this.settings),
+        };
+    }
+
+    @action.bound async downloadExcel() {
+        const url = "/api/v1/polyk/excel/";
+        await fetch(url, this.submissionRequest)
+            .then(response => getBlob(response, "polyk.xlsx"))
+            .then(({blob, filename}) => saveAs(blob, filename));
+    }
+
+    @action.bound async downloadWord() {
+        const url = "/api/v1/polyk/word/";
+        await fetch(url, this.submissionRequest)
+            .then(response => getBlob(response, "polyk.docx"))
+            .then(({blob, filename}) => saveAs(blob, filename));
+    }
+
     @action.bound
     reset() {
         this.settings = {
diff --git a/tests/analysis/test_api.py b/tests/analysis/test_api.py
index 9c127b95..3f43b76f 100644
--- a/tests/analysis/test_api.py
+++ b/tests/analysis/test_api.py
@@ -1,7 +1,11 @@
 import json
+from io import BytesIO
 
+import docx
+import pandas as pd
 import pytest
 from bmds.bmds3.recommender import RecommenderSettings
+from django.urls import reverse
 from rest_framework.test import APIClient
 
 from bmds_server.analysis.models import Analysis
@@ -242,3 +246,32 @@ def test_model_selection(self, bmds3_complete_dichotomous):
         assert response.status_code == 200
         value = response.data["outputs"]["outputs"][0]["frequentist"]["selected"]
         assert value == {"model_index": None, "notes": "no notes"}
+
+
+@pytest.mark.django_db
+class TestPolyKViewSet:
+    def test_create(self, polyk_dataset):
+        client = APIClient()
+        url = reverse("api:polyk-list")
+        response = client.post(url, polyk_dataset, format="json")
+        assert response.status_code == 200
+        assert list(response.json().keys()) == ["df", "df2"]
+
+    def test_excel(self, polyk_dataset):
+        client = APIClient()
+        url = reverse("api:polyk-excel")
+        response = client.post(url, polyk_dataset, format="json")
+        assert response.status_code == 200
+        # ensure that response is a valid workbook with two worksheets
+        data = pd.read_excel(response.content, sheet_name=["adjusted", "summary"])
+        assert isinstance(data["adjusted"], pd.DataFrame)
+        assert isinstance(data["summary"], pd.DataFrame)
+
+    def test_word(self, polyk_dataset):
+        client = APIClient()
+        url = reverse("api:polyk-word")
+        response = client.post(url, polyk_dataset, format="json")
+        assert response.status_code == 200
+        # assert docx loads
+        doc = docx.Document(BytesIO(response.content))
+        assert isinstance(doc, docx.document.Document)
diff --git a/tests/analysis/test_schema.py b/tests/analysis/test_schema.py
index 967583fc..00ab06e4 100644
--- a/tests/analysis/test_schema.py
+++ b/tests/analysis/test_schema.py
@@ -9,9 +9,9 @@
 class TestPolyKInput:
     def test_calculate(self, polyk_dataset):
         analysis = PolyKInput.model_validate(polyk_dataset)
-        df1, df2 = analysis.calculate()
-        assert df1.shape == (200, 4)
-        assert df2.shape == (4, 6)
+        result = analysis.calculate()
+        assert result.adjusted_data.shape == (200, 4)
+        assert result.summary.shape == (4, 6)
 
     def test_validate_dataset(self, polyk_dataset):
         # confirm success

From cf01e687c454802746e9ef5e79fa3cc68a899014 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Wed, 13 Dec 2023 11:02:04 -0500
Subject: [PATCH 17/24] add Desktop mode (#279)

* hello desktop

* start app

* add logging

* wip

* updates

* finish demo

* cleanup

* start server

* start next steps

* updates

* add bmdsdesktop cli option

* hacks for desktop demo

* lint

* enable wal

* update .gitignore

* wip - continue

* double getter?

* demo prep

* add a few updates to the desktop

* desktop updates

* add collections

* refactor homepage

* updates to desktop

* parsimony

* add collections

* include markdown in bundle

* add package versions

* fix integration tests
---
 .gitignore                                    |   2 +-
 MANIFEST.in                                   |   2 +-
 bmds_server/analysis/admin.py                 |   5 +
 bmds_server/analysis/api.py                   |  36 ++-
 bmds_server/analysis/apps.py                  |   3 +
 .../analysis/fixtures/initial_data.json       |   2 +-
 bmds_server/analysis/forms.py                 |  11 +
 .../analysis/migrations/0003_reversions.py    |   3 +-
 ..._last_updated_analysis_starred_and_more.py |  44 ++++
 bmds_server/analysis/models.py                |  28 +++
 bmds_server/analysis/serializers.py           |  10 +
 bmds_server/analysis/signals.py               |  11 +
 .../analysis/analysis_confirm_delete.html     |   2 +-
 .../analysis/collection_confirm_delete.html   |  21 ++
 .../templates/analysis/collection_form.html   |  31 +++
 .../templates/analysis/collection_list.html   |  21 ++
 .../templates/analysis/desktop_home.html      |  95 ++++++++
 bmds_server/analysis/views.py                 |  96 +++++++-
 bmds_server/common/templatetags/bs4.py        |  12 +
 bmds_server/desktop/__init__.py               |   0
 bmds_server/desktop/cli.py                    | 217 ++++++++++++++++++
 bmds_server/desktop/content/app.css           |  32 +++
 bmds_server/desktop/content/top.md            |   7 +
 bmds_server/main/constants.py                 |  15 ++
 bmds_server/main/settings/base.py             |   2 -
 bmds_server/main/settings/desktop.py          |  71 ++++++
 bmds_server/main/urls.py                      |  23 +-
 bmds_server/static/css/epa/bmdsonline.css     |   7 +
 bmds_server/static/css/site.css               |  11 +
 bmds_server/templates/base.html               |   4 +-
 .../templates/includes/base/header.html       |   8 +-
 .../templates/includes/epa/header.html        |   2 +-
 .../templates/includes/pagination.html        |  19 ++
 compose/example.env                           |   1 -
 frontend/src/App.js                           |   7 +-
 .../src/components/Main/Actions/Actions.js    |   8 +
 .../components/Main/Actions/CollectionForm.js |  53 +++++
 .../src/components/Main/Actions/Starred.js    |  35 +++
 .../Main/AnalysisForm/AnalysisForm.js         |   2 +
 .../Main/AnalysisForm/CollectionList.js       |  29 +++
 frontend/src/components/Navigation.js         |   6 +-
 frontend/src/stores/MainStore.js              |  55 +++++
 requirements/base.txt                         |   4 +
 setup.cfg                                     |  23 +-
 tests/analysis/test_views.py                  |   3 +
 tests/data/db.yaml                            |   2 +-
 tests/integration/test_integration.py         |   9 +-
 47 files changed, 1049 insertions(+), 41 deletions(-)
 create mode 100644 bmds_server/analysis/migrations/0004_collection_analysis_last_updated_analysis_starred_and_more.py
 create mode 100644 bmds_server/analysis/signals.py
 create mode 100644 bmds_server/analysis/templates/analysis/collection_confirm_delete.html
 create mode 100644 bmds_server/analysis/templates/analysis/collection_form.html
 create mode 100644 bmds_server/analysis/templates/analysis/collection_list.html
 create mode 100644 bmds_server/analysis/templates/analysis/desktop_home.html
 create mode 100644 bmds_server/desktop/__init__.py
 create mode 100644 bmds_server/desktop/cli.py
 create mode 100644 bmds_server/desktop/content/app.css
 create mode 100644 bmds_server/desktop/content/top.md
 create mode 100644 bmds_server/main/settings/desktop.py
 create mode 100644 bmds_server/templates/includes/pagination.html
 create mode 100644 frontend/src/components/Main/Actions/CollectionForm.js
 create mode 100644 frontend/src/components/Main/Actions/Starred.js
 create mode 100644 frontend/src/components/Main/AnalysisForm/CollectionList.js

diff --git a/.gitignore b/.gitignore
index fd626fcc..b2cf8135 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,7 +20,7 @@ venv/
 # files
 *.log
 *.py[cod]
-*.sqlite3
+*.sqlite3*
 *log
 .coverage
 .env
diff --git a/MANIFEST.in b/MANIFEST.in
index a7abc4a7..9af2e5be 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,4 @@
-recursive-include bmds_server/ *css *.js *.json *.html *.py
+recursive-include bmds_server/ *css *.js *.json *.html *.md *.py
 recursive-include bmds_server/static *
 recursive-include bmds_server/templates *
 global-exclude .DS_Store .gitkeep __pycache__ *.pyc
diff --git a/bmds_server/analysis/admin.py b/bmds_server/analysis/admin.py
index fb18ab5a..ffa4997c 100644
--- a/bmds_server/analysis/admin.py
+++ b/bmds_server/analysis/admin.py
@@ -47,3 +47,8 @@ def edit_url(self, obj):
 class Content(VersionAdmin):
     list_display = ("id", "content_type", "subject", "created", "last_updated")
     list_filter = ("content_type",)
+
+
+@admin.register(models.Collection)
+class CollectionAdmin(VersionAdmin):
+    pass
diff --git a/bmds_server/analysis/api.py b/bmds_server/analysis/api.py
index 334e9e74..b919e895 100644
--- a/bmds_server/analysis/api.py
+++ b/bmds_server/analysis/api.py
@@ -1,4 +1,5 @@
 from bmds.datasets.transforms.polyk import PolyKAdjustment
+from django.conf import settings
 from django.core.exceptions import ValidationError
 from rest_framework import exceptions, mixins, viewsets
 from rest_framework.decorators import action
@@ -17,7 +18,7 @@
 
 class AnalysisViewset(mixins.RetrieveModelMixin, viewsets.GenericViewSet):
     serializer_class = serializers.AnalysisSerializer
-    queryset = models.Analysis.objects.all()
+    queryset = models.Analysis.objects.prefetch_related("collections").all()
 
     @action(detail=False, url_path="default")
     def default(self, request, *args, **kwargs):
@@ -160,6 +161,39 @@ def word(self, request, *args, **kwargs):
 
         return Response(response.model_dump(), content_type="application/json")
 
+    @action(detail=True, methods=("post",))
+    def star(self, request, *args, **kwargs):
+        instance = self.get_object()
+
+        # permissions check
+        if instance.password != request.data.get("editKey", ""):
+            raise exceptions.PermissionDenied()
+
+        # flip the star (but don't change last_updated)
+        if settings.IS_DESKTOP:
+            models.Analysis.objects.filter(id=instance.id).update(starred=not instance.starred)
+            instance.refresh_from_db()
+
+        serializer = self.get_serializer(instance)
+        return Response(serializer.data)
+
+    @action(detail=True, methods=("post",))
+    def collections(self, request, *args, **kwargs):
+        instance = self.get_object()
+
+        # permissions check
+        if instance.password != request.data.get("editKey", ""):
+            raise exceptions.PermissionDenied()
+
+        # update collections
+        if settings.IS_DESKTOP:
+            ids = [d for d in request.data.get("collections", []) if isinstance(d, int)]
+            collections = models.Collection.objects.filter(id__in=ids)
+            instance.collections.set(collections)
+
+        serializer = self.get_serializer(instance)
+        return Response(serializer.data)
+
 
 class PolyKViewset(viewsets.GenericViewSet):
     queryset = models.Analysis.objects.none()
diff --git a/bmds_server/analysis/apps.py b/bmds_server/analysis/apps.py
index 12096dd7..b3f5c17a 100644
--- a/bmds_server/analysis/apps.py
+++ b/bmds_server/analysis/apps.py
@@ -3,3 +3,6 @@
 
 class Config(AppConfig):
     name = "bmds_server.analysis"
+
+    def ready(self):
+        from .signals import init_command  # noqa: F401
diff --git a/bmds_server/analysis/fixtures/initial_data.json b/bmds_server/analysis/fixtures/initial_data.json
index edd9b8db..cb6769af 100644
--- a/bmds_server/analysis/fixtures/initial_data.json
+++ b/bmds_server/analysis/fixtures/initial_data.json
@@ -6,7 +6,7 @@
             "content_type": 1,
             "subject": "Homepage",
             "content": {
-                "template": "<div class=\"row\">\n    <div class=\"col-sm-12\">\n        <h1>Welcome to BMDS online.</h1>\n    </div>\n</div>\n<div class=\"row\">\n    <div class=\"col-md-8\">\n        <div class=\"col-lg\">\n            <p>\n                This web-application executes the US EPA's benchmark dose modeling software (<a href=\"https://www.epa.gov/bmds\">BMDS</a>).\n            </p>\n            <ul>\n                <li>Load example datasets below to view example input files; for more information, see the <a  href=\"http://bmds-server.readthedocs.io/en/latest/\">documentation</a>\n                </li>\n                <li>Software is designed for automated BMDS execution using a\n                    programming language such as Python, R, or Java. To take\n                    advantage of automation, use the <a href=\"/api/v1/\">API</a>,\n                    and see the <a href=\"http://bmds-server.readthedocs.io/en/latest/quickstart.html\">quickstart</a> section.\n                </li>\n            </ul>\n        </div>\n    </div>\n    <div class=\"col-md-4\">\n        <form method=\"post\">\n            {% csrf_token %}\n            <label for=\"id_id\">Create a new analysis:</label>\n            <button type=\"submit\" class=\"btn btn-primary btn-block mb-1\">Create a new BMDS analysis</button>\n            <p class=\"text-muted\">Analyses are deleted after {{days_to_keep_analyses}} days.</p>\n        </form>\n    </div>\n</div>\n"
+                "template": "<div class=\"row\">\n    <div class=\"col-sm-12\">\n        <h1>Welcome to BMDS online.</h1>\n    </div>\n</div>\n<div class=\"row\">\n    <div class=\"col-md-8\">\n        <div class=\"col-lg\">\n            <p>\n                This web-application executes the US EPA's benchmark dose modeling software (<a href=\"https://www.epa.gov/bmds\">BMDS</a>).\n            </p>\n            <ul>\n                <li>Load example datasets below to view example input files; for more information, see the <a  href=\"http://bmds-server.readthedocs.io/en/latest/\">documentation</a>\n                </li>\n                <li>Software is designed for automated BMDS execution using a\n                    programming language such as Python, R, or Java. To take\n                    advantage of automation, use the <a href=\"/api/v1/\">API</a>,\n                    and see the <a href=\"http://bmds-server.readthedocs.io/en/latest/quickstart.html\">quickstart</a> section.\n                </li>\n            </ul>\n        </div>\n    </div>\n    <div class=\"col-md-4\">\n        <form  action=\"{% url 'analysis_create' %}\" method=\"post\">\n            {% csrf_token %}\n            <label for=\"id_id\">Create a new analysis:</label>\n            <button type=\"submit\" class=\"btn btn-primary btn-block mb-1\">Create a new BMDS analysis</button>\n            <p class=\"text-muted\">Analyses are deleted after {{days_to_keep_analyses}} days.</p>\n        </form>\n    </div>\n</div>\n"
             },
             "created": "2021-01-31 08:00:00.123456+00:00",
             "last_updated": "2021-01-31 08:00:00.123456+00:00"
diff --git a/bmds_server/analysis/forms.py b/bmds_server/analysis/forms.py
index bd3ec863..50fe1f76 100644
--- a/bmds_server/analysis/forms.py
+++ b/bmds_server/analysis/forms.py
@@ -11,3 +11,14 @@ class Meta:
     def save(self, commit=True):
         self.instance.inputs = self.instance.default_input()
         return super().save(commit=commit)
+
+
+class CollectionForm(forms.ModelForm):
+    def __init__(self, *args, **kw):
+        super().__init__(*args, **kw)
+        for field in self.fields.values():
+            field.widget.attrs["class"] = "form-control"
+
+    class Meta:
+        model = models.Collection
+        fields = ("name", "description")
diff --git a/bmds_server/analysis/migrations/0003_reversions.py b/bmds_server/analysis/migrations/0003_reversions.py
index 1e476081..dc00654d 100644
--- a/bmds_server/analysis/migrations/0003_reversions.py
+++ b/bmds_server/analysis/migrations/0003_reversions.py
@@ -3,7 +3,8 @@
 
 
 def make_revisions(apps, schema_editor):
-    call_command("createinitialrevisions")
+    # disable; broken w/ migration 0004
+    pass
 
 
 def remove_revisions(apps, schema_editor):
diff --git a/bmds_server/analysis/migrations/0004_collection_analysis_last_updated_analysis_starred_and_more.py b/bmds_server/analysis/migrations/0004_collection_analysis_last_updated_analysis_starred_and_more.py
new file mode 100644
index 00000000..1b0a1804
--- /dev/null
+++ b/bmds_server/analysis/migrations/0004_collection_analysis_last_updated_analysis_starred_and_more.py
@@ -0,0 +1,44 @@
+# Generated by Django 4.2.8 on 2023-12-11 19:27
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("analysis", "0003_reversions"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="Collection",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("name", models.CharField(max_length=128)),
+                ("description", models.TextField(blank=True)),
+                ("created", models.DateTimeField(auto_now_add=True)),
+                ("last_updated", models.DateTimeField(auto_now=True)),
+            ],
+        ),
+        migrations.AddField(
+            model_name="analysis",
+            name="last_updated",
+            field=models.DateTimeField(auto_now=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="analysis",
+            name="starred",
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name="analysis",
+            name="collections",
+            field=models.ManyToManyField(
+                blank=True, related_name="analyses", to="analysis.collection"
+            ),
+        ),
+    ]
diff --git a/bmds_server/analysis/models.py b/bmds_server/analysis/models.py
index 15616c60..59f8ead2 100644
--- a/bmds_server/analysis/models.py
+++ b/bmds_server/analysis/models.py
@@ -47,9 +47,12 @@ class Analysis(models.Model):
     outputs = models.JSONField(default=dict, blank=True)
     errors = models.JSONField(default=dict, blank=True)
     created = models.DateTimeField(auto_now_add=True)
+    last_updated = models.DateTimeField(null=True, auto_now=True)
     started = models.DateTimeField(null=True, blank=True)
     ended = models.DateTimeField(null=True, blank=True)
     deletion_date = models.DateTimeField(null=True, blank=True, default=get_deletion_date)
+    starred = models.BooleanField(default=False)
+    collections = models.ManyToManyField("analysis.Collection", related_name="analyses", blank=True)
 
     class Meta:
         verbose_name_plural = "Analyses"
@@ -110,6 +113,12 @@ def get_excel_url(self):
     def get_word_url(self):
         return reverse("api:analysis-word", args=(str(self.id),))
 
+    def get_star_url(self):
+        return reverse("api:analysis-star", args=(str(self.id),))
+
+    def get_collections_url(self):
+        return reverse("api:analysis-collections", args=(str(self.id),))
+
     def inputs_valid(self) -> bool:
         try:
             validators.validate_input(self.inputs)
@@ -359,6 +368,25 @@ def days_until_deletion(self) -> int | None:
             return None
         return (self.deletion_date - now()).days
 
+    @property
+    def timestamp(self):
+        return self.last_updated or self.ended or self.created
+
+
+@reversion.register()
+class Collection(models.Model):
+    name = models.CharField(max_length=128)
+    description = models.TextField(blank=True)
+    created = models.DateTimeField(auto_now_add=True)
+    last_updated = models.DateTimeField(auto_now=True)
+
+    def __str__(self):
+        return self.name
+
+    @classmethod
+    def opts(cls):
+        return list(cls.objects.values("id", "name").order_by("name"))
+
 
 class ContentType(models.IntegerChoices):
     HOMEPAGE = 1
diff --git a/bmds_server/analysis/serializers.py b/bmds_server/analysis/serializers.py
index af29f587..eb22bc55 100644
--- a/bmds_server/analysis/serializers.py
+++ b/bmds_server/analysis/serializers.py
@@ -3,11 +3,18 @@
 from . import models, validators
 
 
+class CollectionSerializer(serializers.ModelSerializer):
+    class Meta:
+        model = models.Collection
+        fields = ("id", "name")
+
+
 class AnalysisSerializer(serializers.ModelSerializer):
     is_executing = serializers.BooleanField(read_only=True)
     is_finished = serializers.BooleanField(read_only=True)
     has_errors = serializers.BooleanField(read_only=True)
     inputs_valid = serializers.BooleanField(read_only=True)
+    collections = CollectionSerializer(many=True)
     api_url = serializers.URLField(source="get_api_url", read_only=True)
     excel_url = serializers.URLField(source="get_excel_url", read_only=True)
     word_url = serializers.URLField(source="get_word_url", read_only=True)
@@ -19,6 +26,7 @@ class Meta:
             "inputs",
             "errors",
             "outputs",
+            "collections",
             "is_executing",
             "is_finished",
             "has_errors",
@@ -29,11 +37,13 @@ class Meta:
             "created",
             "started",
             "ended",
+            "starred",
         )
         read_only_fields = (
             "id",
             "errors",
             "outputs",
+            "collections",
             "is_executing",
             "is_finished",
             "has_errors",
diff --git a/bmds_server/analysis/signals.py b/bmds_server/analysis/signals.py
new file mode 100644
index 00000000..f4334262
--- /dev/null
+++ b/bmds_server/analysis/signals.py
@@ -0,0 +1,11 @@
+from django.db.backends.signals import connection_created
+from django.dispatch import receiver
+
+
+@receiver(connection_created)
+def init_command(sender, connection, **kwargs) -> None:
+    # https://code.djangoproject.com/ticket/24018
+    command = connection.settings_dict.get("STARTUP_OPTIONS", {}).get("init_command")
+    if connection.vendor == "sqlite" and command:
+        cursor = connection.cursor()
+        cursor.execute(command)
diff --git a/bmds_server/analysis/templates/analysis/analysis_confirm_delete.html b/bmds_server/analysis/templates/analysis/analysis_confirm_delete.html
index 0a14a20a..bb4e631f 100644
--- a/bmds_server/analysis/templates/analysis/analysis_confirm_delete.html
+++ b/bmds_server/analysis/templates/analysis/analysis_confirm_delete.html
@@ -3,7 +3,7 @@
 {% load bs4 %}
 
 {% block content %}
-<div class="alert alert-danger mt-3" role="alert">
+<div class="alert alert-danger" role="alert">
     <form method="post">
         {% csrf_token %}
         <p><strong>Delete analysis?</strong></p>
diff --git a/bmds_server/analysis/templates/analysis/collection_confirm_delete.html b/bmds_server/analysis/templates/analysis/collection_confirm_delete.html
new file mode 100644
index 00000000..bd2110a1
--- /dev/null
+++ b/bmds_server/analysis/templates/analysis/collection_confirm_delete.html
@@ -0,0 +1,21 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class='container'>
+    <div class="row">
+        <div class="col-lg-6">
+            <div class="d-flex">
+                <h3>Collections</h3>
+            </div>
+            <p>Are you sure you want to delete <b>{{object.name}}</b>?</p>
+            <form action="." method="post">
+                {% csrf_token %}
+                <div class="form-group">
+                    <input class="btn btn-danger" type="submit" value="Delete"/>
+                    <a class="btn btn-light" href="{% url 'collection_list' %}">Cancel</a>
+                </div>
+            </form>
+        </div>
+    </div>
+</div>
+{% endblock content %}
diff --git a/bmds_server/analysis/templates/analysis/collection_form.html b/bmds_server/analysis/templates/analysis/collection_form.html
new file mode 100644
index 00000000..331f4074
--- /dev/null
+++ b/bmds_server/analysis/templates/analysis/collection_form.html
@@ -0,0 +1,31 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class='container'>
+    <div class="row">
+        <div class="col-lg-6">
+            <h3>Collections</h3>
+            <form action="." method="post">
+                {% csrf_token %}
+                <div class="form-group">
+                    <label>{{form.name.label}}</label>
+                    {{ form.name }}
+                </div>
+                <div class="form-group">
+                    <label>{{form.description.label}}</label>
+                    {{ form.description }}
+                </div>
+                <div class="form-group d-flex">
+                    <input class="btn btn-primary" type="submit" value="{% if object.id %}Update{% else %}Create{% endif %}"/>
+                    <div class="ml-auto align-self-start flex-shrink-0">
+                        <a class="btn btn-light" href="{% url 'collection_list' %}">Cancel</a>
+                        {% if object.id %}
+                            <a class="btn btn-danger" href="{% url 'collection_delete' object.id %}">Delete</a>
+                        {% endif %}
+                    </div>
+                </div>
+            </form>
+        </div>
+    </div>
+</div>
+{% endblock content %}
diff --git a/bmds_server/analysis/templates/analysis/collection_list.html b/bmds_server/analysis/templates/analysis/collection_list.html
new file mode 100644
index 00000000..ecb570db
--- /dev/null
+++ b/bmds_server/analysis/templates/analysis/collection_list.html
@@ -0,0 +1,21 @@
+{% extends "base.html" %}
+
+{% block content %}
+<div class='container'>
+    <div class="row">
+        <div class="col-lg-6">
+            <div class="d-flex">
+                <h3>Collections</h3>
+                <a class="btn btn-primary ml-auto align-self-start flex-shrink-0" href="{% url 'collection_create' %}">Create</a>
+            </div>
+            {% for object in object_list %}
+            <ul class="mb-0">
+                <li><a href="{% url 'collection_update' object.id %}">{{object.name}}</a></li>
+            </ul>
+            {% empty %}
+            <p class="text-muted">No collections!</p>
+            {% endfor %}
+        </div>
+    </div>
+</div>
+{% endblock content %}
diff --git a/bmds_server/analysis/templates/analysis/desktop_home.html b/bmds_server/analysis/templates/analysis/desktop_home.html
new file mode 100644
index 00000000..691ae2f3
--- /dev/null
+++ b/bmds_server/analysis/templates/analysis/desktop_home.html
@@ -0,0 +1,95 @@
+{% extends "base.html" %}
+
+{% load bs4 %}
+
+{% block content %}
+<div class="row">
+  <div class="col-lg-8">
+
+    <div class="d-flex">
+      <h3>Analyses</h3>
+      <form action="{% url 'analysis_create' %}" method="post" class="ml-auto align-self-start flex-shrink-0">
+        {% csrf_token %}
+        <button type="submit" class="btn btn-primary"><span class="bi bi-plus-square-fill mr-1"></span>Create analysis</button>
+      </form>
+    </div>
+
+    <form method="get" class="form-row align-items-center bg-light py-3">
+      <div class="col-auto">
+        <input class="form-control" name="q" value="{{q}}" type="text" placeholder="Search" />
+      </div>
+      <div class="col-auto">
+        <select class="form-control custom-select" name="collection" id="id_collection">
+          <option>--- Collection ---</option>
+          {% for c in collections %}
+            <option value="{{c.id}}" {% if collection == c.id %}selected {% endif %}>{{c.name}}</option>
+          {% endfor %}
+        </select>
+      </div>
+      <div class="col-auto">
+        <div class="custom-control custom-switch">
+          <input type="checkbox" class="custom-control-input" id="starred" {{starred|yesno:"checked,,"}} name="starred">
+          <label class="custom-control-label" for="starred">Starred</label>
+        </div>
+      </div>
+      <div class="ml-auto">
+        <a href="." class="btn btn-secondary mr-3">Reset</a>
+        <button type="submit" class="btn btn-primary px-3">
+          <span class="bi bi-search mr-1"></span>Search
+        </button>
+      </div>
+    </form>
+
+    {% with objects=object_list %}
+    {% if objects %}
+      <table class="table table-hover table-sm analysis-list">
+        <colgroup>
+          <col width="40px" />
+          <col />
+          <col width="100px" />
+        </colgroup>
+        <tbody>
+          {% for object in objects %}
+          <tr class="stretched-link-parent" >
+            <td class="text-center"><span class="starred bi {{object.starred|yesno:'bi-star-fill,bi-star'}}"></span></td>
+            <td>
+              {% for collection in object.collections.all %}<span class="mr-1 badge badge-info">{{collection}}</span>{% endfor %}
+              <a class="text-dark stretched-link" href="{{object.get_edit_url}}">{{object}}</a>
+            </td>
+            <td>{% table_time now object.timestamp %}</td>
+          </tr>
+          {% endfor %}
+        </tbody>
+      </table>
+      {% include "includes/pagination.html" %}
+    {% else %}
+      <p class="text-muted">No analyses found.</p>
+    {% endif %}
+    {% endwith %}
+  </div>
+  <div class="col-lg-4">
+    <div class="card pane mt-4">
+      <div class="card-header bg-dark">
+        <h4 class="mb-0 text-white text-center">Support</h4>
+      </div>
+      <div class="card-body p-3">
+        <ul class="mb-0">
+          <li><a href="{% url 'collection_list' %}">Collections</a></li>
+          <li><a href="https://www.epa.gov/bmds" target="_blank" rel="noopener noreferrer">BMDS Home Page</a></li>
+          <li><a href="https://www.epa.gov/bmds/how-modeling-dichotomous-data-bmds-online" target="_blank" rel="noopener noreferrer">BMDS Online Tutorial</a></li>
+          <li><a href="https://www.epa.gov/bmds/benchmark-dose-software-bmds-version-32-download" target="_blank" rel="noopener noreferrer">BMDS Downloads</a></li>
+          <li><a href="https://ecomments.epa.gov/bmds/" target="_blank" rel="noopener noreferrer">BMDS Support</a></li>
+        </ul>
+      </div>
+    </div>
+    <div class="card pane mt-4">
+      <div class="card-header bg-dark">
+        <h4 class="mb-0 text-white text-center">Disclaimer</h4>
+      </div>
+      <div class="card-body">
+      <p class="mb-0">This software/application has been approved for release by the U.S. Environmental Protection Agency (USEPA). Although the software has been subjected to rigorous review, the USEPA reserves the right to update the software as needed pursuant to further analysis and review. No warranty, expressed or implied, is made by the USEPA or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. Furthermore, the software is released on condition that neither the USEPA nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use.</p>
+      </div>
+    </div>
+  </div>
+</div>
+{% endblock content %}
diff --git a/bmds_server/analysis/views.py b/bmds_server/analysis/views.py
index b5a35892..99cfa74e 100644
--- a/bmds_server/analysis/views.py
+++ b/bmds_server/analysis/views.py
@@ -1,25 +1,32 @@
+from typing import ClassVar
+
 from django.conf import settings
 from django.contrib.admin.views.decorators import staff_member_required
+from django.db.models.query import QuerySet
 from django.middleware.csrf import get_token
 from django.shortcuts import get_object_or_404
 from django.template import RequestContext, Template
 from django.urls import reverse_lazy
 from django.utils.decorators import method_decorator
-from django.views.generic import CreateView, DeleteView, DetailView, RedirectView, TemplateView
+from django.utils.timezone import now
+from django.views.generic import (
+    CreateView,
+    DeleteView,
+    DetailView,
+    ListView,
+    RedirectView,
+    TemplateView,
+    UpdateView,
+)
 
 from . import forms, models
 from .reporting.analytics import get_cached_analytics
 from .utils import get_citation
 
 
-class Home(CreateView):
-    model = models.Analysis
-    form_class = forms.CreateAnalysisForm
+class Home(TemplateView):
     template_name = "analysis/home.html"
 
-    def get_success_url(self):
-        return self.object.get_edit_url()
-
     def _render_template(self, extra):
         context = RequestContext(self.request, extra)
         content = models.Content.get_cached_content(models.ContentType.HOMEPAGE)
@@ -27,12 +34,57 @@ def _render_template(self, extra):
 
     def get_context_data(self, **kwargs):
         context = super().get_context_data(**kwargs)
-        context["days_to_keep_analyses"] = settings.DAYS_TO_KEEP_ANALYSES
-        context["citation"] = get_citation()
+        context.update(
+            days_to_keep_analyses=settings.DAYS_TO_KEEP_ANALYSES,
+            citation=get_citation(),
+        )
         context["page"] = self._render_template(context)
         return context
 
 
+class DesktopHome(ListView):
+    template_name = "analysis/desktop_home.html"
+    model = models.Analysis
+    queryset = (
+        models.Analysis.objects.defer("outputs", "errors")
+        .all()
+        .order_by("-last_updated", "-created")
+    )
+    paginate_by = 20
+
+    def get_queryset(self) -> QuerySet:
+        qs = super().get_queryset()
+        if q := self.request.GET.get("q"):
+            qs = qs.filter(inputs__analysis_name__icontains=q)
+        if self.request.GET.get("starred"):
+            qs = qs.filter(starred=True)
+        if c := self.request.GET.get("collection"):
+            if c.isnumeric():
+                qs = qs.filter(collections=c)
+        return qs.prefetch_related("collections")
+
+    def get_context_data(self, **kwargs):
+        context = super().get_context_data(**kwargs)
+        collection = self.request.GET.get("collection", "")
+        context.update(
+            q=self.request.GET.get("q", ""),
+            starred=len(self.request.GET.get("starred", "")) > 0,
+            collection=int(collection) if collection.isnumeric() else "",
+            collections=models.Collection.opts(),
+            now=now(),
+        )
+        return context
+
+
+class AnalysisCreate(CreateView):
+    model = models.Analysis
+    form_class = forms.CreateAnalysisForm
+    http_method_names: ClassVar[list[str]] = ["post"]
+
+    def get_success_url(self):
+        return self.object.get_edit_url()
+
+
 class AnalysisHistory(TemplateView):
     template_name: str = "analysis/analysis_history.html"
 
@@ -91,6 +143,8 @@ def get_context_data(self, **kwargs):
                 "editKey": self.object.password,
                 "viewUrl": self.request.build_absolute_uri(self.object.get_absolute_url()),
                 "editUrl": self.request.build_absolute_uri(self.object.get_edit_url()),
+                "starUrl": self.request.build_absolute_uri(self.object.get_star_url()),
+                "collectionUrl": self.request.build_absolute_uri(self.object.get_collections_url()),
                 "renewUrl": self.request.build_absolute_uri(self.object.get_renew_url()),
                 "deleteUrl": self.request.build_absolute_uri(self.object.get_delete_url()),
                 "patchInputUrl": self.object.get_api_patch_inputs_url(),
@@ -98,6 +152,7 @@ def get_context_data(self, **kwargs):
                 "executeResetUrl": self.object.get_api_execute_reset_url(),
                 "deleteDateStr": self.object.deletion_date_str,
                 "deletionDaysUntilDeletion": self.object.days_until_deletion,
+                "collections": models.Collection.opts(),
             }
         return context
 
@@ -125,3 +180,26 @@ def get_object(self, queryset=None):
 
 class PolyKAdjustment(TemplateView):
     template_name: str = "analysis/polyk.html"
+
+
+class CollectionList(ListView):
+    model = models.Collection
+    queryset = models.Collection.objects.all().order_by("name")
+    paginate_by = 1000
+
+
+class CollectionCreate(CreateView):
+    model = models.Collection
+    form_class = forms.CollectionForm
+    success_url = reverse_lazy("collection_list")
+
+
+class CollectionUpdate(UpdateView):
+    model = models.Collection
+    form_class = forms.CollectionForm
+    success_url = reverse_lazy("collection_list")
+
+
+class CollectionDelete(DeleteView):
+    model = models.Collection
+    success_url = reverse_lazy("collection_list")
diff --git a/bmds_server/common/templatetags/bs4.py b/bmds_server/common/templatetags/bs4.py
index d4c0aa0c..8e63219f 100644
--- a/bmds_server/common/templatetags/bs4.py
+++ b/bmds_server/common/templatetags/bs4.py
@@ -1,10 +1,12 @@
 """
 Twitter Bootstrap 4 - helper methods
 """
+from datetime import datetime
 from textwrap import dedent
 from uuid import uuid4
 
 from django import template
+from django.utils import timezone
 from django.utils.html import escapejs
 from django.utils.safestring import mark_safe
 from plotly.graph_objs._figure import Figure
@@ -58,3 +60,13 @@ def plotly(fig: Figure) -> str | None:
     </script>"""
         )
     )
+
+
+@register.simple_tag()
+def table_time(now: datetime, timestamp: datetime):
+    if timestamp.date() == now.date():
+        return timezone.localtime(timestamp).strftime("%I:%M %p")
+    elif timestamp.year == now.year:
+        return timezone.localtime(timestamp).strftime("%b %d")
+    else:
+        return timezone.localtime(timestamp).strftime("%m/%d/%y")
diff --git a/bmds_server/desktop/__init__.py b/bmds_server/desktop/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/bmds_server/desktop/cli.py b/bmds_server/desktop/cli.py
new file mode 100644
index 00000000..f5e48126
--- /dev/null
+++ b/bmds_server/desktop/cli.py
@@ -0,0 +1,217 @@
+import logging
+import os
+from contextlib import redirect_stderr, redirect_stdout
+from importlib.metadata import version
+from io import StringIO
+from pathlib import Path
+from threading import Thread
+from time import sleep
+from typing import ClassVar
+from webbrowser import open_new_tab
+from wsgiref.simple_server import WSGIServer, make_server
+
+from django.conf import settings
+from django.core.management import call_command
+from pydantic import BaseModel, Field
+from textual import on
+from textual.app import App, ComposeResult
+from textual.containers import Container, ScrollableContainer
+from textual.widgets import (
+    Button,
+    Footer,
+    Header,
+    Label,
+    Log,
+    Markdown,
+    Static,
+    TabbedContent,
+    TabPane,
+)
+from whitenoise import WhiteNoise
+
+from ..main.constants import get_app_home
+
+logger = logging.getLogger(__name__)
+
+ROOT = Path(__file__).parent
+
+
+def data_folder() -> Path:
+    path = get_app_home()
+    path.mkdir(parents=True, exist_ok=True)
+    return path
+
+
+class DesktopConfig(BaseModel):
+    path: str = Field(default_factory=lambda: str(data_folder()))
+    host: str = "127.0.0.1"
+    port: int = 5555
+
+
+class LogApp:
+    def __init__(self, app):
+        self.stream = StringIO()
+        self.handler = logging.StreamHandler(self.stream)
+        self.widget = Log(id="log")
+        self.thread = Thread(target=self._run, daemon=True)
+
+    def add_handler(self):
+        logger = logging.getLogger()
+        logger.addHandler(self.handler)
+        logger.setLevel(logging.INFO)
+
+    def start(self):
+        self.add_handler()
+        self.thread.start()
+
+    def _run(self):
+        while True:
+            if log_contents := self.stream.getvalue().strip():
+                self.stream.truncate(0)
+                self.widget.write(log_contents)
+            sleep(1)
+
+
+class AppThread(Thread):
+    def __init__(self, stream: StringIO, host="127.0.0.1", port=5555, **kw):
+        self.stream = stream
+        self.host = host
+        self.port = port
+        self.server: WSGIServer | None = None
+        super().__init__(**kw)
+
+    def run(self):
+        import django
+
+        django.setup()
+
+        from ..main.wsgi import application as django_app
+
+        self.stream.write("\nStart collectstatic\n")
+        call_command(
+            "collectstatic", interactive=False, verbosity=3, stdout=self.stream, stderr=self.stream
+        )
+        self.stream.write("\nEnd collectstatic\n")
+
+        self.stream.write("\nStart migration\n")
+        call_command(
+            "migrate", interactive=False, verbosity=3, stdout=self.stream, stderr=self.stream
+        )
+        self.stream.write("\nEnd migration\n")
+
+        with redirect_stdout(self.stream), redirect_stderr(self.stream):
+            application = WhiteNoise(django_app, root=settings.PUBLIC_DATA_ROOT)
+            self.server = make_server(self.host, self.port, application)
+            url = f"http://{self.host}:{self.port}"
+            self.stream.write(f"\nStart {url}\n\n")
+            open_new_tab(url)
+            try:
+                self.server.serve_forever()
+            except KeyboardInterrupt:
+                self.stream.write(f"\nStop {url}.\n")
+            finally:
+                self.server.shutdown()
+
+    def stop(self):
+        self.stream.write("\nStop server.\n")
+        if isinstance(self.server, WSGIServer):
+            self.server.shutdown()
+
+
+class AppRunner:
+    LABEL: ClassVar = {True: "Stop BMDS Desktop", False: "Start BMDS Desktop"}
+
+    def __init__(self, app: "BmdsDesktop"):
+        self.app = app
+        self.started = False
+        self.widget = Button(label=self.LABEL[self.started], id="runner-button", variant="primary")
+        self.thread: AppThread | None = None
+
+    def toggle(self):
+        host = self.app.config.host
+        port = self.app.config.port
+        self.started = not self.started
+        self.widget.label = self.LABEL[self.started]
+        if self.started:
+            os.environ["BMDS_HOME"] = self.app.config.path
+            os.environ["BMDS_DB"] = str(Path(self.app.config.path) / "bmds.sqlite3")
+            self.thread = AppThread(
+                stream=self.app.log_app.stream,
+                host=host,
+                port=port,
+                daemon=True,
+            )
+            self.thread.start()
+        else:
+            if self.thread:
+                self.thread.stop()
+                self.thread = None
+
+    def start(self):
+        self.thread.start()
+
+
+class BmdsTabs(Static):
+    def __init__(self, _app: "BmdsDesktop", **kw):
+        self._app = _app
+        super().__init__(**kw)
+
+    def compose(self) -> ComposeResult:
+        with TabbedContent(id="tabs"):
+            with TabPane("Application", classes="app"):
+                yield Container(
+                    self._app.runner.widget,
+                )
+                yield Container(
+                    Label(f"[b]Data folder:[/b]\n  {self._app.config.path}"),
+                    Label(f"[b]Port:[/b]\n  {self._app.config.port}"),
+                    Label(f"[b]Host:[/b]\n  {self._app.config.host}"),
+                    classes="app-box",
+                )
+
+            with TabPane("Logging"):
+                yield self._app.log_app.widget
+
+
+class BmdsDesktop(App):
+    """A Textual app for BMDS."""
+
+    TITLE = f"BMDS Desktop (version {version('bmds_server')})"
+    BINDINGS: ClassVar = [("q", "quit", "Quit"), ("d", "toggle_dark", "Toggle dark mode")]
+    CSS_PATH = "content/app.css"
+
+    def __init__(self, **kw):
+        self.config = DesktopConfig()
+        self.log_app = LogApp(self)
+        self.runner = AppRunner(self)
+        self.tabs = BmdsTabs(self)
+        super().__init__(**kw)
+
+    def compose(self) -> ComposeResult:
+        """Create child widgets for the app."""
+        yield Header()
+        yield ScrollableContainer(
+            Markdown((ROOT / "content/top.md").read_text()), self.tabs, classes="main"
+        )
+        yield Footer()
+
+    @on(Button.Pressed, "#runner-button")
+    def toggle_runner(self):
+        self.runner.toggle()
+
+    def action_quit(self):
+        """Exit the application."""
+        self.exit()
+
+    def action_toggle_dark(self):
+        """An action to toggle dark mode."""
+        self.dark = not self.dark
+
+    def on_mount(self) -> None:
+        self.log_app.start()
+
+
+def main():
+    os.environ["DJANGO_SETTINGS_MODULE"] = "bmds_server.main.settings.desktop"
+    app = BmdsDesktop()
+    app.run()
diff --git a/bmds_server/desktop/content/app.css b/bmds_server/desktop/content/app.css
new file mode 100644
index 00000000..493e72fd
--- /dev/null
+++ b/bmds_server/desktop/content/app.css
@@ -0,0 +1,32 @@
+.main {
+    overflow-y: scroll;
+}
+
+Button {
+    width: 30;
+    height: 5;
+    margin: 1;
+    padding: 1;
+    border: heavy white;
+}
+
+#log {
+    height: 15;
+}
+
+#tabs {
+    margin: 0 5;
+}
+
+.app {
+    layout: horizontal;
+}
+
+.app-box {
+    padding: 0 1;
+    margin: 1;
+    border: double grey;
+    width: 70;
+    height: 10;
+    overflow: auto;
+}
diff --git a/bmds_server/desktop/content/top.md b/bmds_server/desktop/content/top.md
new file mode 100644
index 00000000..0ba34739
--- /dev/null
+++ b/bmds_server/desktop/content/top.md
@@ -0,0 +1,7 @@
+# Welcome to BMDS Desktop.
+
+This application is the desktop launcher for the BMDS Desktop application. From this page, you can start the application, as well as review the logs for the application. We hope that you'll have no need to review the logs, but if there's an issue, it makes it possible to send diagnostics to the application developers, should you wish.
+
+BMDS Desktop runs in your browser, but the data and execution all all performed locally, and no data is sent to any external server. To check, you could disable wifi and confirm that the software should perform without error.
+
+An online application exists: [https://bmdsonline.epa.gov](https://bmdsonline.epa.gov).
diff --git a/bmds_server/main/constants.py b/bmds_server/main/constants.py
index 38752da0..a1d5a17b 100644
--- a/bmds_server/main/constants.py
+++ b/bmds_server/main/constants.py
@@ -1,4 +1,6 @@
+import platform
 from enum import IntEnum, StrEnum
+from pathlib import Path
 
 
 class AuthProvider(StrEnum):
@@ -9,3 +11,16 @@ class AuthProvider(StrEnum):
 class SkinStyle(IntEnum):
     Base = 0
     EPA = 1
+
+
+def get_app_home() -> Path:
+    app_home = Path.home()
+    match platform.system():
+        case "Windows":
+            app_home = app_home / "AppData" / "Roaming" / "bmds"
+        case "Darwin":
+            app_home = app_home / "Library" / "Application Support" / "bmds"
+        case "Linux" | _:
+            app_home = app_home / ".bmds"
+    app_home.mkdir(parents=True, exist_ok=True)
+    return app_home
diff --git a/bmds_server/main/settings/base.py b/bmds_server/main/settings/base.py
index a5a41b55..185610ff 100644
--- a/bmds_server/main/settings/base.py
+++ b/bmds_server/main/settings/base.py
@@ -14,12 +14,10 @@
 
 # data paths
 PUBLIC_DATA_ROOT = Path(os.environ.get("PUBLIC_DATA_ROOT", ROOT_DIR / "public"))
-PRIVATE_DATA_ROOT = Path(os.environ.get("PRIVATE_DATA_ROOT", ROOT_DIR / "private"))
 LOGS_PATH = Path(os.environ.get("LOGS_PATH", ROOT_DIR / "logs"))
 
 # make sure these paths exist
 PUBLIC_DATA_ROOT.mkdir(exist_ok=True, parents=False)
-PRIVATE_DATA_ROOT.mkdir(exist_ok=True, parents=False)
 LOGS_PATH.mkdir(exist_ok=True, parents=False)
 
 SKIN = SkinStyle.Base
diff --git a/bmds_server/main/settings/desktop.py b/bmds_server/main/settings/desktop.py
new file mode 100644
index 00000000..96861993
--- /dev/null
+++ b/bmds_server/main/settings/desktop.py
@@ -0,0 +1,71 @@
+import os
+from pathlib import Path
+
+from ..constants import SkinStyle, get_app_home
+from .base import *  # noqa: F403
+
+APP_HOME = Path(os.getenv("BMDS_HOME") or get_app_home())
+ALLOWED_HOSTS = ["*"]
+IS_DESKTOP = True
+
+SKIN = SkinStyle.EPA
+SERVER_ROLE = "production"
+SERVER_BANNER_COLOR = "black"
+
+PUBLIC_DATA_ROOT = APP_HOME / "public"
+LOGS_PATH = APP_HOME / "logs"
+STATIC_ROOT = PUBLIC_DATA_ROOT / "static"
+MEDIA_ROOT = PUBLIC_DATA_ROOT / "media"
+
+PUBLIC_DATA_ROOT.mkdir(exist_ok=True, parents=False)
+LOGS_PATH.mkdir(exist_ok=True, parents=False)
+
+CELERY_TASK_ALWAYS_EAGER = True
+CELERY_TASK_EAGER_PROPAGATES = True
+
+DATABASES = {
+    "default": {
+        "ENGINE": "django.db.backends.sqlite3",
+        "NAME": os.getenv("BMDS_DB", APP_HOME / "bmds.sqlite3"),
+        "STARTUP_OPTIONS": {"init_command": "PRAGMA journal_mode=wal;"},
+    }
+}
+
+LOGGING = {
+    "version": 1,
+    "disable_existing_loggers": True,
+    "filters": {"require_debug_false": {"()": "django.utils.log.RequireDebugFalse"}},
+    "formatters": {"basic": {"format": "%(levelname)s %(asctime)s %(name)s %(message)s"}},
+    "handlers": {
+        "mail_admins": {
+            "level": "ERROR",
+            "filters": ["require_debug_false"],
+            "class": "django.utils.log.AdminEmailHandler",
+        },
+        "console": {"level": "DEBUG", "class": "logging.StreamHandler", "formatter": "basic"},
+        "file": {
+            "level": "DEBUG",
+            "class": "logging.handlers.RotatingFileHandler",
+            "formatter": "basic",
+            "filename": str(LOGS_PATH / "django.log"),
+            "maxBytes": 10 * 1024 * 1024,  # 10 MB
+            "backupCount": 10,
+        },
+        "requests": {
+            "level": "INFO",
+            "class": "logging.handlers.RotatingFileHandler",
+            "formatter": "basic",
+            "filename": str(LOGS_PATH / "requests.log"),
+            "maxBytes": 10 * 1024 * 1024,  # 10 MB
+            "backupCount": 10,
+        },
+        "null": {"class": "logging.NullHandler"},
+    },
+    "loggers": {
+        "": {"handlers": ["console"], "level": "INFO"},
+        "django": {"handlers": ["console"], "propagate": False, "level": "INFO"},
+        "django.request": {"handlers": ["console"], "level": "ERROR", "propagate": True},
+        "bmds_server": {"handlers": ["console"], "propagate": False, "level": "INFO"},
+        "bmds_server.request": {"handlers": ["console"], "propagate": False, "level": "INFO"},
+    },
+}
diff --git a/bmds_server/main/urls.py b/bmds_server/main/urls.py
index d117aa8b..64a1ef84 100644
--- a/bmds_server/main/urls.py
+++ b/bmds_server/main/urls.py
@@ -27,11 +27,16 @@
 
 urlpatterns = [
     # home
-    path("", views.Home.as_view(), name="home"),
+    path(
+        "",
+        views.DesktopHome.as_view() if settings.IS_DESKTOP else views.Home.as_view(),
+        name="home",
+    ),
     path("history/", views.AnalysisHistory.as_view(), name="analysis_history"),
     # api
     api_paths,
     # analysis
+    path("analysis/create/", views.AnalysisCreate.as_view(), name="analysis_create"),
     path("analysis/<uuid:pk>/", views.AnalysisDetail.as_view(), name="analysis"),
     path(edit_pattern, views.AnalysisDetail.as_view(), name="analysis_edit"),
     path(f"{edit_pattern}renew/", views.AnalysisRenew.as_view(), name="analysis_renew"),
@@ -46,6 +51,22 @@
     path("user/logout/", common_views.AppLogoutView.as_view(), name="logout"),
 ]
 
+if settings.IS_DESKTOP:
+    urlpatterns += [
+        path("collection/", views.CollectionList.as_view(), name="collection_list"),
+        path("collection/create/", views.CollectionCreate.as_view(), name="collection_create"),
+        path(
+            "collection/<int:pk>/update/",
+            views.CollectionUpdate.as_view(),
+            name="collection_update",
+        ),
+        path(
+            "collection/<int:pk>/delete/",
+            views.CollectionDelete.as_view(),
+            name="collection_delete",
+        ),
+    ]
+
 if settings.INCLUDE_BETA_FEATURES:
     urlpatterns += [
         path("transforms/polyk/", views.PolyKAdjustment.as_view(), name="polyk"),
diff --git a/bmds_server/static/css/epa/bmdsonline.css b/bmds_server/static/css/epa/bmdsonline.css
index 002ca722..25d72614 100644
--- a/bmds_server/static/css/epa/bmdsonline.css
+++ b/bmds_server/static/css/epa/bmdsonline.css
@@ -67,3 +67,10 @@ a.dropdown-toggle:not([href])::after {
 .popover-header {
   margin-top: 0;
 }
+
+/* desktop analysis list */
+.analysis-list td {
+  border-left: 0px;
+  border-right: 0px;
+  border-color: #dddddd
+}
diff --git a/bmds_server/static/css/site.css b/bmds_server/static/css/site.css
index c74651f6..2d799db7 100644
--- a/bmds_server/static/css/site.css
+++ b/bmds_server/static/css/site.css
@@ -120,3 +120,14 @@ input[type=number] {
 .bi-lg {
   font-size: 1.2rem;
 }
+
+.starred {
+  color: orange;
+}
+.starred:hover {
+  color: darkorange;
+}
+
+.stretched-link-parent {
+  transform: rotate(0);
+}
diff --git a/bmds_server/templates/base.html b/bmds_server/templates/base.html
index ffbcf096..419a5ecd 100644
--- a/bmds_server/templates/base.html
+++ b/bmds_server/templates/base.html
@@ -33,7 +33,7 @@
     {% endif %}
   {% endcache header %}
 
-  <title>{% block title %}BMDS Online{% endblock title %}</title>
+  <title>{% block title %}BMDS {% if IS_DESKTOP %}Desktop{% else %}Online{% endif %}{% endblock title %}</title>
   {% block extra-head %}
   {% endblock extra-head %}
 
@@ -56,7 +56,7 @@
   {% include "includes/epa/header.html" %}
 {% endif %}
 <section class="main-content clearfix" id="main-content">
-  <div class="container-fluid" style="min-height: 90vh !important;">
+  <div class="container-fluid pt-2" style="min-height: 90vh !important;">
 
   {% if messages %}
     {% for message in messages %}
diff --git a/bmds_server/templates/includes/base/header.html b/bmds_server/templates/includes/base/header.html
index 6546721c..23fa58bf 100644
--- a/bmds_server/templates/includes/base/header.html
+++ b/bmds_server/templates/includes/base/header.html
@@ -1,7 +1,7 @@
 {% load bs4 %}
 
 <nav class="navbar navbar-expand-md navbar-dark bg-dark">
-    <a class="navbar-brand" href="{% url 'home' %}">BMDS Online</a>
+    <a class="navbar-brand" href="{% url 'home' %}">Benchmark Dose Tools (BMDS) {% if IS_DESKTOP %}Desktop{% else %}Online{% endif %}</a>
 
     <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent"
         aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
@@ -10,12 +10,6 @@
 
     <div class="collapse navbar-collapse" id="navbarSupportedContent">
         <ul class="nav navbar-nav ml-auto">
-            <li class="nav-item">
-                <a class="nav-link" href="https://github.com/shapiromatron/bmds-server">{% icon "github mr-1" %}Source code</a>
-            </li>
-            <li class="nav-item">
-                <a class="nav-link" href="http://bmds-server.readthedocs.io/en/latest/">{% icon "book mr-1" %}Documentation</a>
-            </li>
             {% if user.is_staff or debug %}
             <li class="nav-item">
                 <a class="nav-link" href="{% url 'admin:index' %}">{% icon "person-badge mr-1" %}Admin</a>
diff --git a/bmds_server/templates/includes/epa/header.html b/bmds_server/templates/includes/epa/header.html
index 40a97f65..b2da8761 100644
--- a/bmds_server/templates/includes/epa/header.html
+++ b/bmds_server/templates/includes/epa/header.html
@@ -98,7 +98,7 @@
     </div>
 </header>
 <nav class="bmds-header navbar justify-content-between">
-    <h2><a href="{% url 'home' %}">Benchmark Dose Tools (BMDS) Online</a></h2>
+    <h2><a href="{% url 'home' %}">BMDS Desktop</a></h2>
     <ul class="nav text-right">
         {% if user.is_staff %}
         <li class="nav-item">
diff --git a/bmds_server/templates/includes/pagination.html b/bmds_server/templates/includes/pagination.html
new file mode 100644
index 00000000..c753e7d6
--- /dev/null
+++ b/bmds_server/templates/includes/pagination.html
@@ -0,0 +1,19 @@
+{% if page_obj.has_previous or page_obj.has_next %}
+<div class="pagination justify-content-center mb-0">
+    {% if page_obj.has_previous %}
+        <li class="page-item">
+            <a class="page-link" href="?page={{ page_obj.previous_page_number }}">previous</a>
+        </li>
+    {% endif %}
+
+    <li class="page-item disabled">
+        <a class="page-link" href="#">{{ page_obj.number }} of {{ page_obj.paginator.num_pages }}</a>
+    </li>
+
+    {% if page_obj.has_next %}
+        <li class="page-item">
+            <a class="page-link" href="?page={{ page_obj.next_page_number }}">next</a>
+        </li>
+    {% endif %}
+</div>
+{% endif %}
diff --git a/compose/example.env b/compose/example.env
index af69dac9..00823b1e 100644
--- a/compose/example.env
+++ b/compose/example.env
@@ -12,7 +12,6 @@ DJANGO_DB_PW=TZU8NUkThcO5FOMQeLHt-fdKHGDxJ1c5qXUnA1eGL0g
 # django
 LOGS_PATH=/app/logs
 PUBLIC_DATA_ROOT=/app/public
-PRIVATE_DATA_ROOT=/app/public
 DJANGO_SETTINGS_MODULE=bmds_server.main.settings.production
 DJANGO_ALLOWED_HOSTS=*
 DJANGO_CSRF_TRUSTED_ORIGINS=https://example.com
diff --git a/frontend/src/App.js b/frontend/src/App.js
index e1ed11b7..169d88c3 100644
--- a/frontend/src/App.js
+++ b/frontend/src/App.js
@@ -19,8 +19,9 @@ class App extends Component {
         autorun(() => {
             const {analysis_name, canEdit} = this.props.mainStore,
                 verb = canEdit ? "Update Analysis" : "Analysis",
-                name = analysis_name ? analysis_name : "";
-            document.title = ["BMDS Online", verb, name].join(" | ");
+                name = analysis_name ? analysis_name : "",
+                app_name = this.props.mainStore.config.is_desktop ? "BMDS Desktop" : "BMDS Online";
+            document.title = [app_name, verb, name].join(" | ");
         });
     }
     render() {
@@ -38,7 +39,7 @@ class App extends Component {
                     {getHeader()}
                     {isFuture ? (
                         <span
-                            className="badge badge-dark px-4 mx-3"
+                            className="badge badge-dark ml-3"
                             title="Future mode: content under active development">
                             <Icon name="lightning-fill" />
                             &nbsp;FUTURE MODE&nbsp;
diff --git a/frontend/src/components/Main/Actions/Actions.js b/frontend/src/components/Main/Actions/Actions.js
index b4b8d9b7..2411111f 100644
--- a/frontend/src/components/Main/Actions/Actions.js
+++ b/frontend/src/components/Main/Actions/Actions.js
@@ -5,6 +5,7 @@ import React, {Component} from "react";
 
 import Button from "../../common/Button";
 import Icon from "../../common/Icon";
+import CollectionForm from "./CollectionForm";
 
 const getDeletionDateText = function(editSettings) {
     const date = editSettings.deleteDateStr,
@@ -106,6 +107,13 @@ class Actions extends Component {
                     ) : (
                         <p className="text-muted pl-4 mb-0">Please save and execute analysis.</p>
                     )}
+                    {mainStore.isDesktop ? (
+                        <>
+                            <div className="dropdown-divider"></div>
+                            <span className="dropdown-header">Collections</span>
+                            <CollectionForm />
+                        </>
+                    ) : null}
                 </div>
             </div>
         );
diff --git a/frontend/src/components/Main/Actions/CollectionForm.js b/frontend/src/components/Main/Actions/CollectionForm.js
new file mode 100644
index 00000000..f06af335
--- /dev/null
+++ b/frontend/src/components/Main/Actions/CollectionForm.js
@@ -0,0 +1,53 @@
+import {inject, observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+import Button from "../../common/Button";
+
+@inject("mainStore")
+@observer
+class CollectionForm extends Component {
+    constructor(props) {
+        super(props);
+        this.state = {selected: props.mainStore.collectionDefaultValues};
+    }
+    render() {
+        const {mainStore} = this.props,
+            {collectionDefaultValues} = mainStore,
+            {collections} = mainStore.config.editSettings;
+
+        if (!mainStore.canEdit || !mainStore.isDesktop) {
+            return null;
+        }
+
+        return (
+            <form className="px-3">
+                <select
+                    multiple
+                    className="form-control"
+                    defaultValue={collectionDefaultValues}
+                    onChange={e =>
+                        this.setState({
+                            selected: Array.from(e.target.selectedOptions, d => parseInt(d.value)),
+                        })
+                    }>
+                    {collections.map(d => (
+                        <option key={d.id} value={d.id}>
+                            {d.name}
+                        </option>
+                    ))}
+                </select>
+                <Button
+                    className="btn btn-primary btn-block btn-sm mt-1"
+                    onClick={() => mainStore.collectionsToggle(this.state.selected)}
+                    icon={"check-circle-fill"}
+                    text="Apply"
+                />
+            </form>
+        );
+    }
+}
+CollectionForm.propTypes = {
+    mainStore: PropTypes.object,
+};
+export default CollectionForm;
diff --git a/frontend/src/components/Main/Actions/Starred.js b/frontend/src/components/Main/Actions/Starred.js
new file mode 100644
index 00000000..bd8d056a
--- /dev/null
+++ b/frontend/src/components/Main/Actions/Starred.js
@@ -0,0 +1,35 @@
+import {inject, observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+import Button from "../../common/Button";
+
+@inject("mainStore")
+@observer
+class Starred extends Component {
+    render() {
+        const {mainStore} = this.props,
+            {starred} = mainStore,
+            icon = starred ? "star-fill" : "star",
+            title = starred ? "Remove star" : "Add star";
+
+        if (!mainStore.canEdit || !mainStore.isDesktop) {
+            return null;
+        }
+
+        return (
+            <li className="nav-item mr-1">
+                <Button
+                    className="btn starred"
+                    onClick={mainStore.starToggle}
+                    icon={icon}
+                    title={title}
+                />
+            </li>
+        );
+    }
+}
+Starred.propTypes = {
+    mainStore: PropTypes.object,
+};
+export default Starred;
diff --git a/frontend/src/components/Main/AnalysisForm/AnalysisForm.js b/frontend/src/components/Main/AnalysisForm/AnalysisForm.js
index ef06fec1..fc87d11a 100644
--- a/frontend/src/components/Main/AnalysisForm/AnalysisForm.js
+++ b/frontend/src/components/Main/AnalysisForm/AnalysisForm.js
@@ -8,6 +8,7 @@ import SelectInput from "../../common/SelectInput";
 import Spinner from "../../common/Spinner";
 import TextAreaInput from "../../common/TextAreaInput";
 import TextInput from "../../common/TextInput";
+import CollectionList from "./CollectionList";
 
 @observer
 class RunChecklist extends Component {
@@ -43,6 +44,7 @@ class AnalysisForm extends Component {
                             value={mainStore.analysis_name}
                             onChange={mainStore.changeAnalysisName}
                         />
+                        <CollectionList />
                     </div>
                     <div className="form-group">
                         <TextAreaInput
diff --git a/frontend/src/components/Main/AnalysisForm/CollectionList.js b/frontend/src/components/Main/AnalysisForm/CollectionList.js
new file mode 100644
index 00000000..8067f9e4
--- /dev/null
+++ b/frontend/src/components/Main/AnalysisForm/CollectionList.js
@@ -0,0 +1,29 @@
+import {inject, observer} from "mobx-react";
+import PropTypes from "prop-types";
+import React, {Component} from "react";
+
+@inject("mainStore")
+@observer
+class CollectionList extends Component {
+    render() {
+        const {collections} = this.props.mainStore;
+
+        if (collections.length == 0) {
+            return null;
+        }
+
+        return (
+            <div className="">
+                {collections.map(d => (
+                    <span className="badge badge-info ml-2" key={d.id}>
+                        {d.name}
+                    </span>
+                ))}
+            </div>
+        );
+    }
+}
+CollectionList.propTypes = {
+    mainStore: PropTypes.object,
+};
+export default CollectionList;
diff --git a/frontend/src/components/Navigation.js b/frontend/src/components/Navigation.js
index d5294b99..0407d214 100644
--- a/frontend/src/components/Navigation.js
+++ b/frontend/src/components/Navigation.js
@@ -7,6 +7,7 @@ import DataTab from "./Data/DataTab";
 import LogicRoot from "./Logic/LogicRoot";
 import Actions from "./Main/Actions/Actions";
 import ShareActions from "./Main/Actions/ShareActions";
+import Starred from "./Main/Actions/Starred";
 import StatusToast from "./Main/Actions/StatusToast";
 import WordReportOptionsModal from "./Main/Actions/WordReportOptionsModal";
 import Main from "./Main/Main";
@@ -44,12 +45,11 @@ class Navigation extends Component {
                         </li>
                     )}
                     {mainStore.canEdit && !mainStore.isDesktop ? (
-                        <li className="nav-item ml-auto mr-1">
-                            <ShareActions />
-                        </li>
+                        <li className="nav-item ml-auto mr-1">{<ShareActions />}</li>
                     ) : (
                         <span className="ml-auto"></span>
                     )}
+                    <Starred />
                     <li
                         className={mainStore.canEdit ? "nav-item" : "nav-item ml-auto"}
                         style={{position: "relative"}}>
diff --git a/frontend/src/stores/MainStore.js b/frontend/src/stores/MainStore.js
index dc3280a9..d991f65d 100644
--- a/frontend/src/stores/MainStore.js
+++ b/frontend/src/stores/MainStore.js
@@ -253,6 +253,8 @@ class MainStore {
         this.rootStore.dataOptionStore.setDatasetOptions(inputs.dataset_options);
         this.rootStore.modelsStore.setModels(inputs.models);
         this.rootStore.logicStore.setLogic(inputs.recommender);
+        this.starred = data.starred;
+        this.collections = data.collections;
         this.isUpdateComplete = true;
         this.analysisSavedAndValidated = data.inputs_valid;
     }
@@ -413,6 +415,59 @@ class MainStore {
         this.downloadReport("wordUrl");
     }
     // *** END REPORT OPTIONS ***
+
+    // *** STAR/UNSTAR ***
+    @observable starred = false;
+    @action.bound
+    async starToggle() {
+        const {csrfToken, starUrl} = this.config.editSettings;
+        await fetch(starUrl, {
+            method: "POST",
+            mode: "cors",
+            headers: getHeaders(csrfToken),
+            body: JSON.stringify({
+                editKey: this.config.editSettings.editKey,
+            }),
+        })
+            .then(response => response.json())
+            .then(data => {
+                this.starred = data.starred;
+            })
+            .catch(error => {
+                this.errorMessage = error;
+                console.error("error", error);
+            });
+    }
+    // *** STAR/UNSTAR ***
+
+    // *** COLLECTIONS ***
+    @observable collections = [];
+    @computed
+    get collectionDefaultValues() {
+        return this.collections.map(d => d.id);
+    }
+    @action.bound
+    async collectionsToggle(collections) {
+        const {csrfToken, collectionUrl} = this.config.editSettings;
+        await fetch(collectionUrl, {
+            method: "POST",
+            mode: "cors",
+            headers: getHeaders(csrfToken),
+            body: JSON.stringify({
+                editKey: this.config.editSettings.editKey,
+                collections,
+            }),
+        })
+            .then(response => response.json())
+            .then(data => {
+                this.collections = data.collections;
+            })
+            .catch(error => {
+                this.errorMessage = error;
+                console.error("error", error);
+            });
+    }
+    // *** COLLECTIONS ***
 }
 
 export default MainStore;
diff --git a/requirements/base.txt b/requirements/base.txt
index 1269f79e..816a224e 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -18,3 +18,7 @@ celery==5.3.4
 
 plotly==5.18.0
 redis==5.0.1
+
+# desktop
+textual==0.45.1
+whitenoise==6.6.0
diff --git a/setup.cfg b/setup.cfg
index 1b630918..6d7eafde 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = bmds_server
-version = 2023.03
+version = 2023.12a1
 description = A service designed to run the USEPA benchmark dose modeling software
 long_description = file: README.rst
 author = Andy Shapiro
@@ -14,7 +14,23 @@ classifiers =
 zip_safe = False
 include_package_data = True
 packages = find:
-requires-python = ">=3.11"
+requires_python = ">=3.11"
+install_requires =
+    Django~=4.2.7
+    django-webpack-loader~=2.0.1
+    djangorestframework~=3.14.0
+    uritemplate~=4.1.1
+    PyYAML~=6.0.1
+    django-reversion~=5.0.6
+    celery~=5.3.4
+    billiard~=4.1.0
+    kombu~=5.3.2
+    plotly~=5.18.0
+    redis~=5.0.1
+    django-anymail~=10.2
+    django-redis~=5.4.0
+    textual~=0.45.1
+    whitenoise~=6.6.0
 
 [options.package_data]
 * =
@@ -26,7 +42,8 @@ requires-python = ">=3.11"
 console_scripts =
     manage.py = bmds_server:manage
     manage = bmds_server:manage
-    bmds = bmds_server:manage
+    bmds = bmds_server.desktop.cli:main
+    bmdsdesktop = bmds_server.desktop.cli:main
 
 [tool:pytest]
 norecursedirs = .git .tox docs static templates
diff --git a/tests/analysis/test_views.py b/tests/analysis/test_views.py
index b62fe27b..ff1ef096 100644
--- a/tests/analysis/test_views.py
+++ b/tests/analysis/test_views.py
@@ -61,12 +61,15 @@ def test_context(self):
                 "editKey": pw,
                 "viewUrl": f"http://testserver/analysis/{pk}/",
                 "editUrl": f"http://testserver/analysis/{pk}/{pw}/",
+                "starUrl": "http://testserver/api/v1/analysis/cc3ca355-a57a-4fba-9dc3-99657562df68/star/",
+                "collectionUrl": "http://testserver/api/v1/analysis/cc3ca355-a57a-4fba-9dc3-99657562df68/collections/",
                 "patchInputUrl": f"/api/v1/analysis/{pk}/patch-inputs/",
                 "renewUrl": f"http://testserver/analysis/{pk}/{pw}/renew/",
                 "deleteUrl": f"http://testserver/analysis/{pk}/{pw}/delete/",
                 "executeUrl": f"/api/v1/analysis/{pk}/execute/",
                 "executeResetUrl": f"/api/v1/analysis/{pk}/execute-reset/",
                 "deleteDateStr": "June 14, 2022",
+                "collections": [],
             },
         }
 
diff --git a/tests/data/db.yaml b/tests/data/db.yaml
index db6e52dc..e5f6cc52 100644
--- a/tests/data/db.yaml
+++ b/tests/data/db.yaml
@@ -5089,7 +5089,7 @@
         R, or Java. To take\n                    advantage of automation, use the
         <a href=\"/api/v1/\">API</a>,\n                    and see the <a href=\"http://bmds-server.readthedocs.io/en/latest/quickstart.html\">quickstart</a>
         section.\n                </li>\n            </ul>\n        </div>\n    </div>\n
-        \   <div class=\"col-md-4\">\n        <form method=\"post\">\n            {%
+        \   <div class=\"col-md-4\">\n        <form  action=\"{% url 'analysis_create' %}\" method=\"post\">\n            {%
         csrf_token %}\n            <label for=\"id_id\">Create a new analysis:</label>\n
         \           <button type=\"submit\" class=\"btn btn-primary btn-block mb-1\">Create
         a new BMDS analysis</button>\n            <p class=\"text-muted\">Analyses
diff --git a/tests/integration/test_integration.py b/tests/integration/test_integration.py
index dd490541..e435ce92 100644
--- a/tests/integration/test_integration.py
+++ b/tests/integration/test_integration.py
@@ -244,11 +244,16 @@ def test_multi_tumor(self):
             # view output summary tables
             page.locator('a:has-text("Output")').click()
 
-            # check one result
-            page.get_by_role("link", name="Multistage Cancer / Multitumor").click()
+            # check one result (multitumor)
+            page.get_by_role("link", name="Multitumor").click()
             expect(page.get_by_role("dialog")).to_contain_text("MS Combo")
             page.locator("#close-modal").click()
 
+            # check one result (individual)
+            page.get_by_role("link", name="Multistage 1°*").click()
+            expect(page.get_by_role("dialog")).to_contain_text("Multistage 1°")
+            page.locator("#close-modal").click()
+
             # Read-only
             page.get_by_role("button", name="Share").click()
             with page.expect_popup() as page2_info:

From a86f2abf449fc19cddbe44f237dd598c7e702640 Mon Sep 17 00:00:00 2001
From: hausman-gdit <karen.hausman@gdit.com>
Date: Mon, 18 Dec 2023 14:35:22 -0500
Subject: [PATCH 18/24] 2, 6

---
 frontend/src/components/Main/OptionsForm/OptionsFormList.js | 2 +-
 frontend/src/components/Output/BayesianResultTable.js       | 4 ++--
 frontend/src/components/Output/FrequentistResultTable.js    | 4 ++--
 frontend/src/components/Output/Multitumor/ResultTable.js    | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/frontend/src/components/Main/OptionsForm/OptionsFormList.js b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
index 075cafea..fc93fe5e 100644
--- a/frontend/src/components/Main/OptionsForm/OptionsFormList.js
+++ b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
@@ -37,7 +37,7 @@ class OptionsFormList extends Component {
                                             <th>BMR Type</th>
                                             <th>BMRF</th>
                                             <th>Tail Probability</th>
-                                            <th>Confidence Level</th>
+                                            <th>Confidence Level (one-sided)</th>
                                             <th>
                                                 Distribution +<br />
                                                 Variance&nbsp;
diff --git a/frontend/src/components/Output/BayesianResultTable.js b/frontend/src/components/Output/BayesianResultTable.js
index b71d7eaa..99a3aaaa 100644
--- a/frontend/src/components/Output/BayesianResultTable.js
+++ b/frontend/src/components/Output/BayesianResultTable.js
@@ -36,8 +36,8 @@ class BayesianResultTable extends Component {
                         <th>BMD</th>
                         <th>BMDU</th>
                         <th>Unnormalized Log Posterior Probability</th>
-                        <th>Scaled Residual for Dose Group near BMD</th>
-                        <th>Scaled Residual for Control Dose Group</th>
+                        <th>Scaled Residual at Control</th>
+                        <th>Scaled Residual near BMD</th>
                     </tr>
                 </thead>
                 <tbody className="table-bordered">
diff --git a/frontend/src/components/Output/FrequentistResultTable.js b/frontend/src/components/Output/FrequentistResultTable.js
index ae3a8bdc..ee120927 100644
--- a/frontend/src/components/Output/FrequentistResultTable.js
+++ b/frontend/src/components/Output/FrequentistResultTable.js
@@ -326,8 +326,8 @@ class FrequentistResultTable extends Component {
                             <i>P</i>-Value
                         </th>
                         <th>AIC</th>
-                        <th>Scaled Residual for Dose Group near BMD</th>
-                        <th>Scaled Residual for Control Dose Group</th>
+                        <th>Scaled Residual at Control</th>
+                        <th>Scaled Residual near BMD</th>
                         {store.recommendationEnabled ? (
                             <th>
                                 <Button
diff --git a/frontend/src/components/Output/Multitumor/ResultTable.js b/frontend/src/components/Output/Multitumor/ResultTable.js
index ce51c436..d96e542b 100644
--- a/frontend/src/components/Output/Multitumor/ResultTable.js
+++ b/frontend/src/components/Output/Multitumor/ResultTable.js
@@ -41,8 +41,8 @@ class ResultTable extends Component {
                             <i>P</i>-Value
                         </th>
                         <th>AIC</th>
-                        <th>Scaled Residual for Dose Group near BMD</th>
-                        <th>Scaled Residual for Control Dose Group</th>
+                        <th>Scaled Residual at Control</th>
+                        <th>Scaled Residual near BMD</th>
                     </tr>
                 </thead>
                 <tbody className="table-bordered">

From 1a878ea355a7e5076ced0b469219cc7313965891 Mon Sep 17 00:00:00 2001
From: hausman-gdit <karen.hausman@gdit.com>
Date: Tue, 19 Dec 2023 09:42:47 -0500
Subject: [PATCH 19/24] Revert "2, 6"

This reverts commit c8ecff526e07ac939bb8be7c41c222be0ea7b2d4.
---
 frontend/src/components/Main/OptionsForm/OptionsFormList.js | 2 +-
 frontend/src/components/Output/BayesianResultTable.js       | 4 ++--
 frontend/src/components/Output/FrequentistResultTable.js    | 4 ++--
 frontend/src/components/Output/Multitumor/ResultTable.js    | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/frontend/src/components/Main/OptionsForm/OptionsFormList.js b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
index fc93fe5e..075cafea 100644
--- a/frontend/src/components/Main/OptionsForm/OptionsFormList.js
+++ b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
@@ -37,7 +37,7 @@ class OptionsFormList extends Component {
                                             <th>BMR Type</th>
                                             <th>BMRF</th>
                                             <th>Tail Probability</th>
-                                            <th>Confidence Level (one-sided)</th>
+                                            <th>Confidence Level</th>
                                             <th>
                                                 Distribution +<br />
                                                 Variance&nbsp;
diff --git a/frontend/src/components/Output/BayesianResultTable.js b/frontend/src/components/Output/BayesianResultTable.js
index 99a3aaaa..b71d7eaa 100644
--- a/frontend/src/components/Output/BayesianResultTable.js
+++ b/frontend/src/components/Output/BayesianResultTable.js
@@ -36,8 +36,8 @@ class BayesianResultTable extends Component {
                         <th>BMD</th>
                         <th>BMDU</th>
                         <th>Unnormalized Log Posterior Probability</th>
-                        <th>Scaled Residual at Control</th>
-                        <th>Scaled Residual near BMD</th>
+                        <th>Scaled Residual for Dose Group near BMD</th>
+                        <th>Scaled Residual for Control Dose Group</th>
                     </tr>
                 </thead>
                 <tbody className="table-bordered">
diff --git a/frontend/src/components/Output/FrequentistResultTable.js b/frontend/src/components/Output/FrequentistResultTable.js
index ee120927..ae3a8bdc 100644
--- a/frontend/src/components/Output/FrequentistResultTable.js
+++ b/frontend/src/components/Output/FrequentistResultTable.js
@@ -326,8 +326,8 @@ class FrequentistResultTable extends Component {
                             <i>P</i>-Value
                         </th>
                         <th>AIC</th>
-                        <th>Scaled Residual at Control</th>
-                        <th>Scaled Residual near BMD</th>
+                        <th>Scaled Residual for Dose Group near BMD</th>
+                        <th>Scaled Residual for Control Dose Group</th>
                         {store.recommendationEnabled ? (
                             <th>
                                 <Button
diff --git a/frontend/src/components/Output/Multitumor/ResultTable.js b/frontend/src/components/Output/Multitumor/ResultTable.js
index d96e542b..ce51c436 100644
--- a/frontend/src/components/Output/Multitumor/ResultTable.js
+++ b/frontend/src/components/Output/Multitumor/ResultTable.js
@@ -41,8 +41,8 @@ class ResultTable extends Component {
                             <i>P</i>-Value
                         </th>
                         <th>AIC</th>
-                        <th>Scaled Residual at Control</th>
-                        <th>Scaled Residual near BMD</th>
+                        <th>Scaled Residual for Dose Group near BMD</th>
+                        <th>Scaled Residual for Control Dose Group</th>
                     </tr>
                 </thead>
                 <tbody className="table-bordered">

From ee3a6e3ac1b52ef28b176497ef901bebb1f7b6c7 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Thu, 1 Feb 2024 09:45:22 -0500
Subject: [PATCH 20/24] Run tests in CI (#5)

* attempt to run tests in cicd

* add PAT

* update coverage reporting

* add coverage report to gitignore
---
 .github/workflows/main.yml | 9 ++++-----
 .gitignore                 | 1 +
 Makefile                   | 5 +++++
 pyproject.toml             | 1 +
 4 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 2eb237e0..2bbf609f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -24,10 +24,10 @@ jobs:
     - name: Checkout bmds@next
       uses: actions/checkout@v3
       with:
-        repository: shapiromatron/bmds
+        repository: USEPA/bmds-private
         path: venv
         ref: next
-        lfs: true
+        token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v4
       with:
         python-version: '3.11'
@@ -71,7 +71,6 @@ jobs:
       run: |
         export "LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH"
         coverage run -m pytest --vcr-record=none
-        coverage html -d coverage_report
         echo "# Python coverage report" >> $GITHUB_STEP_SUMMARY
         coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
 
@@ -145,10 +144,10 @@ jobs:
     - name: Checkout bmds@next
       uses: actions/checkout@v3
       with:
-        repository: shapiromatron/bmds
+        repository: USEPA/bmds-private
         path: venv
         ref: next
-        lfs: true
+        token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v4
       with:
         python-version: '3.11'
diff --git a/.gitignore b/.gitignore
index b2cf8135..3736182e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@
 bmds_server/static/bundles/
 build/
 /data/
+coverage_report/
 dist/
 docs/site/
 node_modules/
diff --git a/Makefile b/Makefile
index 73821d28..cd051965 100644
--- a/Makefile
+++ b/Makefile
@@ -56,6 +56,11 @@ test-integration-debug:  ## Run integration tests in debug mode (requires npm ru
 	@playwright install --with-deps chromium
 	@INTEGRATION_TESTS=1 PWDEBUG=1 py.test -sv tests/integration/
 
+coverage: ## Run test coverage
+	coverage run -m pytest
+	coverage html -d coverage_report
+	$(BROWSER) coverage_report/index.html
+
 docs: ## Build documentation
 	cd docs; mkdocs build --strict
 
diff --git a/pyproject.toml b/pyproject.toml
index 44fe2e9d..c13a9230 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,6 @@
 [tool.coverage.run]
 omit = [
+    "../bmds/*",
     "./bmds_server/main/settings/*",
     "./tests/*",
     "./venv/*",

From 31bac6a5debc177e7469008e3bea94cebd35c558 Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Thu, 1 Feb 2024 10:16:28 -0500
Subject: [PATCH 21/24] 324 random bootstrap seed (#1)

* set seed on dataset select & add options

* attempt to run tests in cicd

* add PAT

* update coverage reporting

* add coverage report to gitignore

* refactor - only set bootstrap_seed for nested dichotomous

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 frontend/src/stores/OptionsStore.js | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/frontend/src/stores/OptionsStore.js b/frontend/src/stores/OptionsStore.js
index 420a10ce..2d5766fb 100644
--- a/frontend/src/stores/OptionsStore.js
+++ b/frontend/src/stores/OptionsStore.js
@@ -1,29 +1,37 @@
 import _ from "lodash";
 import {action, computed, observable} from "mobx";
 
-import {MODEL_CONTINUOUS} from "@/constants/mainConstants";
+import {MODEL_CONTINUOUS, MODEL_NESTED_DICHOTOMOUS} from "@/constants/mainConstants";
 import * as constant from "@/constants/optionsConstants";
 
+const createOption = modelType => {
+    const option = _.cloneDeep(constant.options[modelType]);
+    if (modelType == MODEL_NESTED_DICHOTOMOUS) {
+        // set seed to random number
+        option.bootstrap_seed = Math.ceil(Math.random() * 1000);
+    }
+    return option;
+};
+
 class OptionsStore {
     constructor(rootStore) {
         this.rootStore = rootStore;
     }
 
     @observable optionsList = [];
+
     @computed get canEdit() {
         return this.rootStore.mainStore.canEdit;
     }
 
     @action.bound setDefaultsByDatasetType(force) {
         if (this.optionsList.length === 0 || force) {
-            const option = _.cloneDeep(constant.options[this.getModelType]);
-            this.optionsList = [option];
+            this.optionsList = [createOption(this.getModelType)];
         }
     }
 
     @action.bound addOptions() {
-        const option = _.cloneDeep(constant.options[this.getModelType]);
-        this.optionsList.push(option);
+        this.optionsList.push(createOption(this.getModelType));
         this.rootStore.mainStore.setInputsChangedFlag();
     }
 
@@ -40,6 +48,7 @@ class OptionsStore {
         this.optionsList.splice(val, 1);
         this.rootStore.mainStore.setInputsChangedFlag();
     }
+
     @action.bound setOptions(options) {
         this.optionsList = options;
         this.setDefaultsByDatasetType();
@@ -48,6 +57,7 @@ class OptionsStore {
     @computed get getModelType() {
         return this.rootStore.mainStore.model_type;
     }
+
     @computed get maxItems() {
         return this.rootStore.mainStore.isDesktop
             ? 1000
@@ -55,6 +65,7 @@ class OptionsStore {
             ? 3
             : 6;
     }
+
     @computed get canAddNewOption() {
         return this.optionsList.length < this.maxItems;
     }

From c29ace3996de303cd11966580a843ca4587e7dde Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Wed, 7 Feb 2024 10:10:03 -0500
Subject: [PATCH 22/24] 328 improve error message (#4)

* set seed on dataset select & add options

* basic functionality

* move to utils, test, add node

* attempt to run tests in cicd

* add PAT

* update coverage reporting

* add coverage report to gitignore

* refactor - only set bootstrap_seed for nested dichotomous

* refactorings

* tweak

* standardize server error parsing

* remove

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 frontend/src/common.js                        |  17 --
 .../Main/AnalysisForm/AnalysisForm.js         |   6 +-
 .../src/components/common/ErrorMessage.js     |   6 +-
 frontend/src/stores/DataStore.js              |   2 +-
 frontend/src/stores/MainStore.js              |  14 +-
 frontend/src/utils/parsers.js                 |  73 +++++++++
 frontend/tests/helpers.js                     |   4 +
 frontend/tests/utils/parsers.test.js          | 148 ++++++++++++++++++
 8 files changed, 241 insertions(+), 29 deletions(-)
 create mode 100644 frontend/src/utils/parsers.js
 create mode 100644 frontend/tests/utils/parsers.test.js

diff --git a/frontend/src/common.js b/frontend/src/common.js
index 7626d0a4..76d9c166 100644
--- a/frontend/src/common.js
+++ b/frontend/src/common.js
@@ -28,21 +28,4 @@ export const simulateClick = function(el) {
     },
     getLabel = function(value, mapping) {
         return _.find(mapping, d => d.value == value).label;
-    },
-    parseErrors = errorText => {
-        let errors = [],
-            textErrors = [];
-        try {
-            errors = JSON.parse(errorText);
-        } catch {
-            console.error("Cannot parse error response");
-            return {errors, textErrors};
-        }
-        textErrors = errors.map(error => {
-            if (error.loc && error.msg) {
-                return `${error.loc[0]}: ${error.msg}`;
-            }
-            return JSON.stringify(error);
-        });
-        return {errors, textErrors};
     };
diff --git a/frontend/src/components/Main/AnalysisForm/AnalysisForm.js b/frontend/src/components/Main/AnalysisForm/AnalysisForm.js
index fc87d11a..91ac80d5 100644
--- a/frontend/src/components/Main/AnalysisForm/AnalysisForm.js
+++ b/frontend/src/components/Main/AnalysisForm/AnalysisForm.js
@@ -3,6 +3,7 @@ import PropTypes from "prop-types";
 import React, {Component} from "react";
 
 import Button from "../../common/Button";
+import ErrorMessage from "../../common/ErrorMessage";
 import Icon from "../../common/Icon";
 import SelectInput from "../../common/SelectInput";
 import Spinner from "../../common/Spinner";
@@ -63,10 +64,7 @@ class AnalysisForm extends Component {
                             choices={mainStore.getModelTypeChoices}
                         />
                     </div>
-
-                    {mainStore.errorMessage ? (
-                        <div className="alert alert-danger">{mainStore.errorMessage}</div>
-                    ) : null}
+                    <ErrorMessage error={mainStore.errorMessage} />
                     <div id="controlPanel" className="card bg-light">
                         {mainStore.isExecuting ? (
                             <div className="card-body">
diff --git a/frontend/src/components/common/ErrorMessage.js b/frontend/src/components/common/ErrorMessage.js
index ef8a50f9..b89795a7 100644
--- a/frontend/src/components/common/ErrorMessage.js
+++ b/frontend/src/components/common/ErrorMessage.js
@@ -5,7 +5,11 @@ const ErrorMessage = ({error}) => {
     if (!error) {
         return null;
     }
-    return <p className="text-danger mb-1">{error}</p>;
+    return (
+        <div className="alert alert-danger mb-3">
+            <pre className="text-wrap mb-0">{error}</pre>
+        </div>
+    );
 };
 ErrorMessage.propTypes = {
     error: PropTypes.string,
diff --git a/frontend/src/stores/DataStore.js b/frontend/src/stores/DataStore.js
index 7f8c791b..99621e25 100644
--- a/frontend/src/stores/DataStore.js
+++ b/frontend/src/stores/DataStore.js
@@ -204,7 +204,7 @@ class DataStore {
 
     @computed get selectedDatasetErrorText() {
         const data = this.selectedDatasetErrors;
-        return _.isArray(data) ? data.map(el => el.msg).join(", ") : "";
+        return this.selectedDatasetErrors ? _.uniq(data.map(el => el.msg)).join("\n") : "";
     }
 
     @computed get getMappedArray() {
diff --git a/frontend/src/stores/MainStore.js b/frontend/src/stores/MainStore.js
index d991f65d..ccff27ca 100644
--- a/frontend/src/stores/MainStore.js
+++ b/frontend/src/stores/MainStore.js
@@ -3,8 +3,9 @@ import _ from "lodash";
 import {action, computed, observable, toJS} from "mobx";
 import slugify from "slugify";
 
-import {getHeaders, parseErrors, simulateClick} from "@/common";
+import {getHeaders, simulateClick} from "@/common";
 import * as mc from "@/constants/mainConstants";
+import {parseServerErrors} from "@/utils/parsers";
 
 class MainStore {
     constructor(rootStore) {
@@ -101,9 +102,9 @@ class MainStore {
                     response.json().then(data => this.updateModelStateFromApi(data));
                 } else {
                     response.json().then(errorText => {
-                        const {errors, textErrors} = parseErrors(errorText);
-                        this.errorMessage = textErrors.join(", ");
-                        this.errorData = errors;
+                        const error = parseServerErrors(errorText);
+                        this.errorMessage = error.message;
+                        this.errorData = error.data;
                     });
                 }
             })
@@ -227,8 +228,9 @@ class MainStore {
         this.analysisSavedAndValidated = false;
     }
     @action.bound updateModelStateFromApi(data) {
-        if (data.errors.length > 0) {
-            this.errorMessage = data.errors;
+        const errors = parseServerErrors(data.errors);
+        if (errors) {
+            this.errorMessage = errors.message;
             this.isUpdateComplete = true;
         }
 
diff --git a/frontend/src/utils/parsers.js b/frontend/src/utils/parsers.js
new file mode 100644
index 00000000..6e39aa70
--- /dev/null
+++ b/frontend/src/utils/parsers.js
@@ -0,0 +1,73 @@
+import _ from "lodash";
+
+export const parseServerErrors = errors => {
+        // parse errors from server response. They may come in a variety of formats, so we always
+        // want to show at least an error message if we cannot parse into a better format
+
+        if (_.isEmpty(errors)) {
+            return null;
+        }
+
+        let errorWasParsed = false;
+
+        const container = {
+            data: [],
+            messages: [],
+            message: "",
+        };
+
+        console.warn(`Complete errors:\n\n ${errors}`);
+
+        if (Array.isArray(errors)) {
+            errors.map(error => {
+                if (typeof error === "string") {
+                    const lower = error.toLowerCase();
+                    if (lower.includes("pydantic")) {
+                        errorWasParsed = true;
+                        const msg = JSON.parse(error);
+                        container.data.push(...msg);
+                        container.messages.push(...parsePydanticError(msg));
+                    } else if (lower.includes("traceback")) {
+                        errorWasParsed = true;
+                        container.data.push(error);
+                        container.messages.push(extractErrorFromTraceback(error));
+                    }
+                }
+            });
+        }
+
+        if (!errorWasParsed) {
+            container.data.push(errors);
+            container.messages.push("An error has occurred");
+        }
+
+        // return a single unique set of messages as a single string. This is used in the UI
+        container.message = _.uniq(container.messages)
+            .join("\n")
+            .trim();
+
+        return container;
+    },
+    parsePydanticError = errors => {
+        return errors
+            .map(error => {
+                if (error.loc && error.msg) {
+                    return `${error.loc[0]}: ${error.msg}`;
+                }
+                return JSON.stringify(error);
+            })
+            .sort();
+    },
+    extractErrorFromTraceback = error => {
+        // if this is a traceback from python just return the last line
+        if (!error.includes("Traceback")) {
+            return error;
+        }
+        const lines = error.trim().split("\n"),
+            line = lines[lines.length - 1],
+            colonIndex = line.indexOf(":");
+        if (colonIndex >= 0) {
+            return line.substring(colonIndex + 1).trim();
+        }
+        return line;
+    };
diff --git a/frontend/tests/helpers.js b/frontend/tests/helpers.js
index 7100f5c4..8051c156 100644
--- a/frontend/tests/helpers.js
+++ b/frontend/tests/helpers.js
@@ -8,9 +8,13 @@ const isClose = function(actual, expected, atol) {
         _.zip(actual, expected).map(d => {
             isClose(d[0], d[1], atol);
         });
+    },
+    allEqual = function(actual, expected) {
+        _.zip(actual, expected).map(d => d[0] === d[1]);
     };
 
 assert.isClose = isClose;
 assert.allClose = allClose;
+assert.allEqual = allEqual;
 
 export default assert;
diff --git a/frontend/tests/utils/parsers.test.js b/frontend/tests/utils/parsers.test.js
new file mode 100644
index 00000000..9e9869a5
--- /dev/null
+++ b/frontend/tests/utils/parsers.test.js
@@ -0,0 +1,148 @@
+import {
+    extractErrorFromTraceback,
+    parsePydanticError,
+    parseServerErrors,
+} from "../../src/utils/parsers";
+import assert from "../helpers";
+
+describe("Parsing", function() {
+    describe("parseServerErrors", function() {
+        it("handles no error correct", function() {
+            assert.equal(parseServerErrors(""), null);
+            assert.equal(parseServerErrors(null), null);
+            assert.equal(parseServerErrors(undefined), null);
+            assert.equal(parseServerErrors([]), null);
+        });
+
+        it("handles an unknown format", function() {
+            const expected = {
+                messages: ["An error has occurred"],
+                message: "An error has occurred",
+            };
+
+            expected.data = ["ERROR"];
+            assert.deepStrictEqual(parseServerErrors("ERROR"), expected);
+
+            expected.data = [["ERROR"]];
+            assert.deepStrictEqual(parseServerErrors(["ERROR"]), expected);
+
+            expected.data = [{err: "ERROR"}];
+            assert.deepStrictEqual(parseServerErrors({err: "ERROR"}), expected);
+
+            expected.data = [[{err: "ERROR"}]];
+            assert.deepStrictEqual(parseServerErrors([{err: "ERROR"}]), expected);
+        });
+
+        it("handles tracebacks", function() {
+            assert.deepStrictEqual(
+                parseServerErrors([
+                    'Traceback (most recent call last):\n  File "/bmds-server/bmds_server/analysis/models.py", line 246, in try_run_session\n    return AnalysisSession.run(inputs, dataset_index, option_index)\nValueError: Doses are not unique\n',
+                ]),
+                {
+                    data: [
+                        'Traceback (most recent call last):\n  File "/bmds-server/bmds_server/analysis/models.py", line 246, in try_run_session\n    return AnalysisSession.run(inputs, dataset_index, option_index)\nValueError: Doses are not unique\n',
+                    ],
+                    messages: ["Doses are not unique"],
+                    message: "Doses are not unique",
+                }
+            );
+        });
+
+        it("handles pydantic", function() {
+            assert.deepStrictEqual(
+                parseServerErrors([
+                    '[{"type":"float_type","loc":["datasets",0,"function-after[num_groups(), MaxContinuousDatasetSchema]","doses",1],"msg":"Input should be a valid number","url":"https://errors.pydantic.dev/2.4/v/float_type"},{"type":"float_type","loc":["datasets",0,"function-after[num_groups(), MaxContinuousIndividualDatasetSchema]","doses",1],"msg":"Input should be a valid number","url":"https://errors.pydantic.dev/2.4/v/float_type"},{"type":"missing","loc":["datasets",0,"function-after[num_groups(), MaxContinuousIndividualDatasetSchema]","responses"],"msg":"Field required","url":"https://errors.pydantic.dev/2.4/v/missing"}]',
+                ]),
+                {
+                    data: [
+                        {
+                            loc: [
+                                "datasets",
+                                0,
+                                "function-after[num_groups(), MaxContinuousDatasetSchema]",
+                                "doses",
+                                1,
+                            ],
+                            msg: "Input should be a valid number",
+                            type: "float_type",
+                            url: "https://errors.pydantic.dev/2.4/v/float_type",
+                        },
+                        {
+                            loc: [
+                                "datasets",
+                                0,
+                                "function-after[num_groups(), MaxContinuousIndividualDatasetSchema]",
+                                "doses",
+                                1,
+                            ],
+                            msg: "Input should be a valid number",
+                            type: "float_type",
+                            url: "https://errors.pydantic.dev/2.4/v/float_type",
+                        },
+                        {
+                            loc: [
+                                "datasets",
+                                0,
+                                "function-after[num_groups(), MaxContinuousIndividualDatasetSchema]",
+                                "responses",
+                            ],
+                            msg: "Field required",
+                            type: "missing",
+                            url: "https://errors.pydantic.dev/2.4/v/missing",
+                        },
+                    ],
+                    messages: [
+                        "datasets: Field required",
+                        "datasets: Input should be a valid number",
+                        "datasets: Input should be a valid number",
+                    ],
+                    message: "datasets: Field required\ndatasets: Input should be a valid number",
+                }
+            );
+        });
+    });
+
+    describe("extractErrorFromTraceback", function() {
+        it("extracts the error from a python traceback", function() {
+            const tracebackErrors = [
+                [
+                    'Traceback (most recent call last):\n  File "/bmds-server/bmds_server/analysis/models.py", line 246, in try_run_session\n    return AnalysisSession.run(inputs, dataset_index, option_index)\nValueError: Doses are not unique\n',
+                    "Doses are not unique",
+                ],
+                [
+                    'Traceback (most recent call last):\n  File "/bmds-server/bmds_server/analysis/models.py", line 246, in try_run_session\n    return AnalysisSession.run(inputs, dataset_index, option_index)\nDoses are not unique\n',
+                    "Doses are not unique",
+                ],
+                ["Fallthrough - no change", "Fallthrough - no change"],
+            ];
+
+            tracebackErrors.map(args => {
+                const input = args[0],
+                    result = args[1];
+                assert.equal(extractErrorFromTraceback(input), result);
+            });
+        });
+    });
+
+    describe("parsePydanticError", function() {
+        it("extracts the error from a pydantic exception", function() {
+            const pydanticErrors = [
+                [
+                    [
+                        {
+                            loc: ["datasets", "remove"],
+                            msg: "Input should be a valid number",
+                        },
+                    ],
+                    ["datasets: Input should be a valid number"],
+                ],
+            ];
+
+            pydanticErrors.map(args => {
+                const input = args[0],
+                    result = args[1];
+                assert.allEqual(parsePydanticError(input), result);
+            });
+        });
+    });
+});

From 696efc742d8eeafecaee9a48a9679f9a4c25b117 Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Fri, 9 Feb 2024 18:11:08 -0500
Subject: [PATCH 23/24] 321 improve nomenclature for statistical outputs (#2)

* 8

* 25a, 26, 30 comment

* 27, 29, 33, 34, 35

* 2, 6

* 31

* testfix

* rm comment, 31

* 3 note, 2, 5a, 12, 24, rm comment

* js eol lf

* revert MT

* rename percentile to cummulative probability

* resize tables as needed

* remove change

* fix test w/ degree symbol

* rename log likelihood globally

* fix bug in layout

* rename scaled residual

* rename DOF to d.f.

* change Summary to Modeling Summary

* rename "Abs(Residual of interest)" -> "|Residual near BMD|"

* rename "Frequentist Model Results" to "Maximum Likelihood Approach Model Results"

* title case

* add vertical spacing

* Change "Confidence Level" to "Confidence Level (one-sided)" globally

* add on bound footnote to UI

* handle goodness of fit table

* use < and > instead of less than and greater than

* only show tail probability if hybrid continuous bmr

* make format

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 .../components/IndividualModel/CDFTable.js    |   6 +-
 .../IndividualModel/ContinuousDeviance.js     |   4 +-
 .../IndividualModel/ContinuousSummary.js      |   6 +-
 .../ContinuousTestOfInterest.js               |   4 +-
 .../IndividualModel/DichotomousDeviance.js    |   4 +-
 .../IndividualModel/DichotomousSummary.js     |   6 +-
 .../components/IndividualModel/GoodnessFit.js | 172 ++++++++++++------
 .../IndividualModel/ModelDetailModal.js       |   4 +-
 .../IndividualModel/ModelOptionsTable.js      |  11 +-
 .../IndividualModel/ModelParameters.js        | 109 +++++------
 .../Main/OptionsForm/OptionsFormList.js       |  16 +-
 .../components/Output/BayesianResultTable.js  |   6 +-
 .../Output/FrequentistResultTable.js          |   6 +-
 .../Output/Multitumor/AnalysisOfDeviance.js   |   4 +-
 .../Output/Multitumor/ModelOptions.js         |   2 +-
 .../components/Output/Multitumor/MsCombo.js   |   5 +-
 .../Output/Multitumor/ResultTable.js          |   6 +-
 .../components/Output/Multitumor/Summary.js   |   7 +-
 .../NestedDichotomous/BootstrapResults.js     |   4 +-
 .../Output/NestedDichotomous/Summary.js       |   4 +-
 .../src/components/Output/OptionSetTable.js   |  32 ++--
 frontend/src/components/Output/Output.js      |  10 +-
 frontend/src/constants/logicConstants.js      |   8 +-
 frontend/src/constants/modelConstants.js      |   2 +-
 frontend/src/constants/optionsConstants.js    |   3 +
 frontend/src/constants/plotting.js            |   4 +-
 tests/analysis/test_executor.py               |   6 +-
 tests/analysis/test_validators.py             |   2 +-
 tests/data/db.yaml                            |  14 +-
 tests/integration/test_integration.py         |   4 +-
 30 files changed, 276 insertions(+), 195 deletions(-)

diff --git a/frontend/src/components/IndividualModel/CDFTable.js b/frontend/src/components/IndividualModel/CDFTable.js
index 38362208..d06069e3 100644
--- a/frontend/src/components/IndividualModel/CDFTable.js
+++ b/frontend/src/components/IndividualModel/CDFTable.js
@@ -11,12 +11,16 @@ class CDFTable extends Component {
         const {bmd_dist} = this.props;
         return (
             <table className="table table-sm table-bordered text-right">
+                <colgroup>
+                    <col width="50%" />
+                    <col width="50%" />
+                </colgroup>
                 <thead>
                     <tr className="bg-custom text-left">
                         <th colSpan="2">CDF</th>
                     </tr>
                     <tr>
-                        <th>Percentile</th>
+                        <th>Cumulative Probability</th>
                         <th>BMD</th>
                     </tr>
                 </thead>
diff --git a/frontend/src/components/IndividualModel/ContinuousDeviance.js b/frontend/src/components/IndividualModel/ContinuousDeviance.js
index e5c30b04..6c692bef 100644
--- a/frontend/src/components/IndividualModel/ContinuousDeviance.js
+++ b/frontend/src/components/IndividualModel/ContinuousDeviance.js
@@ -20,11 +20,11 @@ class ContinuousDeviance extends Component {
                 </colgroup>
                 <thead>
                     <tr className="bg-custom">
-                        <th colSpan="9">Likelihoods of Interest</th>
+                        <th colSpan="9">Likelihoods</th>
                     </tr>
                     <tr>
                         <th>Model</th>
-                        <th>Log Likelihood</th>
+                        <th>-2* Log(Likelihood Ratio)</th>
                         <th># of Parameters</th>
                         <th>AIC</th>
                     </tr>
diff --git a/frontend/src/components/IndividualModel/ContinuousSummary.js b/frontend/src/components/IndividualModel/ContinuousSummary.js
index 58acba62..30d211b5 100644
--- a/frontend/src/components/IndividualModel/ContinuousSummary.js
+++ b/frontend/src/components/IndividualModel/ContinuousSummary.js
@@ -19,7 +19,7 @@ class ContinuousSummary extends Component {
                 </colgroup>
                 <thead>
                     <tr className="bg-custom">
-                        <th colSpan="2">Summary</th>
+                        <th colSpan="2">Modeling Summary</th>
                     </tr>
                 </thead>
                 <tbody>
@@ -40,7 +40,7 @@ class ContinuousSummary extends Component {
                         <td>{ff(results.fit.aic)}</td>
                     </tr>
                     <tr>
-                        <td>Log Likelihood</td>
+                        <td>-2* Log(Likelihood Ratio)</td>
                         <td>{ff(results.fit.loglikelihood)}</td>
                     </tr>
                     <tr>
@@ -50,7 +50,7 @@ class ContinuousSummary extends Component {
                         <td>{fractionalFormatter(p_value)}</td>
                     </tr>
                     <tr>
-                        <td>Model DOF</td>
+                        <td>Model d.f.</td>
                         <td>{ff(results.tests.dfs[3])}</td>
                     </tr>
                 </tbody>
diff --git a/frontend/src/components/IndividualModel/ContinuousTestOfInterest.js b/frontend/src/components/IndividualModel/ContinuousTestOfInterest.js
index 6afca764..5058773a 100644
--- a/frontend/src/components/IndividualModel/ContinuousTestOfInterest.js
+++ b/frontend/src/components/IndividualModel/ContinuousTestOfInterest.js
@@ -22,7 +22,7 @@ class ContinuousTestOfInterest extends Component {
                 </colgroup>
                 <thead>
                     <tr className="bg-custom text-left">
-                        <th colSpan="4">Test of Interest</th>
+                        <th colSpan="4">Tests of Mean and Variance Fits</th>
                     </tr>
                     <tr>
                         <th>Test</th>
@@ -30,7 +30,7 @@ class ContinuousTestOfInterest extends Component {
                             LLR
                             <HelpTextPopover title="LLR" content="2 * Log(Likelihood Ratio)" />
                         </th>
-                        <th>Test DOF</th>
+                        <th>Test d.f.</th>
                         <th>
                             <i>P</i>-Value
                         </th>
diff --git a/frontend/src/components/IndividualModel/DichotomousDeviance.js b/frontend/src/components/IndividualModel/DichotomousDeviance.js
index cf7b7add..e948e2ff 100644
--- a/frontend/src/components/IndividualModel/DichotomousDeviance.js
+++ b/frontend/src/components/IndividualModel/DichotomousDeviance.js
@@ -26,10 +26,10 @@ class DichotomousDeviance extends Component {
                     </tr>
                     <tr>
                         <th>Model</th>
-                        <th>Log Likelihood</th>
+                        <th>-2* Log(Likelihood Ratio)</th>
                         <th># Parameters</th>
                         <th>Deviance</th>
-                        <th>Test DOF</th>
+                        <th>Test d.f.</th>
                         <th>
                             <i>P</i>-Value
                         </th>
diff --git a/frontend/src/components/IndividualModel/DichotomousSummary.js b/frontend/src/components/IndividualModel/DichotomousSummary.js
index b06b9aa5..be92923b 100644
--- a/frontend/src/components/IndividualModel/DichotomousSummary.js
+++ b/frontend/src/components/IndividualModel/DichotomousSummary.js
@@ -18,7 +18,7 @@ class DichotomousSummary extends Component {
                 </colgroup>
                 <thead>
                     <tr className="bg-custom">
-                        <th colSpan="2">Summary</th>
+                        <th colSpan="2">Modeling Summary</th>
                     </tr>
                 </thead>
                 <tbody>
@@ -39,7 +39,7 @@ class DichotomousSummary extends Component {
                         <td>{ff(results.fit.aic)}</td>
                     </tr>
                     <tr>
-                        <td>Log Likelihood</td>
+                        <td>-2* Log(Likelihood Ratio)</td>
                         <td>{ff(results.fit.loglikelihood)}</td>
                     </tr>
                     <tr>
@@ -49,7 +49,7 @@ class DichotomousSummary extends Component {
                         <td>{fourDecimalFormatter(results.gof.p_value)}</td>
                     </tr>
                     <tr>
-                        <td>Overall DOF</td>
+                        <td>Overall d.f.</td>
                         <td>{ff(results.gof.df)}</td>
                     </tr>
                     <tr>
diff --git a/frontend/src/components/IndividualModel/GoodnessFit.js b/frontend/src/components/IndividualModel/GoodnessFit.js
index 09ead3d8..b2413c18 100644
--- a/frontend/src/components/IndividualModel/GoodnessFit.js
+++ b/frontend/src/components/IndividualModel/GoodnessFit.js
@@ -6,87 +6,141 @@ import {Dtype} from "@/constants/dataConstants";
 import {isLognormal} from "@/constants/modelConstants";
 import {ff} from "@/utils/formatters";
 
-/* eslint-disable */
-const hdr_c_normal = [
-        "Dose", "Size", "Observed Mean", "Calculated Mean", "Estimated Mean",
-        "Observed SD", "Calculated SD", "Estimated SD", "Scaled Residual",
-    ],
-    hdr_c_lognormal = [
-        "Dose", "Size", "Observed Mean", "Calculated Median", "Estimated Median",
-        "Observed SD", "Calculated GSD", "Estimated GSD", "Scaled Residual",
-    ],
-    hdr_d = [ "Dose", "Size", "Observed", "Expected", "Estimated Probability", "Scaled Residual"];
-/* eslint-enable */
-
 @observer
 class GoodnessFit extends Component {
-    getHeaders(dtype, settings) {
-        if (dtype == Dtype.CONTINUOUS || dtype == Dtype.CONTINUOUS_INDIVIDUAL) {
-            const headers = isLognormal(settings.disttype) ? hdr_c_lognormal : hdr_c_normal;
-            return [headers, [10, 10, 10, 12, 12, 12, 10, 12, 12]];
-        }
-        if (dtype == Dtype.DICHOTOMOUS) {
-            return [hdr_d, [17, 16, 16, 17, 17, 17]];
-        }
-        throw Error("Unknown dtype");
+    getDichotomousData() {
+        const {store} = this.props,
+            gof = store.modalModel.results.gof,
+            dataset = store.selectedDataset;
+        return {
+            headers: [
+                "Dose",
+                "N",
+                "Observed",
+                "Expected",
+                "Estimated Probability",
+                "Scaled Residual",
+            ],
+            colwidths: [17, 16, 16, 17, 17, 17],
+            data: dataset.doses.map((dose, i) => {
+                return [
+                    dose,
+                    dataset.ns[i],
+                    dataset.incidences[i],
+                    ff(gof.expected[i]),
+                    ff(gof.expected[i] / dataset.ns[i]),
+                    ff(gof.residual[i]),
+                ];
+            }),
+        };
+    }
+
+    getContinuousNormalData(dtype) {
+        const {store} = this.props,
+            gof = store.modalModel.results.gof,
+            dataset = store.selectedDataset,
+            useFF = dtype === Dtype.CONTINUOUS_INDIVIDUAL;
+        return {
+            headers: [
+                "Dose",
+                "N",
+                "Sample Mean",
+                "Model Fitted Mean",
+                "Sample SD",
+                "Model Fitted SD",
+                "Scaled Residual",
+            ],
+            colwidths: [1, 1, 1, 1, 1, 1, 1],
+            data: dataset.doses.map((dose, i) => {
+                return [
+                    dose,
+                    dataset.ns[i],
+                    useFF ? ff(gof.obs_mean[i]) : gof.obs_mean[i],
+                    ff(gof.est_mean[i]),
+                    useFF ? ff(gof.obs_sd[i]) : gof.obs_sd[i],
+                    ff(gof.est_sd[i]),
+                    ff(gof.residual[i]),
+                ];
+            }),
+        };
+    }
+
+    getContinuousLognormalData(dtype) {
+        const {store} = this.props,
+            gof = store.modalModel.results.gof,
+            dataset = store.selectedDataset,
+            useFF = dtype === Dtype.CONTINUOUS_INDIVIDUAL;
+        return {
+            headers: [
+                "Dose",
+                "N",
+                "Sample Mean",
+                "Approximate Sample Median",
+                "Model Fitted Median",
+                "Sample SD",
+                "Approximate Sample GSD",
+                "Model Fitted GSD",
+                "Scaled Residual",
+            ],
+            colwidths: [10, 10, 10, 12, 12, 12, 10, 12, 12],
+            data: dataset.doses.map((dose, i) => {
+                return [
+                    dose,
+                    dataset.ns[i],
+                    useFF ? ff(gof.obs_mean[i]) : gof.obs_mean[i],
+                    ff(gof.calc_mean[i]),
+                    ff(gof.est_mean[i]),
+                    useFF ? ff(gof.obs_sd[i]) : gof.obs_sd[i],
+                    ff(gof.calc_mean[i]),
+                    ff(gof.est_sd[i]),
+                    ff(gof.residual[i]),
+                ];
+            }),
+        };
     }
     render() {
         const {store} = this.props,
             settings = store.modalModel.settings,
-            gof = store.modalModel.results.gof,
             dataset = store.selectedDataset,
-            {dtype} = dataset,
-            headers = this.getHeaders(dtype, settings);
+            {dtype} = dataset;
+
+        let data;
+        if (dtype == Dtype.DICHOTOMOUS) {
+            data = this.getDichotomousData();
+        } else {
+            if (isLognormal(settings.disttype)) {
+                data = this.getContinuousLognormalData(dtype);
+            } else {
+                data = this.getContinuousNormalData(dtype);
+            }
+        }
         return (
             <table className="table table-sm table-bordered text-right">
                 <colgroup>
-                    {headers[1].map((d, i) => (
+                    {data.colwidths.map((d, i) => (
                         <col key={i} width={`${d}%`} />
                     ))}
                 </colgroup>
                 <thead>
                     <tr className="bg-custom text-left">
-                        <th colSpan={headers[0].length}>Goodness of Fit</th>
+                        <th colSpan={data.headers.length}>Goodness of Fit</th>
                     </tr>
                     <tr>
-                        {headers[0].map((d, i) => (
+                        {data.headers.map((d, i) => (
                             <th key={i}>{d}</th>
                         ))}
                     </tr>
                 </thead>
                 <tbody>
-                    {dtype == Dtype.CONTINUOUS || dtype == Dtype.CONTINUOUS_INDIVIDUAL
-                        ? gof.dose.map((item, i) => {
-                              const useFF = dtype === Dtype.CONTINUOUS_INDIVIDUAL;
-                              return (
-                                  <tr key={i}>
-                                      <td>{item}</td>
-                                      <td>{gof.size[i]}</td>
-                                      <td>{useFF ? ff(gof.obs_mean[i]) : gof.obs_mean[i]}</td>
-                                      <td>{ff(gof.calc_mean[i])}</td>
-                                      <td>{ff(gof.est_mean[i])}</td>
-                                      <td>{useFF ? ff(gof.obs_sd[i]) : gof.obs_sd[i]}</td>
-                                      <td>{ff(gof.calc_sd[i])}</td>
-                                      <td>{ff(gof.est_sd[i])}</td>
-                                      <td>{ff(gof.residual[i])}</td>
-                                  </tr>
-                              );
-                          })
-                        : null}
-                    {dtype == Dtype.DICHOTOMOUS
-                        ? dataset.doses.map((dose, i) => {
-                              return (
-                                  <tr key={i}>
-                                      <td>{dose}</td>
-                                      <td>{dataset.ns[i]}</td>
-                                      <td>{dataset.incidences[i]}</td>
-                                      <td>{ff(gof.expected[i])}</td>
-                                      <td>{ff(gof.expected[i] / dataset.ns[i])}</td>
-                                      <td>{ff(gof.residual[i])}</td>
-                                  </tr>
-                              );
-                          })
-                        : null}
+                    {data.data.map((row, i) => {
+                        return (
+                            <tr key={i}>
+                                {row.map((cell, j) => (
+                                    <td key={j}>{cell}</td>
+                                ))}
+                            </tr>
+                        );
+                    })}
                 </tbody>
             </table>
         );
diff --git a/frontend/src/components/IndividualModel/ModelDetailModal.js b/frontend/src/components/IndividualModel/ModelDetailModal.js
index 85f985bc..e58e2e78 100644
--- a/frontend/src/components/IndividualModel/ModelDetailModal.js
+++ b/frontend/src/components/IndividualModel/ModelDetailModal.js
@@ -69,7 +69,7 @@ class ModelBody extends Component {
                     </Col>
                 </Row>
                 <Row>
-                    <Col xl={isDichotomous ? 8 : 10}>
+                    <Col xl={isDichotomous ? 8 : 12}>
                         <GoodnessFit store={outputStore} />
                     </Col>
                 </Row>
@@ -82,7 +82,7 @@ class ModelBody extends Component {
                 ) : null}
                 {isContinuous ? (
                     <Row>
-                        <Col xl={6}>
+                        <Col xl={8}>
                             <ContinuousDeviance store={outputStore} />
                             <ContinuousTestOfInterest store={outputStore} />
                         </Col>
diff --git a/frontend/src/components/IndividualModel/ModelOptionsTable.js b/frontend/src/components/IndividualModel/ModelOptionsTable.js
index 690a7fe4..b60a2994 100644
--- a/frontend/src/components/IndividualModel/ModelOptionsTable.js
+++ b/frontend/src/components/IndividualModel/ModelOptionsTable.js
@@ -6,6 +6,7 @@ import {getLabel} from "@/common";
 import TwoColumnTable from "@/components/common/TwoColumnTable";
 import {Dtype} from "@/constants/dataConstants";
 import {hasDegrees} from "@/constants/modelConstants";
+import {isHybridBmr} from "@/constants/optionsConstants";
 import {
     continuousBmrOptions,
     dichotomousBmrOptions,
@@ -39,7 +40,7 @@ class ModelOptionsTable extends Component {
             data = [
                 ["BMR Type", getLabel(model.settings.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(model.settings.bmr)],
-                ["Confidence Level", ff(1 - model.settings.alpha)],
+                ["Confidence Level (one sided)", ff(1 - model.settings.alpha)],
                 hasDegrees.has(model.model_class.verbose)
                     ? ["Degree", ff(model.settings.degree)]
                     : null,
@@ -53,8 +54,10 @@ class ModelOptionsTable extends Component {
                 ["BMRF", ff(model.settings.bmr)],
                 ["Distribution Type", getLabel(model.settings.disttype, distTypeOptions)],
                 ["Direction", model.settings.is_increasing ? "Up" : "Down"],
-                ["Confidence Level", 1 - ff(model.settings.alpha)],
-                ["Tail Probability", ff(model.settings.tail_prob)],
+                ["Confidence Level (one sided)", 1 - ff(model.settings.alpha)],
+                isHybridBmr(model.settings.bmr_type)
+                    ? ["Tail Probability", ff(model.settings.tail_prob)]
+                    : null,
                 hasDegrees.has(model.model_class.verbose)
                     ? ["Degree", ff(model.settings.degree)]
                     : null,
@@ -66,7 +69,7 @@ class ModelOptionsTable extends Component {
             data = [
                 ["BMR Type", getLabel(model.settings.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(model.settings.bmr)],
-                ["Confidence Level", ff(1 - model.settings.alpha)],
+                ["Confidence Level (one sided)", ff(1 - model.settings.alpha)],
                 ["Bootstrap Seed", model.settings.bootstrap_seed],
                 ["Bootstrap Iterations", model.settings.bootstrap_iterations],
                 [
diff --git a/frontend/src/components/IndividualModel/ModelParameters.js b/frontend/src/components/IndividualModel/ModelParameters.js
index d70b58e8..49dcf060 100644
--- a/frontend/src/components/IndividualModel/ModelParameters.js
+++ b/frontend/src/components/IndividualModel/ModelParameters.js
@@ -10,60 +10,65 @@ import {parameterFormatter} from "@/utils/formatters";
 class ModelParameters extends Component {
     render() {
         const {parameters} = this.props,
-            indexes = _.range(parameters.names.length);
+            indexes = _.range(parameters.names.length),
+            anyBounded = _.sum(parameters.bounded) > 0;
 
         return (
-            <table className="table table-sm table-bordered text-right col-l-1">
-                <colgroup>
-                    <col width="20%" />
-                    <col width="20%" />
-                    <col width="20%" />
-                    <col width="20%" />
-                    <col width="20%" />
-                </colgroup>
-                <thead>
-                    <tr className="bg-custom">
-                        <th colSpan="5">Model Parameters</th>
-                    </tr>
-                    <tr>
-                        <th>Variable</th>
-                        <th>Estimate</th>
-                        <th>Standard Error</th>
-                        <th>Lower Confidence</th>
-                        <th>Upper Confidence</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    {indexes.map(i => {
-                        const bounded = parameters.bounded[i];
-                        return (
-                            <tr key={i}>
-                                <td>{parameters.names[i]}</td>
-                                <td>
-                                    {bounded ? (
-                                        <>
-                                            <span>Bounded</span>
-                                            <HelpTextPopover
-                                                title="Bounded"
-                                                content={`The value of this parameter, ${parameters.values[i]}, is within the tolerance of the bound`}
-                                            />
-                                        </>
-                                    ) : (
-                                        parameterFormatter(parameters.values[i])
-                                    )}
-                                </td>
-                                <td>{bounded ? "NA" : parameterFormatter(parameters.se[i])}</td>
-                                <td>
-                                    {bounded ? "NA" : parameterFormatter(parameters.lower_ci[i])}
-                                </td>
-                                <td>
-                                    {bounded ? "NA" : parameterFormatter(parameters.upper_ci[i])}
-                                </td>
-                            </tr>
-                        );
-                    })}
-                </tbody>
-            </table>
+            <>
+                <table className="table table-sm table-bordered text-right col-l-1">
+                    <colgroup>
+                        <col width="34%" />
+                        <col width="33%" />
+                        <col width="33%" />
+                    </colgroup>
+                    <thead>
+                        <tr className="bg-custom">
+                            <th colSpan="3">Model Parameters</th>
+                        </tr>
+                        <tr>
+                            <th>Variable</th>
+                            <th>Estimate</th>
+                            <th>Standard Error</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        {indexes.map(i => {
+                            const bounded = parameters.bounded[i];
+                            return (
+                                <tr key={i}>
+                                    <td>{parameters.names[i]}</td>
+                                    <td>
+                                        {bounded ? (
+                                            <>
+                                                <span>On Bound</span>
+                                                <HelpTextPopover
+                                                    title="On Bound"
+                                                    content={`The value of this parameter, ${parameters.values[i]}, is within the tolerance of the bound`}
+                                                />
+                                            </>
+                                        ) : (
+                                            parameterFormatter(parameters.values[i])
+                                        )}
+                                    </td>
+                                    <td>
+                                        {bounded
+                                            ? "Not Reported"
+                                            : parameterFormatter(parameters.se[i])}
+                                    </td>
+                                </tr>
+                            );
+                        })}
+                    </tbody>
+                </table>
+                {anyBounded ? (
+                    <p>
+                        Standard errors estimates are not generated for parameters estimated on
+                        corresponding bounds, although sampling error is present for all parameters,
+                        as a rule. Standard error estimates may not be reliable as a basis for
+                        confidence intervals or tests when one or more parameters are on bounds.
+                    </p>
+                ) : null}
+            </>
         );
     }
 }
diff --git a/frontend/src/components/Main/OptionsForm/OptionsFormList.js b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
index 075cafea..83ed7b14 100644
--- a/frontend/src/components/Main/OptionsForm/OptionsFormList.js
+++ b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
@@ -23,7 +23,8 @@ class OptionsFormList extends Component {
             modelType = optionsStore.getModelType,
             optionsList = toJS(optionsStore.optionsList),
             distTypeHelpText =
-                "If lognormal is selected, only the Exponential and Hill models can be executed. Other models will be removed during the execution process and will not be shown in the outputs.";
+                "If lognormal is selected, only the Exponential and Hill models can be executed. Other models will be removed during the execution process and will not be shown in the outputs.",
+            tailProbabilityHelpText = "Only used for Hybrid models.";
         return (
             <div>
                 <div className="panel panel-default">
@@ -36,8 +37,13 @@ class OptionsFormList extends Component {
                                         <>
                                             <th>BMR Type</th>
                                             <th>BMRF</th>
-                                            <th>Tail Probability</th>
-                                            <th>Confidence Level</th>
+                                            <th>
+                                                Tail Probability
+                                                <HelpTextPopover
+                                                    content={tailProbabilityHelpText}
+                                                />
+                                            </th>
+                                            <th>Confidence Level (one sided)</th>
                                             <th>
                                                 Distribution +<br />
                                                 Variance&nbsp;
@@ -50,14 +56,14 @@ class OptionsFormList extends Component {
                                         <>
                                             <th>Risk Type</th>
                                             <th>BMR</th>
-                                            <th>Confidence Level</th>
+                                            <th>Confidence Level (one sided)</th>
                                         </>
                                     ) : null}
                                     {modelType === MODEL_NESTED_DICHOTOMOUS ? (
                                         <>
                                             <th>Risk Type</th>
                                             <th>BMR</th>
-                                            <th>Confidence Level</th>
+                                            <th>Confidence Level (one sided)</th>
                                             <th>
                                                 Litter Specific
                                                 <br />
diff --git a/frontend/src/components/Output/BayesianResultTable.js b/frontend/src/components/Output/BayesianResultTable.js
index b71d7eaa..d41fd1a8 100644
--- a/frontend/src/components/Output/BayesianResultTable.js
+++ b/frontend/src/components/Output/BayesianResultTable.js
@@ -36,8 +36,8 @@ class BayesianResultTable extends Component {
                         <th>BMD</th>
                         <th>BMDU</th>
                         <th>Unnormalized Log Posterior Probability</th>
-                        <th>Scaled Residual for Dose Group near BMD</th>
-                        <th>Scaled Residual for Control Dose Group</th>
+                        <th>Scaled Residual at Control</th>
+                        <th>Scaled Residual near BMD</th>
                     </tr>
                 </thead>
                 <tbody className="table-bordered">
@@ -63,8 +63,8 @@ class BayesianResultTable extends Component {
                                 <td>{ff(model.results.bmd)}</td>
                                 <td>{ff(model.results.bmdu)}</td>
                                 <td>{ff(model.results.fit.bic_equiv)}</td>
-                                <td>{ff(model.results.gof.roi)}</td>
                                 <td>{ff(model.results.gof.residual[0])}</td>
+                                <td>{ff(model.results.gof.roi)}</td>
                             </tr>
                         );
                     })}
diff --git a/frontend/src/components/Output/FrequentistResultTable.js b/frontend/src/components/Output/FrequentistResultTable.js
index ae3a8bdc..4420415c 100644
--- a/frontend/src/components/Output/FrequentistResultTable.js
+++ b/frontend/src/components/Output/FrequentistResultTable.js
@@ -242,8 +242,8 @@ class FrequentistRow extends Component {
                 <td>{ff(results.bmdu)}</td>
                 <td>{fractionalFormatter(getPValue(dataset.dtype, results))}</td>
                 <td>{ff(results.fit.aic)}</td>
-                <td>{ff(results.gof.roi)}</td>
                 <td>{ff(results.gof.residual[0])}</td>
+                <td>{ff(results.gof.roi)}</td>
                 <RecommendationTd
                     store={store}
                     data={data}
@@ -326,8 +326,8 @@ class FrequentistResultTable extends Component {
                             <i>P</i>-Value
                         </th>
                         <th>AIC</th>
-                        <th>Scaled Residual for Dose Group near BMD</th>
-                        <th>Scaled Residual for Control Dose Group</th>
+                        <th>Scaled Residual at Control</th>
+                        <th>Scaled Residual near BMD</th>
                         {store.recommendationEnabled ? (
                             <th>
                                 <Button
diff --git a/frontend/src/components/Output/Multitumor/AnalysisOfDeviance.js b/frontend/src/components/Output/Multitumor/AnalysisOfDeviance.js
index 4209aad4..90435817 100644
--- a/frontend/src/components/Output/Multitumor/AnalysisOfDeviance.js
+++ b/frontend/src/components/Output/Multitumor/AnalysisOfDeviance.js
@@ -24,10 +24,10 @@ class AnalysisOfDeviance extends Component {
                     </tr>
                     <tr>
                         <th>Model</th>
-                        <th>Log Likelihood</th>
+                        <th>-2* Log(Likelihood Ratio)</th>
                         <th># Parameters</th>
                         <th>Deviance</th>
-                        <th>Test DOF</th>
+                        <th>Test d.f.</th>
                         <th>
                             <i>P</i>-Value
                         </th>
diff --git a/frontend/src/components/Output/Multitumor/ModelOptions.js b/frontend/src/components/Output/Multitumor/ModelOptions.js
index b073ac4b..85a34715 100644
--- a/frontend/src/components/Output/Multitumor/ModelOptions.js
+++ b/frontend/src/components/Output/Multitumor/ModelOptions.js
@@ -18,7 +18,7 @@ class ModelOptions extends Component {
             data = [
                 ["Risk Type", getLabel(options.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(options.bmr_value)],
-                ["Confidence Level", ff(options.confidence_level)],
+                ["Confidence Level (one sided)", ff(options.confidence_level)],
                 ["Degree", degree],
             ];
         return <TwoColumnTable data={data} label="Model Options" />;
diff --git a/frontend/src/components/Output/Multitumor/MsCombo.js b/frontend/src/components/Output/Multitumor/MsCombo.js
index 5038617d..16b364ac 100644
--- a/frontend/src/components/Output/Multitumor/MsCombo.js
+++ b/frontend/src/components/Output/Multitumor/MsCombo.js
@@ -16,7 +16,7 @@ class MsComboInfo extends Component {
                 ["Model", "Multitumor"],
                 ["Risk Type", getLabel(options.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(options.bmr_value)],
-                ["Confidence Level", ff(options.confidence_level)],
+                ["Confidence Level (one sided)", ff(options.confidence_level)],
             ];
         return <TwoColumnTable data={data} label={label} />;
     }
@@ -29,7 +29,6 @@ MsComboInfo.propTypes = {
 class MsComboSummary extends Component {
     render() {
         const {results} = this.props,
-            label = "Summary",
             data = [
                 ["BMD", ff(results.bmd)],
                 ["BMDL", ff(results.bmdl)],
@@ -38,7 +37,7 @@ class MsComboSummary extends Component {
                 ["Combined Log-Likelihood", ff(results.ll)],
                 ["Combined Log-Likelihood Constant", ff(results.ll_constant)],
             ];
-        return <TwoColumnTable data={data} label={label} />;
+        return <TwoColumnTable data={data} label={"Modeling Summary"} colwidths={[40, 60]} />;
     }
 }
 MsComboSummary.propTypes = {
diff --git a/frontend/src/components/Output/Multitumor/ResultTable.js b/frontend/src/components/Output/Multitumor/ResultTable.js
index ce51c436..7d1255e6 100644
--- a/frontend/src/components/Output/Multitumor/ResultTable.js
+++ b/frontend/src/components/Output/Multitumor/ResultTable.js
@@ -41,8 +41,8 @@ class ResultTable extends Component {
                             <i>P</i>-Value
                         </th>
                         <th>AIC</th>
-                        <th>Scaled Residual for Dose Group near BMD</th>
-                        <th>Scaled Residual for Control Dose Group</th>
+                        <th>Scaled Residual at Control</th>
+                        <th>Scaled Residual near BMD</th>
                     </tr>
                 </thead>
                 <tbody className="table-bordered">
@@ -101,8 +101,8 @@ class ResultTable extends Component {
                                             <td>{ff(model.slope_factor)}</td>
                                             <td>{ff(model.gof.p_value)}</td>
                                             <td>{ff(model.fit.aic)}</td>
-                                            <td>{ff(model.gof.roi)}</td>
                                             <td>{ff(model.gof.residual[0])}</td>
+                                            <td>{ff(model.gof.roi)}</td>
                                         </tr>
                                     );
                                 })
diff --git a/frontend/src/components/Output/Multitumor/Summary.js b/frontend/src/components/Output/Multitumor/Summary.js
index 244f2d09..11db6689 100644
--- a/frontend/src/components/Output/Multitumor/Summary.js
+++ b/frontend/src/components/Output/Multitumor/Summary.js
@@ -21,10 +21,11 @@ class Summary extends Component {
                     </span>,
                     fourDecimalFormatter(model.gof.p_value),
                 ],
-                ["Overall DOF", ff(model.gof.df)],
-                ["Chi²", ff(model.fit.chisq)][("Log Likelihood", ff(model.fit.loglikelihood))],
+                ["Overall d.f.", ff(model.gof.df)],
+                ["Chi²", ff(model.fit.chisq)],
+                ["-2* Log(Likelihood Ratio)", ff(model.fit.loglikelihood)],
             ];
-        return <TwoColumnTable data={data} label="Summary" />;
+        return <TwoColumnTable data={data} label="Modeling Summary" />;
     }
 }
 
diff --git a/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js b/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js
index 0b396ac2..ba2b74ff 100644
--- a/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js
+++ b/frontend/src/components/Output/NestedDichotomous/BootstrapResults.js
@@ -12,7 +12,7 @@ class BootstrapResult extends Component {
             data = [
                 ["# Iterations", settings.bootstrap_iterations],
                 ["Bootstrap Seed", ff(settings.bootstrap_seed)],
-                ["Log-likelihood", ff(results.ll)],
+                ["-2* Log(Likelihood Ratio)", ff(results.ll)],
                 ["Observed Chi-square", ff(results.obs_chi_sq)],
                 [
                     <span key={0}>
@@ -21,7 +21,7 @@ class BootstrapResult extends Component {
                     ff(results.combined_pvalue),
                 ],
             ];
-        return <TwoColumnTable data={data} label="Bootstrap Results" />;
+        return <TwoColumnTable data={data} label="Bootstrap Results" colwidths={[40, 60]} />;
     }
 }
 BootstrapResult.propTypes = {
diff --git a/frontend/src/components/Output/NestedDichotomous/Summary.js b/frontend/src/components/Output/NestedDichotomous/Summary.js
index 9589f6f1..76432a88 100644
--- a/frontend/src/components/Output/NestedDichotomous/Summary.js
+++ b/frontend/src/components/Output/NestedDichotomous/Summary.js
@@ -20,7 +20,7 @@ class Summary extends Component {
                     </span>,
                     ff(results.combined_pvalue),
                 ],
-                ["D.O.F.", ff(results.dof)],
+                ["d.f.", ff(results.dof)],
                 [
                     <span key={1}>
                         Chi<sup>2</sup>
@@ -28,7 +28,7 @@ class Summary extends Component {
                     ff(results.summary.chi_squared),
                 ],
             ];
-        return <TwoColumnTable label="Summary" data={data} />;
+        return <TwoColumnTable label="Modeling Summary" data={data} />;
     }
 }
 Summary.propTypes = {
diff --git a/frontend/src/components/Output/OptionSetTable.js b/frontend/src/components/Output/OptionSetTable.js
index 5f9f9275..68e66f95 100644
--- a/frontend/src/components/Output/OptionSetTable.js
+++ b/frontend/src/components/Output/OptionSetTable.js
@@ -1,3 +1,4 @@
+import _ from "lodash";
 import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
@@ -11,6 +12,7 @@ import {
     distTypeOptions,
     litterSpecificCovariateOptions,
 } from "@/constants/optionsConstants";
+import {isHybridBmr} from "@/constants/optionsConstants";
 import {ff} from "@/utils/formatters";
 
 @inject("outputStore")
@@ -34,14 +36,16 @@ class OptionSetTable extends Component {
                     "Maximum Polynomial Degree",
                     getLabel(selectedDatasetOptions.degree, allDegreeOptions),
                 ],
-                ["Tail Probability", ff(selectedModelOptions.tail_probability)],
-                ["Confidence Level", ff(selectedModelOptions.confidence_level)],
+                isHybridBmr(selectedModelOptions.bmr_type)
+                    ? ["Tail Probability", ff(selectedModelOptions.tail_probability)]
+                    : null,
+                ["Confidence Level (one sided)", ff(selectedModelOptions.confidence_level)],
             ];
         } else if (getModelType === MODEL_DICHOTOMOUS) {
             rows = [
                 ["BMR Type", getLabel(selectedModelOptions.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(selectedModelOptions.bmr_value)],
-                ["Confidence Level", ff(selectedModelOptions.confidence_level)],
+                ["Confidence Level (one sided)", ff(selectedModelOptions.confidence_level)],
                 [
                     "Maximum Multistage Degree",
                     getLabel(selectedDatasetOptions.degree, allDegreeOptions),
@@ -51,7 +55,7 @@ class OptionSetTable extends Component {
             rows = [
                 ["BMR Type", getLabel(selectedModelOptions.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(selectedModelOptions.bmr_value)],
-                ["Confidence Level", ff(selectedModelOptions.confidence_level)],
+                ["Confidence Level (one sided)", ff(selectedModelOptions.confidence_level)],
                 ["Bootstrap Seed", selectedModelOptions.bootstrap_seed],
                 ["Bootstrap Iterations", selectedModelOptions.bootstrap_iterations],
                 [
@@ -66,7 +70,7 @@ class OptionSetTable extends Component {
             rows = [
                 ["BMR Type", getLabel(selectedModelOptions.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(selectedModelOptions.bmr_value)],
-                ["Confidence Level", ff(selectedModelOptions.confidence_level)],
+                ["Confidence Level (one sided)", ff(selectedModelOptions.confidence_level)],
                 ["Degree Setting", outputStore.multitumorDegreeInputSettings.join(", ")],
             ];
         } else {
@@ -83,14 +87,16 @@ class OptionSetTable extends Component {
                         <col width="40%" />
                     </colgroup>
                     <tbody>
-                        {rows.map((d, i) => {
-                            return (
-                                <tr key={i}>
-                                    <th className="bg-custom">{d[0]}</th>
-                                    <td>{d[1]}</td>
-                                </tr>
-                            );
-                        })}
+                        {rows
+                            .filter(d => !_.isNull(d))
+                            .map((d, i) => {
+                                return (
+                                    <tr key={i}>
+                                        <th className="bg-custom">{d[0]}</th>
+                                        <td>{d[1]}</td>
+                                    </tr>
+                                );
+                            })}
                     </tbody>
                 </table>
             </>
diff --git a/frontend/src/components/Output/Output.js b/frontend/src/components/Output/Output.js
index f3aea0b9..f87c1085 100644
--- a/frontend/src/components/Output/Output.js
+++ b/frontend/src/components/Output/Output.js
@@ -81,7 +81,7 @@ class Output extends Component {
 
         return (
             <div className="container-fluid mb-3">
-                <div className="row">
+                <div className="row py-2">
                     {outputStore.outputs.length > 1 ? (
                         <div className="col-lg-2">
                             <SelectInput
@@ -117,9 +117,9 @@ class Output extends Component {
                             </div>
                         </div>
                     ) : (
-                        <div className="row">
+                        <div className="row py-2">
                             <div className="col-lg-8">
-                                <h4>Frequentist Model Results</h4>
+                                <h4>Maximum Likelihood Approach Model Results</h4>
                                 <FrequentistResultTable />
                                 {canEdit ? <SelectModel /> : null}
                             </div>
@@ -134,7 +134,7 @@ class Output extends Component {
                     )
                 ) : null}
                 {selectedBayesian ? (
-                    <div className="row">
+                    <div className="row py-2">
                         <div className="col-lg-12">
                             <h4>Bayesian Model Results</h4>
                             <BayesianResultTable />
@@ -150,7 +150,7 @@ class Output extends Component {
                 ) : null}
 
                 {isFuture && !outputStore.isMultiTumor ? (
-                    <div className="row">
+                    <div className="row py-2">
                         {selectedFrequentist ? (
                             <div className="col col-lg-6">
                                 <DoseResponsePlot
diff --git a/frontend/src/constants/logicConstants.js b/frontend/src/constants/logicConstants.js
index 9cb9dd62..8b184a96 100644
--- a/frontend/src/constants/logicConstants.js
+++ b/frontend/src/constants/logicConstants.js
@@ -136,15 +136,15 @@ export const RULES = Object.freeze({
             enabledNested: true,
         },
         [RULES.ROI_LARGE]: {
-            name: "Abs(Residual of interest) too large",
-            notes: val => `|Residual for Dose Group Near BMD| > ${val}`,
+            name: "|Residual near BMD| too large",
+            notes: val => `|Residual Near BMD| > ${val}`,
             hasThreshold: true,
             enabledContinuous: true,
             enabledDichotomous: true,
             enabledNested: true,
         },
         [RULES.WARNINGS]: {
-            name: "BMDS model Warning",
+            name: "BMDS model warning",
             notes: val => "BMD output file included warning",
             hasThreshold: false,
             enabledContinuous: false,
@@ -200,7 +200,7 @@ export const RULES = Object.freeze({
             enabledNested: true,
         },
         [RULES.CONTROL_RESIDUAL_HIGH]: {
-            name: "Abs(Residual at control) too large",
+            name: "|Residual at control| too large",
             notes: val => `|Residual at control| > ${val}`,
             hasThreshold: true,
             enabledContinuous: true,
diff --git a/frontend/src/constants/modelConstants.js b/frontend/src/constants/modelConstants.js
index 35dfcc18..4fda10c1 100644
--- a/frontend/src/constants/modelConstants.js
+++ b/frontend/src/constants/modelConstants.js
@@ -78,7 +78,7 @@ const modelsList = {
     hasDegrees = new Set(["Multistage", "Polynomial"]),
     getNameFromDegrees = function(model) {
         const degree = model.parameters.names.length - 1;
-        return `Multistage ${degree}°`;
+        return `Multistage ${degree}`;
     };
 
 export {allModelOptions, getNameFromDegrees, hasDegrees, isLognormal, models, modelsList};
diff --git a/frontend/src/constants/optionsConstants.js b/frontend/src/constants/optionsConstants.js
index e79cf094..c471f673 100644
--- a/frontend/src/constants/optionsConstants.js
+++ b/frontend/src/constants/optionsConstants.js
@@ -44,6 +44,9 @@ export const options = {
         {value: 6, label: "Hybrid-Extra Risk"},
         {value: 7, label: "Hybrid-Added Risk"},
     ],
+    isHybridBmr = function(val) {
+        return val === 6 || val === 7;
+    },
     distTypeOptions = [
         {value: 1, label: "Normal + Constant"},
         {value: 2, label: "Normal + Non-constant"},
diff --git a/frontend/src/constants/plotting.js b/frontend/src/constants/plotting.js
index 2135a8ff..014695e0 100644
--- a/frontend/src/constants/plotting.js
+++ b/frontend/src/constants/plotting.js
@@ -112,9 +112,9 @@ export const getResponse = dataset => {
     },
     getCdfLayout = function(dataset) {
         let layout = _.cloneDeep(doseResponseLayout);
-        layout.title.text = "BMD Cumulative distribution function";
+        layout.title.text = "BMD Cumulative Distribution Function";
         layout.xaxis.title.text = getDoseLabel(dataset);
-        layout.yaxis.title.text = "Percentile";
+        layout.yaxis.title.text = "Cumulative Probability";
         layout.yaxis.range = [0, 1];
         return layout;
     },
diff --git a/tests/analysis/test_executor.py b/tests/analysis/test_executor.py
index fec5669b..8fbf25cf 100644
--- a/tests/analysis/test_executor.py
+++ b/tests/analysis/test_executor.py
@@ -169,17 +169,17 @@ def test_disttype(self, bmds3_complete_continuous):
         session = AnalysisSession.create(data, 0, 0)
         assert len(session.frequentist.models) == 5
         names = [model.name() for model in session.frequentist.models]
-        assert names == ["ExponentialM3", "ExponentialM5", "Hill", "Linear", "Power"]
+        assert names == ["Exponential 3", "Exponential 5", "Hill", "Linear", "Power"]
 
         data["options"][0]["dist_type"] = 2
         session = AnalysisSession.create(data, 0, 0)
         assert len(session.frequentist.models) == 5
         names = [model.name() for model in session.frequentist.models]
-        assert names == ["ExponentialM3", "ExponentialM5", "Hill", "Linear", "Power"]
+        assert names == ["Exponential 3", "Exponential 5", "Hill", "Linear", "Power"]
 
         # lognormal
         data["options"][0]["dist_type"] = 3
         session = AnalysisSession.create(data, 0, 0)
         assert len(session.frequentist.models) == 2
         names = [model.name() for model in session.frequentist.models]
-        assert names == ["ExponentialM3", "ExponentialM5"]
+        assert names == ["Exponential 3", "Exponential 5"]
diff --git a/tests/analysis/test_validators.py b/tests/analysis/test_validators.py
index 425e9aca..879b7573 100644
--- a/tests/analysis/test_validators.py
+++ b/tests/analysis/test_validators.py
@@ -350,7 +350,7 @@ def test_dichotomous(self, bmds3_complete_dichotomous):
         # check incidence > n
         check = deepcopy(dataset)
         check["incidences"][0] = check["ns"][0] + 1
-        with pytest.raises(PydanticValidationError, match="Incidence cannot be greater than N"):
+        with pytest.raises(PydanticValidationError, match="Incidence > N"):
             datasets.MaxDichotomousDatasetSchema(**check)
 
         # check minimums
diff --git a/tests/data/db.yaml b/tests/data/db.yaml
index e5f6cc52..4d7e79b3 100644
--- a/tests/data/db.yaml
+++ b/tests/data/db.yaml
@@ -1612,10 +1612,10 @@
               - 1
               model_notes:
               - '0':
-                - Control stdev. fit greater than threshold (2.312 > 1.5)
+                - Control stdev. fit > threshold (2.312 > 1.5)
                 '1':
-                - Goodness of fit p-value less than threshold (0 < 0.1)
-                - Abs(Residual of interest) greater than threshold (2.246 > 2.0)
+                - Goodness of fit p-value < threshold (0 < 0.1)
+                - '|Residual near BMD| > threshold (2.246 > 2.0)'
                 - Variance test failed (Test 2 p-value 2 < 0.05)
                 - Incorrect variance model (p-value 2 = 0), constant variance selected
                 '2': []
@@ -7067,8 +7067,8 @@
       2.0, "enabled_dichotomous": true, "enabled_continuous": false, "enabled_nested":
       true}]}, "results": {"recommended_model_index": null, "recommended_model_variable":
       null, "model_bin": [1], "model_notes": [{"0": ["Control stdev. fit greater than
-      threshold (2.312 > 1.5)"], "1": ["Goodness of fit p-value less than threshold
-      (0 < 0.1)", "Abs(Residual of interest) greater than threshold (2.246 > 2.0)",
+      threshold (2.312 > 1.5)"], "1": ["Goodness of fit p-value < threshold
+      (0 < 0.1)", "|Residual near BMD| > threshold (2.246 > 2.0)",
       "Constant variance test failed (p-value 2 < 0.05)", "Incorrect variance model
       (p-value 2 = 0), constant variance selected"], "2": []}]}}, "selected": {"model_index":
       null, "notes": ""}}, "bayesian": null}]}, "errors": [], "created": "2021-11-15T18:42:28.857Z",
@@ -7342,8 +7342,8 @@
       2.0, "enabled_dichotomous": true, "enabled_continuous": false, "enabled_nested":
       true}]}, "results": {"recommended_model_index": null, "recommended_model_variable":
       null, "model_bin": [1], "model_notes": [{"0": ["Control stdev. fit greater than
-      threshold (2.312 > 1.5)"], "1": ["Goodness of fit p-value less than threshold
-      (0 < 0.1)", "Abs(Residual of interest) greater than threshold (2.246 > 2.0)",
+      threshold (2.312 > 1.5)"], "1": ["Goodness of fit p-value < threshold
+      (0 < 0.1)", "|Residual near BMD| > threshold (2.246 > 2.0)",
       "Constant variance test failed (p-value 2 < 0.05)", "Incorrect variance model
       (p-value 2 = 0), constant variance selected"], "2": []}]}}, "selected": {"model_index":
       null, "notes": "No best fitting model selected"}}, "bayesian": null}], "analysis_id":
diff --git a/tests/integration/test_integration.py b/tests/integration/test_integration.py
index e435ce92..a05acc87 100644
--- a/tests/integration/test_integration.py
+++ b/tests/integration/test_integration.py
@@ -250,8 +250,8 @@ def test_multi_tumor(self):
             page.locator("#close-modal").click()
 
             # check one result (individual)
-            page.get_by_role("link", name="Multistage 1°*").click()
-            expect(page.get_by_role("dialog")).to_contain_text("Multistage 1°")
+            page.get_by_role("link", name="Multistage 1*").click()
+            expect(page.get_by_role("dialog")).to_contain_text("Multistage 1")
             page.locator("#close-modal").click()
 
             # Read-only

From 67ed92319d15ecddf5c9487169b30c1839cd59f1 Mon Sep 17 00:00:00 2001
From: Karen Hausman <74921039+hausman-gdit@users.noreply.github.com>
Date: Mon, 12 Feb 2024 16:20:50 -0500
Subject: [PATCH 24/24] 332 remove bmds 2.7 (#6)

* bmds3 collapse changes

* dueling formatters

* fixup gitlab actions?

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
---
 .github/workflows/main.yml                   | 14 ++++++--------
 bmds_server/analysis/executor.py             |  9 ++++-----
 bmds_server/analysis/models.py               |  6 +++---
 bmds_server/analysis/reporting/docx.py       |  3 +--
 bmds_server/analysis/reporting/excel.py      |  2 +-
 bmds_server/analysis/schema.py               |  2 +-
 bmds_server/analysis/transforms.py           |  8 ++++----
 bmds_server/analysis/validators/__init__.py  |  2 +-
 bmds_server/analysis/validators/options.py   |  8 ++++----
 bmds_server/analysis/validators/selectors.py |  2 +-
 compose/app/Dockerfile                       |  2 +-
 compose/app/test.py                          |  2 +-
 tests/analysis/test_api.py                   |  2 +-
 tests/analysis/test_executor.py              |  4 ++--
 tests/analysis/test_transforms.py            |  4 ++--
 tests/conftest.py                            |  2 +-
 16 files changed, 34 insertions(+), 38 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 2bbf609f..69c65e03 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -21,12 +21,12 @@ jobs:
     steps:
     - name: Checkout bmds-server
       uses: actions/checkout@v3
-    - name: Checkout bmds@next
+    - name: Checkout bmds@main
       uses: actions/checkout@v3
       with:
         repository: USEPA/bmds-private
         path: venv
-        ref: next
+        ref: main
         token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v4
       with:
@@ -55,8 +55,7 @@ jobs:
         export "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib:/usr/lib"
         sudo cp vendor/libnlopt.so /usr/local/lib/libnlopt.so.0
         sudo ln -s /lib/x86_64-linux-gnu/libgsl.so /usr/local/lib/libgsl.so.25
-        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bin/BMDS330/libDRBMD.so"
-        echo $BMD_DLL
+        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bmdscore.cpython-*-x86_64-linux-gnu.so"
         ldd $BMD_DLL
     - name: lint
       run: |
@@ -141,12 +140,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Checkout bmds@next
+    - name: Checkout bmds@main
       uses: actions/checkout@v3
       with:
         repository: USEPA/bmds-private
         path: venv
-        ref: next
+        ref: main
         token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v4
       with:
@@ -176,8 +175,7 @@ jobs:
         export "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib:/usr/lib"
         sudo cp vendor/libnlopt.so /usr/local/lib/libnlopt.so.0
         sudo ln -s /lib/x86_64-linux-gnu/libgsl.so /usr/local/lib/libgsl.so.25
-        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bin/BMDS330/libDRBMD.so"
-        echo $BMD_DLL
+        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bmdscore.cpython-*-x86_64-linux-gnu.so"
         ldd $BMD_DLL
     # https://github.community/t/how-to-retry-a-failed-step-in-github-actions-workflow/125880
     - name: run integration tests
diff --git a/bmds_server/analysis/executor.py b/bmds_server/analysis/executor.py
index 5b1d24e6..c09f9f98 100644
--- a/bmds_server/analysis/executor.py
+++ b/bmds_server/analysis/executor.py
@@ -3,11 +3,10 @@
 from typing import NamedTuple, Self
 
 import bmds
-from bmds.bmds3.constants import DistType
-from bmds.bmds3.models.multi_tumor import Multitumor, MultitumorBase
-from bmds.bmds3.sessions import BmdsSession
-from bmds.bmds3.types.nested_dichotomous import IntralitterCorrelation, LitterSpecificCovariate
-from bmds.constants import ModelClass
+from bmds.constants import DistType, ModelClass
+from bmds.models.multi_tumor import Multitumor, MultitumorBase
+from bmds.sessions import BmdsSession
+from bmds.types.nested_dichotomous import IntralitterCorrelation, LitterSpecificCovariate
 
 from .schema import AnalysisSessionSchema
 from .transforms import (
diff --git a/bmds_server/analysis/models.py b/bmds_server/analysis/models.py
index 59f8ead2..984bdcc9 100644
--- a/bmds_server/analysis/models.py
+++ b/bmds_server/analysis/models.py
@@ -8,10 +8,10 @@
 import bmds
 import pandas as pd
 import reversion
-from bmds.bmds3.batch import BatchBase, BmdsSessionBatch, MultitumorBatch
-from bmds.bmds3.recommender.recommender import RecommenderSettings
-from bmds.bmds3.types.sessions import VersionSchema
+from bmds.batch import BatchBase, BmdsSessionBatch, MultitumorBatch
 from bmds.constants import ModelClass
+from bmds.recommender.recommender import RecommenderSettings
+from bmds.types.sessions import VersionSchema
 from django.conf import settings
 from django.core.cache import cache
 from django.core.exceptions import ValidationError
diff --git a/bmds_server/analysis/reporting/docx.py b/bmds_server/analysis/reporting/docx.py
index 15c8bb48..d70dec8c 100644
--- a/bmds_server/analysis/reporting/docx.py
+++ b/bmds_server/analysis/reporting/docx.py
@@ -5,9 +5,8 @@
 
 import docx
 from bmds import __version__
-from bmds.bmds3.reporting import write_setting_p
 from bmds.datasets.transforms.polyk import PolyKAdjustment
-from bmds.reporting.styling import Report
+from bmds.reporting.styling import Report, write_setting_p
 from django.conf import settings
 from django.utils.timezone import now
 
diff --git a/bmds_server/analysis/reporting/excel.py b/bmds_server/analysis/reporting/excel.py
index cf2f893b..49b84bc3 100644
--- a/bmds_server/analysis/reporting/excel.py
+++ b/bmds_server/analysis/reporting/excel.py
@@ -3,8 +3,8 @@
 from typing import Any
 
 import pandas as pd
-from bmds.bmds3.sessions import BmdsSession
 from bmds.constants import Dtype
+from bmds.sessions import BmdsSession
 
 from ..executor import AnalysisSession, MultiTumorSession
 
diff --git a/bmds_server/analysis/schema.py b/bmds_server/analysis/schema.py
index 4ca46f1c..5c9fb13d 100644
--- a/bmds_server/analysis/schema.py
+++ b/bmds_server/analysis/schema.py
@@ -2,8 +2,8 @@
 from io import StringIO
 
 import pandas as pd
-from bmds.bmds3.types.sessions import VersionSchema
 from bmds.datasets.transforms.polyk import PolyKAdjustment
+from bmds.types.sessions import VersionSchema
 from pydantic import BaseModel, Field, field_validator
 from rest_framework.schemas.openapi import SchemaGenerator
 
diff --git a/bmds_server/analysis/transforms.py b/bmds_server/analysis/transforms.py
index 61383872..6f2ee2f0 100644
--- a/bmds_server/analysis/transforms.py
+++ b/bmds_server/analysis/transforms.py
@@ -2,11 +2,11 @@
 from enum import StrEnum
 
 import bmds
-from bmds.bmds3.types.continuous import ContinuousModelSettings
-from bmds.bmds3.types.dichotomous import DichotomousModelSettings
-from bmds.bmds3.types.nested_dichotomous import NestedDichotomousModelSettings
-from bmds.bmds3.types.priors import PriorClass
 from bmds.constants import Dtype
+from bmds.types.continuous import ContinuousModelSettings
+from bmds.types.dichotomous import DichotomousModelSettings
+from bmds.types.nested_dichotomous import NestedDichotomousModelSettings
+from bmds.types.priors import PriorClass
 
 from .validators.datasets import AdverseDirection
 
diff --git a/bmds_server/analysis/validators/__init__.py b/bmds_server/analysis/validators/__init__.py
index 3836a137..b13f9db7 100644
--- a/bmds_server/analysis/validators/__init__.py
+++ b/bmds_server/analysis/validators/__init__.py
@@ -1,4 +1,4 @@
-from bmds.bmds3.recommender import RecommenderSettings
+from bmds.recommender import RecommenderSettings
 
 from ...common.validation import pydantic_validate
 from .datasets import validate_datasets
diff --git a/bmds_server/analysis/validators/options.py b/bmds_server/analysis/validators/options.py
index 33778f65..3bce3d8e 100644
--- a/bmds_server/analysis/validators/options.py
+++ b/bmds_server/analysis/validators/options.py
@@ -1,10 +1,10 @@
 from typing import Any
 
 import bmds
-from bmds.bmds3.constants import DistType
-from bmds.bmds3.types.continuous import ContinuousRiskType
-from bmds.bmds3.types.dichotomous import DichotomousRiskType
-from bmds.bmds3.types.nested_dichotomous import LitterSpecificCovariate
+from bmds.constants import DistType
+from bmds.types.continuous import ContinuousRiskType
+from bmds.types.dichotomous import DichotomousRiskType
+from bmds.types.nested_dichotomous import LitterSpecificCovariate
 from django.conf import settings
 from django.core.exceptions import ValidationError
 from pydantic import BaseModel, Field
diff --git a/bmds_server/analysis/validators/selectors.py b/bmds_server/analysis/validators/selectors.py
index 6cd38d69..4cc01e0a 100644
--- a/bmds_server/analysis/validators/selectors.py
+++ b/bmds_server/analysis/validators/selectors.py
@@ -1,4 +1,4 @@
-from bmds.bmds3.selected import SelectedModelSchema
+from bmds.selected import SelectedModelSchema
 from pydantic import BaseModel
 
 
diff --git a/compose/app/Dockerfile b/compose/app/Dockerfile
index b44fd73c..c48a853a 100644
--- a/compose/app/Dockerfile
+++ b/compose/app/Dockerfile
@@ -42,5 +42,5 @@ USER app
 
 ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
-RUN ldd /usr/local/lib/python3.11/site-packages/bmds/bmdscore.cpython-311-x86_64-linux-gnu.so && \
+RUN ldd /usr/local/lib/python3.11/site-packages/bmds/bmdscore.cpython-*-x86_64-linux-gnu.so && \
     python /app/test.py
diff --git a/compose/app/test.py b/compose/app/test.py
index c326ec45..ff6c8563 100644
--- a/compose/app/test.py
+++ b/compose/app/test.py
@@ -1,5 +1,5 @@
 import bmds
-from bmds.bmds3.models.dichotomous import Logistic
+from bmds.models.dichotomous import Logistic
 
 dataset = bmds.DichotomousDataset(
     doses=[0, 50, 100, 150, 200], ns=[100, 100, 100, 100, 100], incidences=[0, 5, 30, 65, 90]
diff --git a/tests/analysis/test_api.py b/tests/analysis/test_api.py
index 3f43b76f..1b03aed5 100644
--- a/tests/analysis/test_api.py
+++ b/tests/analysis/test_api.py
@@ -4,7 +4,7 @@
 import docx
 import pandas as pd
 import pytest
-from bmds.bmds3.recommender import RecommenderSettings
+from bmds.recommender import RecommenderSettings
 from django.urls import reverse
 from rest_framework.test import APIClient
 
diff --git a/tests/analysis/test_executor.py b/tests/analysis/test_executor.py
index 8fbf25cf..ff950713 100644
--- a/tests/analysis/test_executor.py
+++ b/tests/analysis/test_executor.py
@@ -1,7 +1,7 @@
 from copy import deepcopy
 
-from bmds.bmds3.constants import ContinuousModelIds, DichotomousModelIds
-from bmds.bmds3.types.priors import PriorClass
+from bmds.constants import ContinuousModelIds, DichotomousModelIds
+from bmds.types.priors import PriorClass
 
 from bmds_server.analysis.executor import AnalysisSession
 
diff --git a/tests/analysis/test_transforms.py b/tests/analysis/test_transforms.py
index 484c6db8..d138cc43 100644
--- a/tests/analysis/test_transforms.py
+++ b/tests/analysis/test_transforms.py
@@ -1,8 +1,8 @@
 import bmds
 import pytest
-from bmds.bmds3.types.continuous import ContinuousRiskType
-from bmds.bmds3.types.dichotomous import DichotomousRiskType
 from bmds.constants import M_Exponential, M_ExponentialM3, M_ExponentialM5
+from bmds.types.continuous import ContinuousRiskType
+from bmds.types.dichotomous import DichotomousRiskType
 
 from bmds_server.analysis import transforms
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 87336b19..365942d3 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 
 import pytest
-from bmds.bmds3.recommender import RecommenderSettings
+from bmds.recommender import RecommenderSettings
 from django.core.management import call_command