diff --git a/bmds_ui/analysis/executor.py b/bmds_ui/analysis/executor.py
index e31f03e2..edff5d8a 100644
--- a/bmds_ui/analysis/executor.py
+++ b/bmds_ui/analysis/executor.py
@@ -4,7 +4,6 @@
import pybmds
from pybmds.constants import DistType, ModelClass
-from pybmds.models.multi_tumor import Multitumor
from pybmds.session import Session
from pybmds.types.nested_dichotomous import IntralitterCorrelation, LitterSpecificCovariate
@@ -179,7 +178,7 @@ class MultiTumorSession(NamedTuple):
"""
option_index: int
- session: Multitumor | None
+ session: pybmds.Multitumor | None
@classmethod
def run(cls, inputs: dict, option_index: int) -> AnalysisSessionSchema:
@@ -202,7 +201,7 @@ def create(cls, inputs: dict, option_index: int) -> Self:
model_settings = build_model_settings(
dataset_type, PriorEnum.frequentist_restricted, options, {}
)
- session = Multitumor(datasets, degrees=degrees, settings=model_settings)
+ session = pybmds.Multitumor(datasets, degrees=degrees, settings=model_settings)
return cls(option_index=option_index, session=session)
def execute(self):
@@ -213,7 +212,7 @@ def deserialize(cls, data: dict) -> Self:
obj = AnalysisSessionSchema.model_validate(data)
return cls(
option_index=obj.option_index,
- session=Multitumor.from_serialized(obj.frequentist),
+ session=pybmds.Multitumor.from_serialized(obj.frequentist),
)
def to_schema(self) -> AnalysisSessionSchema:
diff --git a/bmds_ui/desktop/actions.py b/bmds_ui/desktop/actions.py
index 2d58617b..0eb4657a 100644
--- a/bmds_ui/desktop/actions.py
+++ b/bmds_ui/desktop/actions.py
@@ -203,8 +203,8 @@ def create_shortcut(no_input: bool = False):
shortcut.write_text(script)
console = Console()
- console.print("BMDS Desktop Manger Created:", style="magenta")
- console.print("----------------------------", style="magenta")
+ console.print("BMDS Desktop Manager Created:", style="magenta")
+ console.print("-----------------------------", style="magenta")
console.print(shortcut, style="cyan")
console.print("\nOpening this file will start BMDS Desktop.")
console.print("You can move this file or create a shortcut to it.\n")
diff --git a/bmds_ui/desktop/components/database_form.py b/bmds_ui/desktop/components/database_form.py
index 9e5e75b2..c7194e18 100644
--- a/bmds_ui/desktop/components/database_form.py
+++ b/bmds_ui/desktop/components/database_form.py
@@ -73,6 +73,18 @@ def additional_path_checks(path: Path):
raise ValueError(f"Cannot edit database {path}. Is this a sqlite database?") from None
+def check_duplicates(dbs: list[Database], db: Database):
+ duplicate = next((el for el in dbs if el.id != db.id and el.path == db.path), None)
+ if duplicate:
+ raise ValueError(
+ f"An existing project ({duplicate.name}) already exists with this filename: {db.path}"
+ )
+
+ duplicate = next((el for el in dbs if el.id != db.id and el.name == db.name), None)
+ if duplicate:
+ raise ValueError(f"An existing project already exists with this name: {db.name}")
+
+
class NullWidget(Widget):
DEFAULT_CSS = """
NullWidget {
@@ -190,12 +202,19 @@ def compose(self) -> ComposeResult:
)
def db_valid(self) -> Database:
- db = Database(
+ kw = dict(
name=self.query_one("#name").value,
description=self.query_one("#description").value,
path=Path(self.query_one("#path").value) / self.query_one("#filename").value,
)
+ if self.db is None:
+ db = Database(**kw)
+ else:
+ db = self.db.model_copy()
+ for key, value in kw.items():
+ setattr(db, key, value)
additional_path_checks(db.path)
+ check_duplicates(Config.get().databases, db)
return db
@on(Button.Pressed, "#db-create")
diff --git a/docs/development.md b/docs/development.md
index 3c3be36b..f98fab38 100644
--- a/docs/development.md
+++ b/docs/development.md
@@ -3,10 +3,10 @@
Make sure you have the following applications installed locally:
- [Git](https://git-scm.com/)
-- [Python](https://www.python.org/) == 3.11
-- [Node.js](https://nodejs.org) == 18
+- [Python](https://www.python.org/) ≥ 3.12
+- [Node.js](https://nodejs.org) ≥ 20
- [Yarn](https://yarnpkg.com/)
-- [PostgreSQL](https://www.postgresql.org/) >= 16
+- [PostgreSQL](https://www.postgresql.org/) ≥ 16
If installing on Windows, these packages are available using [miniconda](https://docs.conda.io/en/latest/miniconda.html).
diff --git a/frontend/src/components/Data/SelectModelType.js b/frontend/src/components/Data/SelectModelType.js
index be92bf46..f84c0d31 100644
--- a/frontend/src/components/Data/SelectModelType.js
+++ b/frontend/src/components/Data/SelectModelType.js
@@ -20,9 +20,9 @@ class SelectModelType extends Component {
text="New"
onClick={dataStore.addDataset}
/>
- {" "}
+
dataStore.setModelType(value)}
value={dataStore.model_type}
choices={dataStore.getFilteredDatasetTypes.map(item => {
diff --git a/frontend/src/components/IndividualModel/Summary.js b/frontend/src/components/IndividualModel/Summary.js
index 7aa06ab7..2e498af8 100644
--- a/frontend/src/components/IndividualModel/Summary.js
+++ b/frontend/src/components/IndividualModel/Summary.js
@@ -51,7 +51,7 @@ class Summary extends Component {
}
}
- return ;
+ return ;
}
}
Summary.propTypes = {
diff --git a/scripts/bmds-online-api.ipynb b/scripts/bmds-online-api.ipynb
deleted file mode 100644
index b52553b0..00000000
--- a/scripts/bmds-online-api.ipynb
+++ /dev/null
@@ -1,400 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# BMDS Online API\n",
- "\n",
- "A work in progress to demonstrate how to use the BMDS Online API."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 1,
- "metadata": {},
- "outputs": [],
- "source": [
- "import json\n",
- "import time\n",
- "from pathlib import Path\n",
- "\n",
- "import requests"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "metadata": {},
- "outputs": [],
- "source": [
- "payload = \"\"\"{\"editKey\":\"gs2bhkbqu4q0\",\"partial\":true,\"data\":{\"analysis_name\":\"demo\",\"analysis_description\":\"test\",\"dataset_type\":\"D\",\"models\":{\"frequentist_restricted\":[\"Dichotomous-Hill\",\"Gamma\",\"LogLogistic\",\"LogProbit\",\"Weibull\"]},\"datasets\":[{\"ns\":[9,9,11,10,7],\"doses\":[0,0.46,1.39,4.17,12.5],\"enabled\":true,\"dataset_id\":0,\"incidences\":[0,0,3,2,3],\"model_type\":\"DM\",\"column_names\":{\"ns\":\"N\",\"doses\":\"Dose\",\"incidences\":\"Incidence\"},\"dataset_name\":\"Dataset #1\"}],\"options\":[{\"bmr_type\":\"Extra\",\"bmr_value\":0.1,\"background\":\"Estimated\",\"confidence_level\":0.95}],\"logic\":{\"rules\":{\"gof\":{\"threshold\":0.1,\"failure_bin\":0,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"dof_zero\":{\"threshold\":\"\",\"failure_bin\":0,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"high_bmd\":{\"threshold\":1,\"failure_bin\":1,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"warnings\":{\"threshold\":\"\",\"failure_bin\":1,\"enabled_nested\":false,\"enabled_continuous\":false,\"enabled_dichotomous\":false},\"high_bmdl\":{\"threshold\":1,\"failure_bin\":1,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"roi_large\":{\"threshold\":2,\"failure_bin\":0,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"gof_cancer\":{\"threshold\":0.05,\"failure_bin\":0,\"enabled_nested\":false,\"enabled_continuous\":false,\"enabled_dichotomous\":true},\"aic_missing\":{\"threshold\":\"\",\"failure_bin\":2,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"bmd_missing\":{\"threshold\":\"\",\"failure_bin\":2,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"roi_missing\":{\"threshold\":\"\",\"failure_bin\":2,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"bmdl_missing\":{\"threshold\":\"\",\"failure_bin\":2,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"bmdu_missing\":{\"threshold\":\"\",\"failure_bin\":1,\"enabled_nested\":false,\"enabled_continuous\":false,\"enabled_dichotomous\":false},\"low_bmd_fail\":{\"threshold\":10,\"failure_bin\":0,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"low_bmd_warn\":{\"threshold\":3,\"failure_bin\":1,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"variance_fit\":{\"threshold\":0.05,\"failure_bin\":0,\"enabled_nested\":false,\"enabled_continuous\":true,\"enabled_dichotomous\":false},\"low_bmdl_fail\":{\"threshold\":10,\"failure_bin\":0,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"low_bmdl_warn\":{\"threshold\":3,\"failure_bin\":1,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"variance_type\":{\"threshold\":0.05,\"failure_bin\":1,\"enabled_nested\":false,\"enabled_continuous\":true,\"enabled_dichotomous\":false},\"control_stdev_fit\":{\"threshold\":1.5,\"failure_bin\":1,\"enabled_nested\":false,\"enabled_continuous\":true,\"enabled_dichotomous\":false},\"bmd_bmdl_ratio_fail\":{\"threshold\":20,\"failure_bin\":0,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"bmd_bmdl_ratio_warn\":{\"threshold\":3,\"failure_bin\":1,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true},\"control_residual_high\":{\"threshold\":2,\"failure_bin\":1,\"enabled_nested\":true,\"enabled_continuous\":true,\"enabled_dichotomous\":true}},\"recommend_viable\":true,\"recommend_questionable\":false,\"sufficiently_close_bmdl\":3}}}\"\"\"\n",
- "logic = json.loads(payload)['data']['logic']"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "metadata": {},
- "outputs": [],
- "source": [
- "data = {\n",
- " \"analysis_name\": \"demo\",\n",
- " \"analysis_description\": \"test\",\n",
- " \"dataset_type\": \"D\",\n",
- " \"models\": {\n",
- " \"frequentist_unrestricted\": [\n",
- " \"Dichotomous-Hill\",\n",
- " \"Gamma\",\n",
- " \"LogLogistic\",\n",
- " \"LogProbit\",\n",
- " \"Logistic\",\n",
- " \"Probit\",\n",
- " \"Weibull\",\n",
- " ]\n",
- " },\n",
- " \"datasets\": [\n",
- " {\n",
- " \"ns\": [9, 9, 11, 10, 7],\n",
- " \"doses\": [0, 0.46, 1.39, 4.17, 12.5],\n",
- " \"enabled\": True,\n",
- " \"dataset_id\": 0,\n",
- " \"incidences\": [0, 0, 3, 2, 3],\n",
- " \"model_type\": \"DM\",\n",
- " \"column_names\": {\n",
- " \"ns\": \"N\",\n",
- " \"doses\": \"Dose\",\n",
- " \"incidences\": \"Incidence\"\n",
- " },\n",
- " \"dataset_name\": \"Dataset #1\",\n",
- " }\n",
- " ],\n",
- " \"options\": [\n",
- " {\"bmr_type\": \"Extra\", \"bmr_value\": 0.1, \"background\": \"Estimated\", \"confidence_level\": 0.95}\n",
- " ],\n",
- " \"logic\": logic\n",
- "}"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
- "metadata": {},
- "outputs": [],
- "source": [
- "root = \"http://127.0.0.1:5550\"\n",
- "create_url = \"/api/v1/job/\""
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "201\n"
- ]
- }
- ],
- "source": [
- "resp = requests.post(root + create_url, json=dict(inputs=data))\n",
- "print(resp.status_code)\n",
- "output = resp.json()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Polling...\n"
- ]
- }
- ],
- "source": [
- "poll_url = root + output['api_url']\n",
- "while output['is_finished'] is False:\n",
- " print(\"Polling...\")\n",
- " time.sleep(1)\n",
- " resp = requests.get(poll_url)\n",
- " output = resp.json()\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "{'results': {'aic': 41.50669368126711,\n",
- " 'bmd': 0.9447511030013629,\n",
- " 'fit': {'cov': [[1964909.0730664653,\n",
- " 2.2908012128639843,\n",
- " 1.7985458979813416,\n",
- " -83.8552592379433],\n",
- " [2.2908012130249538,\n",
- " 0.2556226264923172,\n",
- " -1.009759410085084,\n",
- " -1.1009683696920616],\n",
- " [1.7985459004171105,\n",
- " -1.0097594100850777,\n",
- " 24.85841578447824,\n",
- " -21.093255211304268],\n",
- " [-83.85525924116398,\n",
- " -1.1009683696920571,\n",
- " -21.093255211304324,\n",
- " 131.99131800494922]],\n",
- " 'max': 16.753346840633554,\n",
- " 'model': {'id': 1, 'params': ['a', 'b', 'c', 'd'], 'verbose': 'Hill'},\n",
- " 'params': [-17.999987391264558,\n",
- " -0.8564043055751586,\n",
- " -0.27239291611321903,\n",
- " 7.234503578715854],\n",
- " 'bmd_dist': [[0.7288911813952538,\n",
- " 0.7354971392376395,\n",
- " 0.7422288004574837,\n",
- " 0.7491445964995801,\n",
- " 0.7562259655003359,\n",
- " 0.7634975845152987,\n",
- " 0.7709282140764542,\n",
- " 0.7784700949637998,\n",
- " 0.7861591092594095,\n",
- " 0.7940647828450534,\n",
- " 0.8021347049384774,\n",
- " 0.8102664655046556,\n",
- " 0.8184908988066019,\n",
- " 0.8268243073394,\n",
- " 0.8352766355476002,\n",
- " 0.8439030835661998,\n",
- " 0.852650071757209,\n",
- " 0.8614612942044027,\n",
- " 0.8702535099862481,\n",
- " 0.8787698923348418,\n",
- " 0.8871733900662253,\n",
- " 0.8957078237978783,\n",
- " 0.9043130920840636,\n",
- " 0.9130542853836429,\n",
- " 0.921855955566993,\n",
- " 0.9299878265352295,\n",
- " 0.9374189207649705,\n",
- " 0.9447511030013629,\n",
- " 0.9523006554929304,\n",
- " 0.9598128523233402,\n",
- " 0.9670620880212893,\n",
- " 0.9740329260788917,\n",
- " 0.9809184720749853,\n",
- " 0.9879053941521294,\n",
- " 0.9949346574431424,\n",
- " 1.0017645838607359,\n",
- " 1.0082257310596825,\n",
- " 1.014416147773569,\n",
- " 1.020471522945165,\n",
- " 1.026498362113175,\n",
- " 1.0324527303658582,\n",
- " 1.0382915429776782,\n",
- " 1.0439768743621032,\n",
- " 1.0494868039253518,\n",
- " 1.0548500581718536,\n",
- " 1.0601049459417218,\n",
- " 1.0652874723821535,\n",
- " 1.0703817216017375,\n",
- " 1.0753826385651981,\n",
- " 1.0803012241845844,\n",
- " 1.0851484793719464,\n",
- " 1.0898970172862983,\n",
- " 1.094541748161996,\n",
- " 1.099131268224416,\n",
- " 1.103714184405928],\n",
- " [0.365,\n",
- " 0.37,\n",
- " 0.375,\n",
- " 0.38,\n",
- " 0.385,\n",
- " 0.39,\n",
- " 0.395,\n",
- " 0.4,\n",
- " 0.405,\n",
- " 0.41,\n",
- " 0.415,\n",
- " 0.42,\n",
- " 0.425,\n",
- " 0.43,\n",
- " 0.435,\n",
- " 0.44,\n",
- " 0.445,\n",
- " 0.45,\n",
- " 0.455,\n",
- " 0.46,\n",
- " 0.465,\n",
- " 0.47,\n",
- " 0.475,\n",
- " 0.48,\n",
- " 0.485,\n",
- " 0.49,\n",
- " 0.495,\n",
- " 0.5,\n",
- " 0.505,\n",
- " 0.51,\n",
- " 0.515,\n",
- " 0.52,\n",
- " 0.525,\n",
- " 0.53,\n",
- " 0.535,\n",
- " 0.54,\n",
- " 0.545,\n",
- " 0.55,\n",
- " 0.555,\n",
- " 0.56,\n",
- " 0.565,\n",
- " 0.57,\n",
- " 0.575,\n",
- " 0.58,\n",
- " 0.585,\n",
- " 0.59,\n",
- " 0.595,\n",
- " 0.6,\n",
- " 0.605,\n",
- " 0.61,\n",
- " 0.615,\n",
- " 0.62,\n",
- " 0.625,\n",
- " 0.63,\n",
- " 0.635]],\n",
- " 'model_df': 3.9999999999999782,\n",
- " 'total_df': 0.0,\n",
- " 'dist_numE': 200,\n",
- " 'num_params': 4},\n",
- " 'gof': {'df': 1.0000000000000218,\n",
- " 'p_value': 0.3922799121202948,\n",
- " 'expected': [1.3707154390275478e-07,\n",
- " 0.007401528275540834,\n",
- " 2.924434609814579,\n",
- " 2.980783751678894,\n",
- " 2.0866379971131757],\n",
- " 'residual': [-0.00037023174351040564,\n",
- " -0.08603213513298874,\n",
- " 0.044187758489693876,\n",
- " -0.568078074124869,\n",
- " 0.6322944716390008],\n",
- " 'test_statistic': 0.7318632205140916},\n",
- " 'bmdl': 0.0,\n",
- " 'bmdu': -9999.0,\n",
- " 'bounded': [False, False, False, False],\n",
- " 'model_name': 'Hill',\n",
- " 'model_class': 'Hill'},\n",
- " 'settings': {'bmr': 0.1,\n",
- " 'alpha': 0.95,\n",
- " 'burnin': 20,\n",
- " 'degree': 3,\n",
- " 'samples': 100,\n",
- " 'bmr_type': 2},\n",
- " 'has_output': True,\n",
- " 'model_name': 'Hill',\n",
- " 'model_class': 1,\n",
- " 'model_index': 0,\n",
- " 'model_version': 'BMDS330',\n",
- " 'execution_halted': False}"
- ]
- },
- "execution_count": 7,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "output['outputs']['outputs'][0]['models'][0]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 8,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "44082"
- ]
- },
- "execution_count": 8,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "excel_url = root + output['word_url']\n",
- "resp = requests.get(excel_url)\n",
- "Path('~/Desktop/demo.docx').write_bytes(resp.content)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 9,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "6292"
- ]
- },
- "execution_count": 9,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "word_url = root + output['excel_url']\n",
- "resp = requests.get(word_url)\n",
- "Path('~/Desktop/demo.xlsx').write_bytes(resp.content)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 10,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "complete!\n"
- ]
- }
- ],
- "source": [
- "print('complete!')"
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.11.9"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/tests/analysis/test_api.py b/tests/analysis/test_api.py
index 0dd7b62b..507c673d 100644
--- a/tests/analysis/test_api.py
+++ b/tests/analysis/test_api.py
@@ -17,6 +17,15 @@ def check_error(response: dict, type: str, loc: list, msg: str):
assert response["msg"] == msg
+analyses = [
+ "432a6083-f9aa-4de2-a71f-a6488b4c5bf1", # dichotomous
+ "cfe458aa-2313-44c0-9346-f4931567bef0", # continuous summary
+ "09c09d22-2e1a-413c-b350-6b19969f6533", # continuous individual
+ "4459f728-05f7-4057-a27c-174822a0313d", # nested dichotomous
+ "2f86f324-911d-4194-97d1-fc7c3f5d0c72", # multitumor
+]
+
+
@pytest.mark.django_db
class TestAnalysisViewSet:
def test_auth(self, complete_continuous):
@@ -245,16 +254,18 @@ def test_model_selection(self, complete_dichotomous):
value = response.data["outputs"]["outputs"][0]["frequentist"]["selected"]
assert value == {"model_index": None, "notes": "no notes"}
- def test_excel(self):
+ @pytest.mark.parametrize("pk", analyses)
+ def test_excel(self, pk):
client = APIClient()
- analysis = Analysis.objects.get(pk="ded15870-8986-4d5b-b924-ef9036b2e17e")
+ analysis = Analysis.objects.get(pk=pk)
url = reverse("api:analysis-excel", args=(analysis.id,))
resp = client.get(url)
assert resp.status_code == 200
- def test_word(self):
+ @pytest.mark.parametrize("pk", analyses)
+ def test_word(self, pk):
client = APIClient()
- analysis = Analysis.objects.get(pk="ded15870-8986-4d5b-b924-ef9036b2e17e")
+ analysis = Analysis.objects.get(pk=pk)
url = reverse("api:analysis-word", args=(analysis.id,))
resp = client.get(url)
assert resp.status_code == 200
diff --git a/tests/analysis/test_models.py b/tests/analysis/test_models.py
index 5f9276ac..445b907e 100644
--- a/tests/analysis/test_models.py
+++ b/tests/analysis/test_models.py
@@ -95,7 +95,6 @@ def test_dichotomous(self, complete_dichotomous, data_path, rewrite_data_files):
write_excel(df, data_path / "reports/dichotomous.xlsx")
(data_path / "reports/dichotomous.docx").write_bytes(docx.getvalue())
- @pytest.mark.xfail
def test_nested_dichotomous(self, bmds_complete_nd, data_path, rewrite_data_files):
analysis = Analysis.objects.create(inputs=bmds_complete_nd)
diff --git a/tests/data/db.yaml b/tests/data/db.yaml
index abc1e4a9..dacf9f6a 100644
--- a/tests/data/db.yaml
+++ b/tests/data/db.yaml
@@ -699,7 +699,7 @@
recommend_questionable: false
sufficiently_close_bmdl: 3
dataset_type: C
- analysis_name: continuous
+ analysis_name: continuous summary
dataset_options:
- degree: 0
enabled: true
@@ -1767,7 +1767,6 @@
- model: analysis.analysis
pk: ded15870-8986-4d5b-b924-ef9036b2e17e
fields:
- collections: []
created: 2024-05-14 19:17:13.442351+00:00
deletion_date: 2024-11-10 19:18:13.839491+00:00
ended: 2024-05-14 19:18:13.839482+00:00
@@ -5141,6 +5140,9414 @@
option_index: 0
starred: false
started: 2024-05-14 19:18:13.442351+00:00
+- model: analysis.analysis
+ pk: 432a6083-f9aa-4de2-a71f-a6488b4c5bf1
+ fields:
+ password: up37taqueuwm
+ inputs:
+ models:
+ frequentist_unrestricted:
+ - Logistic
+ - Probit
+ options:
+ - bmr_type: 1
+ bmr_value: 0.1
+ confidence_level: 0.95
+ datasets:
+ - ns:
+ - 20
+ - 20
+ - 20
+ - 20
+ - 20
+ doses:
+ - 0
+ - 50
+ - 100
+ - 200
+ - 400
+ dtype: D
+ metadata:
+ id: 0
+ name: 'Dataset #1'
+ dose_name: Dose
+ dose_units: ''
+ response_name: Incidence
+ response_units: ''
+ incidences:
+ - 0
+ - 1
+ - 2
+ - 10
+ - 19
+ recommender:
+ rules:
+ - threshold: 0.1
+ rule_class: gof
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: dof_zero
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 1
+ rule_class: high_bmd
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: warnings
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: false
+ enabled_dichotomous: false
+ - threshold: 1
+ rule_class: high_bmdl
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 2
+ rule_class: roi_large
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 0.05
+ rule_class: gof_cancer
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: false
+ enabled_dichotomous: false
+ - threshold: null
+ rule_class: aic_missing
+ failure_bin: 2
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: bmd_missing
+ failure_bin: 2
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: roi_missing
+ failure_bin: 2
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: bmdl_missing
+ failure_bin: 2
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: bmdu_missing
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: false
+ enabled_dichotomous: false
+ - threshold: 10
+ rule_class: low_bmd_fail
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 3
+ rule_class: low_bmd_warn
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 0.05
+ rule_class: variance_fit
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: true
+ enabled_dichotomous: false
+ - threshold: 10
+ rule_class: low_bmdl_fail
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 3
+ rule_class: low_bmdl_warn
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 0.05
+ rule_class: variance_type
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: false
+ enabled_dichotomous: false
+ - threshold: 1.5
+ rule_class: control_stdev_fit
+ failure_bin: 0
+ enabled_nested: false
+ enabled_continuous: true
+ enabled_dichotomous: false
+ - threshold: 20
+ rule_class: bmd_bmdl_ratio_fail
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 3
+ rule_class: bmd_bmdl_ratio_warn
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 2
+ rule_class: control_residual_high
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ enabled: true
+ recommend_viable: true
+ recommend_questionable: false
+ sufficiently_close_bmdl: 3
+ dataset_type: D
+ analysis_name: dichotomous
+ dataset_options:
+ - degree: 3
+ enabled: true
+ dataset_id: 0
+ outputs:
+ outputs:
+ - error: null
+ bayesian: null
+ frequentist:
+ id: null
+ name: ''
+ models:
+ - name: Logistic
+ results:
+ bmd: 102.86343217689623
+ fit:
+ aic: 61.897203949777676
+ chisq: 0.97883107598887
+ bmd_dist:
+ - - 72.70299512909745
+ - 73.7871236124494
+ - 74.73646852250444
+ - 75.58369807800183
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+ model_df: 2.0
+ total_df: 0.0
+ bic_equiv: -24.153070876789652
+ loglikelihood: -28.948601974888838
+ gof:
+ df: 3.0
+ roi: -0.16379073945264083
+ p_value: 0.8063740234536434
+ eb_lower:
+ - 0.004574749374156553
+ - 0.0026155551366913435
+ - 0.017512638773429286
+ - 0.2785367024207322
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+ eb_upper:
+ - 0.15655040867866274
+ - 0.242397087110846
+ - 0.3113874876688261
+ - 0.7214632975792677
+ - 1.02443110332393
+ expected:
+ - 0.3770364540353177
+ - 0.9362459814799984
+ - 2.230579020833315
+ - 9.011628298304203
+ - 19.44451043906993
+ residual:
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+ - 0.4441881766764077
+ - -0.604867854750647
+ test_statistic: 0.97883107598887
+ bmdl: 77.07242298367221
+ bmdu: 131.54556240658434
+ deviance:
+ df:
+ - -9999
+ - 3
+ - 4
+ ll:
+ - -28.30521281286277
+ - -28.948601974888838
+ - -62.686945757242626
+ names:
+ - Full model
+ - Fitted model
+ - Reduced model
+ params:
+ - 5
+ - 2
+ - 1
+ p_value:
+ - -9999.0
+ - 0.7322750633195843
+ - 4.141131881851834e-14
+ deviance:
+ - -9999.0
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+ plotting:
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+ analysis_name: Nested Dichotomous
+ dataset_options:
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+ name: ''
+ models:
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+ last_updated: 2024-08-22 15:25:46.872461+00:00
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+ min_value: -100.0
+ initial_value: 0.0
+ - name: v
+ type: 0
+ stdev: 0.0
+ max_value: 100.0
+ min_value: -100.0
+ initial_value: 0.0
+ - name: k
+ type: 0
+ stdev: 0.0
+ max_value: 5.0
+ min_value: 0.0
+ initial_value: 0.0
+ - name: n
+ type: 0
+ stdev: 0.0
+ max_value: 18.0
+ min_value: 1.0
+ initial_value: 1.0
+ overrides: null
+ prior_class: 1
+ variance_priors:
+ - name: rho
+ type: 0
+ stdev: 0.0
+ max_value: 18.0
+ min_value: -18.0
+ initial_value: 0.0
+ - name: alpha
+ type: 0
+ stdev: 0.0
+ max_value: 18.0
+ min_value: -18.0
+ initial_value: 0.0
+ samples: 0
+ bmr_type: 2
+ disttype: 2
+ tail_prob: 0.01
+ is_increasing: true
+ model_class:
+ id: 6
+ params:
+ - g
+ - v
+ - k
+ - n
+ verbose: Hill
+ model_form_str: P[dose] = g + v * dose ^ n / (k ^ n + dose ^ n)
+ variance_params:
+ - rho
+ - alpha
+ dataset:
+ anova: null
+ doses:
+ - 0.0
+ - 0.0
+ - 0.0
+ - 0.0
+ - 0.0
+ - 0.0
+ - 0.0
+ - 0.0
+ - 0.1
+ - 0.1
+ - 0.1
+ - 0.1
+ - 0.1
+ - 0.1
+ - 1.0
+ - 1.0
+ - 1.0
+ - 1.0
+ - 1.0
+ - 1.0
+ - 10.0
+ - 10.0
+ - 10.0
+ - 10.0
+ - 10.0
+ - 10.0
+ - 100.0
+ - 100.0
+ - 100.0
+ - 100.0
+ - 100.0
+ - 100.0
+ - 300.0
+ - 300.0
+ - 300.0
+ - 300.0
+ - 300.0
+ - 300.0
+ - 500.0
+ - 500.0
+ - 500.0
+ - 500.0
+ - 500.0
+ - 500.0
+ dtype: CI
+ metadata:
+ id: 0
+ name: 'Dataset #1'
+ dose_name: Dose
+ dose_units: ''
+ response_name: Response
+ response_units: ''
+ responses:
+ - 8.1079
+ - 9.3063
+ - 9.7431
+ - 9.7814
+ - 10.0517
+ - 10.6132
+ - 10.7509
+ - 11.0567
+ - 9.1556
+ - 9.6821
+ - 9.8256
+ - 10.2095
+ - 10.2222
+ - 12.0382
+ - 9.5661
+ - 9.7059
+ - 9.9905
+ - 10.2716
+ - 10.471
+ - 11.0602
+ - 8.8514
+ - 10.0107
+ - 10.0854
+ - 10.5683
+ - 11.1394
+ - 11.4875
+ - 9.5427
+ - 9.7211
+ - 9.8267
+ - 10.0231
+ - 10.1833
+ - 10.8685
+ - 11.368
+ - 13.5176
+ - 12.3168
+ - 14.002
+ - 17.1186
+ - 13.6368
+ - 19.9572
+ - 20.1347
+ - 16.7743
+ - 20.0571
+ - 15.1564
+ - 15.0368
+ version:
+ dll: 24.1a4
+ python: 24.1a4
+ selected:
+ notes: User selected best fitting model
+ model_index: 0
+ description: ''
+ recommender:
+ results:
+ model_bin:
+ - 0
+ model_notes:
+ - '0': []
+ '1': []
+ '2': []
+ recommended_model_index: 0
+ recommended_model_variable: aic
+ settings:
+ rules:
+ - threshold: 0.1
+ rule_class: gof
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: dof_zero
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 1.0
+ rule_class: high_bmd
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: warnings
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: false
+ enabled_dichotomous: false
+ - threshold: 1.0
+ rule_class: high_bmdl
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 2.0
+ rule_class: roi_large
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 0.05
+ rule_class: gof_cancer
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: false
+ enabled_dichotomous: false
+ - threshold: null
+ rule_class: aic_missing
+ failure_bin: 2
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: bmd_missing
+ failure_bin: 2
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: roi_missing
+ failure_bin: 2
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: bmdl_missing
+ failure_bin: 2
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: null
+ rule_class: bmdu_missing
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: false
+ enabled_dichotomous: false
+ - threshold: 10.0
+ rule_class: low_bmd_fail
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 3.0
+ rule_class: low_bmd_warn
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 0.05
+ rule_class: variance_fit
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: true
+ enabled_dichotomous: false
+ - threshold: 10.0
+ rule_class: low_bmdl_fail
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 3.0
+ rule_class: low_bmdl_warn
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 0.05
+ rule_class: variance_type
+ failure_bin: 1
+ enabled_nested: false
+ enabled_continuous: false
+ enabled_dichotomous: false
+ - threshold: 1.5
+ rule_class: control_stdev_fit
+ failure_bin: 0
+ enabled_nested: false
+ enabled_continuous: true
+ enabled_dichotomous: false
+ - threshold: 20.0
+ rule_class: bmd_bmdl_ratio_fail
+ failure_bin: 1
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 3.0
+ rule_class: bmd_bmdl_ratio_warn
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ - threshold: 2.0
+ rule_class: control_residual_high
+ failure_bin: 0
+ enabled_nested: true
+ enabled_continuous: true
+ enabled_dichotomous: true
+ enabled: true
+ recommend_viable: true
+ recommend_questionable: false
+ sufficiently_close_bmdl: 3.0
+ model_average: null
+ option_index: 0
+ dataset_index: 0
+ analysis_id: 09c09d22-2e1a-413c-b350-6b19969f6533
+ bmds_ui_version: 24.1a4
+ bmds_python_version:
+ dll: 24.1a4
+ python: 24.1a4
+ analysis_schema_version: '1.1'
+ errors: []
+ created: 2024-08-22 15:23:53.050405+00:00
+ last_updated: 2024-08-22 15:24:59.827826+00:00
+ started: 2024-08-22 15:24:55.537289+00:00
+ ended: 2024-08-22 15:24:55.791463+00:00
+ deletion_date: null
+ starred: false
+ collections: [1]
- model: analysis.collection
pk: 1
fields:
diff --git a/tests/desktop/components/test_database_form.py b/tests/desktop/components/test_database_form.py
index c35203fe..637678b3 100644
--- a/tests/desktop/components/test_database_form.py
+++ b/tests/desktop/components/test_database_form.py
@@ -5,6 +5,7 @@
import pytest
from bmds_ui.desktop.components import database_form
+from bmds_ui.desktop.config import Database
def test_additional_path_checks():
@@ -27,3 +28,31 @@ def test_additional_path_checks():
p = Path(f.name)
with pytest.raises(ValueError, match="Cannot edit database"):
database_form.additional_path_checks(p)
+
+
+def test_check_duplicates():
+ existing = [
+ Database(name="a", path=Path("a.db")),
+ Database(name="b", path=Path("b.db")),
+ ]
+
+ # check pass; new filename
+ new_db = Database(name="c", path=Path("c.db"))
+ assert database_form.check_duplicates(existing, new_db) is None
+
+ # check pass; editing existing file
+ new_db = existing[0].model_copy()
+ new_db.name = "d"
+ assert database_form.check_duplicates(existing, new_db) is None
+
+ # check failure; new database with same path
+ new_db = Database(name="b", path=Path("b.db"))
+ with pytest.raises(
+ ValueError, match=r"An existing project \([\w]+\) already exists with this filename"
+ ):
+ database_form.check_duplicates(existing, new_db)
+
+ # check failure; new database with same name
+ new_db = Database(name="b", path=Path("d.db"))
+ with pytest.raises(ValueError, match="An existing project already exists with this name"):
+ database_form.check_duplicates(existing, new_db)
diff --git a/tests/desktop/test_actions.py b/tests/desktop/test_actions.py
index 467b294f..33d58860 100644
--- a/tests/desktop/test_actions.py
+++ b/tests/desktop/test_actions.py
@@ -47,4 +47,4 @@ def test_write_startup_script():
def test_create_shortcut(capsys):
actions.create_shortcut(no_input=True)
captured = capsys.readouterr()
- assert "BMDS Desktop Manger Created" in captured.out
+ assert "BMDS Desktop Manager Created" in captured.out
diff --git a/tests/desktop/test_app.py b/tests/desktop/test_app.py
index cb116673..90667ce7 100644
--- a/tests/desktop/test_app.py
+++ b/tests/desktop/test_app.py
@@ -1,4 +1,5 @@
import os
+import secrets
import tempfile
from pathlib import Path
@@ -138,7 +139,7 @@ async def test_db_form(self, rollback_get_app):
await pilot.pause()
# fill out form w/ valid data
- app.query_one("#name").value = "test name"
+ app.query_one("#name").value = f"Test {secrets.token_urlsafe(8)}"
app.query_one("#filename").value = "test-db.db"
app.query_one("#description").value = "test description"
@@ -171,7 +172,7 @@ async def test_db_form(self, rollback_get_app):
await pilot.press("enter")
assert isinstance(app.screen, components.database_form.DatabaseFormModel)
- assert app.query_one("#name").value == "test name"
+ assert app.query_one("#name").value.startswith("Test ")
assert app.query_one("#filename").value == "test-db.db"
assert app.query_one("#path").value == resolved_temp_dir
assert app.query_one("#description").value == "test description"
diff --git a/tests/integration/common.py b/tests/integration/common.py
index 85235350..c4d69923 100644
--- a/tests/integration/common.py
+++ b/tests/integration/common.py
@@ -5,7 +5,6 @@
from django.test import TestCase
from playwright.sync_api import Page
-CAN_EXECUTE = os.getenv("CI") is None
RUN_INTEGRATION = os.environ.get("INTEGRATION_TESTS") is not None
if RUN_INTEGRATION:
os.environ["DJANGO_ALLOW_ASYNC_UNSAFE"] = "true"
@@ -25,7 +24,6 @@ class PlaywrightTestCase(StaticLiveServerTestCase, TestCase):
@pytest.fixture(autouse=True)
def set_fixtures(self, page: Page):
- self.can_execute: bool = CAN_EXECUTE
self.page: Page = page
def url(self, path: str) -> str:
diff --git a/tests/integration/test_integration.py b/tests/integration/test_integration.py
index a7553c4e..696afe81 100644
--- a/tests/integration/test_integration.py
+++ b/tests/integration/test_integration.py
@@ -1,16 +1,28 @@
-import pytest
-from playwright.sync_api import expect
+from playwright.sync_api import Page, expect
+
+from bmds_ui.analysis.models import Analysis
from .common import PlaywrightTestCase
+# current version: {"analysis_schema_version": "1.1"}
+analysis_pks = [
+ ("432a6083-f9aa-4de2-a71f-a6488b4c5bf1", "dichotomous"),
+ ("cfe458aa-2313-44c0-9346-f4931567bef0", "continuous summary"),
+ ("09c09d22-2e1a-413c-b350-6b19969f6533", "continuous individual"),
+ ("4459f728-05f7-4057-a27c-174822a0313d", "nested dichotomous"),
+ ("2f86f324-911d-4194-97d1-fc7c3f5d0c72", "multitumor"),
+]
+
class TestContinuousIntegration(PlaywrightTestCase):
- def test_continuous(self):
- page = self.page
- page.goto(self.url("/"))
+ def _create_new_analysis(self) -> Page:
+ self.page.goto(self.url("/"))
+ with self.page.expect_navigation():
+ self.page.get_by_role("button", name="Create a new BMDS analysis").click()
+ return self.page
- with page.expect_navigation():
- page.get_by_role("button", name="Create a new BMDS analysis").click()
+ def _test_continuous(self, option: str):
+ page = self._create_new_analysis()
# set main input
page.locator("#analysis_name").fill("abc")
@@ -22,6 +34,7 @@ def test_continuous(self):
# view data tab
page.get_by_role("link", name="Data").click()
+ page.locator("#datasetType").select_option(option)
page.get_by_role("button", name="New").click()
page.get_by_role("button", name="Load an example dataset").click()
@@ -29,54 +42,57 @@ def test_continuous(self):
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...")
+ # 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()
- expect(page.locator("#frequentist-model-result tbody tr")).to_have_count(2)
+ # view output summary tables
+ page.locator('a:has-text("Output")').click()
+ expect(page.locator("#frequentist-model-result tbody tr")).to_have_count(2)
- # display frequentist modal
- page.locator("#freq-result-0").click()
- expect(page.locator("#info-table tbody tr")).to_have_count(3)
- page.locator("#close-modal").click()
+ # display frequentist modal
+ page.locator("#freq-result-0").click()
+ expect(page.locator("#info-table tbody tr")).to_have_count(3)
+ page.locator("#close-modal").click()
- page.locator("#selection_model").select_option("0")
- page.locator("#selection_notes").fill("selected!")
- page.locator("#selection_submit").click()
- expect(page.locator(".toast")).to_contain_text("Model selection updated.")
+ page.locator("#selection_model").select_option("0")
+ page.locator("#selection_notes").fill("selected!")
+ page.locator("#selection_submit").click()
+ expect(page.locator(".toast")).to_contain_text("Model selection updated.")
page.locator('a:has-text("Logic")').click()
expect(page.locator("#decision-logic tbody tr")).to_have_count(4)
expect(page.locator("#rule-table tbody tr")).to_have_count(20)
# 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
+ 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="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="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="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()
+ 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("/"))
+ def test_continuous_summary(self):
+ # create new analysis and make sure we can execute, view results, and view read-only page
+ self._test_continuous(option="CS")
+
+ def test_continuous_individual(self):
+ # create new analysis and make sure we can execute, view results, and view read-only page
+ self._test_continuous(option="I")
- with page.expect_navigation():
- page.get_by_role("button", name="Create a new BMDS analysis").click()
+ def test_dichotomous(self):
+ # create new analysis and make sure we can execute, view results, and view read-only page
+ page = self._create_new_analysis()
# set main input
page.locator("#analysis_name").fill("abc")
@@ -98,66 +114,60 @@ def test_dichotomous(self):
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...")
+ # 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()
- expect(page.locator("#frequentist-model-result tbody tr")).to_have_count(2)
- expect(page.locator("#bayesian-model-result tbody tr")).to_have_count(2)
+ # view output summary tables
+ page.locator('a:has-text("Output")').click()
+ expect(page.locator("#frequentist-model-result tbody tr")).to_have_count(2)
+ expect(page.locator("#bayesian-model-result tbody tr")).to_have_count(2)
- # display frequentist modal
- page.locator("#freq-result-0").click()
- expect(page.locator("#info-table tbody tr")).to_have_count(3)
- page.locator("#close-modal").click()
+ # display frequentist modal
+ page.locator("#freq-result-0").click()
+ expect(page.locator("#info-table tbody tr")).to_have_count(3)
+ page.locator("#close-modal").click()
- # display bayesian modal
- page.locator("#bayesian-result-0").click()
- expect(page.locator("#info-table tbody tr")).to_have_count(3)
- page.locator("#close-modal").click()
+ # display bayesian modal
+ page.locator("#bayesian-result-0").click()
+ expect(page.locator("#info-table tbody tr")).to_have_count(3)
+ page.locator("#close-modal").click()
- # display bayesian model average modal
- page.locator("td", has_text="Model Average").click()
- expect(page.locator("#ma-result-summary tbody tr")).to_have_count(3)
- page.locator("#close-modal").click()
+ # display bayesian model average modal
+ page.locator("td", has_text="Model Average").click()
+ expect(page.locator("#ma-result-summary tbody tr")).to_have_count(3)
+ page.locator("#close-modal").click()
- page.locator("#selection_model").select_option("0")
- page.locator("#selection_notes").fill("selected!")
- page.locator("#selection_submit").click()
- expect(page.locator(".toast")).to_contain_text("Model selection updated.")
+ page.locator("#selection_model").select_option("0")
+ page.locator("#selection_notes").fill("selected!")
+ page.locator("#selection_submit").click()
+ expect(page.locator(".toast")).to_contain_text("Model selection updated.")
page.locator('a:has-text("Logic")').click()
expect(page.locator("#decision-logic tbody tr")).to_have_count(4)
expect(page.locator("#rule-table tbody tr")).to_have_count(18)
# 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
+ 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="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="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="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()
+ page2.get_by_role("link", name="Logic").click()
+ expect(page2.get_by_role("cell", name="Decision Logic")).to_be_visible()
- @pytest.mark.xfail
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()
+ # create new analysis and make sure we can execute, view results, and view read-only page
+ page = self._create_new_analysis()
# set main input
page.locator("#analysis_name").fill("abc")
@@ -175,45 +185,41 @@ def test_nested_dichotomous(self):
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...")
+ # 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)
+ # 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()
+ # 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
+ # 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="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="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="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()
+ 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()
+ # create new analysis and make sure we can execute, view results, and view read-only page
+ page = self._create_new_analysis()
# set main input
page.locator("#analysis_name").fill("abc")
@@ -238,35 +244,87 @@ def test_multi_tumor(self):
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...")
+ # 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()
+ # view output summary tables
+ page.locator('a:has-text("Output")').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 (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()
+ # check one result (individual)
+ expect(page.get_by_role("link", name="Multistage 2*")).to_have_count(3)
+ page.get_by_role("link", name="Multistage 2*").nth(1).click()
+ expect(page.get_by_role("dialog")).to_contain_text("Multistage 2")
+ 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
+ # 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="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="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()
- page2.get_by_role("link", name="Output").click()
- expect(page2.get_by_text("Model Results")).to_be_visible()
+ def test_read_view(self):
+ # load existing analyses in our database and confirm we can view everything in read-only mode
+ page = self.page
+ for pk, model_type in analysis_pks:
+ a = Analysis.objects.get(pk=pk)
+ self.page.goto(self.url(a.get_absolute_url()))
+
+ # check main tab loads
+ expect(page.get_by_role("cell", name="Analysis Name:")).to_be_visible()
+
+ # check data tab loads
+ page.get_by_role("link", name="Data").click()
+ expect(page.get_by_text("Dataset Name:")).to_be_visible()
+
+ # check output tab loads
+ page.get_by_role("link", name="Output").click()
+ if model_type == "multitumor":
+ expect(page.get_by_role("heading", name="Model Results")).to_be_visible()
+ else:
+ expect(page.locator("#frequentist-model-result")).to_be_visible()
+
+ # check logic tab loads (not present with multitumor)
+ if model_type != "multitumor":
+ page.get_by_role("link", name="Logic").click()
+ expect(page.get_by_role("cell", name="Decision Logic")).to_be_visible()
+
+ def test_edit_view(self):
+ # load existing analyses in our database and confirm we can view everything in editable mode
+ page = self.page
+ for pk, model_type in analysis_pks:
+ a = Analysis.objects.get(pk=pk)
+ self.page.goto(self.url(a.get_edit_url()))
+
+ # check main tab loads
+ expect(page.locator("#analysis_name")).to_be_visible()
+
+ # check data tab loads
+ page.get_by_role("link", name="Data").click()
+ expect(page.get_by_role("button", name="New")).to_be_visible()
+
+ # check output tab loads
+ page.get_by_role("link", name="Output").click()
+ if model_type == "multitumor":
+ expect(page.get_by_role("heading", name="Model Results")).to_be_visible()
+ else:
+ expect(page.locator("#frequentist-model-result")).to_be_visible()
+
+ # check logic tab loads (not present with multitumor)
+ if model_type != "multitumor":
+ page.get_by_role("link", name="Logic").click()
+ expect(page.get_by_role("cell", name="Decision Logic")).to_be_visible()