334 output refactoring (#14)

* merge GOF

* gof tweak, infotable merge

* modal first pass

* tweak imports

* merge summary, fix import

* remove lollipop

* fix after merge w/ floating point hover

* wip

* updates

* fix test failures and warnings

* use CamelCase

* version updates

* remove multitumor analysis of deviance

* add cdf plot to individual multitumor models

* remove special multitumor components

* use new <Table> component

* add ruff check to windows batch file

* make summary results consistent across types

* remove duplicative parameter components

* revert to psycopg2

---------

Co-authored-by: Andy Shapiro <[email protected]>

Makefile

@@ -80,10 +80,10 @@ lint: lint-py lint-js  ## Check formatting issues
 format: format-py format-js  ## Fix formatting issues where possible
 
 lint-py:  ## Check python formatting issues
-	@ruff format . --check && ruff .
+	@ruff format . --check && ruff check .
 
 format-py:  ## Fix python formatting issues where possible
-	@ruff format . && ruff . --fix --show-fixes
+	@ruff format . && ruff check . --fix --show-fixes
 
 lint-js:  ## Check javascript formatting issues
 	@npm --prefix ./frontend run lint

bmds_server/analysis/api.py

@@ -4,6 +4,7 @@
 from rest_framework import exceptions, mixins, viewsets
 from rest_framework.decorators import action
 from rest_framework.response import Response
+from rest_framework.schemas.openapi import AutoSchema
 
 from ..common import renderers
 from ..common.renderers import BinaryFile
@@ -19,6 +20,7 @@
 class AnalysisViewset(mixins.RetrieveModelMixin, viewsets.GenericViewSet):
     serializer_class = serializers.AnalysisSerializer
     queryset = models.Analysis.objects.prefetch_related("collections").all()
+    schema = AutoSchema(operation_id_base="Analysis")
 
     @action(detail=False, url_path="default")
     def default(self, request, *args, **kwargs):
@@ -198,6 +200,7 @@ def collections(self, request, *args, **kwargs):
 class PolyKViewset(viewsets.GenericViewSet):
     queryset = models.Analysis.objects.none()
     serializer_class = UnusedSerializer
+    schema = AutoSchema(operation_id_base="PolyK")
 
     def _run_analysis(self, request) -> PolyKAdjustment:
         try:

bmds_server/common/templatetags/bs4.py

@@ -1,6 +1,7 @@
 """
 Twitter Bootstrap 4 - helper methods
 """
+
 from datetime import datetime
 from textwrap import dedent
 from uuid import uuid4

frontend/package.json

@@ -46,7 +46,7 @@
     "rimraf": "^2.4.3",
     "style-loader": "^0.19.0",
     "webpack": "^5.88.1",
-    "webpack-bundle-tracker": "^2.0.1",
+    "webpack-bundle-tracker": "^3.1.0",
     "webpack-cli": "^5.1.4",
     "webpack-dev-middleware": "^6.1.1"
   },
@@ -58,7 +58,7 @@
     "lodash": "^4.17.21",
     "mobx": "^5.15.7",
     "mobx-react": "^6.3.1",
-    "plotly.js": "2.27.0",
+    "plotly.js": "2.30.0",
     "popper.js": "^1.16.1",
     "prop-types": "^15.7.2",
     "react": "^17.0.2",

frontend/src/components/IndividualModel/GoodnessFit.js

@@ -8,10 +8,8 @@ import {ff} from "@/utils/formatters";
 
 @observer
 class GoodnessFit extends Component {
-    getDichotomousData() {
-        const {store} = this.props,
-            gof = store.modalModel.results.gof,
-            dataset = store.selectedDataset;
+    getDichotomousData(dataset, model) {
+        const gof = model.results.gof;
         return {
             headers: [
                 "Dose",
@@ -35,10 +33,8 @@ class GoodnessFit extends Component {
         };
     }
 
-    getContinuousNormalData(dtype) {
-        const {store} = this.props,
-            gof = store.modalModel.results.gof,
-            dataset = store.selectedDataset,
+    getContinuousNormalData(dataset, dtype, model) {
+        const gof = model.results.gof,
             useFF = dtype === Dtype.CONTINUOUS_INDIVIDUAL;
         return {
             headers: [
@@ -65,10 +61,8 @@ class GoodnessFit extends Component {
         };
     }
 
-    getContinuousLognormalData(dtype) {
-        const {store} = this.props,
-            gof = store.modalModel.results.gof,
-            dataset = store.selectedDataset,
+    getContinuousLognormalData(dataset, dtype, model) {
+        const gof = model.results.gof,
             useFF = dtype === Dtype.CONTINUOUS_INDIVIDUAL;
         return {
             headers: [
@@ -98,22 +92,22 @@ class GoodnessFit extends Component {
             }),
         };
     }
+
     render() {
         const {store} = this.props,
             settings = store.modalModel.settings,
-            dataset = store.selectedDataset,
+            model = store.modalModel,
+            dataset = store.isMultiTumor ? store.modalDataset : store.selectedDataset,
             {dtype} = dataset;
-
         let data;
-        if (dtype == Dtype.DICHOTOMOUS) {
-            data = this.getDichotomousData();
+        if (store.isMultiTumor || dtype == Dtype.DICHOTOMOUS) {
+            data = this.getDichotomousData(dataset, model);
+        } else if (isLognormal(settings.disttype)) {
+            data = this.getContinuousLognormalData(dataset, dtype, model);
         } else {
-            if (isLognormal(settings.disttype)) {
-                data = this.getContinuousLognormalData(dtype);
-            } else {
-                data = this.getContinuousNormalData(dtype);
-            }
+            data = this.getContinuousNormalData(dataset, dtype, model);
         }
+
         return (
             <table className="table table-sm table-bordered text-right">
                 <colgroup>

frontend/src/components/IndividualModel/InfoTable.js

@@ -10,7 +10,9 @@ class InfoTable extends Component {
     render() {
         const {outputStore} = this.props,
             model = outputStore.modalModel,
-            dataset = outputStore.selectedDataset,
+            dataset = outputStore.isMultiTumor
+                ? outputStore.modalDataset
+                : outputStore.selectedDataset,
             data = [
                 ["Dataset", dataset.metadata.name],
                 ["Model", model.name],