integrate de search into fold change temporarily

Author: asizemore

packages/libs/eda/src/lib/notebook/ComputeNotebookCell.tsx

@@ -22,6 +22,7 @@ export function ComputeNotebookCell(
     computationId,
     cells,
     getAdditionalCollectionPredicate,
+    hidden=false,
   } = cell;
   const computation = analysis.descriptor.computations.find(
     (comp) => comp.computationId === computationId
@@ -102,7 +103,7 @@ export function ComputeNotebookCell(
     getAdditionalCollectionPredicate &&
     getAdditionalCollectionPredicate(projectId);
 
-  return computation && appOverview ? (
+  return computation && appOverview && !hidden ? (
     <>
       {cell.helperText && (
         <div className="NotebookCellHelpText">

packages/libs/eda/src/lib/notebook/NotebookPresets.tsx

@@ -54,6 +54,7 @@ export interface ComputeCellDescriptor
   getAdditionalCollectionPredicate?: (
     projectId?: string
   ) => (variableCollection: CollectionVariableTreeNode) => boolean;
+  hidden?: boolean; // Whether to hide this computation cell in the UI. Useful for computations where the entire configuration is already known.
 }
 
 export interface TextCellDescriptor extends NotebookCellDescriptorBase<'text'> {
@@ -102,6 +103,7 @@ export const presetNotebooks: Record<string, PresetNotebook> = {
         title: 'Configure PCA',
         computationName: 'dimensionalityreduction',
         computationId: 'pca_1',
+        hidden: true, // Hide in UI since config is already known.
         helperText: (
           <NumberedHeader
             number={2}

packages/sites/genomics-site/webapp/wdkCustomization/js/client/components/questions/EdaNotebookParameter.tsx

@@ -46,9 +46,11 @@ type EdaNotebookParameterProps = {
 export function EdaNotebookParameter(props: EdaNotebookParameterProps) {
   const { value, datasetIdParamName, notebookTypeParamName, wdkState } = props;
 
+  console.log("Rendering EdaNotebookParameter with props:", props);
+
   // TEMPORARY: We don't have this value coming from the wdk yet.
   const studyId = datasetIdParamName ?? 'DS_82dc5abc7f';
-  const notebookType = notebookTypeParamName ?? 'wgcnaCorrelationNotebook';
+  const notebookType = notebookTypeParamName ?? 'differentialExpressionNotebook';
 
   // we need to maintain the analysis as regular "live" React state somewhere
   const [analysis, setAnalysis] = useState<NewAnalysis | Analysis | undefined>(

packages/sites/genomics-site/webapp/wdkCustomization/js/client/components/questions/EdaNotebookQuestionForm.tsx

@@ -12,6 +12,9 @@ export const EdaNotebookQuestionForm = (props: Props) => {
     throw new Error('No search defined.');
   }
 
+  console.log("in EdaNotebookQuestionForm with searchName:", searchName);
+  console.log("EDANotebookQuestionForm props:", props);
+
   // We'll use this function throughout the notebook to update any wdk parameters.
   const updateParamValue = useCallback(
     (parameter: Parameter, newParamValue: string) => {
@@ -33,8 +36,9 @@ export const EdaNotebookQuestionForm = (props: Props) => {
 
   // An override that renders the notebook instead of any default parameter or parameter group ui.
   // NOTE: this function is run for every visible parameter group. May cause
-  // an issue if the wdk question has multipl parameter groups.
+  // an issue if the wdk question has multiple parameter groups.
   const renderParamGroup = () => {
+    console.log("Rendering EdaNotebookParameter with wdkState:", wdkState);
     return <EdaNotebookParameter value={'test'} wdkState={wdkState} />;
   };
 

packages/sites/genomics-site/webapp/wdkCustomization/js/client/pluginConfig.tsx

@@ -44,7 +44,6 @@ import {
 } from './components/questions/ByLocation';
 import { DynSpansBySourceId } from './components/questions/DynSpansBySourceId';
 import { GenesByBindingSiteFeature } from './components/questions/GenesByBindingSiteFeature';
-import { GenesByWGCNAModules } from './components/questions/GenesByWGCNAModules';
 import { GenesByOrthologPattern } from './components/questions/GenesByOrthologPattern';
 import { InternalGeneDataset } from './components/questions/InternalGeneDataset';
 import { hasChromosomeAndSequenceIDXorGroup } from './components/questions/MutuallyExclusiveParams/utils';
@@ -194,11 +193,12 @@ const apiPluginConfig: ClientPluginRegistryEntry<any>[] = [
   },
   {
     type: 'questionForm',
-    test: ({ question }) =>
-      question?.queryName === 'GenesByGenericFoldChange' ||
-      question?.queryName === 'GenesByRnaSeqFoldChange' ||
-      question?.queryName === 'GenesByUserDatasetRnaSeq',
-    component: GenericFoldChangeForm,
+    test: ({ question }) => { 
+      console.log(question?.queryName);
+      return question?.queryName === 'GenesByGenericFoldChange' ||
+      question?.queryName === 'GenesByRnaSeqFoldChange'
+    },
+    component: EdaNotebookQuestionForm,
   },
   {
     type: 'questionForm',
@@ -290,6 +290,12 @@ const apiPluginConfig: ClientPluginRegistryEntry<any>[] = [
     test: ({ question }) => question?.queryName === 'GenesByWGCNAModule',
     component: EdaNotebookQuestionForm,
   },
+    {
+    type: 'questionForm',
+    test: ({ question }) => question?.queryName === 'GenesByDESeqAnalysis',
+    // Possibly GenesByDESeqAnalysis but check.
+    component: EdaNotebookQuestionForm,
+  },
 ];
 
 export default apiPluginConfig;