Disable apps based on study metadata

packages/libs/eda/src/lib/core/components/computations/Types.ts

@@ -6,6 +6,7 @@ import { GeoConfig } from '../../types/geoConfig';
 import { Computation, ComputationAppOverview } from '../../types/visualization';
 import { Filter, StudyEntity } from '../..';
 import { VisualizationPlugin } from '../visualizations/VisualizationPlugin';
+import { IsEnabledInPickerParams } from '../visualizations/VisualizationTypes';
 
 export interface ComputationProps {
   analysisState: AnalysisState;
@@ -50,4 +51,8 @@ export interface ComputationPlugin {
     rootEntity: StudyEntity
   ) => Record<string, unknown> | undefined;
   isConfigurationComplete: (configuration: unknown) => boolean;
+  /** Function used to determine if visualization is compatible with study */
+  isEnabledInPicker?: (props: IsEnabledInPickerParams) => boolean;
+  /** Human-readable study requirements for this computation */
+  studyRequirements?: string;
 }

packages/libs/eda/src/lib/core/components/computations/plugins/abundance.tsx

@@ -18,6 +18,8 @@ import { ComputationStepContainer } from '../ComputationStepContainer';
 import './Plugins.scss';
 import { makeClassNameHelper } from '@veupathdb/wdk-client/lib/Utils/ComponentUtils';
 import { VariableCollectionSelectList } from '../../variableSelectors/VariableCollectionSingleSelect';
+import { IsEnabledInPickerParams } from '../../visualizations/VisualizationTypes';
+import { entityTreeToArray } from '../../../utils/study-metadata';
 
 const cx = makeClassNameHelper('AppStepConfigurationContainer');
 
@@ -95,6 +97,9 @@ export const plugin: ComputationPlugin = {
       hideShowMissingnessToggle: true,
     }),
   },
+  isEnabledInPicker: isEnabledInPicker,
+  studyRequirements:
+    'These visualizations are only available for studies with compatible assay data.',
 };
 
 function AbundanceConfigDescriptionComponent({
@@ -195,3 +200,19 @@ export function AbundanceConfiguration(props: ComputationConfigProps) {
     </ComputationStepContainer>
   );
 }
+
+// The abundance app's only requirement for the study is that the study
+// contains at least one collection.
+function isEnabledInPicker({
+  studyMetadata,
+}: IsEnabledInPickerParams): boolean {
+  if (!studyMetadata) return false;
+
+  const entities = entityTreeToArray(studyMetadata.rootEntity);
+  // Ensure there are collections in this study. Otherwise, disable app
+  const studyHasCollections = entities.some(
+    (entity) => !!entity.collections?.length
+  );
+
+  return studyHasCollections;
+}

packages/libs/eda/src/lib/core/components/computations/plugins/alphaDiv.tsx

@@ -17,6 +17,8 @@ import { ComputationStepContainer } from '../ComputationStepContainer';
 import './Plugins.scss';
 import { makeClassNameHelper } from '@veupathdb/wdk-client/lib/Utils/ComponentUtils';
 import { VariableCollectionSelectList } from '../../variableSelectors/VariableCollectionSingleSelect';
+import { IsEnabledInPickerParams } from '../../visualizations/VisualizationTypes';
+import { entityTreeToArray } from '../../../utils/study-metadata';
 
 const cx = makeClassNameHelper('AppStepConfigurationContainer');
 
@@ -60,6 +62,9 @@ export const plugin: ComputationPlugin = {
       hideShowMissingnessToggle: true,
     }),
   },
+  isEnabledInPicker: isEnabledInPicker,
+  studyRequirements:
+    'These visualizations are only available for studies with compatible assay data.',
 };
 
 function AlphaDivConfigDescriptionComponent({
@@ -159,3 +164,19 @@ export function AlphaDivConfiguration(props: ComputationConfigProps) {
     </ComputationStepContainer>
   );
 }
+
+// Alpha div's only requirement of the study is that
+// the study contains at least one collection.
+function isEnabledInPicker({
+  studyMetadata,
+}: IsEnabledInPickerParams): boolean {
+  if (!studyMetadata) return false;
+  const entities = entityTreeToArray(studyMetadata.rootEntity);
+
+  // Ensure there are collections in this study. Otherwise, disable app
+  const studyHasCollections = entities.some(
+    (entity) => !!entity.collections?.length
+  );
+
+  return studyHasCollections;
+}

packages/libs/eda/src/lib/core/components/computations/plugins/betadiv.tsx

@@ -18,6 +18,8 @@ import { ComputationStepContainer } from '../ComputationStepContainer';
 import './Plugins.scss';
 import { makeClassNameHelper } from '@veupathdb/wdk-client/lib/Utils/ComponentUtils';
 import { VariableCollectionSelectList } from '../../variableSelectors/VariableCollectionSingleSelect';
+import { IsEnabledInPickerParams } from '../../visualizations/VisualizationTypes';
+import { entityTreeToArray } from '../../../utils/study-metadata';
 
 const cx = makeClassNameHelper('AppStepConfigurationContainer');
 
@@ -63,6 +65,9 @@ export const plugin: ComputationPlugin = {
       })
       .withSelectorIcon(ScatterBetadivSVG),
   },
+  isEnabledInPicker: isEnabledInPicker,
+  studyRequirements:
+    'These visualizations are only available for studies with compatible assay data.',
 };
 
 function BetaDivConfigDescriptionComponent({
@@ -172,3 +177,19 @@ export function BetaDivConfiguration(props: ComputationConfigProps) {
     </ComputationStepContainer>
   );
 }
+
+// Beta div's only requirement of the study is that it contains
+// at least one collection
+function isEnabledInPicker({
+  studyMetadata,
+}: IsEnabledInPickerParams): boolean {
+  if (!studyMetadata) return false;
+  const entities = entityTreeToArray(studyMetadata.rootEntity);
+
+  // Ensure there are collections in this study. Otherwise, disable app
+  const studyHasCollections = entities.some(
+    (entity) => !!entity.collections?.length
+  );
+
+  return studyHasCollections;
+}

packages/libs/eda/src/lib/core/components/computations/plugins/correlationAssayAssay.tsx

@@ -18,6 +18,8 @@ import { bipartiteNetworkVisualization } from '../../visualizations/implementati
 import { variableCollectionsAreUnique } from '../../../utils/visualization';
 import PluginError from '../../visualizations/PluginError';
 import { VariableCollectionSelectList } from '../../variableSelectors/VariableCollectionSingleSelect';
+import { IsEnabledInPickerParams } from '../../visualizations/VisualizationTypes';
+import { entityTreeToArray } from '../../../utils/study-metadata';
 
 const cx = makeClassNameHelper('AppStepConfigurationContainer');
 
@@ -73,6 +75,9 @@ export const plugin: ComputationPlugin = {
       },
     }), // Must match name in data service and in visualization.tsx
   },
+  isEnabledInPicker: isEnabledInPicker,
+  studyRequirements:
+    'These visualizations are only available for studies with metagenomic data.',
 };
 
 // Renders on the thumbnail page to give a summary of the app instance
@@ -198,3 +203,21 @@ export function CorrelationAssayAssayConfiguration(
     </ComputationStepContainer>
   );
 }
+
+// The correlation assay x assay app should only be available
+// for studies with metagenomic data.
+function isEnabledInPicker({
+  studyMetadata,
+}: IsEnabledInPickerParams): boolean {
+  if (!studyMetadata) return false;
+
+  const entities = entityTreeToArray(studyMetadata.rootEntity);
+
+  // Check that the metagenomic entity exists _and_ that it has
+  // at least one collection.
+  const hasMetagenomicData = entities.some(
+    (entity) => entity.id === 'OBI_0002623' && !!entity.collections?.length
+  ); // OBI_0002623 = Metagenomic sequencing assay
+
+  return hasMetagenomicData;
+}

packages/libs/eda/src/lib/core/components/computations/plugins/correlationAssayMetadata.tsx

@@ -16,6 +16,9 @@ import { makeClassNameHelper } from '@veupathdb/wdk-client/lib/Utils/ComponentUt
 import { H6 } from '@veupathdb/coreui';
 import { bipartiteNetworkVisualization } from '../../visualizations/implementations/BipartiteNetworkVisualization';
 import { VariableCollectionSelectList } from '../../variableSelectors/VariableCollectionSingleSelect';
+import { entityTreeToArray } from '../../../utils/study-metadata';
+import { IsEnabledInPickerParams } from '../../visualizations/VisualizationTypes';
+import { ancestorEntitiesForEntityId } from '../../../utils/data-element-constraints';
 
 const cx = makeClassNameHelper('AppStepConfigurationContainer');
 
@@ -62,6 +65,9 @@ export const plugin: ComputationPlugin = {
       },
     }), // Must match name in data service and in visualization.tsx
   },
+  isEnabledInPicker: isEnabledInPicker,
+  studyRequirements:
+    'These visualizations are only available for studies with compatible metadata.',
 };
 
 // Renders on the thumbnail page to give a summary of the app instance
@@ -155,3 +161,65 @@ export function CorrelationAssayMetadataConfiguration(
     </ComputationStepContainer>
   );
 }
+
+const ASSAY_ENTITIES = [
+  'OBI_0002623',
+  'EUPATH_0000809',
+  'EUPATH_0000813',
+  'EUPATH_0000812',
+];
+
+// The correlation assay x metadata app is only available for studies
+// with appropriate metadata. Specifically, the study
+// must have at least one continuous metadata variable that is on a one-to-one path
+// from the assay entity.
+// See PR #74 in service-eda-compute for the matching logic on the backend.
+function isEnabledInPicker({
+  studyMetadata,
+}: IsEnabledInPickerParams): boolean {
+  if (!studyMetadata) return false;
+
+  const entities = entityTreeToArray(studyMetadata.rootEntity);
+  // Ensure there are collections in this study. Otherwise, disable app
+  const studyHasCollections = entities.some(
+    (entity) => !!entity.collections?.length
+  );
+  if (!studyHasCollections) return false;
+
+  // Check for appropriate metadata
+  // Step 1. Find the first assay node. Doesn't need to be any assay in particular just any mbio assay will do
+  const firstAssayEntityIndex = entities.findIndex((entity) =>
+    ASSAY_ENTITIES.includes(entity.id)
+  );
+  if (firstAssayEntityIndex === -1) return false;
+
+  // Step 2. Find all ancestor entites of the assayEntity that are on a one-to-one path with assayEntity.
+  // Step 2a. Grab ancestor entities.
+  const ancestorEntities = ancestorEntitiesForEntityId(
+    entities[firstAssayEntityIndex].id,
+    entities
+  ).reverse(); // Reverse so that the ancestorEntities[0] is the assay and higher indices are further up the tree.
+
+  // Step 2b. Trim the ancestorEntities so that we only keep those that are on
+  // a 1:1 path. Once we find an ancestor that is many to one with its parent, we
+  // know we've hit the end of the 1:1 path.
+  const lastOneToOneAncestorIndex = ancestorEntities.findIndex(
+    (entity) => entity.isManyToOneWithParent
+  );
+  const oneToOneAncestors = ancestorEntities.slice(
+    1, // removing the assay itself
+    lastOneToOneAncestorIndex + 1
+  );
+
+  // Step 3. Check if there are any continuous variables in the filtered entities
+  const hasContinuousVariable = oneToOneAncestors
+    .flatMap((entity) => entity.variables)
+    .some(
+      (variable) =>
+        'dataShape' in variable &&
+        variable.dataShape === 'continuous' &&
+        (variable.type === 'number' || variable.type === 'integer') // Support for dates coming soon! Can remove this line once the backend is ready.
+    );
+
+  return hasContinuousVariable;
+}

packages/libs/eda/src/lib/core/components/computations/plugins/differentialabundance.tsx

@@ -40,6 +40,8 @@ import {
   getBinRanges,
 } from '../../../../map/analysis/utils/defaultOverlayConfig';
 import { VariableCollectionSelectList } from '../../variableSelectors/VariableCollectionSingleSelect';
+import { IsEnabledInPickerParams } from '../../visualizations/VisualizationTypes';
+import { entityTreeToArray } from '../../../utils/study-metadata';
 
 const cx = makeClassNameHelper('AppStepConfigurationContainer');
 
@@ -126,6 +128,9 @@ export const plugin: ComputationPlugin = {
       },
     }), // Must match name in data service and in visualization.tsx
   },
+  isEnabledInPicker: isEnabledInPicker,
+  studyRequirements:
+    'These visualizations are only available for studies with compatible assay data.',
 };
 
 function DifferentialAbundanceConfigDescriptionComponent({
@@ -462,3 +467,19 @@ function assertConfigWithComparator(
     );
   }
 }
+
+// Differential abundance requires that the study
+// has at least one collection.
+function isEnabledInPicker({
+  studyMetadata,
+}: IsEnabledInPickerParams): boolean {
+  if (!studyMetadata) return false;
+
+  const entities = entityTreeToArray(studyMetadata.rootEntity);
+  // Ensure there are collections in this study. Otherwise, disable app
+  const studyHasCollections = entities.some(
+    (entity) => !!entity.collections?.length
+  );
+
+  return studyHasCollections;
+}

packages/libs/eda/src/lib/core/components/visualizations/Visualizations.scss

@@ -97,6 +97,14 @@
       font-weight: 300;
     }
   }
+  // Add disabled effects for the app rows
+  &-AppPicker {
+    &__disabled {
+      cursor: not-allowed;
+      border-radius: 20px;
+      color: #a6a6a6;
+    }
+  }
 
   // add hover effect for thumbnail icons
   &-ConfiguredVisualization:hover &-ConfiguredVisualizationActions {

packages/libs/eda/src/lib/core/utils/study-metadata.ts

@@ -12,7 +12,7 @@ import {
 } from '../types/variable';
 import { preorder } from '@veupathdb/wdk-client/lib/Utils/TreeUtils';
 
-export function entityTreeToArray(rootEntity: StudyEntity) {
+export function entityTreeToArray(rootEntity: StudyEntity): StudyEntity[] {
   return Array.from(preorder(rootEntity, (e) => e.children ?? []));
 }