Merge branch 'main' into 426-donut-marker-config-panel

VEuPathDB · Sep 11, 2023 · 2610930 · 2610930
2 parents 7e2b51a + e267f16
commit 2610930
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diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/abundance.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/abundance.tsx
@@ -150,14 +150,20 @@ export function AbundanceConfiguration(props: ComputationConfigProps) {
   );
 
   const collectionVarItems = useMemo(() => {
-    return collections.map((collectionVar) => ({
-      value: {
-        variableId: collectionVar.id,
-        entityId: collectionVar.entityId,
-      },
-      display:
-        collectionVar.entityDisplayName + ' > ' + collectionVar.displayName,
-    }));
+    return collections
+      .filter((collectionVar) => {
+        return collectionVar.normalizationMethod
+          ? collectionVar.normalizationMethod !== 'NULL'
+          : true;
+      })
+      .map((collectionVar) => ({
+        value: {
+          variableId: collectionVar.id,
+          entityId: collectionVar.entityId,
+        },
+        display:
+          collectionVar.entityDisplayName + ' > ' + collectionVar.displayName,
+      }));
   }, [collections]);
 
   const selectedCollectionVar = useMemo(() => {

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/alphaDiv.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/alphaDiv.tsx
@@ -133,14 +133,20 @@ export function AlphaDivConfiguration(props: ComputationConfigProps) {
   );
 
   const collectionVarItems = useMemo(() => {
-    return collections.map((collectionVar) => ({
-      value: {
-        variableId: collectionVar.id,
-        entityId: collectionVar.entityId,
-      },
-      display:
-        collectionVar.entityDisplayName + ' > ' + collectionVar.displayName,
-    }));
+    return collections
+      .filter((collectionVar) => {
+        return collectionVar.normalizationMethod
+          ? collectionVar.normalizationMethod !== 'NULL'
+          : true;
+      })
+      .map((collectionVar) => ({
+        value: {
+          variableId: collectionVar.id,
+          entityId: collectionVar.entityId,
+        },
+        display:
+          collectionVar.entityDisplayName + ' > ' + collectionVar.displayName,
+      }));
   }, [collections]);
 
   const selectedCollectionVar = useMemo(() => {

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/betadiv.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/betadiv.tsx
@@ -136,14 +136,20 @@ export function BetaDivConfiguration(props: ComputationConfigProps) {
   );
 
   const collectionVarItems = useMemo(() => {
-    return collections.map((collectionVar) => ({
-      value: {
-        variableId: collectionVar.id,
-        entityId: collectionVar.entityId,
-      },
-      display:
-        collectionVar.entityDisplayName + ' > ' + collectionVar.displayName,
-    }));
+    return collections
+      .filter((collectionVar) => {
+        return collectionVar.normalizationMethod
+          ? collectionVar.normalizationMethod !== 'NULL'
+          : true;
+      })
+      .map((collectionVar) => ({
+        value: {
+          variableId: collectionVar.id,
+          entityId: collectionVar.entityId,
+        },
+        display:
+          collectionVar.entityDisplayName + ' > ' + collectionVar.displayName,
+      }));
   }, [collections]);
 
   const selectedCollectionVar = useMemo(() => {

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/differentialabundance.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/differentialabundance.tsx
@@ -175,14 +175,22 @@ export function DifferentialAbundanceConfiguration(
     );
 
   const collectionVarItems = useMemo(() => {
-    return collections.map((collectionVar) => ({
-      value: {
-        variableId: collectionVar.id,
-        entityId: collectionVar.entityId,
-      },
-      display:
-        collectionVar.entityDisplayName + ' > ' + collectionVar.displayName,
-    }));
+    return collections
+      .filter((collectionVar) => {
+        return collectionVar.normalizationMethod
+          ? !collectionVar.isProportion &&
+              collectionVar.normalizationMethod === 'NULL' &&
+              !collectionVar.displayName?.includes('pathway')
+          : true;
+      })
+      .map((collectionVar) => ({
+        value: {
+          variableId: collectionVar.id,
+          entityId: collectionVar.entityId,
+        },
+        display:
+          collectionVar.entityDisplayName + ' > ' + collectionVar.displayName,
+      }));
   }, [collections]);
 
   const selectedCollectionVar = useMemo(() => {

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts b/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
@@ -12,7 +12,7 @@ export const plugins: Record<string, ComputationPlugin> = {
   abundance,
   alphadiv,
   betadiv,
-  differentialabundance,
+  // differentialabundance,
   countsandproportions,
   distributions,
   pass,

diff --git a/packages/libs/eda/src/lib/core/types/study.ts b/packages/libs/eda/src/lib/core/types/study.ts
@@ -220,6 +220,9 @@ export const CollectionVariableTreeNode = t.intersection([
     units: t.string,
     entityId: t.string,
     entityDisplayName: t.string,
+    isCompositional: t.boolean,
+    isProportion: t.boolean,
+    normalizationMethod: t.string,
   }),
 ]);
 

diff --git a/...genomics-site/webapp/wdkCustomization/js/client/components/homepage/VEuPathDBHomePage.tsx b/...genomics-site/webapp/wdkCustomization/js/client/components/homepage/VEuPathDBHomePage.tsx
@@ -601,7 +601,8 @@ const useHeaderMenuItems = (
           type: 'reactRoute',
           display: (
             <>
-              Multi-study Interactive Map <img alt="BETA" src={betaImage} />
+              MapVEu - Multi-study Interactive Map{' '}
+              <img alt="BETA" src={betaImage} />
             </>
           ),
           key: 'map--mega-study',