Merge branch 'main' into bug/membership-table-search-filter

VEuPathDB · Aug 23, 2023 · 920d6fd · 920d6fd
2 parents 889ae77 + c90abd2
commit 920d6fd
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Showing 14 changed files with 3,777 additions and 2,668 deletions.
diff --git a/.github/workflows/pr-check.yml b/.github/workflows/pr-check.yml
@@ -17,3 +17,4 @@ jobs:
       - uses: nrwl/nx-set-shas@v3
       - run: yarn
       - run: yarn nx affected --target=build-npm-modules --parallel=3
+      - run: yarn nx affected --target=compile:check
diff --git a/Dockerfile b/Dockerfile
@@ -33,7 +33,10 @@ COPY package.json package.json
 COPY yarn.lock yarn.lock
 COPY packages packages
 
+ARG NODE_OPTIONS=--max-old-space-size=4096
+
 # Build the client bundles
+RUN echo "Building with NODE_OPTIONS=$NODE_OPTIONS"
 RUN yarn \
     && yarn nx bundle:npm @veupathdb/clinepi-site \
     && yarn nx bundle:npm @veupathdb/genomics-site \

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,7 +1,5 @@
 version: "3.5"
 
-name: "web-client"
-
 networks:
   traefik:
     external: true

diff --git a/packages/libs/components/src/plots/VolcanoPlot.tsx b/packages/libs/components/src/plots/VolcanoPlot.tsx
@@ -363,11 +363,17 @@ function VolcanoPlot(props: VolcanoPlotProps, ref: Ref<HTMLDivElement>) {
                   }}
                 >
                   <ul>
-                    {data?.pointIDs?.map((id) => (
-                      <li key={id}>
-                        <span>{id}</span>
-                      </li>
-                    ))}
+                    {data?.displayLabels
+                      ? data.displayLabels.map((label) => (
+                          <li key={label}>
+                            <span>{label}</span>
+                          </li>
+                        ))
+                      : data?.pointIDs?.map((id) => (
+                          <li key={id}>
+                            <span>{id}</span>
+                          </li>
+                        ))}
                   </ul>
                   <div
                     className="pseudo-hr"

diff --git a/packages/libs/components/src/types/plots/volcanoplot.ts b/packages/libs/components/src/types/plots/volcanoplot.ts
@@ -11,6 +11,8 @@ export type VolcanoPlotDataPoint = {
   pointIDs?: string[];
   // Used to determine color of data point in the plot
   significanceColor?: string;
+  // Optional user-friendly label. One for each pointID
+  displayLabels?: string[];
 };
 
 export type VolcanoPlotData = Array<VolcanoPlotDataPoint>;
diff --git a/...s/eda/src/lib/core/components/visualizations/implementations/VolcanoPlotVisualization.tsx b/...s/eda/src/lib/core/components/visualizations/implementations/VolcanoPlotVisualization.tsx
@@ -52,6 +52,7 @@ import SliderWidget, {
 } from '@veupathdb/components/lib/components/widgets/Slider';
 import { ResetButtonCoreUI } from '../../ResetButton';
 import AxisRangeControl from '@veupathdb/components/lib/components/plotControls/AxisRangeControl';
+import { fixVarIdLabel } from '../../../utils/visualization';
 // end imports
 
 const DEFAULT_SIG_THRESHOLD = 0.05;
@@ -270,9 +271,18 @@ function VolcanoPlotViz(props: VisualizationProps<Options>) {
          */
         .map((d) => {
           const { pointID, ...remainingProperties } = d;
+          // Try to find a user-friendly label for the point. Note that pointIDs are in entityID.variableID format.
+          const displayLabel =
+            pointID &&
+            fixVarIdLabel(
+              pointID.split('.')[1],
+              pointID.split('.')[0],
+              entities
+            );
           return {
             ...remainingProperties,
             pointIDs: pointID ? [pointID] : undefined,
+            displayLabels: displayLabel ? [displayLabel] : undefined,
             significanceColor: assignSignificanceColor(
               Number(d.log2foldChange),
               Number(d.pValue),
@@ -299,19 +309,24 @@ function VolcanoPlotViz(props: VisualizationProps<Options>) {
         if (foundIndex === -1) {
           aggregatedData.push(entry);
         } else {
-          const { pointIDs } = aggregatedData[foundIndex];
+          const { pointIDs, displayLabels } = aggregatedData[foundIndex];
           if (pointIDs) {
             aggregatedData[foundIndex] = {
               ...aggregatedData[foundIndex],
               pointIDs: [
                 ...pointIDs,
                 ...(entry.pointIDs ? entry.pointIDs : []),
               ],
+              displayLabels: displayLabels && [
+                ...displayLabels,
+                ...(entry.displayLabels ? entry.displayLabels : []),
+              ],
             };
           } else {
             aggregatedData[foundIndex] = {
               ...aggregatedData[foundIndex],
               pointIDs: entry.pointIDs,
+              displayLabels: entry.displayLabels,
             };
           }
         }

diff --git a/packages/libs/eda/src/lib/map/analysis/utils/defaultOverlayConfig.ts b/packages/libs/eda/src/lib/map/analysis/utils/defaultOverlayConfig.ts
@@ -65,7 +65,8 @@ export async function getDefaultOverlayConfig(
           overlayVariable: overlayVariableDescriptor,
           aggregationConfig: {
             overlayType: 'categorical',
-            numeratorValues: numeratorValues ?? [],
+            numeratorValues:
+              numeratorValues ?? overlayVariable.vocabulary ?? [],
             denominatorValues:
               denominatorValues ?? overlayVariable.vocabulary ?? [],
           },

diff --git a/packages/libs/user-datasets/src/lib/Components/Detail/UserDatasetDetail.jsx b/packages/libs/user-datasets/src/lib/Components/Detail/UserDatasetDetail.jsx
@@ -519,6 +519,11 @@ class UserDatasetDetail extends React.Component {
 
    -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= */
 
+  // This is needed to resolve downstream typescript errors.
+  // TypeScript infers that this method returns JSX.Element[].
+  // Some classes extending this will return (JSX.Element | null)[].
+  // The ReactNode type is better suited, here, since it allows for null values.
+  /** @return {import("react").ReactNode[]} */
   getPageSections() {
     return [
       this.renderHeaderSection,

diff --git a/packages/libs/wdk-client/src/Utils/UserPreferencesUtils.ts b/packages/libs/wdk-client/src/Utils/UserPreferencesUtils.ts
@@ -65,7 +65,9 @@ export async function getResultTableColumnsPref(
 
   const [knownColumns, unknownColumns] = partition(
     columns,
-    (columnName) => columnName in recordClass.attributesMap
+    (columnName) =>
+      recordClass.attributes.some((a) => a.name === columnName) ||
+      question.dynamicAttributes.some((a) => a.name === columnName)
   );
 
   if (unknownColumns.length > 0) {

diff --git a/packages/sites/clinepi-site/package.json b/packages/sites/clinepi-site/package.json
@@ -8,6 +8,7 @@
     "clean": "rm -rf dist && mkdir dist",
     "copy:webapp": "cp -r webapp/* dist",
     "copy:images": "cp -r ../../../node_modules/@veupathdb/web-common/images dist",
+    "compile:check": "tsc --noEmit",
     "bundle:dev": "npm-run-all clean copy:webapp copy:images && BROWSERSLIST_ENV=modern webpack --mode=development",
     "bundle:npm": "npm-run-all clean copy:webapp copy:images && BROWSERSLIST_ENV=modern webpack --mode=production && BROWSERSLIST_ENV=legacy webpack --mode=production"
   },

diff --git a/packages/sites/genomics-site/package.json b/packages/sites/genomics-site/package.json
@@ -8,6 +8,7 @@
     "clean": "rm -rf dist && mkdir dist",
     "copy:webapp": "cp -r webapp/* dist",
     "copy:images": "cp -r ../../../node_modules/@veupathdb/web-common/images dist",
+    "compile:check": "tsc --noEmit",
     "bundle:dev": "npm-run-all clean copy:webapp copy:images && BROWSERSLIST_ENV=modern webpack --mode=development",
     "bundle:npm": "npm-run-all clean copy:webapp copy:images && BROWSERSLIST_ENV=modern webpack --mode=production && BROWSERSLIST_ENV=legacy webpack --mode=production"
   },

diff --git a/packages/sites/mbio-site/package.json b/packages/sites/mbio-site/package.json
@@ -8,6 +8,7 @@
     "clean": "rm -rf dist && mkdir dist",
     "copy:webapp": "cp -r webapp/* dist",
     "copy:images": "cp -r ../../../node_modules/@veupathdb/web-common/images dist",
+    "compile:check": "tsc --noEmit",
     "bundle:dev": "npm-run-all clean copy:webapp copy:images && BROWSERSLIST_ENV=modern webpack --mode=development",
     "bundle:npm": "npm-run-all clean copy:webapp copy:images && BROWSERSLIST_ENV=modern webpack --mode=production && BROWSERSLIST_ENV=legacy webpack --mode=production"
   },

diff --git a/packages/sites/ortho-site/package.json b/packages/sites/ortho-site/package.json
@@ -9,6 +9,7 @@
     "clean": "rm -rf dist && mkdir dist",
     "copy:webapp": "cp -r webapp/* dist",
     "copy:images": "cp -r ../../../node_modules/@veupathdb/web-common/images dist",
+    "compile:check": "tsc --noEmit",
     "bundle:dev": "npm-run-all clean copy:webapp copy:images && BROWSERSLIST_ENV=modern webpack --mode=development",
     "bundle:npm": "npm-run-all clean copy:webapp copy:images && BROWSERSLIST_ENV=modern webpack --mode=production && BROWSERSLIST_ENV=legacy webpack --mode=production"
   },