Merge branch 'main' into typeahead

packages/libs/components/src/map/SemanticMarkers.tsx

@@ -211,7 +211,7 @@ function constrainLongitudeToMainWorld({
   // but we need to make sure that west is slightly greater than east
   // so that they "wrap around" the whole globe
   // (if west was slightly less than east, it would represent a very tiny sliver)
-  if (newWest === newEast) newWest = newWest + 1e-8;
+  if (Math.abs(newEast - newWest) < 1e-8) newWest = newEast + 1e-8;
 
   return {
     southWest: { lat: south, lng: newWest },

packages/libs/eda/src/lib/core/components/visualizations/implementations/LineplotVisualization.tsx

@@ -651,14 +651,14 @@ function LineplotViz(props: VisualizationProps<Options>) {
     [options, providedOverlayVariable, providedOverlayVariableDescriptor]
   );
 
-  // define showMarginalHistogram
-  const showMarginalHistogram = options?.showMarginalHistogram ?? false;
   // check banner condition
   const showIndependentAxisBanner =
     vizConfig.independentAxisLogScale && vizConfig.useBinning;
   const showDependentAxisBanner =
     vizConfig.dependentAxisLogScale && vizConfig.showErrorBars;
 
+  const showMarginalHistogram = options?.showMarginalHistogram ?? false;
+
   const data = usePromise(
     useCallback(async (): Promise<LinePlotDataWithCoverage | undefined> => {
       if (

packages/libs/eda/src/lib/core/hooks/workspace.ts

@@ -130,11 +130,11 @@ export function useStudyEntities(filters?: Filter[]) {
                             min:
                               filter.type === 'numberRange'
                                 ? filter.min
-                                : filter.min.split('T00:00:00Z')[0],
+                                : filter.min.split(/T00:00:00(?:\.000)?Z?/)[0],
                             max:
                               filter.type === 'numberRange'
                                 ? filter.max
-                                : filter.max.split('T00:00:00Z')[0],
+                                : filter.max.split(/T00:00:00(?:\.000)?Z?/)[0],
                           }
                         : undefined;
 

packages/libs/eda/src/lib/map/analysis/hooks/standaloneVizPlugins.ts

@@ -23,6 +23,8 @@ import { barplotRequest } from './plugins/barplot';
 import { lineplotRequest } from './plugins/lineplot';
 import { histogramRequest } from './plugins/histogram';
 import { scatterplotRequest } from './plugins/scatterplot';
+//TO DO import timeline SVGIcon
+import LineSVG from '../../../core/components/visualizations/implementations/selectorIcons/LineSVG';
 
 interface Props {
   selectedOverlayConfig?: OverlayConfig;
@@ -40,10 +42,6 @@ export function useStandaloneVizPlugins({
       return visualization.withOptions({
         hideFacetInputs: true, // will also enable table-only mode for mosaic
         hideShowMissingnessToggle: true,
-        // TODO: need to distinguish lineplot from lineplot with marginal histogram?
-        // perhaps need to make another function only for lineplot with marginal histogram
-        // or define xxx.withOptions({}) directly at corresponding visualizationPlugins below
-        showMarginalHistogram: false,
         layoutComponent: FloatingLayout,
         // why are we providing three functions to access the properties of
         // one object? Because in the pre-SAM world, getOverlayVariable was already
@@ -108,6 +106,17 @@ export function useStandaloneVizPlugins({
             vizWithOptions(lineplotVisualization),
             lineplotRequest
           ),
+          // activate timeline Viz
+          timeseries: vizWithCustomizedGetRequest(
+            vizWithOptions(
+              lineplotVisualization
+                .withOptions({
+                  showMarginalHistogram: true,
+                })
+                .withSelectorIcon(LineSVG)
+            ),
+            lineplotRequest
+          ),
         },
       },
       'standalone-map-distributions': {

packages/libs/wdk-client/src/Controllers/QuestionController.tsx

@@ -377,9 +377,9 @@ const enhance = connect<
   (stateProps, dispatchProps, ownProps) => ({
     ...stateProps,
     ...dispatchProps,
+    ...omit(ownProps, ['question', 'recordClass']),
     searchName: ownProps.question,
     recordClassName: ownProps.recordClass,
-    ...omit(ownProps, ['question', 'recordClass']),
   })
 );
 

packages/libs/wdk-client/src/Views/Question/Params/FilterParamNew/FilterParamObserver.ts

@@ -139,6 +139,8 @@ const observeInitialParamData: Observer = (action$, state$, services) => {
           } as Filter);
         }
       }
+      // If filters is empty, assume there is no initialParamData for this param.
+      if (filters.length === 0) return EMPTY;
       return of(
         updateParamValue({
           paramValue: JSON.stringify({ filters }),

packages/sites/genomics-site/webapp/wdkCustomization/js/client/componentWrappers.jsx

@@ -525,4 +525,4 @@ export { SiteSearchInput } from './component-wrappers/SiteSearchInput';
 
 export { AnswerController } from './component-wrappers/AnswerController';
 
-export { QuestionController } from './component-wrappers/QuestionController';
+// export { QuestionController } from './component-wrappers/QuestionController';

packages/sites/ortho-site/webapp/wdkCustomization/js/client/utils/dataSummary.tsx

@@ -7,24 +7,30 @@ import {
   nullValue,
   oneOf,
   record,
-  string
+  string,
 } from '@veupathdb/wdk-client/lib/Utils/Json';
 
 import { DataTableColumns } from 'ortho-client/utils/dataTables';
 import { TaxonUiMetadata } from 'ortho-client/utils/taxons';
+import { renderAttributeValue } from '@veupathdb/wdk-client/lib/Utils/ComponentUtils';
+
+const linkAttributeValue = record({
+  url: string,
+  displayText: string,
+});
 
 const proteomeSummaryRowDecoder = record({
   clustered_sequences: string,
   core_peripheral: oneOf(constant('Core'), constant('Peripheral')),
   resource_version: oneOf(string, nullValue),
   groups: string,
   name: string,
-  resource_name: string,
-  resource_url: string,
+  ncbi_taxon_url_link: linkAttributeValue,
+  resource_url_link: linkAttributeValue,
   sequences: string,
   root_taxon: string,
   three_letter_abbrev: string,
-  most_recent: string
+  most_recent: string,
 });
 
 type ProteomeSummaryRow = Unpack<typeof proteomeSummaryRowDecoder>;
@@ -40,99 +46,106 @@ export const RELEASE_SUMMARY_COLUMNS: DataTableColumns<
   core_peripheral: {
     key: 'core_peripheral',
     name: 'Core/Peripheral',
-    helpText: 'There are 150 Core species whose proteomes were used to form the initial core groups. The remaining species on the site are Peripheral species. The Peripheral proteins were mapped into core groups if they met sequence similarity thresholds. Proteins that did not map into core groups were collected and used to form Residual groups.',
-    sortable: true
+    helpText:
+      'There are 150 Core species whose proteomes were used to form the initial core groups. The remaining species on the site are Peripheral species. The Peripheral proteins were mapped into core groups if they met sequence similarity thresholds. Proteins that did not map into core groups were collected and used to form Residual groups.',
+    sortable: true,
   },
   name: {
     key: 'name',
     name: 'Name',
     helpText: 'Genus, species and strain name',
-    sortable: true
+    sortable: true,
+  },
+  ncbi_taxon_url_link: {
+    key: 'ncbi_taxon_url_link',
+    name: 'NCBI Taxon ID',
+    helpText: 'The URL of the NCBI site for this taxon.',
+    sortable: true,
+    renderCell: ({ value }) => renderAttributeValue(value),
   },
   root_taxon: {
     key: 'root_taxon',
     name: 'Category',
-    helpText: 'The taxonomic category of the organism. ALVE: Alveolata, AMOE: Amoeba, ARCH: Archaea, EUGL: Euglenozoa, FUNG: Fungi, META: Metazoa, OBAC: Other Bacteria, OEUK: Other Eukaryota, PROT: Proteobacteria, VIRI: Viridiplantae',
-    sortable: true
+    helpText:
+      'The taxonomic category of the organism. ALVE: Alveolata, AMOE: Amoeba, ARCH: Archaea, EUGL: Euglenozoa, FUNG: Fungi, META: Metazoa, OBAC: Other Bacteria, OEUK: Other Eukaryota, PROT: Proteobacteria, VIRI: Viridiplantae',
+    sortable: true,
   },
   three_letter_abbrev: {
     key: 'three_letter_abbrev',
     name: 'Abbreviation',
-    helpText: 'Usually, this a four-letter abbreviation for this organism at OrthoMCL. Sometimes, the name follows the format abcd-old, in which case it is a core organism that also has an updated proteome which has been added to OrthoMCL as a peripheral organism. The updated name in this case is abcd.',
-    sortable: true
+    helpText:
+      'Usually, this a four-letter abbreviation for this organism at OrthoMCL. Sometimes, the name follows the format abcd-old, in which case it is a core organism that also has an updated proteome which has been added to OrthoMCL as a peripheral organism. The updated name in this case is abcd.',
+    sortable: true,
   },
   clustered_sequences: {
     key: 'clustered_sequences',
     name: '# Grouped Sequences',
-    helpText: 'Number of proteins that are part of an ortholog group. A protein would not be part of a group if it was poor quality (e.g., several stop codons or very few amino acids).',
+    helpText:
+      'Number of proteins that are part of an ortholog group. A protein would not be part of a group if it was poor quality (e.g., several stop codons or very few amino acids).',
     sortable: true,
-    makeOrder: ({ clustered_sequences }) => Number(clustered_sequences)
+    makeOrder: ({ clustered_sequences }) => Number(clustered_sequences),
   },
   groups: {
     key: 'groups',
     name: '# Groups',
-    helpText: 'Number of ortholog groups in which the organism proteins are found.',
+    helpText:
+      'Number of ortholog groups in which the organism proteins are found.',
     sortable: true,
-    makeOrder: ({ groups }) => Number(groups)
+    makeOrder: ({ groups }) => Number(groups),
   },
   sequences: {
     key: 'sequences',
     name: '# Sequences',
-    helpText: 'Number of proteins in the organism that have been processed by OrthoMCL. This will depend on whether the gene was structurally annotated to encode a protein.',
+    helpText:
+      'Number of proteins in the organism that have been processed by OrthoMCL. This will depend on whether the gene was structurally annotated to encode a protein.',
     sortable: true,
-    makeOrder: ({ sequences }) => Number(sequences)
+    makeOrder: ({ sequences }) => Number(sequences),
   },
-  resource_name: {
-    key: 'resource_name',
+  resource_url_link: {
+    key: 'resource_url_link',
     name: 'Resource',
     helpText: 'The source of the organism proteome.',
-    sortable: true
-  },
-  resource_url: {
-    key: 'resource_url',
-    name: 'URL',
-    helpText: 'The URL of the site from which the organism proteome was obtained.',
-    sortable: true
+    sortable: true,
+    renderCell: ({ value }) => renderAttributeValue(value),
   },
   most_recent: {
     key: 'most_recent',
     name: 'Most recent version',
     sortable: true,
-    helpText: 'Type most_recent in the search box to show only the most recent version.',
+    helpText:
+      'Type most_recent in the search box to show only the most recent version.',
   },
   resource_version: {
     key: 'resource_version',
     name: 'Proteome version',
     sortable: true,
     makeOrder: ({ resource_version }) => resource_version || '',
-    makeSearchableString: resource_version => resource_version || 'N/A',
+    makeSearchableString: (resource_version) => resource_version || 'N/A',
     renderCell: ({ value }) =>
-      value ? value : <span className="EmptyResourceVersion">N/A</span>
-  }
+      value ? value : <span className="EmptyResourceVersion">N/A</span>,
+  },
 };
 
 export function makeReleaseSummaryRows(
   { species }: TaxonUiMetadata,
   proteomeSummaryRows: ProteomeSummaryRows
 ): ProteomeSummaryRows {
-  return proteomeSummaryRows.map(
-    proteomeSummaryRow => ({
-      ...proteomeSummaryRow,
-      root_taxon: species[proteomeSummaryRow.three_letter_abbrev].rootTaxon
-    })
-  );
+  return proteomeSummaryRows.map((proteomeSummaryRow) => ({
+    ...proteomeSummaryRow,
+    root_taxon: species[proteomeSummaryRow.three_letter_abbrev].rootTaxon,
+  }));
 }
 
 export const RELEASE_SUMMARY_COLUMN_ORDER = [
   'root_taxon',
   'name',
+  'ncbi_taxon_url_link',
   'core_peripheral',
   'three_letter_abbrev',
-  'resource_name',
-  'resource_url',
+  'resource_url_link',
   'resource_version',
   'most_recent',
   'sequences',
   'clustered_sequences',
-  'groups'
+  'groups',
 ] as const;