@vitessce/biomarker-select 3.5.10 → 3.5.11

package/dist/index.js

@@ -1023,6 +1023,7 @@ const CoordinationType = {
   FEATURE_VALUE_COLORMAP: "featureValueColormap",
   FEATURE_VALUE_TRANSFORM: "featureValueTransform",
   FEATURE_VALUE_COLORMAP_RANGE: "featureValueColormapRange",
+  FEATURE_AGGREGATION_STRATEGY: "featureAggregationStrategy",
   OBS_COLOR_ENCODING: "obsColorEncoding",
   SPATIAL_IMAGE_LAYER: "spatialImageLayer",
   SPATIAL_SEGMENTATION_LAYER: "spatialSegmentationLayer",
@@ -1165,6 +1166,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_SELECTION,
     CoordinationType.FEATURE_VALUE_COLORMAP,
     CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.OBS_COLOR_ENCODING,
     CoordinationType.ADDITIONAL_OBS_SETS,
     CoordinationType.TOOLTIPS_VISIBLE,
@@ -1208,6 +1210,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_SELECTION,
     CoordinationType.FEATURE_VALUE_COLORMAP,
     CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.OBS_COLOR_ENCODING,
     CoordinationType.ADDITIONAL_OBS_SETS,
     CoordinationType.TOOLTIPS_VISIBLE,
@@ -1287,6 +1290,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_SELECTION,
     CoordinationType.FEATURE_VALUE_COLORMAP,
     CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.OBS_COLOR_ENCODING,
     CoordinationType.ADDITIONAL_OBS_SETS,
     CoordinationType.MOLECULE_HIGHLIGHT,
@@ -1324,6 +1328,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_SELECTION,
     CoordinationType.FEATURE_VALUE_COLORMAP,
     CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.OBS_COLOR_ENCODING,
     CoordinationType.ADDITIONAL_OBS_SETS,
     CoordinationType.MOLECULE_HIGHLIGHT,
@@ -1437,6 +1442,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_SELECTION,
     CoordinationType.FEATURE_VALUE_TRANSFORM,
     CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.OBS_SET_SELECTION,
     CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_HIGHLIGHT,
@@ -1452,6 +1458,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_TYPE,
     CoordinationType.FEATURE_VALUE_TYPE,
     CoordinationType.FEATURE_SELECTION,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.ADDITIONAL_OBS_SETS,
     CoordinationType.OBS_SET_COLOR,
     CoordinationType.OBS_COLOR_ENCODING,
@@ -1530,6 +1537,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_VALUE_COLORMAP,
     CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
     CoordinationType.FEATURE_SELECTION,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.TOOLTIPS_VISIBLE,
     CoordinationType.TOOLTIP_CROSSHAIRS_VISIBLE,
     CoordinationType.LEGEND_VISIBLE,
@@ -1570,6 +1578,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
     CoordinationType.FEATURE_VALUE_POSITIVITY_THRESHOLD,
     CoordinationType.FEATURE_VALUE_COLORMAP,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.OBS_SET_SELECTION,
     CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_HIGHLIGHT,
@@ -1598,6 +1607,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_SELECTION,
     CoordinationType.FEATURE_VALUE_TRANSFORM,
     CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.OBS_SET_SELECTION,
     CoordinationType.OBS_SET_HIGHLIGHT,
     CoordinationType.OBS_HIGHLIGHT,
@@ -1702,6 +1712,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.OBS_TYPE,
     CoordinationType.SAMPLE_TYPE,
     CoordinationType.FEATURE_SELECTION,
+    CoordinationType.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType.SAMPLE_SET_SELECTION,
     CoordinationType.SAMPLE_SET_FILTER,
     CoordinationType.OBS_SET_SELECTION,
@@ -33366,7 +33377,7 @@ function loadPathwayNodes() {
       kgId: d.id,
       label: d.pathway,
       // For reactome
-      term: `reactome:${d.acc}`,
+      term: `REACTOME:${d.acc}`,
       // For reactome
       // label: d.ontology_label, // For GO_BP
       // term: d.acc, // For GO_BP
@@ -33436,7 +33447,11 @@ async function loadPathwayToGeneEdges() {
     }));
   });
 }
-async function transformFeature({ queryClient }, node, targetModality) {
+async function transformFeature({ queryClient }, nodeOrig, targetModality) {
+  var _a2;
+  const node = {
+    ...nodeOrig
+  };
   if (targetModality === node.nodeType) {
     return [node];
   }
@@ -33452,6 +33467,19 @@ async function transformFeature({ queryClient }, node, targetModality) {
         staleTime: Infinity,
         queryFn: loadPathwayToGeneEdges
       });
+      if (!node.kgId) {
+        const pathwayNodes = await queryClient.fetchQuery({
+          queryKey: ["pathwayNodes"],
+          staleTime: Infinity,
+          queryFn: loadPathwayNodes
+        });
+        const foundId = (_a2 = pathwayNodes.find((n2) => n2.term === node.term)) == null ? void 0 : _a2.kgId;
+        if (foundId) {
+          node.kgId = foundId;
+        } else {
+          console.warn("Could not find matching pathway node based on term.");
+        }
+      }
       const matchingEdges = pathwayGeneEdges.filter((d) => d.source === node.kgId);
       const matchingGeneIds = matchingEdges.map((d) => d.target);
       const matchingGenes = geneNodes.filter((d) => matchingGeneIds.includes(d.kgId));

package/dist-tsc/default-async-functions.d.ts

@@ -13,13 +13,13 @@ export function autocompleteFeature({ queryClient }: {
  * @satisfies {TransformFeatureFunc}
  * @param {object} ctx
  * @param {QueryClient} ctx.queryClient
- * @param {KgNode} node
+ * @param {KgNode} nodeOrig
  * @param {TargetModalityType} targetModality
  * @returns {Promise<KgNode[]>}
  */
 export function transformFeature({ queryClient }: {
     queryClient: QueryClient;
-}, node: KgNode, targetModality: TargetModalityType): Promise<KgNode[]>;
+}, nodeOrig: KgNode, targetModality: TargetModalityType): Promise<KgNode[]>;
 /**
  * @satisfies {GetAlternativeTermsFunc}
  * @param {object} ctx

package/dist-tsc/default-async-functions.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"default-async-functions.d.ts","sourceRoot":"","sources":["../src/default-async-functions.js"],"names":[],"mappings":"AAyHA;;;;;;;GAOG;AACH,qDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,WAAQ,MAAM,kBACN,IAAI,GAAG,kBAAkB,GACvB,OAAO,CAAC,MAAM,EAAE,CAAC,CAiB7B;AAkBD;;;;;;;GAOG;AACH,kDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,QAAQ,MAAM,kBACN,kBAAkB,GAChB,OAAO,CAAC,MAAM,EAAE,CAAC,CAmC7B;AAED;;;;;;GAMG;AACH,qDAJG;IAAyB,WAAW,EAA5B,WAAW;CACnB,SAAQ,MAAM,GACJ,OAAO,CAAC,MAAM,EAAE,CAAC,CA2B7B;AAED;;;;;;;GAOG;AACH,gDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,kBAAQ,MAAM,kBACN,MAAM,GACJ,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAoBxC;iCAjQsD,uBAAuB;wCADsE,iBAAiB;4BAAjB,iBAAiB"}
+{"version":3,"file":"default-async-functions.d.ts","sourceRoot":"","sources":["../src/default-async-functions.js"],"names":[],"mappings":"AAyHA;;;;;;;GAOG;AACH,qDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,WAAQ,MAAM,kBACN,IAAI,GAAG,kBAAkB,GACvB,OAAO,CAAC,MAAM,EAAE,CAAC,CAiB7B;AAkBD;;;;;;;GAOG;AACH,kDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,YAAQ,MAAM,kBACN,kBAAkB,GAChB,OAAO,CAAC,MAAM,EAAE,CAAC,CAoD7B;AAED;;;;;;GAMG;AACH,qDAJG;IAAyB,WAAW,EAA5B,WAAW;CACnB,SAAQ,MAAM,GACJ,OAAO,CAAC,MAAM,EAAE,CAAC,CA2B7B;AAED;;;;;;;GAOG;AACH,gDALG;IAAyB,WAAW,EAA5B,WAAW;CACnB,kBAAQ,MAAM,kBACN,MAAM,GACJ,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAoBxC;iCAlRsD,uBAAuB;wCADsE,iBAAiB;4BAAjB,iBAAiB"}

package/dist-tsc/default-async-functions.js

@@ -53,7 +53,7 @@ function loadPathwayNodes() {
         return result.map((/** @type {any} */ d) => ({
             kgId: d.id,
             label: d.pathway, // For reactome
-            term: `reactome:${d.acc}`, // For reactome
+            term: `REACTOME:${d.acc}`, // For reactome
             // label: d.ontology_label, // For GO_BP
             // term: d.acc, // For GO_BP
             nodeType: 'pathway',
@@ -146,11 +146,14 @@ async function loadPathwayToGeneEdges() {
  * @satisfies {TransformFeatureFunc}
  * @param {object} ctx
  * @param {QueryClient} ctx.queryClient
- * @param {KgNode} node
+ * @param {KgNode} nodeOrig
  * @param {TargetModalityType} targetModality
  * @returns {Promise<KgNode[]>}
  */
-export async function transformFeature({ queryClient }, node, targetModality) {
+export async function transformFeature({ queryClient }, nodeOrig, targetModality) {
+    const node = {
+        ...nodeOrig,
+    };
     if (targetModality === node.nodeType) {
         // For example, if the target modality is gene and the node is already a gene node.
         return [node];
@@ -168,6 +171,20 @@ export async function transformFeature({ queryClient }, node, targetModality) {
                 staleTime: Infinity,
                 queryFn: loadPathwayToGeneEdges,
             });
+            if (!node.kgId) {
+                const pathwayNodes = await queryClient.fetchQuery({
+                    queryKey: ['pathwayNodes'],
+                    staleTime: Infinity,
+                    queryFn: loadPathwayNodes,
+                });
+                const foundId = pathwayNodes.find(n => n.term === node.term)?.kgId;
+                if (foundId) {
+                    node.kgId = foundId;
+                }
+                else {
+                    console.warn('Could not find matching pathway node based on term.');
+                }
+            }
             // TODO: support matching using ontology term (rather than requiring kgId)?
             const matchingEdges = pathwayGeneEdges.filter((/** @type {KgEdge} */ d) => d.source === node.kgId);
             const matchingGeneIds = matchingEdges.map((/** @type {KgEdge} */ d) => d.target);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/biomarker-select",
-  "version": "3.5.10",
+  "version": "3.5.11",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -25,9 +25,9 @@
     "fuse.js": "^7.0.0",
     "d3-dsv": "^1.1.1",
     "clsx": "^1.1.1",
-    "@vitessce/constants-internal": "3.5.10",
-    "@vitessce/vit-s": "3.5.10",
-    "@vitessce/types": "3.5.10"
+    "@vitessce/constants-internal": "3.5.11",
+    "@vitessce/vit-s": "3.5.11",
+    "@vitessce/types": "3.5.11"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^5.16.4",

package/src/default-async-functions.js

@@ -58,7 +58,7 @@ function loadPathwayNodes() {
       return result.map((/** @type {any} */ d) => ({
         kgId: d.id,
         label: d.pathway, // For reactome
-        term: `reactome:${d.acc}`, // For reactome
+        term: `REACTOME:${d.acc}`, // For reactome
         // label: d.ontology_label, // For GO_BP
         // term: d.acc, // For GO_BP
         nodeType: 'pathway',
@@ -164,11 +164,14 @@ async function loadPathwayToGeneEdges() {
  * @satisfies {TransformFeatureFunc}
  * @param {object} ctx
  * @param {QueryClient} ctx.queryClient
- * @param {KgNode} node
+ * @param {KgNode} nodeOrig
  * @param {TargetModalityType} targetModality
  * @returns {Promise<KgNode[]>}
  */
-export async function transformFeature({ queryClient }, node, targetModality) {
+export async function transformFeature({ queryClient }, nodeOrig, targetModality) {
+  const node = {
+    ...nodeOrig,
+  };
   if (targetModality === node.nodeType) {
     // For example, if the target modality is gene and the node is already a gene node.
     return [node];
@@ -187,6 +190,20 @@ export async function transformFeature({ queryClient }, node, targetModality) {
         queryFn: loadPathwayToGeneEdges,
       });
 
+      if (!node.kgId) {
+        const pathwayNodes = await queryClient.fetchQuery({
+          queryKey: ['pathwayNodes'],
+          staleTime: Infinity,
+          queryFn: loadPathwayNodes,
+        });
+        const foundId = pathwayNodes.find(n => n.term === node.term)?.kgId;
+        if (foundId) {
+          node.kgId = foundId;
+        } else {
+          console.warn('Could not find matching pathway node based on term.');
+        }
+      }
+
       // TODO: support matching using ontology term (rather than requiring kgId)?
       const matchingEdges = pathwayGeneEdges.filter((/** @type {KgEdge} */ d) => d.source === node.kgId);
       const matchingGeneIds = matchingEdges.map((/** @type {KgEdge} */ d) => d.target);