@weng-lab/genomebrowser-ui 0.2.7 → 0.2.9

package/src/TrackSelect/Folders/biosamples/data/notes.md

@@ -0,0 +1,17 @@
+# Notes
+
+## Missing data
+
+mouse chrom hmm file missing
+
+```json
+        {
+          "id": "chromhmm-ENCFF491PKK",
+          "assay": "chromhmm",
+          "url": "https://downloads.wenglab.org/Registry-V4/ENCFF491PKK.bigBed",
+          "experimentAccession": "",
+          "fileAccession": "ENCFF491PKK"
+        },
+```
+
+also intestine 15.5 days sometimes 416's

package/src/TrackSelect/Folders/biosamples/shared/columns.tsx

@@ -5,11 +5,12 @@ import {
   useGridApiContext,
 } from "@mui/x-data-grid-premium";
 import { Stack, capitalize } from "@mui/material";
-import Check from "@mui/icons-material/Check";
 import { AssayIcon, ontologyTypes, assayTypes, lifeStages } from "./constants";
-import { BiosampleRowInfo } from "./types";
+import { BiosampleRowInfo, CollectionType } from "./types";
 
-function CoreCollectionCell(params: GridRenderCellParams<BiosampleRowInfo>) {
+const collectionTypes: CollectionType[] = ["Core", "Ancillary", "Partial"];
+
+function CollectionCell(params: GridRenderCellParams<BiosampleRowInfo>) {
   const apiRef = useGridApiContext();
 
   if (params.rowNode.type !== "group") {
@@ -30,11 +31,7 @@ function CoreCollectionCell(params: GridRenderCellParams<BiosampleRowInfo>) {
     childIds[0],
   ) as BiosampleRowInfo | null;
 
-  if (firstChildRow?.coreCollection) {
-    return <Check color="primary" />;
-  }
-
-  return null;
+  return firstChildRow?.collection ?? null;
 }
 
 const displayNameCol: GridColDef<BiosampleRowInfo> = {
@@ -140,12 +137,13 @@ const lifeStageCol: GridColDef<BiosampleRowInfo> = {
   valueFormatter: (value) => value && capitalize(value),
 };
 
-const coreCollectionCol: GridColDef<BiosampleRowInfo> = {
-  field: "coreCollection",
-  headerName: "Core Collection",
-  type: "boolean",
-  width: 120,
-  renderCell: (params) => <CoreCollectionCell {...params} />,
+const collectionCol: GridColDef<BiosampleRowInfo> = {
+  field: "collection",
+  headerName: "Collection",
+  type: "singleSelect",
+  valueOptions: collectionTypes,
+  width: 100,
+  renderCell: (params) => <CollectionCell {...params} />,
 };
 
 const experimentCol: GridColDef<BiosampleRowInfo> = {
@@ -167,7 +165,7 @@ const idCol: GridColDef<BiosampleRowInfo> = {
 export const sortedByAssayColumns: GridColDef<BiosampleRowInfo>[] = [
   displayNameCol,
   sortedByAssayOntologyCol,
-  coreCollectionCol,
+  collectionCol,
   sampleTypeCol,
   lifeStageCol,
   sortedByAssayAssayCol,
@@ -179,7 +177,7 @@ export const sortedByAssayColumns: GridColDef<BiosampleRowInfo>[] = [
 /** Default columns (ontology as top-level grouping) */
 export const defaultColumns: GridColDef<BiosampleRowInfo>[] = [
   defaultAssayCol,
-  coreCollectionCol,
+  collectionCol,
   sampleTypeCol,
   lifeStageCol,
   defaultOntologyCol,

package/src/TrackSelect/Folders/biosamples/shared/createFolder.ts

@@ -24,7 +24,7 @@ import { BiosampleTreeItem } from "./BiosampleTreeItem";
  * @returns Array of flattened BiosampleRowInfo objects, one per assay
  */
 function flattenTrackIntoRows(track: BiosampleTrackInfo): BiosampleRowInfo[] {
-  const { ontology, lifeStage, sampleType, displayName, core } = track;
+  const { ontology, lifeStage, sampleType, displayName, collection } = track;
 
   // Sort assays so cCRE comes first, then maintain original order for the rest
   const sortedAssays = [...track.assays].sort((a, b) => {
@@ -46,7 +46,7 @@ function flattenTrackIntoRows(track: BiosampleTrackInfo): BiosampleRowInfo[] {
       experimentAccession,
       fileAccession,
       url,
-      coreCollection: core ?? false,
+      collection,
     }),
   );
 }

package/src/TrackSelect/Folders/biosamples/shared/types.ts

@@ -2,6 +2,8 @@
  * Types for biosample folder data
  */
 
+export type CollectionType = "Core" | "Ancillary" | "Partial";
+
 /**
  * Assay information from the JSON data
  */
@@ -23,7 +25,7 @@ export type BiosampleTrackInfo = {
   sampleType: string;
   displayName: string;
   assays: BiosampleAssayInfo[];
-  core?: boolean;
+  collection: CollectionType;
 };
 
 /**
@@ -39,7 +41,7 @@ export type BiosampleRowInfo = {
   experimentAccession: string;
   fileAccession: string;
   url: string;
-  coreCollection: boolean;
+  collection: CollectionType;
 };
 
 /**

package/test/main.tsx

@@ -79,7 +79,7 @@ function injectCallbacks(track: Track, callbacks: TrackCallbacks): Track {
 
 function Main() {
   const [open, setOpen] = useState(false);
-  const currentAssembly: Assembly = "GRCh38";
+  const currentAssembly: Assembly = "mm10";
 
   const browserStore = createBrowserStoreMemo({
     // chr7:19,695,494-19,699,803

package/vite.config.ts

@@ -30,6 +30,9 @@ export default defineConfig({
       },
     },
   },
+  server: {
+    allowedHosts: true,
+  },
   build: {
     lib: {
       entry: path.resolve(__dirname, "src/lib.ts"),