@sjcrh/proteinpaint-types 2.137.1-0 → 2.137.2-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.137.1-0",
+  "version": "2.137.2-0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -743,14 +743,13 @@ export type SingleCellGeneExpressionGdc = {
 }
 
 export type SingleCellSamples = {
-	/** if missing refer to the samples as 'sample', this provides override e.g. 'case' */
 	/** logic to decide sample table columns (the one shown on singlecell app ui, displaying a table of samples with sc data)
 	a sample table will always have a sample column, to show sample.sample value
 	- use uiLabels.Sample to customize the name of the first column
 	- the other two properties allow to declare additional columns to be shown in table, that are for display only
 	when sample.experiments[] are used, a last column of experiment id will be auto added
 	*/
-	/** any columns to be added to sample table. each is a term id */
+	/** any columns to be added to sample table. each is a term id, limited to categorical/numeric dictionary terms */
 	sampleColumns?: { termid: string }[]
 	/** used on client but not on ds */
 	experimentColumns?: { label: string }[]
@@ -803,7 +802,9 @@ type SingleCellPlot = {
 	/** value is display as plot name on ui and also used as identifier for a plot, must be unique */
 	name: string
 	/** folder in which per-sample files are stored.
-	each file is a tabular text file with all cells (rows) from that sample.
+	- each file is a tabular text file with all cells (rows) from that sample. each file is named by the sample and includes optional suffix
+	- folder must only contain per-sample files! files with names that cannot be matched to sample will crash dataset. this improves debugging
+
 	all files must have same set of columns:
 	- 1st column is cell barcode
 	- x/y coordinate column number is defined in coordsColumns{x,y} below
@@ -1539,7 +1540,16 @@ type PlotConfigByCohort = {
 type Tw = {
 	id: string
 	q: unknown
-	baseURL?: string //Only appears as a quick fix in SAMD9-SAMD9L.hg19?
+	/** quick fix for generating URL links in mds3 tk sample table! adhoc design. may move to tw.term.baseURL and not specific to mds3 tk
+	 */
+	baseURL?: string
+	/** quick fix. such a "publication" term can have values either pmid or doi, need to generate different links
+	cannot use ds-defined callback to compute the link as the links are only generated on client
+	thus this work around for client code to apply the url-building logic
+	a doi value must be defined as "doi: 10.1038/s41408-025-01309-6", beginning with "doi: ", this allows client code to recognize it is doi;
+	otherwise it is treated as pmid and joined to pubmed link as-is
+	*/
+	pmidOrDoi?: true
 }
 
 type Variant2Samples = GdcApi & {