@sjcrh/proteinpaint-shared 2.176.1-0 → 2.177.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.176.1-0",
+  "version": "2.177.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -17,21 +17,22 @@ import { getWrappedTvslst } from './filter.js'
 // part of 'common' argument to exported dataset js function, at server runtime
 export const TermTypeGroups = {
 	DICTIONARY_VARIABLES: 'Dictionary Variables',
-	MUTATION_CNV_FUSION: 'Mutation/CNV/Fusion',
-	VARIANT_GENOTYPE: 'Variant Genotype',
 	DNA_METHYLATION: 'DNA Methylation',
 	GENE_DEPENDENCY: 'Gene Dependency',
 	GENE_EXPRESSION: 'Gene Expression',
-	PROTEIN_EXPRESSION: 'Protein Expression',
-	SPLICE_JUNCTION: 'Splice Junction',
-	METABOLITE_INTENSITY: 'Metabolite Intensity',
 	GSEA: 'GSEA',
+	METABOLITE_INTENSITY: 'Metabolite Intensity',
+	MUTATION_CNV_FUSION: 'Mutation/CNV/Fusion',
 	MUTATION_SIGNATURE: 'Mutation Signature',
+	PROTEIN_EXPRESSION: 'Protein Expression',
+	SINGLECELL_CELLTYPE: 'Single-cell Cell Type',
 	SNP: 'SNP Genotype',
 	SNP_LIST: 'SNP List',
 	SNP_LOCUS: 'SNP Locus',
+	SPLICE_JUNCTION: 'Splice Junction',
 	SSGSEA: 'Geneset Expression',
-	TERM_COLLECTION: 'Term Collection'
+	TERM_COLLECTION: 'Term Collection',
+	VARIANT_GENOTYPE: 'Variant Genotype'
 }
 
 export const defaultcolor = rgb('#8AB1D4').darker()

package/src/termdb.usecase.js

@@ -113,23 +113,7 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 			}
 			return uses
 		case 'runChart2':
-			if (usecase.detail == 'date') {
-				if (term.type == 'date') {
-					uses.add('plot')
-				}
-				if (child_types.includes('date')) uses.add('branch')
-			} else if (usecase.detail == 'numeric') {
-				if (isNumericTerm(term) && term.type != 'date') {
-					uses.add('plot')
-				}
-				if (hasNumericChild(child_types)) uses.add('branch')
-			} else {
-				if (graphableTypes.has(term.type)) uses.add('plot')
-				if (!term.isleaf) uses.add('branch')
-			}
-			return uses
-		case 'frequencyChart':
-			if (usecase.detail == 'term') {
+			if (usecase.detail == 'date' || usecase.detail == 'xtw') {
 				if (term.type == 'date') {
 					uses.add('plot')
 				}

package/src/terms.js

@@ -70,7 +70,8 @@ export const typeGroup = {
 	[TermTypes.GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
 	[TermTypes.SSGSEA]: TermTypeGroups.SSGSEA,
 	[TermTypes.METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
-	[TermTypes.TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION
+	[TermTypes.TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,
+	[TermTypes.SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE
 }
 
 const nonDictTypes = new Set([
@@ -196,6 +197,7 @@ export function getParentType(types, ds) {
 	if (!ids || ids.length == 0) return null
 	for (const id of ids) {
 		const typeObj = ds.cohort.termdb.sampleTypes[id]
+		if (!typeObj) continue
 		if (typeObj.parent_id == null) return id //this is the root type
 		//if my parent is in the list, then I am not the parent
 		if (ids.includes(typeObj.parent_id)) continue