@sjcrh/proteinpaint-shared 2.137.3 → 2.138.3-7

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.137.3",
+  "version": "2.138.3-7",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -29,7 +29,8 @@ export const TermTypeGroups = {
 	MUTATION_SIGNATURE: 'Mutation Signature',
 	SNP: 'SNP Genotype',
 	SNP_LIST: 'SNP List',
-	SNP_LOCUS: 'SNP Locus'
+	SNP_LOCUS: 'SNP Locus',
+	SSGSEA: 'Geneset Expression'
 }
 
 export const defaultcolor = rgb('#8AB1D4').darker()
@@ -61,7 +62,8 @@ export const dtnloss = 8
 export const dtcloss = 9
 export const dtloh = 10
 export const dtmetaboliteintensity = 11
-// add new dt value here, and DO NOT change value of existing dt!
+export const dtssgsea = 12
+// add new dt value here. !!!DO NOT change value of existing dt!!!
 
 export const dt2label = {
 	[dtsnvindel]: 'SNV/indel',

package/src/termdb.usecase.js

@@ -16,6 +16,7 @@ export const graphableTypes = new Set([
 	'dtfusion',
 	'dtsv',
 	'date',
+	TermTypes.SSGSEA,
 	TermTypes.METABOLITE_INTENSITY,
 	TermTypes.SINGLECELL_GENE_EXPRESSION,
 	TermTypes.SINGLECELL_CELLTYPE,

package/src/terms.js

@@ -1,4 +1,4 @@
-import { dtgeneexpression, dtmetaboliteintensity, TermTypeGroups, dtTerms } from './common.js'
+import { dtgeneexpression, dtssgsea, dtmetaboliteintensity, TermTypeGroups, dtTerms } from './common.js'
 import { roundValueAuto } from './roundValue.js'
 
 // moved TermTypeGroups to `server/src/common.js`, so now has to re-export
@@ -26,6 +26,7 @@ export const NumericModes = {
 export const TermTypes = {
 	GENE_VARIANT: 'geneVariant',
 	GENE_EXPRESSION: 'geneExpression',
+	SSGSEA: 'ssGSEA',
 	CATEGORICAL: 'categorical',
 	INTEGER: 'integer',
 	FLOAT: 'float',
@@ -50,11 +51,11 @@ export const NUMERIC_DICTIONARY_TERM = 'numericDictTerm'
 
 export const TermTypes2Dt = {
 	[TermTypes.GENE_EXPRESSION]: dtgeneexpression,
+	[TermTypes.SSGSEA]: dtssgsea,
 	[TermTypes.METABOLITE_INTENSITY]: dtmetaboliteintensity
 }
 
-//The dataset provides the allowed term types that are then mapped to the term type groups
-//Depending on the dataset types and the use case only certain term type groups/tabs are allowed
+// maps term type to group (as is shown as toggles in search ui)
 export const typeGroup = {
 	[TermTypes.CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,
 	[TermTypes.CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,
@@ -67,6 +68,7 @@ export const typeGroup = {
 	[TermTypes.SNP_LIST]: TermTypeGroups.SNP_LIST,
 	[TermTypes.SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
 	[TermTypes.GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
+	[TermTypes.SSGSEA]: TermTypeGroups.SSGSEA,
 	[TermTypes.METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY
 }
 
@@ -75,6 +77,7 @@ const nonDictTypes = new Set([
 	TermTypes.SNP_LIST,
 	TermTypes.SNP_LOCUS,
 	TermTypes.GENE_EXPRESSION,
+	TermTypes.SSGSEA,
 	TermTypes.GENE_VARIANT,
 	TermTypes.METABOLITE_INTENSITY,
 	TermTypes.SINGLECELL_GENE_EXPRESSION,
@@ -88,6 +91,7 @@ export const numericTypes = new Set([
 	TermTypes.INTEGER,
 	TermTypes.FLOAT,
 	TermTypes.GENE_EXPRESSION,
+	TermTypes.SSGSEA,
 	TermTypes.METABOLITE_INTENSITY,
 	TermTypes.SINGLECELL_GENE_EXPRESSION,
 	TermTypes.DATE
@@ -131,6 +135,8 @@ export function equals(t1, t2) {
 	switch (t1.type) {
 		case TermTypes.GENE_EXPRESSION:
 			return t1.gene == t2.gene
+		case TermTypes.SSGSEA:
+			return t1.id == t2.id
 		case TermTypes.METABOLITE_INTENSITY:
 			return t1.name == t2.name
 		case TermTypes.GENE_VARIANT:
@@ -207,6 +213,7 @@ const typeMap = {
 	float: 'Numerical',
 	integer: 'Numerical',
 	geneExpression: 'Gene Expression',
+	ssGSEA: 'Geneset Expression',
 	geneVariant: 'Gene Variant',
 	metaboliteIntensity: 'Metabolite Intensity',
 	multiValue: 'Multi Value',