@sjcrh/proteinpaint-shared 2.163.1 → 2.167.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.163.1",
+  "version": "2.167.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -30,7 +30,8 @@ export const TermTypeGroups = {
 	SNP: 'SNP Genotype',
 	SNP_LIST: 'SNP List',
 	SNP_LOCUS: 'SNP Locus',
-	SSGSEA: 'Geneset Expression'
+	SSGSEA: 'Geneset Expression',
+	TERM_COLLECTION: 'Term Collection'
 }
 
 export const defaultcolor = rgb('#8AB1D4').darker()

package/src/mds3tk.js

@@ -1,4 +1,4 @@
-import { dtcnv } from './common.js'
+import { dtcnv, dtsnvindel, dtsv, dtfusionrna } from './common.js'
 
 // this script should contain mds3 track-related stuff shared between client and backend
 
@@ -49,3 +49,50 @@ export function summarize_mclass(mlst) {
 	}
 	return [...m2c].sort((i, j) => j[1] - i[1])
 }
+
+/*
+ssmid is not specific for ssm, it covers all alterations
+gdc ssm are identified by a specific uuid, thus the design
+*/
+export function guessSsmid(ssmid) {
+	const l = ssmid.split(ssmIdFieldsSeparator)
+	if (l.length == 4) {
+		const [chr, tmp, ref, alt] = l
+		const pos = Number(tmp)
+		if (Number.isNaN(pos)) throw 'ssmid snvindel pos not integer'
+		return { dt: dtsnvindel, l: [chr, pos, ref, alt] }
+	}
+	if (l.length == 5) {
+		// cnv. if type=cat, _value is blank string
+		const [chr, _start, _stop, _class, _value] = l
+		const start = Number(_start),
+			stop = Number(_stop),
+			value = _value == '' ? null : Number(_value)
+		if (Number.isNaN(start) || Number.isNaN(stop)) throw 'ssmid cnv start/stop not integer'
+		return { dt: dtcnv, l: [chr, start, stop, _class, value] }
+	}
+	if (l.length == 6) {
+		if (l[3] == '+' || l[3] == '-') {
+			// sv/fusion
+			const [_dt, chr, _pos, strand, _pi, _mname] = l
+
+			// mname is encoded in case it contains comma (and is same as ssmIdFieldsSeparator)
+			const mname = decodeURIComponent(_mname)
+			const dt = Number(_dt)
+			if (dt != dtsv && dt != dtfusionrna) throw 'ssmid dt not sv/fusion'
+			const pos = Number(_pos)
+			if (Number.isNaN(pos)) throw 'ssmid svfusion position not integer'
+			const pairlstIdx = Number(_pi)
+			if (Number.isNaN(pairlstIdx)) throw 'ssmid pairlstIdx not integer'
+			return { dt, l: [dt, chr, pos, strand, pairlstIdx, mname] }
+		}
+		// cnv with sample
+		const [chr, _start, _stop, _class, _value, sample] = l
+		const start = Number(_start),
+			stop = Number(_stop),
+			value = _value == '' ? null : Number(_value) // if cnv not using value, must avoid `Number('')=0`
+		if (Number.isNaN(start) || Number.isNaN(stop)) throw 'ssmid cnv start/stop not integer'
+		return { dt: dtcnv, l: [chr, start, stop, _class, value, sample] }
+	}
+	throw 'unknown ssmid'
+}

package/src/terms.js

@@ -39,7 +39,8 @@ export const TermTypes = {
 	SINGLECELL_GENE_EXPRESSION: 'singleCellGeneExpression',
 	SINGLECELL_CELLTYPE: 'singleCellCellType',
 	MULTIVALUE: 'multivalue',
-	DATE: 'date'
+	DATE: 'date',
+	TERM_COLLECTION: 'termCollection'
 }
 export const dtTermTypes = new Set(dtTerms.map(t => t.type))
 for (const dtTermType of dtTermTypes) {
@@ -68,7 +69,8 @@ export const typeGroup = {
 	[TermTypes.SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
 	[TermTypes.GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
 	[TermTypes.SSGSEA]: TermTypeGroups.SSGSEA,
-	[TermTypes.METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY
+	[TermTypes.METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
+	[TermTypes.TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION
 }
 
 const nonDictTypes = new Set([
@@ -218,7 +220,8 @@ const typeMap = {
 	snplocus: 'SNP Locus',
 	snp: 'SNP',
 	snplst: 'SNP List',
-	numericDictTerm: 'Numeric Dictionary Term'
+	numericDictTerm: 'Numeric Dictionary Term',
+	termCollection: 'Term Collection'
 }
 
 export function termType2label(type) {