@sjcrh/proteinpaint-shared 2.180.1 → 2.181.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.180.1",
+  "version": "2.181.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -15,27 +15,32 @@ import { getWrappedTvslst } from "./filter.js"
 
 // moved from `#shared/terms` to here, so that this can be passed as
 // part of 'common' argument to exported dataset js function, at server runtime
-export const TermTypeGroups = {
-	DICTIONARY_VARIABLES: "Dictionary Variables",
-	DNA_METHYLATION: "DNA Methylation",
-	GENE_DEPENDENCY: "Gene Dependency",
-	GENE_EXPRESSION: "Gene Expression",
-	GSEA: "GSEA",
-	METABOLITE_INTENSITY: "Metabolite Intensity",
-	PROTEOME_ABUNDANCE: "Whole Proteome Abundance",
-	MUTATION_CNV_FUSION: "Mutation/CNV/Fusion",
-	MUTATION_SIGNATURE: "Mutation Signature",
-	PROTEIN_EXPRESSION: "Protein Expression",
-	SINGLECELL_CELLTYPE: "Single-cell Cell Type",
-	SINGLECELL_GENE_EXPRESSION: "Single-cell Gene Expression",
-	SNP: "SNP Genotype",
-	SNP_LIST: "SNP List",
-	SNP_LOCUS: "SNP Locus",
-	SPLICE_JUNCTION: "Splice Junction",
-	SSGSEA: "Geneset Expression",
-	TERM_COLLECTION: "Term Collection",
-	VARIANT_GENOTYPE: "Variant Genotype",
-}
+// 3/30/2026 - changed from literal object to a class with static properties
+// to make it easier for IDEs and tsc compiler to catch typos in consumer code
+export class TermTypeGroups {
+	static DICTIONARY_VARIABLES = "Dictionary Variables"
+	static DNA_METHYLATION = "DNA Methylation"
+	static GENE_DEPENDENCY = "Gene Dependency"
+	static GENE_EXPRESSION = "Gene Expression"
+	static ISOFORM_EXPRESSION = "Isoform Expression"
+	static GSEA = "GSEA"
+	static METABOLITE_INTENSITY = "Metabolite Intensity"
+	static PROTEOME_ABUNDANCE = "Whole Proteome Abundance"
+	static MUTATION_CNV_FUSION = "Mutation/CNV/Fusion"
+	static MUTATION_SIGNATURE = "Mutation Signature"
+	static PROTEIN_EXPRESSION = "Protein Expression"
+	static SINGLECELL_CELLTYPE = "Single-cell Cell Type"
+	static SINGLECELL_GENE_EXPRESSION = "Single-cell Gene Expression"
+	static SNP = "SNP Genotype"
+	static SNP_LIST = "SNP List"
+	static SNP_LOCUS = "SNP Locus"
+	static SPLICE_JUNCTION = "Splice Junction"
+	static SSGSEA = "Geneset Expression"
+	static TERM_COLLECTION = "Term Collection"
+	static VARIANT_GENOTYPE = "Variant Genotype"
+}
+// freeze so that mutating any of the static properties above will throw at runtime
+Object.freeze(TermTypeGroups)
 
 export const defaultcolor = rgb("#8AB1D4").darker()
 export const default_text_color = rgb("#aaa").darker().darker()

package/src/termdb.usecase.js

@@ -3,6 +3,7 @@ import {
 	isNumericTerm,
 	SINGLECELL_CELLTYPE,
 	SINGLECELL_GENE_EXPRESSION,
+	ISOFORM_EXPRESSION,
 } from "./terms.js"
 
 export const graphableTypes = new Set([
@@ -16,6 +17,7 @@ export const graphableTypes = new Set([
 	"geneVariant",
 	"samplelst",
 	"geneExpression",
+	ISOFORM_EXPRESSION,
 	"dtcnv",
 	"dtsnvindel",
 	"dtfusion",

package/src/terms.js

@@ -21,6 +21,7 @@ const DNA_METHYLATION = "dnaMethylation"
 const FLOAT = "float"
 const GENE_VARIANT = "geneVariant"
 const GENE_EXPRESSION = "geneExpression"
+const ISOFORM_EXPRESSION = "isoformExpression"
 const INTEGER = "integer"
 const METABOLITE_INTENSITY = "metaboliteIntensity"
 const MULTIVALUE = "multivalue"
@@ -37,6 +38,7 @@ const PROTEOME_ABUNDANCE = "proteomeAbundance"
 const TermTypes = {
 	GENE_VARIANT,
 	GENE_EXPRESSION,
+	ISOFORM_EXPRESSION,
 	SSGSEA,
 	DNA_METHYLATION,
 	CATEGORICAL,
@@ -81,6 +83,7 @@ const typeGroup = {
 	[SNP_LIST]: TermTypeGroups.SNP_LIST,
 	[SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
 	[GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
+	[ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,
 	[SSGSEA]: TermTypeGroups.SSGSEA,
 	[DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,
 	[METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
@@ -94,6 +97,7 @@ const nonDictTypes = /* @__PURE__ */ new Set([
 	SNP_LIST,
 	SNP_LOCUS,
 	GENE_EXPRESSION,
+	ISOFORM_EXPRESSION,
 	SSGSEA,
 	DNA_METHYLATION,
 	GENE_VARIANT,
@@ -109,6 +113,7 @@ const numericTypes = /* @__PURE__ */ new Set([
 	INTEGER,
 	FLOAT,
 	GENE_EXPRESSION,
+	ISOFORM_EXPRESSION,
 	SSGSEA,
 	DNA_METHYLATION,
 	METABOLITE_INTENSITY,
@@ -141,6 +146,10 @@ function isNonDictionaryType(type) {
 	if (!type) throw new Error("Type is not defined")
 	return nonDictTypes.has(type)
 }
+function isNumTermCollection(term) {
+	if (!term || !term.type) throw new Error("Term or term type is not defined")
+	return term.type === TERM_COLLECTION
+}
 function equals(t1, t2) {
 	if (!t1) throw new Error("First term is not defined ")
 	if (!t2) throw new Error("Second term is not defined ")
@@ -154,6 +163,8 @@ function equals(t1, t2) {
 	switch (t1.type) {
 		case GENE_EXPRESSION:
 			return t1.gene == t2.gene
+		case ISOFORM_EXPRESSION:
+			return t1.isoform == t2.isoform
 		case SSGSEA:
 			return t1.id == t2.id
 		case DNA_METHYLATION:
@@ -226,6 +237,7 @@ const typeMap = {
 	float: "Numerical",
 	integer: "Numerical",
 	geneExpression: "Gene Expression",
+	isoformExpression: "Isoform Expression",
 	ssGSEA: "Geneset Expression",
 	dnaMethylation: "DNA Methylation",
 	geneVariant: "Gene Variant",
@@ -285,6 +297,7 @@ export {
 	GENE_EXPRESSION,
 	GENE_VARIANT,
 	INTEGER,
+	ISOFORM_EXPRESSION,
 	METABOLITE_INTENSITY,
 	MULTIVALUE,
 	NumericModes,
@@ -316,6 +329,7 @@ export {
 	isCategoricalTerm,
 	isDictionaryType,
 	isNonDictionaryType,
+	isNumTermCollection,
 	isNumericTerm,
 	isSingleCellTerm,
 	numericTypes,