@sjcrh/proteinpaint-shared 2.177.0 → 2.178.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.177.0",
+  "version": "2.178.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -22,10 +22,12 @@ export const TermTypeGroups = {
 	GENE_EXPRESSION: 'Gene Expression',
 	GSEA: 'GSEA',
 	METABOLITE_INTENSITY: 'Metabolite Intensity',
+	WHOLE_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',
@@ -65,6 +67,8 @@ export const dtcloss = 9
 export const dtloh = 10
 export const dtmetaboliteintensity = 11
 export const dtssgsea = 12
+export const dtdnamethylation = 13
+export const dtwholeproteomeabundance = 14
 // add new dt value here. !!!DO NOT change value of existing dt!!!
 
 export const dt2label = {
@@ -78,7 +82,8 @@ export const dt2label = {
 	[dtcloss]: 'C-loss',
 	[dtloh]: 'LOH',
 	[dtgeneexpression]: 'Gene Expression',
-	[dtmetaboliteintensity]: 'Metabolite Intensity'
+	[dtmetaboliteintensity]: 'Metabolite Intensity',
+	[dtwholeproteomeabundance]: 'Whole Proteome Abundance'
 }
 
 // Maps dt types to UI labels and lesion types for GRIN2

package/src/fetch-helpers.js

@@ -9,7 +9,9 @@ import { deepFreeze } from './helpers.js'
 	- this addresses issues with ky.json() or got.json(), where a HTTP 404 NOT FOUND
 		response with text/html can break error handling/logging, making it harder to debug
 
-	- this also automatically handles multipart responses 
+	- this also automatically handles multipart responses
+
+  - NOTE: for backend, use xfetch() instead, it uses ky() and its built-in retry support
 
 	arguments:
 	url
@@ -221,22 +223,27 @@ export async function memFetch(url, init, opts = {}) {
 						dataCache.set(dataKey, { response, exp: Date.now() + cacheLifetime })
 						return response
 				  })
-				: fetch(url, init).then(async r => {
-						const response = await processResponse(r)
-						if (!r.ok) {
-							console.trace(response)
-							throw (
-								'memFetch error ' +
-								r.status +
-								': ' +
-								(typeof response == 'object' ? response.message || response.error : response)
-							)
-						}
-						// replace the cached promise result with the actual data,
-						// since persisting a cached promise for a long time is likely not best practice
-						dataCache.set(dataKey, { response: deepFreeze(response), exp: Date.now() + cacheLifetime })
-						return response
-				  })
+				: fetch(url, init)
+						.then(async r => {
+							const response = await processResponse(r)
+							if (!r.ok) {
+								console.trace(response)
+								throw (
+									'memFetch error ' +
+									r.status +
+									': ' +
+									(typeof response == 'object' ? response.message || response.error : response)
+								)
+							}
+							// replace the cached promise result with the actual data,
+							// since persisting a cached promise for a long time is likely not best practice
+							dataCache.set(dataKey, { response: deepFreeze(response), exp: Date.now() + cacheLifetime })
+							return response
+						})
+						.catch(e => {
+							if (dataCache.get(dataKey)) dataCache.delete(dataKey)
+							throw e
+						})
 
 			dataCache.set(dataKey, { response: result, exp: Date.now() + cacheLifetime })
 			manageCacheSize(now)
@@ -244,7 +251,7 @@ export async function memFetch(url, init, opts = {}) {
 		} catch (e) {
 			// delete this cache only if it is a promise;
 			// do not delete a valid resolved data cache
-			if (dataCache.get(dataKey) instanceof Promise) delete dataCache.delete(dataKey)
+			if (dataCache.get(dataKey) instanceof Promise) dataCache.delete(dataKey)
 			throw e
 		}
 	}

package/src/termdb.usecase.js

@@ -17,7 +17,9 @@ export const graphableTypes = new Set([
 	'dtsv',
 	'date',
 	TermTypes.SSGSEA,
+	TermTypes.DNA_METHYLATION,
 	TermTypes.METABOLITE_INTENSITY,
+	TermTypes.WHOLE_PROTEOME_ABUNDANCE,
 	TermTypes.SINGLECELL_GENE_EXPRESSION,
 	TermTypes.SINGLECELL_CELLTYPE,
 	TermTypes.SNP,
@@ -66,8 +68,8 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 	const usecase = _usecase || {}
 
 	// may apply dataset specific override filter for a use case
-	if (typeof ds?.usecase?.[use.target] == 'function') {
-		return ds.usecase[use.target](term, use)
+	if (typeof ds?.usecase?.[usecase.target] == 'function') {
+		return ds.usecase[usecase.target](term, usecase)
 	}
 
 	// if (term.isprivate && !user.roleCanUse(term)) return false
@@ -75,10 +77,11 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 	const uses = new Set()
 	// note: expects term.child_types to be null if term.isleaf == true
 	const child_types = term.child_types || []
-
 	// default handling
 	switch (usecase.target) {
 		case 'barchart':
+		case 'violin':
+		case 'boxplot':
 		case 'summary':
 			if (term.type && term.type !== 'survival') uses.add('plot')
 			if (hasAllowedChildTypes(child_types, ['survival'])) uses.add('branch')
@@ -89,6 +92,10 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 				if (term.type && term.type !== 'survival') uses.add('plot')
 				if (hasAllowedChildTypes(child_types, ['survival'])) uses.add('branch')
 				return uses
+			} else {
+				if (graphableTypes.has(term.type)) uses.add('plot')
+				if (!term.isleaf) uses.add('branch')
+				return uses
 			}
 
 		case 'matrix':
@@ -107,6 +114,13 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 					uses.add('plot')
 				}
 				if (hasNumericChild(child_types)) uses.add('branch')
+			} else if (usecase?.vocab?.type == 'singleCell') {
+				/** TODO: Revisit this approach. Seems chaotic.  */
+				if (term.type && term.type.startsWith('singleCell')) {
+					if (term.plot && term.plot == usecase.vocab?.config.name) {
+						uses.add('plot')
+					}
+				}
 			} else {
 				if (graphableTypes.has(term.type)) uses.add('plot')
 				if (!term.isleaf) uses.add('branch')
@@ -139,7 +153,7 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 			}
 			return uses
 
-		case 'numericTermCollections':
+		case 'termCollections':
 			if (usecase.detail?.termIds?.includes(term.id)) uses.add('plot')
 			if (usecase.detail?.branchIds?.includes(term.id)) uses.add('branch')
 			return uses
@@ -170,6 +184,7 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 				if (hasAllowedChildTypes(child_types, ['condition', 'survival'])) uses.add('branch')
 				return uses
 			}
+			return uses
 
 		case 'survival':
 			if (usecase.detail == 'term') {
@@ -182,6 +197,7 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 				if (hasAllowedChildTypes(child_types, ['survival'])) uses.add('branch')
 				return uses
 			}
+			return uses
 
 		case 'regression':
 			if (usecase.detail == 'outcome') {
@@ -207,8 +223,9 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 				if (hasChildTypes(child_types, ['categorical', 'float', 'integer'])) uses.add('branch')
 				return uses
 			}
+			return uses
 
-		case 'filter':
+		case 'filter': {
 			// apply "exlst" to other targets as needed
 			const exlst = termdbConfig?.excludedTermtypeByTarget?.filter
 			if (exlst) {
@@ -216,7 +233,11 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 				if (child_types.find(t => !exlst.includes(t))) uses.add('branch') // there's a non-excluded child type, allow branch to show
 				return uses
 			}
-		// no specific rule for filter. pass and use default rules
+			// no specific rule for filter. use default rules
+			if (graphableTypes.has(term.type)) uses.add('plot')
+			if (!term.isleaf) uses.add('branch')
+			return uses
+		}
 
 		case 'correlationVolcano':
 			if (usecase.detail == 'numeric') {

package/src/terms.js

@@ -1,4 +1,12 @@
-import { dtgeneexpression, dtssgsea, dtmetaboliteintensity, TermTypeGroups, dtTerms } from './common.js'
+import {
+	dtgeneexpression,
+	dtssgsea,
+	dtdnamethylation,
+	dtmetaboliteintensity,
+	dtwholeproteomeabundance,
+	TermTypeGroups,
+	dtTerms
+} from './common.js'
 
 // moved TermTypeGroups to `server/src/common.js`, so now has to re-export
 export { TermTypeGroups } from './common.js'
@@ -26,6 +34,7 @@ export const TermTypes = {
 	GENE_VARIANT: 'geneVariant',
 	GENE_EXPRESSION: 'geneExpression',
 	SSGSEA: 'ssGSEA',
+	DNA_METHYLATION: 'dnaMethylation',
 	CATEGORICAL: 'categorical',
 	INTEGER: 'integer',
 	FLOAT: 'float',
@@ -36,6 +45,7 @@ export const TermTypes = {
 	SURVIVAL: 'survival',
 	SAMPLELST: 'samplelst',
 	METABOLITE_INTENSITY: 'metaboliteIntensity',
+	WHOLE_PROTEOME_ABUNDANCE: 'wholeProteomeAbundance',
 	SINGLECELL_GENE_EXPRESSION: 'singleCellGeneExpression',
 	SINGLECELL_CELLTYPE: 'singleCellCellType',
 	MULTIVALUE: 'multivalue',
@@ -52,7 +62,9 @@ export const NUMERIC_DICTIONARY_TERM = 'numericDictTerm'
 export const TermTypes2Dt = {
 	[TermTypes.GENE_EXPRESSION]: dtgeneexpression,
 	[TermTypes.SSGSEA]: dtssgsea,
-	[TermTypes.METABOLITE_INTENSITY]: dtmetaboliteintensity
+	[TermTypes.DNA_METHYLATION]: dtdnamethylation,
+	[TermTypes.METABOLITE_INTENSITY]: dtmetaboliteintensity,
+	[TermTypes.WHOLE_PROTEOME_ABUNDANCE]: dtwholeproteomeabundance
 }
 
 // maps term type to group (as is shown as toggles in search ui)
@@ -69,9 +81,12 @@ export const typeGroup = {
 	[TermTypes.SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
 	[TermTypes.GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
 	[TermTypes.SSGSEA]: TermTypeGroups.SSGSEA,
+	[TermTypes.DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,
 	[TermTypes.METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
+	[TermTypes.WHOLE_PROTEOME_ABUNDANCE]: TermTypeGroups.WHOLE_PROTEOME_ABUNDANCE,
 	[TermTypes.TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,
-	[TermTypes.SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE
+	[TermTypes.SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,
+	[TermTypes.SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION
 }
 
 const nonDictTypes = new Set([
@@ -80,8 +95,10 @@ const nonDictTypes = new Set([
 	TermTypes.SNP_LOCUS,
 	TermTypes.GENE_EXPRESSION,
 	TermTypes.SSGSEA,
+	TermTypes.DNA_METHYLATION,
 	TermTypes.GENE_VARIANT,
 	TermTypes.METABOLITE_INTENSITY,
+	TermTypes.WHOLE_PROTEOME_ABUNDANCE,
 	TermTypes.SINGLECELL_GENE_EXPRESSION,
 	TermTypes.SINGLECELL_CELLTYPE
 ])
@@ -94,7 +111,9 @@ export const numericTypes = new Set([
 	TermTypes.FLOAT,
 	TermTypes.GENE_EXPRESSION,
 	TermTypes.SSGSEA,
+	TermTypes.DNA_METHYLATION,
 	TermTypes.METABOLITE_INTENSITY,
+	TermTypes.WHOLE_PROTEOME_ABUNDANCE,
 	TermTypes.SINGLECELL_GENE_EXPRESSION,
 	TermTypes.DATE
 ])
@@ -105,7 +124,7 @@ export const annoNumericTypes = new Set([TermTypes.INTEGER, TermTypes.FLOAT, Ter
 
 const categoricalTypes = new Set([TermTypes.CATEGORICAL, TermTypes.SNP])
 
-const singleSampleTerms = new Set([TermTypes.SINGLECELL_GENE_EXPRESSION])
+const singleSampleTerms = new Set([TermTypes.SINGLECELL_CELLTYPE, TermTypes.SINGLECELL_GENE_EXPRESSION])
 
 export function isSingleSampleTerm(term) {
 	if (!term) return false
@@ -139,7 +158,10 @@ export function equals(t1, t2) {
 			return t1.gene == t2.gene
 		case TermTypes.SSGSEA:
 			return t1.id == t2.id
+		case TermTypes.DNA_METHYLATION:
+			return t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop
 		case TermTypes.METABOLITE_INTENSITY:
+		case TermTypes.WHOLE_PROTEOME_ABUNDANCE:
 			return t1.name == t2.name
 		case TermTypes.GENE_VARIANT:
 			return t1.gene == t2.gene || (t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop)
@@ -214,8 +236,10 @@ const typeMap = {
 	integer: 'Numerical',
 	geneExpression: 'Gene Expression',
 	ssGSEA: 'Geneset Expression',
+	dnaMethylation: 'DNA Methylation',
 	geneVariant: 'Gene Variant',
 	metaboliteIntensity: 'Metabolite Intensity',
+	wholeProteomeAbundance: 'Whole Proteome Abundance',
 	multiValue: 'Multi Value',
 	singleCellGeneExpression: 'Single Cell, Gene Expression',
 	singleCellCellType: 'Single Cell, Cell Type',