@sjcrh/proteinpaint-shared 2.167.0 → 2.170.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.167.0",
+  "version": "2.170.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -1323,9 +1323,7 @@ const dtTerms_temp = [
 		isleaf: true,
 		type: 'dtsnvindel',
 		dt: dtsnvindel,
-		values: Object.fromEntries(
-			mutationClasses.filter(key => key != 'Blank').map(key => [key, { label: mclass[key].label }])
-		)
+		values: {}
 	},
 	{
 		id: 'cnv',
@@ -1335,7 +1333,7 @@ const dtTerms_temp = [
 		isleaf: true,
 		type: 'dtcnv',
 		dt: dtcnv,
-		values: Object.fromEntries([...CNVClasses, 'WT'].map(key => [key, { label: mclass[key].label }]))
+		values: {}
 	},
 	{
 		id: 'fusion',
@@ -1345,7 +1343,7 @@ const dtTerms_temp = [
 		isleaf: true,
 		type: 'dtfusion',
 		dt: dtfusionrna,
-		values: Object.fromEntries([mclassfusionrna, 'WT'].map(key => [key, { label: mclass[key].label }]))
+		values: {}
 	},
 	{
 		id: 'sv',
@@ -1355,7 +1353,7 @@ const dtTerms_temp = [
 		isleaf: true,
 		type: 'dtsv',
 		dt: dtsv,
-		values: Object.fromEntries([mclasssv, 'WT'].map(key => [key, { label: mclass[key].label }]))
+		values: {}
 	}
 ]
 // add origin annotations to dt terms

package/src/fetch-helpers.js

@@ -161,8 +161,13 @@ export async function memFetch(url, init, opts = {}) {
 				fetch(url, init).then(async r => {
 					const response = await processResponse(r)
 					if (!r.ok) {
-						console.log(response)
-						throw 'memFetch error ' + r.status
+						console.trace(response)
+						throw (
+							'memFetch error ' +
+							r.status +
+							': ' +
+							(typeof response == 'object' ? response.message || response.error : response)
+						)
 					}
 					// to-do: support opt.freeze to enforce deep freeze of data.json()
 					dataCache.set(dataKey, response)

package/src/index.js

@@ -9,6 +9,7 @@ export * from './filter.js'
 export * from './hash.js'
 export * from './helpers.js'
 export * from './joinUrl.js'
+export * from './manhattan.js'
 export * from './mds3tk.js'
 export * from './roundValue.js'
 export * from './termdb.bins.js'

package/src/manhattan.js

@@ -0,0 +1,3 @@
+// Contains shared constants for Manhattan plots
+// This constant defines the log cutoff for q-values in Manhattan plots before scaling the y-axis.
+export const MANHATTAN_LOG_QVALUE_CUTOFF = 40

package/src/termdb.usecase.js

@@ -20,7 +20,8 @@ export const graphableTypes = new Set([
 	TermTypes.METABOLITE_INTENSITY,
 	TermTypes.SINGLECELL_GENE_EXPRESSION,
 	TermTypes.SINGLECELL_CELLTYPE,
-	TermTypes.SNP
+	TermTypes.SNP,
+	TermTypes.TERM_COLLECTION
 ])
 
 /*