@sjcrh/proteinpaint-shared 2.85.0 → 2.87.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.85.0",
+  "version": "2.87.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/termdb.usecase.js

@@ -108,20 +108,19 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 			}
 			return uses
 
-		case 'profile':
+		case 'profileForms':
 			if (!term.isleaf) {
-				uses.add('branch')
 				const ancestors = term.id.split('__').length //depends on using the __ naming convension!
-				if (ancestors > 2) {
+				if (ancestors == 2) {
 					uses.add('plot')
-				}
+				} else if (ancestors < 2) uses.add('branch')
 			}
 			return uses
 
-		case 'boxplot':
-			if (term.type == 'float' || term.type == 'integer') uses.add('plot')
-			if (usecase.detail === 'term2' && hasNumericChild(child_types)) uses.add('branch')
-			return uses
+		// case 'boxplot':
+		// 	if (term.type == 'float' || term.type == 'integer') uses.add('plot')
+		// 	if (usecase.detail === 'term2' && hasNumericChild(child_types)) uses.add('branch')
+		// 	return uses
 
 		case 'cuminc':
 			if (usecase.detail == 'term') {

package/src/terms.js

@@ -36,7 +36,8 @@ export const TermTypes = {
 	SAMPLELST: 'samplelst',
 	METABOLITE_INTENSITY: 'metaboliteIntensity',
 	SINGLECELL_GENE_EXPRESSION: 'singleCellGeneExpression',
-	SINGLECELL_CELLTYPE: 'singleCellCellType'
+	SINGLECELL_CELLTYPE: 'singleCellCellType',
+	MULTIVALUE: 'multivalue'
 }
 
 export const NUMERIC_DICTIONARY_TERM = 'numericDictTerm'
@@ -150,9 +151,15 @@ export function getBin(lst, value) {
 		)
 	return bin
 }
-
+//Terms may  have a sample type associated to them, in datasets with multiple types of samples.
+//For example the gender is associated to the patient while the age is associated to the type sample. This function is used
+//for example when calling getData or getFilter, to return either the parent or the child samples, depending on the use case.
 export function getSampleType(term, ds) {
 	if (!term) return null
+	//non dict terms annotate only samples, eg: gene expression, metabolite intensity, gene variant.
+	//Their sample type is the default sample type that may or may not have a parent type, depending on the dataset
+	if (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE
+	//dictionary terms may annotate different types of samples, eg: patient and sample or mouse and crop.
 	if (term.id) return ds.cohort.termdb.term2SampleType.get(term.id)
 	if (term.type == 'samplelst') {
 		const key = Object.keys(term.values)[0]