@sjcrh/proteinpaint-shared 2.135.1 → 2.135.2-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.135.1",
+  "version": "2.135.2-0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -1242,7 +1242,7 @@ export const CNVClasses = Object.values(mclass)
 	.map(m => m.key)
 
 // dt terms used for filtering variants for geneVariant term
-const _dtTerms = [
+const dtTerms_temp = [
 	{
 		id: 'snvindel',
 		query: 'snvindel',
@@ -1287,11 +1287,10 @@ const _dtTerms = [
 	}
 ]
 // add origin annotations to dt terms
-export const dtTerms = []
-for (const _dtTerm of _dtTerms) {
-	const dtTerm = structuredClone(_dtTerm)
+const dtTerms_temp2 = []
+for (const dtTerm of dtTerms_temp) {
 	dtTerm.name_noOrigin = dtTerm.name // for labeling groups in groupsetting
-	dtTerms.push(dtTerm) // no origin
+	dtTerms_temp2.push(dtTerm) // no origin
 	for (const origin of ['somatic', 'germline']) {
 		// add origins
 		const addOrigin = {
@@ -1299,9 +1298,10 @@ for (const _dtTerm of _dtTerms) {
 			name: `${dtTerm.name} (${origin})`,
 			origin
 		}
-		dtTerms.push(Object.assign({}, dtTerm, addOrigin))
+		dtTerms_temp2.push(Object.assign({}, dtTerm, addOrigin))
 	}
 }
+export const dtTerms = dtTerms_temp2
 
 export const colorScaleMap = {
 	blueWhiteRed: { domain: [0, 0.5, 1], range: ['blue', 'white', 'red'] },

package/src/index.js

@@ -10,7 +10,6 @@ export * from './filter.js'
 export * from './hash.js'
 export * from './helpers.js'
 export * from './joinUrl.js'
-export * from './mds.termdb.termvaluesetting.js' // deprecated?
 export * from './mds3tk.js'
 export * from './roundValue.js'
 export * from './termdb.bins.js'

package/src/terms.js

@@ -41,7 +41,7 @@ export const TermTypes = {
 	MULTIVALUE: 'multivalue',
 	DATE: 'date'
 }
-const dtTermTypes = new Set(dtTerms.map(t => t.type))
+export const dtTermTypes = new Set(dtTerms.map(t => t.type))
 for (const dtTermType of dtTermTypes) {
 	TermTypes[dtTermType.toUpperCase()] = dtTermType
 }

package/src/mds.termdb.termvaluesetting.js

@@ -1,81 +0,0 @@
-export function validate_termvaluesetting ( lst, from ) {
-/*
-shared between client and server
-for validating a list of term-value setting
-TODO also work for termdb filter
-*/
-	if(!lst) throw '.terms[] list missing from '+from
-	if(!Array.isArray(lst)) throw '.terms[] is not an array from '+from
-
-	// allow the array to be blank!!!
-
-	for(const t of lst) {
-		if(!t.term) throw '.term{} missing from a '+from+' term'
-		if(!t.term.id) throw '.term.term.id missing from a '+from+' term'
-		if( t.term.iscategorical ) {
-			if(!t.values) throw '.values[] missing from a '+from+' term'
-			if(!Array.isArray(t.values)) throw '.values[] is not an array from a '+from+' term'
-			for(const i of t.values) {
-				if(typeof i != 'object') throw 'an element is not object from values of '+t.term.id+' from '+from
-				if(!i.key) throw '.key missing from a value of '+t.term.id+' from '+from
-				if(!i.label) i.label = i.key
-			}
-			continue
-		}
-		if(t.term.isinteger || t.term.isfloat) {
-			if(!t.ranges) throw '.ranges[] missing from a numerical term of '+from
-			for(const range of t.ranges) {
-				if( range.value != undefined ) {
-					// is a special category, not a value from numerical range
-					if(!range.label) throw '.label missing for is_unannotated category'
-				} else {
-					validate_single_numericrange( range, from )
-				}
-			}
-			continue
-		}
-		if(t.term.iscondition) {
-			if( t.grade_and_child ) {
-				if(!Array.isArray(t.grade_and_child)) throw 'grade_and_child[] is not array from '+from
-				for(const i of t.grade_and_child) {
-					if(!Number.isInteger(i.grade)) throw '.grade is not an integer from one of grade_and_child[] from '+from
-					if(i.child_id==undefined) throw 'child_id is missing from one of grade_and_child[] from '+from
-				}
-				if(!t.value_by_max_grade && !t.value_by_most_recent && !t.value_by_computable_grade) throw 'unknown value_type for a bar_by_grade condition term from '+from
-			} else {
-				if(!t.values) throw '.values[] missing from a condition term of '+from
-				if(!Array.isArray(t.values)) throw '.values[] is not an array from a '+from+' term'
-				for(const i of t.values) {
-					if(typeof i != 'object') throw 'an element is not object from values of '+t.term.id+' from '+from
-					// i.key == 0 should be valid, check for presence of the object["key"] property instead 
-					if(!('key' in i)) throw '.key missing from a value of '+t.term.id+' from '+from
-					if(!i.label) i.label = i.key
-				}
-				if( t.bar_by_grade ) {
-					if(!t.value_by_max_grade && !t.value_by_most_recent && !t.value_by_computable_grade) throw 'unknown value_type for a bar_by_grade condition term from '+from
-				} else if(t.bar_by_children) {
-				} else {
-					throw 'neither bar_by_grade or bar_by_children is set for a condition term from '+from
-				}
-			}
-			continue
-		}
-		throw 'unknown term type from a '+from+' term'
-	}
-}
-
-
-
-export function validate_single_numericrange ( r, from ) {
-	// a regular range
-	if(r.startunbounded) {
-		if(r.stopunbounded) throw 'both start & stop are unbounded from '+from
-		if(!Number.isFinite(r.stop)) throw '.stop undefined when start is unbounded from '+from
-	} else if(r.stopunbounded) {
-		if(!Number.isFinite(r.start)) throw '.start undefined when stop is unbounded from '+from
-	} else {
-		if(!Number.isFinite(r.start)) throw '.start undefined when start is not unbounded from '+from
-		if(!Number.isFinite(r.stop)) throw '.stop undefined when stop is not unbounded from '+from
-		if(r.start >= r.stop ) throw '.start is not lower than stop from '+from
-	}
-}