@sjcrh/proteinpaint-server 2.173.0 → 2.174.1

package/src/mds3.gdc.filter.js

@@ -6,35 +6,42 @@ f{}
 returns a GDC filter object, or null if no filter
 
 GDC filter: https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval/
-
-TODO !!support nested filter!!
 */
-export function filter2GDCfilter(f) {
+export function filter2GDCfilter(f, level = 0) {
 	// gdc filter that will be returned
-	const obj = {
-		op: f.in ? 'and' : 'not',
+	let obj = {
+		op: f.join || 'and',
 		content: []
 	}
-	if (!Array.isArray(f.lst)) throw 'filter.lst[] not array'
+	if (!Array.isArray(f.lst)) throw new Error('filter.lst[] not array')
+	if (f.in === false) throw `negation of nested filters is not supported`
+
 	for (const item of f.lst) {
-		if (item.type != 'tvs') throw 'filter.lst[] item.type!="tvs"'
-		if (!item.tvs) throw 'item.tvs missing'
-		if (!item.tvs.term) throw 'item.tvs.term missing'
+		if (item.type != 'tvs') {
+			const f = filter2GDCfilter(item, level + 1)
+			if (f) obj.content.push(f)
+			continue
+		}
+		if (!item.tvs) throw new Error('item.tvs missing')
+		if (!item.tvs.term) throw new Error('item.tvs.term missing')
 		if (dtTermTypes.has(item.tvs.term.type)) {
 			// geneVariant/dt term filtering will be performed during post-processing
 			// (see mayFilterByGeneVariant() in server/src/mds3.init.js)
 			continue
 		}
 		if (item.tvs.term.type == 'geneExpression') {
+			if (level > 0) throw new Error(`gene expression filters are only supported at the root level of a nested filter`)
 			// geneExpression term filtering will be performed during post-processing (see mayFilterByExpression() in server/src/mds3.gdc.js)
 			continue
 		}
 		if (item.tvs.term.type == 'survival') {
+			if (level > 0) throw new Error(`survival filters are only supported at the root level of a nested filter`)
 			// survival term filtering will be performed during post-processing (see mayFilterBySurvival() in server/src/mds3.gdc.js)
 			continue
 		}
 
-		if (item.tvs.values) {
+		// sometimes, numeric filters have a values entry
+		if (item.tvs.values && !item.tvs.ranges) {
 			// categorical
 			const f = {
 				op: item.tvs.isnot ? '!=' : 'in',
@@ -47,65 +54,24 @@ export function filter2GDCfilter(f) {
 			continue
 		}
 		if (item.tvs.ranges) {
-			for (const range of item.tvs.ranges) {
-				if (range.startunbounded) {
-					obj.content.push({
-						op: range.stopinclusive ? (item.tvs.isnot ? '>' : '<=') : item.tvs.isnot ? '>=' : '<',
-						content: { field: mayChangeCase2Cases(item.tvs.term), value: range.stop }
-					})
-					continue
-				}
-				if (range.stopunbounded) {
-					obj.content.push({
-						op: range.startinclusive ? (item.tvs.isnot ? '<' : '>=') : item.tvs.isnot ? '<=' : '>',
-						content: { field: mayChangeCase2Cases(item.tvs.term), value: range.start }
-					})
-					continue
-				}
-				if (item.tvs.isnot) {
-					obj.content.push({
-						op: 'or',
-						content: [
-							{
-								op: 'and',
-								content: [
-									{
-										op: range.startinclusive ? '<' : '<=',
-										content: { field: mayChangeCase2Cases(item.tvs.term), value: range.start }
-									}
-								]
-							},
-							{
-								op: 'and',
-								content: [
-									{
-										op: range.stopinclusive ? '>' : '>=',
-										content: { field: mayChangeCase2Cases(item.tvs.term), value: range.stop }
-									}
-								]
-							}
-						]
-					})
-				} else {
-					obj.content.push({
-						op: 'and',
-						content: [
-							{
-								op: range.startinclusive ? '>=' : '>',
-								content: { field: mayChangeCase2Cases(item.tvs.term), value: range.start }
-							},
-							{
-								op: range.stopinclusive ? '<=' : '<',
-								content: { field: mayChangeCase2Cases(item.tvs.term), value: range.stop }
-							}
-						]
-					})
+			let f
+			if (!item.tvs.ranges.length) throw new Error('item.tvs.ranges[] is empty')
+			if (item.tvs.ranges.length == 1) {
+				const range = item.tvs.ranges[0]
+				f = range2GDCrange(range, item)
+			} else {
+				f = { op: 'or', content: [] }
+				for (const range of item.tvs.ranges) {
+					f.content.push(range2GDCrange(range, item))
 				}
 			}
+			//if (item.tvs.isnot) f = { op: '!=', content: f }
+			obj.content.push(f)
 			continue
 		}
-		throw 'unknown tvs structure when converting to gdc filter'
+		throw new Error('unknown tvs structure when converting to gdc filter')
 	}
+	if (!level) console.log(JSON.stringify(obj, null, '  '))
 	return obj.content.length ? obj : null
 }
 
@@ -123,3 +89,31 @@ function mayChangeCase2Cases(t) {
 	if (l[0] == 'case') l[0] = 'cases'
 	return l.join('.')
 }
+
+function range2GDCrange(range, item) {
+	if (range.startunbounded) {
+		return {
+			op: range.stopinclusive ? (item.tvs.isnot ? '>' : '<=') : item.tvs.isnot ? '>=' : '<',
+			content: { field: mayChangeCase2Cases(item.tvs.term), value: range.stop }
+		}
+	}
+	if (range.stopunbounded) {
+		return {
+			op: range.startinclusive ? (item.tvs.isnot ? '<' : '>=') : item.tvs.isnot ? '<=' : '>',
+			content: { field: mayChangeCase2Cases(item.tvs.term), value: range.start }
+		}
+	}
+	return {
+		op: 'and',
+		content: [
+			{
+				op: range.startinclusive ? (item.tvs.isnot ? '<' : '>=') : item.tvs.isnot ? '>=' : '>',
+				content: { field: mayChangeCase2Cases(item.tvs.term), value: range.start }
+			},
+			{
+				op: range.stopinclusive ? (item.tvs.isnot ? '>' : '<=') : item.tvs.isnot ? '<=' : '<',
+				content: { field: mayChangeCase2Cases(item.tvs.term), value: range.stop }
+			}
+		]
+	}
+}