Merge pull request #7 from biothings/subclassing-fix

Pass source with descendants
biothings · Aug 22, 2024 · d140a26 · d140a26
2 parents 271c64e + d44f248
commit d140a26
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Showing 2 changed files with 44 additions and 26 deletions.
diff --git a/__test__/index.test.js b/__test__/index.test.js
@@ -5,69 +5,69 @@ const { getDescendants } = require('../src/index');
 test('chebi', () => {
   let curies = ['CHEBI:26218'];
   let descendants = getDescendants(curies);
-  expect(descendants['CHEBI:26218']).toContain('CHEBI:50394');
-  expect(descendants['CHEBI:26218']).toContain('CHEBI:51700');
+  expect(descendants['CHEBI:26218']).toHaveProperty('CHEBI:50394');
+  expect(descendants['CHEBI:26218']).toHaveProperty('CHEBI:51700');
 });
 
 //DOID:0060524 -> DOID:0040001 -> DOID:0060527
 //crustacean allergy -> shrimp allergy -> indian prawn allergy
 test('doid', () => {
   let curies = ['DOID:0060524'];
   let descendants = getDescendants(curies);
-  expect(descendants['DOID:0060524']).toContain('DOID:0040001');
-  expect(descendants['DOID:0060524']).toContain('DOID:0060527');
+  expect(descendants['DOID:0060524']).toHaveProperty('DOID:0040001');
+  expect(descendants['DOID:0060524']).toHaveProperty('DOID:0060527');
 });
 
 //GO:0032553 -> GO:0032555 -> GO:0032559 
 //ribonucleotide binding -> purine ribonucleotide binding -> adenyl ribonucleotide binding
 test('go', () => {
   let curies = ['GO:0032553'];
   let descendants = getDescendants(curies);
-  expect(descendants['GO:0032553']).toContain('GO:0032555');
-  expect(descendants['GO:0032553']).toContain('GO:0032559');
+  expect(descendants['GO:0032553']).toHaveProperty('GO:0032555');
+  expect(descendants['GO:0032553']).toHaveProperty('GO:0032559');
 });
 
 //HP:0003812 -> HP:0003828
 //Phenotypic variability -> Variable expressivity
 test('hp', () => {
   let curies = ['HP:0003812'];
   let descendants = getDescendants(curies);
-  expect(descendants['HP:0003812']).toContain('HP:0003828');
+  expect(descendants['HP:0003812']).toHaveProperty('HP:0003828');
 });
 
 //MONDO:0001517 -> MONDO:0001955 -> MONDO:0024275
 //dysentery -> protozoal dysentery -> amebic dysentery
 test('mondo', () => {
   let curies = ['MONDO:0001517'];
   let descendants = getDescendants(curies);
-  expect(descendants['MONDO:0001517']).toContain('MONDO:0001955');
-  expect(descendants['MONDO:0001517']).toContain('MONDO:0024275');
+  expect(descendants['MONDO:0001517']).toHaveProperty('MONDO:0001955');
+  expect(descendants['MONDO:0001517']).toHaveProperty('MONDO:0024275');
 });
 
 //UMLS:C0680344 -> UMLS:C0003114 -> UMLS:C0680369
 //sociocultural values, norms, and social control -> anomie -> anomie(normless)
 test('umls', () => {
   let curies = ['UMLS:C0680344'];
   let descendants = getDescendants(curies);
-  expect(descendants['UMLS:C0680344']).toContain('UMLS:C0003114');
-  expect(descendants['UMLS:C0680344']).toContain('UMLS:C0680369');
+  expect(descendants['UMLS:C0680344']).toHaveProperty('UMLS:C0003114');
+  expect(descendants['UMLS:C0680344']).toHaveProperty('UMLS:C0680369');
 });
 
 test('multiple', () => {
   let curies = ['HP:0003812', 'MONDO:0001517'];
   let descendants = getDescendants(curies);
-  expect(descendants['HP:0003812']).toContain('HP:0003828');
-  expect(descendants['MONDO:0001517']).toContain('MONDO:0001955');
-  expect(descendants['MONDO:0001517']).toContain('MONDO:0024275');
+  expect(descendants['HP:0003812']).toHaveProperty('HP:0003828');
+  expect(descendants['MONDO:0001517']).toHaveProperty('MONDO:0001955');
+  expect(descendants['MONDO:0001517']).toHaveProperty('MONDO:0024275');
 });
 
 test('no descendants', () => {
   let curies = ['DOID:0060527'];
   let descendants = getDescendants(curies);
-  expect(descendants['DOID:0060527'].length).toBe(0);
+  expect(Object.keys(descendants['DOID:0060527']).length).toBe(0);
 });
 
 test('recursive', () => {
   let curies = ['UMLS:C0012634'];
   let descendants = getDescendants(curies);
-});
+});
diff --git a/src/index.js b/src/index.js
@@ -13,7 +13,9 @@ const loadData = () => {
   for (let ontology in ONTOLOGIES) {
     const filename = `../data/${ontology}-parsed.json`;
     const ontologyData = require(filename);
-    data = { ...data, ...ontologyData };
+    Object.entries(ontologyData).forEach(([parent, descendants]) => {
+      data[parent] = { source: ontology.toUpperCase(), descendants };
+    });
   }
   // const end = performance.now();
   // console.log(`loadData took ${end - start} milliseconds.`);
@@ -28,27 +30,43 @@ exports.getDescendants = (curies, recursive = true) => {
     const children = {};
 
     for (let curie of curies) {
-      children[curie] = [];
+      children[curie] = {};
       level = [curie];
-      while (level.length > 0 && children[curie].length < ENTITY_CAP) {
+      while (
+        level.length > 0 &&
+        Object.keys(children[curie]).length < ENTITY_CAP
+      ) {
         next_level = [];
         for (let c of level) {
           if (data[c]) {
-            children[curie].push(...data[c]);
-            next_level.push(...data[c]);
+            data[c].descendants.forEach(
+              child => (children[curie][child] = data[c].source),
+            );
+            next_level.push(
+              ...data[c].descendants.filter(child => child !== curie),
+            );
           }
         }
         level = next_level;
       }
-      children[curie] = _.uniq(children[curie])
-        .filter(child => child !== curie)
-        .slice(0, ENTITY_CAP);
+
+      delete children[curie][curie]; // Ensure no self-children
+      children[curie] = Object.fromEntries(
+        Object.entries(children[curie]).slice(0, ENTITY_CAP),
+      );
     }
     return children;
   } else {
     return Object.fromEntries(
-      Object.entries(_.pick(data, curies)).map(([curie, descendants]) => {
-        return [curie, descendants.filter(descendant => descendant !== curie)];
+      Object.entries(_.pick(data, curies)).map(([curie, descendantInfo]) => {
+        return [
+          curie,
+          Object.fromEntries(
+            descendantInfo.descendants
+              .filter(descendant => descendant !== curie)
+              .map(descendant => [descendant, source]),
+          ),
+        ];
       }),
     );
   }