Rename getReference & getType to getReferenceRID & getTypeRID

Author: mathieulemieux

src/repo/upload/positionalvariant.js

@@ -39,7 +39,7 @@ const formatReferenceDisplayName = (ref) => {
  * @param {string} opt.type the variant type name
  * @returns {string} the strignify record's RID
  */
-const getType = async (session, type) => {
+const getTypeRID = async (session, type) => {
     const result = await select(
         session,
         parse({
@@ -65,7 +65,7 @@ const getType = async (session, type) => {
  * @param {string} [opt.preferedRefSrcName] the name of the prefered reference source
  * @returns {string} the strignify record's RID
  */
-const getReference = async (session, ref, { preferedRefSrcName } = {}) => {
+const getReferenceRID = async (session, ref, { preferedRefSrcName } = {}) => {
     // Chromosome support
     const referenceDisplayName = formatReferenceDisplayName(ref);
 
@@ -123,17 +123,17 @@ const getContent = async (session, notation, { preferedRefSrcName } = {}) => {
     );
 
     // Replacing variant type by its RID
-    content.type = await getType(session, content.type);
+    content.type = await getTypeRID(session, content.type);
 
     // Replacing variant references by their RIDs
-    content.reference1 = await getReference(
+    content.reference1 = await getReferenceRID(
         session,
         content.reference1,
         { preferedRefSrcName },
     );
 
     if (content.reference2) {
-        content.reference2 = await getReference(
+        content.reference2 = await getReferenceRID(
             session,
             content.reference2,
             { preferedRefSrcName },
@@ -188,18 +188,18 @@ const uploadPositionalVariant = async (session, user, content, {
 
     // Make sure type is an RID
     if (!looksLikeRID(payload.type, true)) {
-        payload.type = await getType(session, payload.type);
+        payload.type = await getTypeRID(session, payload.type);
     }
     // Make sure references are RIDs
     if (!looksLikeRID(payload.reference1, true)) {
-        payload.reference1 = await getReference(
+        payload.reference1 = await getReferenceRID(
             session,
             payload.reference1,
             { preferedRefSrcName },
         );
     }
     if (payload.reference2 && !looksLikeRID(payload.reference2, true)) {
-        payload.reference2 = await getReference(
+        payload.reference2 = await getReferenceRID(
             session,
             payload.reference2,
             { preferedRefSrcName },
@@ -238,8 +238,8 @@ const uploadPositionalVariant = async (session, user, content, {
 module.exports = {
     formatReferenceDisplayName,
     getContent,
-    getReference,
-    getType,
+    getReferenceRID,
+    getTypeRID,
     positionalVariantQueryFilters,
     uploadPositionalVariant,
 };

test/repo/upload/positionalvariant.test.js

@@ -40,8 +40,8 @@ const {
 const {
     formatReferenceDisplayName,
     getContent,
-    getReference,
-    getType,
+    getReferenceRID,
+    getTypeRID,
     positionalVariantQueryFilters,
     uploadPositionalVariant,
 } = require('../../../src/repo/upload/positionalvariant');
@@ -69,7 +69,7 @@ describe('formatReferenceDisplayName', () => {
     });
 });
 
-describe('getType', () => {
+describe('getTypeRID', () => {
     const session = {};
 
     beforeEach(() => {
@@ -80,25 +80,25 @@ describe('getType', () => {
         jest.clearAllMocks();
     });
 
-    test('type is formatted to lowercase', async () => {
-        await getType(session, 'Substitution');
+    test('type arg gets formatted to lowercase', async () => {
+        await getTypeRID(session, 'Substitution');
         expect(parse).toHaveBeenCalledWith(expect.objectContaining({
             filters: { name: 'substitution' },
         }));
     });
 
     test('returns RID when vocabulary is found', async () => {
-        await expect(getType(session, 'substitution')).resolves.toBe('#123:45');
+        await expect(getTypeRID(session, 'substitution')).resolves.toBe('#123:45');
     });
 
     test('throws NotImplementedError when vocabulary is not found', async () => {
         select.mockResolvedValue([]);
 
-        await expect(getType(session, 'unknown')).rejects.toBeInstanceOf(NotImplementedError);
+        await expect(getTypeRID(session, 'unknown')).rejects.toBeInstanceOf(NotImplementedError);
     });
 });
 
-describe('getReference', () => {
+describe('getReferenceRID', () => {
     const session = {};
 
     beforeEach(() => {
@@ -110,24 +110,24 @@ describe('getReference', () => {
     });
 
     test('normalizes chromosome notation before querying', async () => {
-        await getReference(session, '12');
+        await getReferenceRID(session, '12');
         expect(parse).toHaveBeenCalledWith(expect.objectContaining({
             filters: { displayName: 'chr12' },
         }));
     });
 
     test('returns first RID when there is no preferedRefSrcName provided', async () => {
-        await expect(getReference(session, 'BRCA2', {})).resolves.toBe('#123:45');
+        await expect(getReferenceRID(session, 'BRCA2', {})).resolves.toBe('#123:45');
     });
 
     test('uses preferred source if preferedRefSrcName is provided', async () => {
-        await expect(getReference(session, 'BRCA2', { preferedRefSrcName: 'entrez gene' })).resolves.toBe('#123:46');
+        await expect(getReferenceRID(session, 'BRCA2', { preferedRefSrcName: 'entrez gene' })).resolves.toBe('#123:46');
     });
 
     test('throws NotImplementedError when no feature is found', async () => {
         select.mockResolvedValue([]);
 
-        await expect(getReference(session, 'BRCA2', {})).rejects.toBeInstanceOf(NotImplementedError);
+        await expect(getReferenceRID(session, 'BRCA2', {})).rejects.toBeInstanceOf(NotImplementedError);
     });
 });
 
@@ -137,9 +137,9 @@ describe('getContent', () => {
     beforeEach(() => {
         jest.clearAllMocks();
         select
-            .mockResolvedValueOnce([{ '@rid': '#123:45' }]) // getType()
-            .mockResolvedValueOnce([{ '@rid': '#123:46', source: { name: 'hgnc' } }]) // getReference()
-            .mockResolvedValueOnce([{ '@rid': '#123:47', source: { name: 'hgnc' } }]); // getReference()
+            .mockResolvedValueOnce([{ '@rid': '#123:45' }]) // getTypeRID()
+            .mockResolvedValueOnce([{ '@rid': '#123:46', source: { name: 'hgnc' } }]) // getReferenceRID()
+            .mockResolvedValueOnce([{ '@rid': '#123:47', source: { name: 'hgnc' } }]); // getReferenceRID()
     });
 
     test('throws ValidationError when notation is empty string', async () => {
@@ -216,9 +216,9 @@ describe('uploadPositionalVariant', () => {
     test('conversion to RIDs and create new record', async () => {
         create.mockResolvedValue({ '@rid': '#21:1' });
         select
-            .mockResolvedValueOnce([{ '@rid': '#20:1' }]) // getType()
-            .mockResolvedValueOnce([{ '@rid': '#20:2', source: { name: 'hgnc' } }]) // getReference()
-            .mockResolvedValueOnce([{ '@rid': '#20:3', source: { name: 'hgnc' } }]); // getReference()
+            .mockResolvedValueOnce([{ '@rid': '#20:1' }]) // getTypeRID()
+            .mockResolvedValueOnce([{ '@rid': '#20:2', source: { name: 'hgnc' } }]) // getReferenceRID()
+            .mockResolvedValueOnce([{ '@rid': '#20:3', source: { name: 'hgnc' } }]); // getReferenceRID()
 
         const content = {
             reference1: 'BRCA2',