jbrowse-plugin-msaview 2.8.2 → 2.9.0

package/dist/MsaViewPanel/doLaunchOrthologs.test.js

@@ -0,0 +1,127 @@
+import { beforeEach, describe, expect, test, vi } from 'vitest';
+import { doLaunchOrthologs } from './doLaunchOrthologs';
+import { launchMSA } from '../utils/msa';
+import { COMMON_SPECIES, fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils/ncbiOrthologs';
+// Every network call is mocked and nothing else is. What is under test is the
+// argument shaping either side of those calls -- which taxa get asked for, what
+// becomes the QUERY row, and whether the row earns the Accession that drives the
+// CDD overlay -- so the real COMMON_SPECIES list and the real
+// cleanProteinSequence stay in the picture.
+vi.mock('../utils/ncbiOrthologs', async (importOriginal) => ({
+    ...(await importOriginal()),
+    resolveGeneId: vi.fn(),
+    fetchProteinForGene: vi.fn(),
+    fetchOrthologRows: vi.fn(),
+}));
+vi.mock('../utils/msa', () => ({ launchMSA: vi.fn() }));
+const mockResolveGeneId = vi.mocked(resolveGeneId);
+const mockFetchProtein = vi.mocked(fetchProteinForGene);
+const mockFetchRows = vi.mocked(fetchOrthologRows);
+const mockLaunchMSA = vi.mocked(launchMSA);
+const HUMAN = 9606;
+const GENE_ID = '22861';
+const REPRESENTATIVE = { accession: 'NP_127497.1', sequence: 'MAGGAWGRLACY' };
+function makeModel(orthologParams) {
+    return {
+        orthologParams,
+        setProgress: () => { },
+    };
+}
+function params(extra = {}) {
+    return {
+        taxId: HUMAN,
+        geneCandidates: ['NLRP1'],
+        msaAlgorithm: 'clustalo',
+        ...extra,
+    };
+}
+// What fetchOrthologRows was asked for, which is the only place the taxa
+// default is observable.
+function taxaAskedFor() {
+    return [...mockFetchRows.mock.calls[0][0].taxa].sort((a, b) => a - b);
+}
+// The QUERY row as it went to the aligner, read back out of the FASTA rather
+// than out of an intermediate, since the FASTA is what the alignment is of.
+function queryRowSent() {
+    return mockLaunchMSA.mock.calls[0][0].sequence.split('\n')[1];
+}
+function queryMetadata(result) {
+    return JSON.parse(result.treeMetadata).QUERY;
+}
+beforeEach(() => {
+    vi.clearAllMocks();
+    mockResolveGeneId.mockResolvedValue({ geneId: GENE_ID, matched: 'NLRP1' });
+    mockFetchProtein.mockResolvedValue(REPRESENTATIVE);
+    mockFetchRows.mockResolvedValue([]);
+    mockLaunchMSA.mockResolvedValue({ msa: '', tree: '' });
+});
+describe('taxa', () => {
+    test('omitted asks for every species the dialog offers, less the query', async () => {
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(taxaAskedFor()).toEqual(COMMON_SPECIES.map(s => s.taxId)
+            .filter(t => t !== HUMAN)
+            .sort((a, b) => a - b));
+    });
+    test('given is taken as written, less the query', async () => {
+        await doLaunchOrthologs({
+            self: makeModel(params({ taxa: [HUMAN, 10090, 9615] })),
+        });
+        expect(taxaAskedFor()).toEqual([9615, 10090]);
+    });
+    test('an empty list is a request for no rows, not a request for all of them', async () => {
+        await doLaunchOrthologs({ self: makeModel(params({ taxa: [] })) });
+        expect(taxaAskedFor()).toEqual([]);
+    });
+});
+describe('the QUERY row', () => {
+    test('omitted proteinSequence falls back to the representative protein', async () => {
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(queryRowSent()).toBe(REPRESENTATIVE.sequence);
+    });
+    test('a supplied sequence is used, and is cleaned first', async () => {
+        await doLaunchOrthologs({
+            self: makeModel(params({ proteinSequence: 'MAGG*AWGR&' })),
+        });
+        expect(queryRowSent()).toBe('MAGGAWGR');
+    });
+    test('throws when neither a sequence nor a representative is available', async () => {
+        mockFetchProtein.mockResolvedValue(undefined);
+        await expect(doLaunchOrthologs({ self: makeModel(params()) })).rejects.toThrow(/No query protein/);
+        expect(mockLaunchMSA).not.toHaveBeenCalled();
+    });
+    test('a failed representative lookup does not take down a launch that brought its own sequence', async () => {
+        vi.spyOn(console, 'warn').mockImplementation(() => { });
+        mockFetchProtein.mockRejectedValue(new Error('429'));
+        await doLaunchOrthologs({
+            self: makeModel(params({ proteinSequence: REPRESENTATIVE.sequence })),
+        });
+        expect(queryRowSent()).toBe(REPRESENTATIVE.sequence);
+    });
+});
+// The Accession is what afterCreateAutoruns.autoLoadProteinDomains keys the CDD
+// overlay off, and attaching it to a row that is NOT the protein it names draws
+// every domain box at an offset. So the byte-identity guard is the assertion
+// here, in both directions.
+describe('the Accession that drives the domain overlay', () => {
+    test('is attached when the query row IS the representative protein', async () => {
+        const result = await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(queryMetadata(result)).toMatchObject({
+            'Gene ID': GENE_ID,
+            Accession: REPRESENTATIVE.accession,
+        });
+    });
+    test('is withheld from a non-representative isoform', async () => {
+        const result = await doLaunchOrthologs({
+            self: makeModel(params({ proteinSequence: 'MDIFFERENTISOFORM' })),
+        });
+        expect(queryMetadata(result).Accession).toBeUndefined();
+    });
+    test('is withheld when the representative lookup failed', async () => {
+        vi.spyOn(console, 'warn').mockImplementation(() => { });
+        mockFetchProtein.mockRejectedValue(new Error('429'));
+        const result = await doLaunchOrthologs({
+            self: makeModel(params({ proteinSequence: REPRESENTATIVE.sequence })),
+        });
+        expect(queryMetadata(result).Accession).toBeUndefined();
+    });
+});

package/dist/MsaViewPanel/model.d.ts

@@ -1,6 +1,6 @@
 export type { MSAFormat } from 'msa-parsers';
 import type { MafRegion, MsaViewInitState } from './types';
-import type { BlastDatabase, BlastProgram, MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
+import type { BlastDatabase, MsaAlgorithm } from '../LaunchMsaView/components/BlastQuery/consts';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
@@ -12,13 +12,10 @@ export interface IRegion {
     end: number;
 }
 export interface BlastParams {
-    baseUrl: string;
     blastDatabase: BlastDatabase;
     msaAlgorithm: MsaAlgorithm;
-    blastProgram: BlastProgram;
     selectedTranscript?: Feature;
     proteinSequence: string;
-    rid?: string;
 }
 export interface OrthologParams {
     /** NCBI taxon id of the assembly the query gene came from */