jbrowse-plugin-msaview 3.5.0 → 3.7.0

package/dist/MsaViewPanel/genomeToMSA.test.js

@@ -6,12 +6,40 @@ vi.mock('@jbrowse/core/util', () => ({
     getSession: vi.fn(),
 }));
 const mockGetSession = vi.mocked(getSession);
+// What the assembly calls each chromosome. Empty means every name is already
+// canonical, which is the config where the raw comparison this replaced
+// happened to work.
+let aliases = {};
+// core's assembly throws from getCanonicalRefName until its aliases load, and
+// answers `initialized` false until then -- so the stand-in throws too, or the
+// guard is asserted against a method that never had the failure mode
+let assemblyInitialized = true;
+function mockSession(session) {
+    mockGetSession.mockReturnValue({
+        assemblyManager: {
+            get: () => ({
+                get initialized() {
+                    return assemblyInitialized;
+                },
+                getCanonicalRefName: (refName) => {
+                    if (!assemblyInitialized) {
+                        throw new Error('aliases not loaded');
+                    }
+                    return aliases[refName] ?? refName;
+                },
+            }),
+        },
+        ...session,
+    });
+}
 describe('genomeToMSA', () => {
     beforeEach(() => {
         vi.clearAllMocks();
+        aliases = {};
+        assemblyInitialized = true;
     });
     test('returns undefined when connectedView is not initialized', () => {
-        mockGetSession.mockReturnValue({
+        mockSession({
             hovered: {
                 hoverFeature: {},
                 hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -19,7 +47,7 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'hg38.chr1',
-            rows: [['hg38.chr1', 'ACGTACGTAC']],
+            rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
             transcriptToMsaMap: undefined,
             mafRegion: {
                 refName: 'chr1',
@@ -27,19 +55,19 @@ describe('genomeToMSA', () => {
                 end: 1010,
                 assemblyName: 'hg38',
             },
-            connectedView: { initialized: false },
+            connectedView: { initialized: false, assemblyNames: ['hg38'] },
             seqPosToVisibleCol: vi.fn(),
         };
         const result = genomeToMSA({ model });
         expect(result).toBeUndefined();
     });
     test('returns undefined when hovered is not valid', () => {
-        mockGetSession.mockReturnValue({
+        mockSession({
             hovered: null,
         });
         const model = {
             querySeqName: 'hg38.chr1',
-            rows: [['hg38.chr1', 'ACGTACGTAC']],
+            rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
             transcriptToMsaMap: undefined,
             mafRegion: {
                 refName: 'chr1',
@@ -47,7 +75,7 @@ describe('genomeToMSA', () => {
                 end: 1010,
                 assemblyName: 'hg38',
             },
-            connectedView: { initialized: true },
+            connectedView: { initialized: true, assemblyNames: ['hg38'] },
             seqPosToVisibleCol: vi.fn(),
         };
         const result = genomeToMSA({ model });
@@ -55,7 +83,7 @@ describe('genomeToMSA', () => {
     });
     describe('mafRegion mapping', () => {
         test('returns visible column for valid hover within mafRegion', () => {
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -64,7 +92,7 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn().mockReturnValue(5);
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -77,6 +105,7 @@ describe('genomeToMSA', () => {
                     assemblyNames: ['hg38'],
                 },
                 seqPosToVisibleCol: mockSeqPosToVisibleCol,
+                visibleColToSeqPos: () => 4,
             };
             const result = genomeToMSA({ model });
             // hover coord 1005 is 1-based, so the 0-based genome position is 1004,
@@ -84,8 +113,36 @@ describe('genomeToMSA', () => {
             expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 4);
             expect(result).toBe(5);
         });
+        test('a position past the end of the row lights nothing', () => {
+            mockSession({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1009, refName: 'chr1' },
+                },
+            });
+            // react-msaview answers one column past the end for a residue the row
+            // does not have, and that column maps back to no residue
+            const model = {
+                querySeqName: 'hg38.chr1',
+                rowMap: new Map([['hg38.chr1', 'ACGTACG']]),
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                connectedView: {
+                    initialized: true,
+                    assemblyNames: ['hg38'],
+                },
+                seqPosToVisibleCol: () => 7,
+                visibleColToSeqPos: () => undefined,
+            };
+            expect(genomeToMSA({ model })).toBeUndefined();
+        });
         test('returns undefined when hover refName does not match mafRegion', () => {
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1005, refName: 'chr2' },
@@ -93,7 +150,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -112,7 +169,7 @@ describe('genomeToMSA', () => {
         });
         test('returns undefined when hover coord is before mafRegion start', () => {
             // 1-based coord 1000 is the 0-based base 999, one before the region
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1000, refName: 'chr1' },
@@ -120,7 +177,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -139,7 +196,7 @@ describe('genomeToMSA', () => {
         });
         test('returns undefined when hover coord is at or after mafRegion end', () => {
             // 1-based coord 1011 is the 0-based base 1010, one past the region
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1011, refName: 'chr1' },
@@ -147,7 +204,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -165,7 +222,7 @@ describe('genomeToMSA', () => {
             expect(result).toBeUndefined();
         });
         test('returns undefined when assembly does not match', () => {
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -173,7 +230,7 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'hg38.chr1',
-                rows: [['hg38.chr1', 'ACGTACGTAC']],
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
                 transcriptToMsaMap: undefined,
                 mafRegion: {
                     refName: 'chr1',
@@ -193,7 +250,7 @@ describe('genomeToMSA', () => {
     });
     describe('transcriptToMsaMap mapping (original behavior)', () => {
         test('returns visible column using g2p mapping', () => {
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -203,14 +260,14 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 0,
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     // g2p is keyed by 0-based genome position, the hover coord is 1-based
                     g2p: { 1004: 10 },
                 },
                 mafRegion: undefined,
-                connectedView: { initialized: true },
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
                 seqPosToVisibleCol: mockSeqPosToVisibleCol,
                 visibleColToSeqPos: (_name, col) => col,
             };
@@ -221,7 +278,7 @@ describe('genomeToMSA', () => {
         test('returns undefined when the hover is on another refName', () => {
             // session.hovered is global, so a hover on an unrelated chromosome can
             // carry a coordinate that happens to be a g2p key
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1005, refName: 'chr2' },
@@ -230,13 +287,13 @@ describe('genomeToMSA', () => {
             const mockSeqPosToVisibleCol = vi.fn();
             const model = {
                 querySeqName: 'QUERY',
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     g2p: { 1004: 10 },
                 },
                 mafRegion: undefined,
-                connectedView: { initialized: true },
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
                 seqPosToVisibleCol: mockSeqPosToVisibleCol,
             };
             expect(genomeToMSA({ model })).toBeUndefined();
@@ -245,7 +302,7 @@ describe('genomeToMSA', () => {
         // a pasted alignment often carries only the region BLAST aligned, and
         // querySeqOffset says how much of the protein comes before it
         test('shifts a trimmed query row by querySeqOffset', () => {
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -255,10 +312,10 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 4,
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
                 mafRegion: undefined,
-                connectedView: { initialized: true },
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
                 seqPosToVisibleCol,
                 visibleColToSeqPos: (_name, col) => col,
             };
@@ -266,7 +323,7 @@ describe('genomeToMSA', () => {
             expect(seqPosToVisibleCol).toHaveBeenCalledWith('QUERY', 6);
         });
         test('maps nothing for a residue before the trimmed row starts', () => {
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -276,10 +333,10 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 20,
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
                 mafRegion: undefined,
-                connectedView: { initialized: true },
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
                 seqPosToVisibleCol,
                 visibleColToSeqPos: (_name, col) => col,
             };
@@ -289,7 +346,7 @@ describe('genomeToMSA', () => {
         // react-msaview answers one column past the end for a residue the row does
         // not have, which would light the last column for everything beyond it
         test('maps nothing for a residue the row stops short of', () => {
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -298,17 +355,17 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 querySeqOffset: 0,
-                rows: [['QUERY', 'MKV']],
+                rowMap: new Map([['QUERY', 'MKV']]),
                 transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
                 mafRegion: undefined,
-                connectedView: { initialized: true },
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
                 seqPosToVisibleCol: () => 3,
                 visibleColToSeqPos: () => undefined,
             };
             expect(genomeToMSA({ model })).toBeUndefined();
         });
         test('returns undefined when g2p has no mapping for coord', () => {
-            mockGetSession.mockReturnValue({
+            mockSession({
                 hovered: {
                     hoverFeature: {},
                     hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -316,13 +373,13 @@ describe('genomeToMSA', () => {
             });
             const model = {
                 querySeqName: 'QUERY',
-                rows: [['QUERY', 'MKVLTAEEK']],
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
                 transcriptToMsaMap: {
                     refName: 'chr1',
                     g2p: { 1000: 0 }, // No entry for 1004
                 },
                 mafRegion: undefined,
-                connectedView: { initialized: true },
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
                 seqPosToVisibleCol: vi.fn(),
             };
             const result = genomeToMSA({ model });
@@ -330,7 +387,7 @@ describe('genomeToMSA', () => {
         });
     });
     test('returns undefined when neither mafRegion nor transcriptToMsaMap is set', () => {
-        mockGetSession.mockReturnValue({
+        mockSession({
             hovered: {
                 hoverFeature: {},
                 hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -338,21 +395,17 @@ describe('genomeToMSA', () => {
         });
         const model = {
             querySeqName: 'QUERY',
-            rows: [['QUERY', 'MKVLTAEEK']],
+            rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
             transcriptToMsaMap: undefined,
             mafRegion: undefined,
-            connectedView: { initialized: true },
+            connectedView: { initialized: true, assemblyNames: ['hg38'] },
             seqPosToVisibleCol: vi.fn(),
         };
         const result = genomeToMSA({ model });
         expect(result).toBeUndefined();
     });
-    // seqPosToVisibleCol answers 0 for a row name it does not know, so without a
-    // guard an alignment whose query row is missing -- the default 'QUERY' on an
-    // uploaded file, or the empty name the manual panel leaves when it matches
-    // nothing -- lights column 0 on every genome hover
     test('returns undefined when querySeqName names no row here', () => {
-        mockGetSession.mockReturnValue({
+        mockSession({
             hovered: {
                 hoverFeature: {},
                 hoverPosition: { coord: 1005, refName: 'chr1' },
@@ -361,13 +414,134 @@ describe('genomeToMSA', () => {
         const seqPosToVisibleCol = vi.fn(() => 0);
         const model = {
             querySeqName: 'QUERY',
-            rows: [['some_other_row', 'MKVLTAEEK']],
+            rowMap: new Map([['some_other_row', 'MKVLTAEEK']]),
             transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 3 } },
             mafRegion: undefined,
-            connectedView: { initialized: true },
+            connectedView: { initialized: true, assemblyNames: ['hg38'] },
             seqPosToVisibleCol,
         };
         expect(genomeToMSA({ model })).toBeUndefined();
         expect(seqPosToVisibleCol).not.toHaveBeenCalled();
     });
+    test('a query row folded into a collapsed clade still maps', () => {
+        mockSession({
+            hovered: {
+                hoverFeature: {},
+                hoverPosition: { coord: 1005, refName: 'chr1' },
+            },
+        });
+        const model = {
+            querySeqName: 'QUERY',
+            querySeqOffset: 0,
+            rows: [['collapsed_clade', 'MKVLTAEEK']],
+            rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
+            transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 3 } },
+            mafRegion: undefined,
+            connectedView: { initialized: true, assemblyNames: ['hg38'] },
+            seqPosToVisibleCol: (_name, pos) => pos,
+            visibleColToSeqPos: (_name, col) => col,
+        };
+        expect(genomeToMSA({ model })).toBe(3);
+    });
+    // A hover names the chromosome the assembly's way and the transcript names it
+    // the annotation file's way, so on GENCODE-on-hg38 -- jbrowse.org's own
+    // config -- the two are '1' and 'chr1' and pointing at a codon lit nothing.
+    describe('a config whose assembly and annotation spell the refName apart', () => {
+        beforeEach(() => {
+            aliases = { chr1: '1', chr2: '2' };
+        });
+        test('maps a hover named 1 onto a transcript named chr1', () => {
+            mockSession({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: '1' },
+                },
+            });
+            const seqPosToVisibleCol = vi.fn().mockReturnValue(10);
+            const model = {
+                querySeqName: 'QUERY',
+                querySeqOffset: 0,
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
+                transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
+                mafRegion: undefined,
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
+                seqPosToVisibleCol,
+                visibleColToSeqPos: (_name, col) => col,
+            };
+            expect(genomeToMSA({ model })).toBe(10);
+            expect(seqPosToVisibleCol).toHaveBeenCalledWith('QUERY', 10);
+        });
+        // the gate still has to reject another chromosome, which is the whole
+        // reason it is there
+        test('still rejects a hover on another chromosome', () => {
+            mockSession({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: '2' },
+                },
+            });
+            const seqPosToVisibleCol = vi.fn();
+            const model = {
+                querySeqName: 'QUERY',
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
+                transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
+                mafRegion: undefined,
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
+                seqPosToVisibleCol,
+            };
+            expect(genomeToMSA({ model })).toBeUndefined();
+            expect(seqPosToVisibleCol).not.toHaveBeenCalled();
+        });
+        // this runs from a hover autorun, and mafRegion names an assembly off a
+        // frozen spec that nothing here waited for -- so the aliases may not be
+        // loaded, and asking for them throws
+        test('falls back to the raw name while the aliases are still loading', () => {
+            assemblyInitialized = false;
+            mockSession({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: 'chr1' },
+                },
+            });
+            const seqPosToVisibleCol = vi.fn().mockReturnValue(10);
+            const model = {
+                querySeqName: 'QUERY',
+                querySeqOffset: 0,
+                rowMap: new Map([['QUERY', 'MKVLTAEEK']]),
+                transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 10 } },
+                mafRegion: undefined,
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
+                seqPosToVisibleCol,
+                visibleColToSeqPos: (_name, col) => col,
+            };
+            expect(() => genomeToMSA({ model })).not.toThrow();
+            // both sides spell it 'chr1' here, so the raw comparison still answers
+            expect(genomeToMSA({ model })).toBe(10);
+        });
+        test('maps a hover named 1 into a mafRegion named chr1', () => {
+            mockSession({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: '1' },
+                },
+            });
+            const seqPosToVisibleCol = vi.fn().mockReturnValue(5);
+            const model = {
+                querySeqName: 'hg38.chr1',
+                rowMap: new Map([['hg38.chr1', 'ACGTACGTAC']]),
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                connectedView: { initialized: true, assemblyNames: ['hg38'] },
+                seqPosToVisibleCol,
+                visibleColToSeqPos: () => 4,
+            };
+            expect(genomeToMSA({ model })).toBe(5);
+            expect(seqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 4);
+        });
+    });
 });

package/dist/MsaViewPanel/launchAutoruns.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/MsaViewPanel/launchAutoruns.test.js

@@ -0,0 +1,36 @@
+import { expect, test, vi } from 'vitest';
+import { doLaunchBlast } from './doLaunchBlast';
+import stateModelFactory from './model';
+vi.mock('@jbrowse/core/util', async (importOriginal) => ({
+    ...(await importOriginal()),
+    getSession: () => ({ views: [], hovered: undefined }),
+}));
+vi.mock('./doLaunchBlast', () => ({ doLaunchBlast: vi.fn() }));
+vi.mock('./msaDataStore', () => ({
+    cleanupOldData: vi.fn(async () => { }),
+    deleteMsaData: vi.fn(async () => { }),
+    generateDataStoreId: vi.fn(),
+    retrieveMsaData: vi.fn(),
+    storeMsaData: vi.fn(),
+}));
+// the real launch reads querySeqName before its first await, as resolveQuery
+// does, which used to make that name a reason to launch again
+test('a write the launch body read does not start a second launch', () => {
+    vi.mocked(doLaunchBlast).mockImplementation(({ self }) => {
+        void self.querySeqName;
+        return new Promise(() => { });
+    });
+    const model = stateModelFactory().create({
+        type: 'MsaView',
+        id: 'msa1',
+        blastParams: {
+            searchProgram: 'blastp',
+            blastDatabase: 'uniprotkb_swissprot',
+            msaAlgorithm: 'clustalo',
+            proteinSequence: 'MKV',
+        },
+    });
+    expect(doLaunchBlast).toHaveBeenCalledTimes(1);
+    model.setQuerySeqName('P53_HUMAN_query');
+    expect(doLaunchBlast).toHaveBeenCalledTimes(1);
+});