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Oncoprinter enable submitting of data in same format as MutationMapper fix #11214 #5145

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Oncoprinter enable submitting of data in same format as MutationMapper fix #11214 #5145

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1 change: 1 addition & 0 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -356,6 +356,7 @@
"es-abstract": "1.18.0-next.2",
"expect": "^1.20.2",
"expect-jsx": "5.0.0",
"glob": "7.2.0",
"http-server": "0.11.1",
"identity-obj-proxy": "^3.0.0",
"jasmine-core": "^3.9.0",
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214 changes: 104 additions & 110 deletions src/pages/staticPages/tools/oncoprinter/OncoprinterGeneticUtils.spec.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -3,111 +3,107 @@ import { parseGeneticInput } from './OncoprinterGeneticUtils';

describe('OncoprinterGeneticUtils', () => {
describe('parseGeneticInput', () => {
it('skips header line', () => {
assert.deepEqual(
parseGeneticInput(
'sample gene alteration type\nsample_id TP53 FUSION FUSION\n'
),
{
parseSuccess: true,
result: [
{
sampleId: 'sample_id',
hugoGeneSymbol: 'TP53',
alteration: 'structuralVariant',
eventInfo: 'FUSION',
trackName: undefined,
},
],
error: undefined,
}
it('skips header line', async () => {
const parsed = await parseGeneticInput(
'sample gene alteration type\nsample_id TP53 FUSION FUSION\n'
);
assert.deepEqual(parsed, {
parseSuccess: true,
result: [
{
sampleId: 'sample_id',
hugoGeneSymbol: 'TP53',
alteration: 'structuralVariant',
eventInfo: 'FUSION',
trackName: undefined,
},
],
error: undefined,
});
});
it('parses fusion command correctly', () => {
assert.deepEqual(
parseGeneticInput('sample_id TP53 FUSION FUSION'),
{
parseSuccess: true,
result: [
{
sampleId: 'sample_id',
hugoGeneSymbol: 'TP53',
alteration: 'structuralVariant',
eventInfo: 'FUSION',
trackName: undefined,
},
],
error: undefined,
}
it('parses fusion command correctly', async () => {
const parsed = await parseGeneticInput(
'sample_id TP53 FUSION FUSION'
);
assert.deepEqual(parsed, {
parseSuccess: true,
result: [
{
sampleId: 'sample_id',
hugoGeneSymbol: 'TP53',
alteration: 'structuralVariant',
eventInfo: 'FUSION',
trackName: undefined,
},
],
error: undefined,
});
});
it('throws an error if fusion is not specified correctly', () => {
it('throws an error if fusion is not specified correctly', async () => {
try {
const parsed = parseGeneticInput(
const parsed = await parseGeneticInput(
'sample_id TP53 FUSION apsoidjfpaos'
);
assert(false);
} catch (e) {}
});
it('parses germline mutation correctly', () => {
assert.deepEqual(
parseGeneticInput('sampleid BRCA1 Q1538A MISSENSE_GERMLINE'),
{
parseSuccess: true,
result: [
{
sampleId: 'sampleid',
hugoGeneSymbol: 'BRCA1',
alteration: 'missense',
proteinChange: 'Q1538A',
isGermline: true,
trackName: undefined,
},
],
error: undefined,
}
it('parses germline mutation correctly', async () => {
const parsed = await parseGeneticInput(
'sampleid BRCA1 Q1538A MISSENSE_GERMLINE'
);
assert.deepEqual(parsed, {
parseSuccess: true,
result: [
{
sampleId: 'sampleid',
hugoGeneSymbol: 'BRCA1',
alteration: 'missense',
proteinChange: 'Q1538A',
isGermline: true,
trackName: undefined,
},
],
error: undefined,
});
});
it('parses driver mutation correctly', () => {
assert.deepEqual(
parseGeneticInput('sampleid BRCA1 Q1538A TRUNC_DRIVER'),
{
parseSuccess: true,
result: [
{
sampleId: 'sampleid',
hugoGeneSymbol: 'BRCA1',
alteration: 'trunc',
proteinChange: 'Q1538A',
isCustomDriver: true,
trackName: undefined,
},
],
error: undefined,
}
it('parses driver mutation correctly', async () => {
const parsed = await parseGeneticInput(
'sampleid BRCA1 Q1538A TRUNC_DRIVER'
);
assert.deepEqual(parsed, {
parseSuccess: true,
result: [
{
sampleId: 'sampleid',
hugoGeneSymbol: 'BRCA1',
alteration: 'trunc',
proteinChange: 'Q1538A',
isCustomDriver: true,
trackName: undefined,
},
],
error: undefined,
});
});
it('parses germline & driver mutation correctly', () => {
assert.deepEqual(
parseGeneticInput(
'sampleid BRCA1 Q1538A MISSENSE_GERMLINE_DRIVER'
),
{
parseSuccess: true,
result: [
{
sampleId: 'sampleid',
hugoGeneSymbol: 'BRCA1',
alteration: 'missense',
proteinChange: 'Q1538A',
isGermline: true,
isCustomDriver: true,
trackName: undefined,
},
],
error: undefined,
}
it('parses germline & driver mutation correctly', async () => {
const parsed = await parseGeneticInput(
'sampleid BRCA1 Q1538A MISSENSE_GERMLINE_DRIVER'
);
assert.deepEqual(parsed, {
parseSuccess: true,
result: [
{
sampleId: 'sampleid',
hugoGeneSymbol: 'BRCA1',
alteration: 'missense',
proteinChange: 'Q1538A',
isGermline: true,
isCustomDriver: true,
trackName: undefined,
},
],
error: undefined,
});
});
it('throws an error for an invalid mutation modifier', () => {
try {
Expand All @@ -117,27 +113,25 @@ describe('OncoprinterGeneticUtils', () => {
assert(false);
} catch (e) {}
});
it('parses a line with a given track name correctly', () => {
assert.deepEqual(
parseGeneticInput(
'sampleid BRCA1 Q1538A MISSENSE_GERMLINE_DRIVER testTrackName'
),
{
parseSuccess: true,
result: [
{
sampleId: 'sampleid',
hugoGeneSymbol: 'BRCA1',
alteration: 'missense',
proteinChange: 'Q1538A',
isGermline: true,
isCustomDriver: true,
trackName: 'testTrackName',
},
],
error: undefined,
}
it('parses a line with a given track name correctly', async () => {
const parsed = await parseGeneticInput(
'sampleid BRCA1 Q1538A MISSENSE_GERMLINE_DRIVER testTrackName'
);
assert.deepEqual(parsed, {
parseSuccess: true,
result: [
{
sampleId: 'sampleid',
hugoGeneSymbol: 'BRCA1',
alteration: 'missense',
proteinChange: 'Q1538A',
isGermline: true,
isCustomDriver: true,
trackName: 'testTrackName',
},
],
error: undefined,
});
});
});
});
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