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Merged
RyanRatcliff merged 1 commit into from
Jul 24, 2019
Merged

removing use existing sequence option since it's now the default and … #101

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6 changes: 3 additions & 3 deletions lib/cmds/tasks_cmds/create-foundation-task.js
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,8 @@ exports.builder = yargs => {
choices: ['all', 'variant', 'cnv', 'fnv'],
type: 'string',
demandOption: false
}).option('use-existing-sequence', {
describe: 'Attempt to add indexed values to existing sequence.',
}).option('re-ingest-file', {
describe: 'Force a re-ingestion of a file that has already been ingested.',
type: 'Boolean',
default: false,
demandOption: false
Expand All @@ -61,7 +61,7 @@ exports.handler = async argv => {
indexedDate: argv.indexedDate,
performerId: argv.performerId,
indexType: argv.indexType,
useExistingSequence: argv.useExistingSequence
reIngestFile: argv.reIngestFile
});
print(response.data, argv);
};
6 changes: 3 additions & 3 deletions lib/cmds/tasks_cmds/create-nantomics-task.js
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Expand Up @@ -49,8 +49,8 @@ exports.builder = yargs => {
alias: 'u',
demandOption: false,
type: 'string'
}).option('use-existing-sequence', {
describe: 'Attempt to add indexed values to existing sequence.',
}).option('re-ingest-file', {
describe: 'Force a re-ingestion of a file that has already been ingested.',
type: 'Boolean',
default: false,
demandOption: false
Expand All @@ -69,7 +69,7 @@ exports.handler = async argv => {
indexedDate: argv.indexedDate,
performerId: argv.performerId,
uploadType: argv.uploadType,
useExistingSequence: argv.useExistingSequence
reIngestFile: argv.reIngestFile
});
print(response.data, argv);
};
16 changes: 8 additions & 8 deletions test/unit/commands/task.test.js
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Expand Up @@ -101,7 +101,7 @@ test.serial.cb('The "create-foundation-xml-import" command should create a found
performerId: 'performer1',
indexedDate: '1999-01-01 12:00',
indexType: 'all',
useExistingSequence: false
reIngestFile: false
});
t.is(printSpy.callCount, 1);
t.is(printSpy.getCall(0).args[0], res.data);
Expand All @@ -112,7 +112,7 @@ test.serial.cb('The "create-foundation-xml-import" command should create a found
.parse('create-foundation-xml-import db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3 -x c8ef7300-1373-4e51-8eb9-ff333600f6a5 -r 1234 -s 2a6dc73e-ed30-4387-94c1-0cd661da56d9 -n test3 --test-type test1 --performer-id performer1 --indexed-date "1999-01-01 12:00" --index-type all');
});

test.serial.cb('The "create-foundation-xml-import" accepts use-existing-sequence as an optional boolean flag', t => {
test.serial.cb('The "create-foundation-xml-import" accepts re-ingest-file as an optional boolean flag', t => {
const res = { data: {} };
postStub.onFirstCall().returns(res);
callback = () => {
Expand All @@ -128,15 +128,15 @@ test.serial.cb('The "create-foundation-xml-import" accepts use-existing-sequence
performerId: 'performer1',
indexedDate: '1999-01-01 12:00',
indexType: 'all',
useExistingSequence: true
reIngestFile: true
});
t.is(printSpy.callCount, 1);
t.is(printSpy.getCall(0).args[0], res.data);
t.end();
};

yargs.command(createFoundationTask)
.parse('create-foundation-xml-import db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3 -x c8ef7300-1373-4e51-8eb9-ff333600f6a5 -r 1234 -s 2a6dc73e-ed30-4387-94c1-0cd661da56d9 -n test3 --test-type test1 --performer-id performer1 --indexed-date "1999-01-01 12:00" --index-type all --use-existing-sequence');
.parse('create-foundation-xml-import db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3 -x c8ef7300-1373-4e51-8eb9-ff333600f6a5 -r 1234 -s 2a6dc73e-ed30-4387-94c1-0cd661da56d9 -n test3 --test-type test1 --performer-id performer1 --indexed-date "1999-01-01 12:00" --index-type all --re-ingest-file');
});

test.serial.cb('The "create-nantomics-vcf-import" command should create a Nantomics ingest task', t => {
Expand All @@ -156,7 +156,7 @@ test.serial.cb('The "create-nantomics-vcf-import" command should create a Nantom
performerId: 'performer1',
indexedDate: '1999-01-01 12:00',
uploadType: 'variant',
useExistingSequence: false
reIngestFile: false
});
t.is(printSpy.callCount, 1);
t.is(printSpy.getCall(0).args[0], res.data);
Expand All @@ -167,7 +167,7 @@ test.serial.cb('The "create-nantomics-vcf-import" command should create a Nantom
.parse('create-nantomics-vcf-import db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3 -v c8ef7300-1373-4e51-8eb9-ff333600f6a5 -p converted -s 2a6dc73e-ed30-4387-94c1-0cd661da56d9 -e germline -n test4 --test-type test1 --performer-id performer1 --indexed-date "1999-01-01 12:00" --upload-type variant');
});

test.serial.cb('The "create-nantomics-vcf-import" command accepts use-existing-sequence as an optional boolean flag', t => {
test.serial.cb('The "create-nantomics-vcf-import" command accepts re-ingest-file as an optional boolean flag', t => {
const res = { data: {} };
postStub.onFirstCall().returns(res);
callback = () => {
Expand All @@ -184,15 +184,15 @@ test.serial.cb('The "create-nantomics-vcf-import" command accepts use-existing-s
performerId: 'performer1',
indexedDate: '1999-01-01 12:00',
uploadType: 'variant',
useExistingSequence: true
reIngestFile: true
});
t.is(printSpy.callCount, 1);
t.is(printSpy.getCall(0).args[0], res.data);
t.end();
};

yargs.command(createNantomicsTask)
.parse('create-nantomics-vcf-import db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3 -v c8ef7300-1373-4e51-8eb9-ff333600f6a5 -p converted -s 2a6dc73e-ed30-4387-94c1-0cd661da56d9 -e germline -n test4 --test-type test1 --performer-id performer1 --indexed-date "1999-01-01 12:00" --upload-type variant --use-existing-sequence');
.parse('create-nantomics-vcf-import db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3 -v c8ef7300-1373-4e51-8eb9-ff333600f6a5 -p converted -s 2a6dc73e-ed30-4387-94c1-0cd661da56d9 -e germline -n test4 --test-type test1 --performer-id performer1 --indexed-date "1999-01-01 12:00" --upload-type variant --re-ingest-file');
});

test.serial.cb('The "tasks-cancel" command should cancel a task', t => {
Expand Down