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Dump json #163

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08ae5a0
fix merge conflict
stevekm Jan 22, 2020
9bf2ce7
Merge branch 'develop' into test-pairing
stevekm Jan 28, 2020
d77be1d
add tests for base RoslinQcOperator class
stevekm Jan 29, 2020
563009c
add test to Makefile
stevekm Feb 4, 2020
ce2a2c5
Merge branch 'develop' into roslin-qc
stevekm Feb 4, 2020
0d4dfb9
merge against develop
stevekm Feb 5, 2020
da2449a
update fixture dump script for dumping Run's
stevekm Feb 5, 2020
bd4bf07
start Roslin QC operator and input parsing with tests and fixtures
stevekm Feb 5, 2020
a4816de
merge against develop
stevekm Feb 5, 2020
83bf428
add tests for serializer using output_metadata field
stevekm Feb 11, 2020
b1406d9
merge against develop
stevekm Feb 11, 2020
9e3419b
update demo run methods and input.json template
stevekm Feb 12, 2020
33a8c19
add fixture duplication script
stevekm Feb 15, 2020
6cd29d2
Merge branch 'duplication-script' into roslin-qc
stevekm Feb 15, 2020
d452748
add multiple run handling for roslin qc input, update fixtures and sc…
stevekm Feb 16, 2020
1464afc
merge against develop
stevekm Feb 16, 2020
40f49f6
merge against develop
stevekm Feb 16, 2020
300bea2
add RoslinQCOperator to get by classname for Operator Factory
stevekm Feb 18, 2020
de58404
make Roslin operator data easier to read
stevekm Feb 19, 2020
e9670d1
update Makefile and operator tests
stevekm Feb 19, 2020
30284a2
add roslin qc pipeline fixture
stevekm Feb 19, 2020
84d182a
clean up Roslin operator
stevekm Feb 19, 2020
5eccbf1
add sorting to QC inputs for reproducibility
stevekm Feb 19, 2020
851ad77
update Roslin qc operator and tests
stevekm Feb 19, 2020
cdeb92d
disable bid to cwl conversion since its handled elsewhere
stevekm Feb 20, 2020
40869d4
remove CWL conversion
stevekm Feb 20, 2020
2787baa
refactor job data generation methods
stevekm Feb 24, 2020
0d2bc2b
update Roslin QC operator tests
stevekm Feb 24, 2020
e615bf4
update test for input generation
stevekm Feb 24, 2020
0a7c95a
merge against develop and fix conflicts
stevekm Feb 24, 2020
145fd99
merge against develop
stevekm Feb 25, 2020
39f13c8
merge against roslin-qc
stevekm Feb 25, 2020
c43cc7d
update serializer tests
stevekm Feb 25, 2020
8e70561
merge against roslin-qc
stevekm Feb 25, 2020
70e55ae
update import recipe
stevekm Feb 25, 2020
188eddf
move server log to logs dir
stevekm Feb 25, 2020
fbd7acb
update API run view to support Run IDs, fixes #157
stevekm Feb 25, 2020
b235fc6
fix service checking in Makefile before trying to start server
stevekm Feb 26, 2020
89d58b6
add job JSON dumping
stevekm Feb 26, 2020
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merge against develop
  • Loading branch information
stevekm committed Feb 25, 2020
commit 145fd99aec15eff2e189b5e8c3023804beaa86cc
11 changes: 10 additions & 1 deletion runner/operator/roslin_operator/roslin_operator.py
Original file line number Diff line number Diff line change
@@ -39,11 +39,20 @@ def get_jobs(self):
tumor_sample_name = job['pair'][0]['ID']
normal_sample_name = job['pair'][1]['ID']
name = "ROSLIN %s, %i of %i" % (self.request_id, i + 1, number_of_inputs)
assay = job['assay']
pi = job['pi']
pi_email = job['pi_email']
data = {
'app': self.get_pipeline_id(),
'inputs': roslin_inputs,
'name': name,
'tags': {'requestId': self.request_id}
'tags': {
'requestId': self.request_id,
'sampleNameTumor': tumor_sample_name,
'sampleNameNormal': normal_sample_name,
'labHeadName': pi,
'labHeadEmail': pi_email
}
}
run = APIRunCreateSerializer(data = data)
roslin_jobs.append((run, job))
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