def coverage(context, re_upload, family_id):
"""Upload coverage from an analysis to Chanjo."""
chanjo_api = coverage_app.ChanjoAPI(context.obj)
family_obj = context.obj['status'].family(family_id)
api = UploadCoverageApi(context.obj['status'],
context.obj['housekeeper_api'], chanjo_api)
coverage_data = api.data(family_obj.analyses[0])
api.upload(coverage_data, replace=re_upload)
def coverage(context, re_upload, family_id):
"""Upload coverage from an analysis to Chanjo."""
click.echo(click.style("----------------- COVERAGE --------------------"))
if not family_id:
_suggest_cases_to_upload(context)
context.abort()
chanjo_api = coverage_app.ChanjoAPI(context.obj)
family_obj = context.obj["status"].family(family_id)
api = UploadCoverageApi(context.obj["status"],
context.obj["housekeeper_api"], chanjo_api)
coverage_data = api.data(family_obj.analyses[0])
api.upload(coverage_data, replace=re_upload)
def coverage_upload_api(chanjo_config_dict, populated_housekeeper_api):
"""Fixture for coverage upload API"""
hk_api = populated_housekeeper_api
status_api = None
coverage_api = MockCoverage(chanjo_config_dict)
_api = UploadCoverageApi(status_api=status_api, hk_api=hk_api, chanjo_api=coverage_api)
return _api
def coverage(context: CGConfig, re_upload, family_id):
"""Upload coverage from an analysis to Chanjo."""
click.echo(click.style("----------------- COVERAGE --------------------"))
status_db: Store = context.status_db
if not family_id:
suggest_cases_to_upload(status_db=status_db)
raise click.Abort
case_obj: models.Family = status_db.family(family_id)
upload_coverage_api = UploadCoverageApi(
status_api=status_db,
hk_api=context.housekeeper_api,
chanjo_api=context.chanjo_api,
)
coverage_data = upload_coverage_api.data(case_obj.analyses[0])
upload_coverage_api.upload(coverage_data, replace=re_upload)
def test_upload(chanjo_config_dict, populated_housekeeper_api, analysis_store,
mocker, case_id):
"""test uploading with chanjo"""
# GIVEN a coverage api and a data dictionary
mock_upload = mocker.patch.object(ChanjoAPI, "upload")
mock_sample = mocker.patch.object(ChanjoAPI, "sample")
mock_remove = mocker.patch.object(ChanjoAPI, "delete_sample")
hk_api = populated_housekeeper_api
chanjo_api = ChanjoAPI(config=chanjo_config_dict)
coverage_api = UploadCoverageApi(status_api=None,
hk_api=hk_api,
chanjo_api=chanjo_api)
family_name = case_id
family_obj = analysis_store.family(family_name)
analysis_obj = MockAnalysis(family_obj=family_obj)
data = coverage_api.data(analysis_obj=analysis_obj)
# WHEN uploading samples in data dictionary
coverage_api.upload(data=data, replace=True)
# THEN methods sample, and upload should each have been called three times
assert mock_upload.call_count == len(data["samples"])
assert mock_sample.call_count == len(data["samples"])