def test_upload_rna_coverage_bigwig_to_scout(
caplog: Generator[LogCaptureFixture, None, None],
dna_sample_son_id: str,
mip_rna_analysis_hk_api: HousekeeperAPI,
rna_case_id: str,
rna_sample_son_id: str,
rna_store: Store,
upload_scout_api: UploadScoutAPI,
):
"""Test that A RNA case's bigWig file for all samples can be loaded via a cg CLI
command into an already existing DNA case"""
# GIVEN an existing RNA case with related sample
# GIVEN an existing DNA case with related sample
# GIVEN a sample in the RNA case is connected to a sample in the DNA case via subject_id (i.e. same subject_id)
upload_scout_api.status_db = rna_store
# GIVEN the connected RNA sample has a bigWig in Housekeeper
# WHEN running the method to upload RNA files to Scout
caplog.set_level(logging.INFO)
upload_scout_api.upload_rna_coverage_bigwig_to_scout(case_id=rna_case_id,
dry_run=True)
# THEN the bigWig file should have been uploaded to the connected sample on the dna case in scout
assert "Upload RNA coverage bigwig file finished!" in caplog.text
# THEN the customers dna samples name should have been mentioned in the logging (and used in the upload)
dna_customer_sample_name: str = rna_store.sample(
internal_id=dna_sample_son_id).name
assert dna_customer_sample_name in caplog.text
def test_upload_rna_fusion_report_to_scout_no_subject_id(
caplog: Generator[LogCaptureFixture, None, None],
dna_case_id: str,
mip_rna_analysis_hk_api: HousekeeperAPI,
rna_case_id: str,
rna_store: Store,
upload_scout_api: UploadScoutAPI,
):
"""Test that A RNA case's gene fusion report"""
# GIVEN a sample in the RNA case is NOT connected to a sample in the DNA case via subject_id (i.e. same subject_id)
for link in rna_store.family(rna_case_id).links:
link.sample.subject_id = ""
for link in rna_store.family(dna_case_id).links:
link.sample.subject_id = ""
rna_store.commit()
upload_scout_api.status_db = rna_store
# GIVEN the connected RNA case has a research fusion report in Housekeeper
# WHEN running the method to upload RNA files to Scout
caplog.set_level(logging.INFO)
# THEN an exception should be raised on unconnected data
with pytest.raises(CgDataError):
upload_scout_api.upload_fusion_report_to_scout(case_id=rna_case_id,
dry_run=True)
def test_upload_splice_junctions_bed_to_scout_no_subject_id(
caplog: Generator[LogCaptureFixture, None, None],
dna_case_id: str,
mip_rna_analysis_hk_api: HousekeeperAPI,
rna_case_id: str,
rna_store: Store,
upload_scout_api: UploadScoutAPI,
):
"""Test that A RNA case's junction splice files for all samples can be loaded via a cg CLI
command into an already existing DNA case"""
# GIVEN a sample in the RNA case is NOT connected to a sample in the DNA case via subject_id (i.e. same subject_id)
for link in rna_store.family(rna_case_id).links:
link.sample.subject_id = ""
for link in rna_store.family(dna_case_id).links:
link.sample.subject_id = ""
rna_store.commit()
upload_scout_api.status_db = rna_store
# GIVEN the connected RNA sample has a junction bed in Housekeeper
# WHEN running the method to upload RNA files to Scout
caplog.set_level(logging.INFO)
# THEN an exception should be raised on unconnected data
with pytest.raises(CgDataError):
upload_scout_api.upload_splice_junctions_bed_to_scout(
case_id=rna_case_id, dry_run=True)
def test_upload_rna_junctions_to_scout(
caplog: Generator[LogCaptureFixture, None, None],
mip_rna_analysis_hk_api: HousekeeperAPI,
rna_case_id: str,
rna_store: Store,
upload_scout_api: UploadScoutAPI,
):
"""Test that A RNA case's gene fusion report and junction splice files for all samples can be loaded via a cg CLI
command into an already existing DNA case"""
# GIVEN an existing RNA case with related sample
# GIVEN an existing DNA case with related sample
# GIVEN a sample in the RNA case is connected to a sample in the DNA case via subject_id (i.e. same subject_id)
upload_scout_api.status_db = rna_store
# GIVEN the connected RNA sample has a junction bed in Housekeeper
# GIVEN the connected RNA sample has a bigWig in Housekeeper
# WHEN running the method to upload RNA files to Scout
caplog.set_level(logging.INFO)
upload_scout_api.upload_rna_junctions_to_scout(case_id=rna_case_id,
dry_run=True)
# THEN the 2 files should have been uploaded to the connected sample on the dna case in scout
assert "Upload splice junctions bed file finished!" in caplog.text
assert "Upload RNA coverage bigwig file finished!" in caplog.text