def fixture_real_populated_compress_fastq_api(
real_compress_api: CompressAPI, compress_hk_fastq_bundle: dict,
helpers: StoreHelpers) -> CompressAPI:
"""Populated compress api fixture"""
helpers.ensure_hk_bundle(real_compress_api.hk_api,
compress_hk_fastq_bundle)
return real_compress_api
def test_clean_hk_bundle_files_dry_run(
caplog,
case_id: str,
cg_context: CGConfig,
cli_runner: CliRunner,
helpers: StoreHelpers,
mocker,
timestamp: datetime,
):
# GIVEN a housekeeper api with some alignment files
file_path = "path/to_file.cram"
tag = "cram"
hk_bundle_data = {
"name": case_id,
"created": timestamp,
"expires": timestamp,
"files": [
{
"path": file_path,
"archive": False,
"tags": [case_id, tag]
},
],
}
store = cg_context.status_db
case = helpers.ensure_case(store=store, case_id=case_id)
helpers.add_analysis(store=store,
case=case,
started_at=timestamp,
completed_at=timestamp)
helpers.ensure_hk_bundle(cg_context.housekeeper_api,
bundle_data=hk_bundle_data)
# WHEN running the clean command in dry run mode
caplog.set_level(logging.INFO)
result = cli_runner.invoke(hk_bundle_files,
["-c", case_id, "--dry-run", "--tags", tag],
obj=cg_context)
# THEN assert it exits with success
assert result.exit_code == 0
# THEN assert that the files where removed
assert f"{file_path} not on disk" in caplog.text
def fixture_mip_dna_housekeeper(
real_housekeeper_api: HousekeeperAPI,
mip_delivery_bundle: dict,
fastq_delivery_bundle: dict,
helpers: StoreHelpers,
) -> HousekeeperAPI:
helpers.ensure_hk_bundle(real_housekeeper_api,
bundle_data=mip_delivery_bundle)
helpers.ensure_hk_bundle(real_housekeeper_api,
bundle_data=fastq_delivery_bundle)
# assert that the files exists
version_obj_mip: hk_models.Version = real_housekeeper_api.last_version(
mip_delivery_bundle["name"])
version_obj_fastq: hk_models.Version = real_housekeeper_api.last_version(
fastq_delivery_bundle["name"])
real_housekeeper_api.include(version_obj=version_obj_mip)
real_housekeeper_api.include(version_obj=version_obj_fastq)
return real_housekeeper_api
def test_clean_hk_alignment_files_dry_run(
cli_runner: CliRunner,
cg_context: CGConfig,
helpers: StoreHelpers,
case_id: str,
timestamp: datetime,
caplog,
):
# GIVEN a housekeeper api with some alignment files
file_path = "path/to_file.cram"
hk_bundle_data = {
"name":
case_id,
"created":
timestamp,
"expires":
timestamp,
"files": [
{
"path": file_path,
"archive": False,
"tags": [case_id, "cram"]
},
],
}
helpers.ensure_hk_bundle(cg_context.housekeeper_api,
bundle_data=hk_bundle_data)
# WHEN running the clean command in dry run mode
caplog.set_level(logging.INFO)
result = cli_runner.invoke(hk_alignment_files,
[case_id, "--yes", "--dry-run"],
obj=cg_context)
# THEN assert it exits with success
assert result.exit_code == 0
# THEN assert that the files where removed
assert f"Deleting {file_path} from database" in caplog.text
def fixture_mip_hk_store(
helpers: StoreHelpers,
real_housekeeper_api: HousekeeperAPI,
timestamp: datetime,
case_id: str,
) -> HousekeeperAPI:
deliver_hk_bundle_data = {
"name":
case_id,
"created":
timestamp,
"expires":
timestamp,
"files": [
{
"path": "tests/fixtures/apps/mip/dna/store/case_config.yaml",
"archive": False,
"tags": ["mip-config"],
},
{
"path":
"tests/fixtures/apps/mip/dna/store/case_qc_sample_info.yaml",
"archive": False,
"tags": ["sampleinfo"],
},
{
"path":
"tests/fixtures/apps/mip/case_metrics_deliverables.yaml",
"archive": False,
"tags": [HkMipAnalysisTag.QC_METRICS],
},
{
"path": "tests/fixtures/apps/mip/case_file.txt",
"archive": False,
"tags": ["case-tag"],
},
{
"path": "tests/fixtures/apps/mip/sample_file.txt",
"archive": False,
"tags": ["sample-tag", "ADM1"],
},
],
}
helpers.ensure_hk_bundle(real_housekeeper_api,
deliver_hk_bundle_data,
include=True)
empty_deliver_hk_bundle_data = {
"name":
"case_missing_data",
"created":
timestamp,
"expires":
timestamp,
"files": [
{
"path":
"tests/fixtures/apps/mip/dna/store/empty_case_config.yaml",
"archive": False,
"tags": ["mip-config"],
},
{
"path":
"tests/fixtures/apps/mip/dna/store/empty_case_qc_sample_info.yaml",
"archive": False,
"tags": ["sampleinfo"],
},
{
"path":
"tests/fixtures/apps/mip/dna/store/empty_case_metrics_deliverables.yaml",
"archive": False,
"tags": [HkMipAnalysisTag.QC_METRICS],
},
{
"path": "tests/fixtures/apps/mip/case_file.txt",
"archive": False,
"tags": ["case-tag"],
},
{
"path": "tests/fixtures/apps/mip/sample_file.txt",
"archive": False,
"tags": ["sample-tag", "ADM1"],
},
],
}
helpers.ensure_hk_bundle(real_housekeeper_api,
empty_deliver_hk_bundle_data,
include=True)
return real_housekeeper_api
