def test_get_presence_status_status_db(
caplog,
helpers: StoreHelpers,
wipe_demultiplex_api: DeleteDemuxAPI,
flowcell_name: str,
):
"""Test to see if the presence of a flowcell is detected in status-db"""
caplog.set_level(logging.INFO)
# GIVEN DeleteDemuxAPI objects, one with amd one without a flowcell in status-db
wipe_demux_api: DeleteDemuxAPI = wipe_demultiplex_api
# WHEN the flowcell name is parsed and fetched fetching the presence of a flowcell in either context
empty_presence: bool = wipe_demux_api.status_db_presence
# THEN there should be an appropriate presence in both cases
assert not empty_presence
# WHEN adding a flowcell into the statusdb and checking its updated presence
helpers.add_flowcell(store=wipe_demux_api.status_db,
flowcell_id=flowcell_name,
sequencer_type="novaseq")
populated_presence: bool = wipe_demux_api.status_db_presence
# THEN the presence should be updated
assert populated_presence
def fluffy_context(
cg_context: CGConfig,
helpers: StoreHelpers,
real_housekeeper_api: HousekeeperAPI,
fluffy_samplesheet_bundle_data,
fluffy_fastq_hk_bundle_data,
fluffy_case_id_existing,
fluffy_sample_lims_id,
) -> CGConfig:
cg_context.housekeeper_api_ = real_housekeeper_api
fluffy_analysis_api = FluffyAnalysisAPI(config=cg_context)
helpers.ensure_hk_version(fluffy_analysis_api.housekeeper_api,
bundle_data=fluffy_samplesheet_bundle_data)
helpers.ensure_hk_version(fluffy_analysis_api.housekeeper_api,
fluffy_fastq_hk_bundle_data)
example_fluffy_case = helpers.add_case(
fluffy_analysis_api.status_db,
internal_id=fluffy_case_id_existing,
name=fluffy_case_id_existing,
data_analysis=Pipeline.FLUFFY,
)
example_fluffy_sample = helpers.add_sample(
fluffy_analysis_api.status_db,
internal_id=fluffy_sample_lims_id,
is_tumour=False,
application_type="tgs",
reads=100,
sequenced_at=dt.datetime.now(),
)
helpers.add_flowcell(fluffy_analysis_api.status_db,
flowcell_id="flowcell",
samples=[example_fluffy_sample])
helpers.add_relationship(fluffy_analysis_api.status_db,
case=example_fluffy_case,
sample=example_fluffy_sample)
cg_context.meta_apis["analysis_api"] = fluffy_analysis_api
return cg_context
def test_get_sample_flowcells_with_flowcell(cli_runner: CliRunner,
base_context: CGConfig,
disk_store: Store,
helpers: StoreHelpers):
"""Test that we can query samples and hide flowcell, ensuring that no flowcell name is in the output"""
# GIVEN a database with a sample and a related flowcell
flowcell = helpers.add_flowcell(disk_store)
sample = helpers.add_sample(disk_store, flowcell=flowcell)
assert flowcell in disk_store.Sample.query.first().flowcells
sample_id = sample.internal_id
# WHEN getting a sample with the --flowcells flag
result = cli_runner.invoke(get, ["sample", sample_id, "--hide-flowcell"],
obj=base_context)
# THEN the related flowcell should be listed in the output
assert result.exit_code == 0
for flowcell in disk_store.Sample.query.first().flowcells:
assert flowcell.name not in result.output
