def test_select_command(
cli_runner: CliRunner,
populated_stats_api: StatsAPI,
demux_results_finished_dir: Path,
flowcell_object: Flowcell,
demultiplex_context: CGConfig,
):
demultiplex_context.cg_stats_api_ = populated_stats_api
# GIVEN a stats api with some information about a flowcell
flowcell_id: str = flowcell_object.flowcell_id
full_flowcell_name: str = flowcell_object.flowcell_full_name
assert find.get_flowcell_id(flowcell_id)
demux_results = DemuxResults(
demux_dir=demux_results_finished_dir / full_flowcell_name,
flowcell=flowcell_object,
bcl_converter="bcl2fastq",
)
# GIVEN a project id
project_id: str = ""
for project in demux_results.projects:
project_id = project.split("_")[-1]
assert project_id
# WHEN exporting the sample information
result = cli_runner.invoke(select_project_cmd,
[flowcell_id, "--project", project_id],
obj=demultiplex_context)
# THEN assert that the command exits with success
assert result.exit_code == 0
# THEN assert that the flowcell id if in the printing
assert flowcell_id in result.output
def fixture_nipt_upload_api_context(
cg_context: CGConfig, nipt_stats_api: StatsAPI,
re_sequenced_sample_store: Store) -> CGConfig:
cg_context.status_db_ = re_sequenced_sample_store
cg_context.cg_stats_api_ = nipt_stats_api
return cg_context
def fixture_demultiplex_context(
demultiplexing_api: DemultiplexingAPI,
stats_api: StatsAPI,
real_housekeeper_api: HousekeeperAPI,
cg_context: CGConfig,
) -> CGConfig:
cg_context.demultiplex_api_ = demultiplexing_api
cg_context.cg_stats_api_ = stats_api
cg_context.housekeeper_api_ = real_housekeeper_api
return cg_context
def fixture_wipe_demultiplex_api(
cg_context: CGConfig,
demultiplexed_flowcells_working_directory: Path,
flowcell_full_name: str,
stats_api: StatsAPI,
) -> DeleteDemuxAPI:
"""Yield an initialized DeleteDemuxAPI"""
cg_context.cg_stats_api_ = stats_api
return DeleteDemuxAPI(
config=cg_context,
demultiplex_base=demultiplexed_flowcells_working_directory,
dry_run=False,
run_path=Path(flowcell_full_name),
)
def test_set_dry_run_delete_demux_api(
caplog,
cg_context: CGConfig,
demultiplexed_flowcells_working_directory: Path,
flowcell_full_name: str,
stats_api: StatsAPI,
):
"""Test to test function to set the API to run in dry run mode"""
caplog.set_level(logging.DEBUG)
cg_context.cg_stats_api_ = stats_api
# WHEN setting the dry_run mode on a DeleteDemuxAPI
wipe_demultiplex_api: DeleteDemuxAPI = DeleteDemuxAPI(
config=cg_context,
demultiplex_base=demultiplexed_flowcells_working_directory,
dry_run=True,
run_path=flowcell_full_name,
)
# THEN the dry run parameter should be set to True and it should be logged
assert wipe_demultiplex_api.dry_run
assert f"DeleteDemuxAPI: Setting dry run mode to True" in caplog.text