def test_cli_init(cli_runner: CliRunner, base_context: CGConfig, caplog):
caplog.set_level(logging.INFO)
# GIVEN you want to setup a new database using the CLI
database = "./test_db.sqlite3"
database_path = Path(database)
database_uri = f"sqlite:///{database}"
base_context.status_db_ = Store(uri=database_uri)
with cli_runner.isolated_filesystem():
assert database_path.exists() is False
# WHEN calling "init"
result = cli_runner.invoke(init, [], obj=base_context)
# THEN it should setup the database with some tables
assert result.exit_code == 0
assert database_path.exists()
assert len(Store(database_uri).engine.table_names()) > 0
# GIVEN the database already exists
# WHEN calling the init function
result = cli_runner.invoke(init, [], obj=base_context)
# THEN it should print an error and give error exit code
assert result.exit_code != 0
assert "Database already exists" in caplog.text
# GIVEN the database already exists
# WHEN calling "init" with "--reset"
result = cli_runner.invoke(init, ["--reset"],
input="Yes",
obj=base_context)
# THEN it should re-setup the tables and print new tables
assert result.exit_code == 0
assert "Success!" in caplog.text
def test_upload_genotype(
upload_context: CGConfig,
case_id: str,
cli_runner: CliRunner,
analysis_store_trio: Store,
upload_genotypes_hk_api: HousekeeperAPI,
caplog,
):
"""Test to upload genotypes via the CLI"""
caplog.set_level(logging.DEBUG)
# GIVEN a context with a case that is ready for upload sequence genotypes
upload_context.status_db_ = analysis_store_trio
upload_context.housekeeper_api_ = upload_genotypes_hk_api
case_obj = upload_context.status_db.family(case_id)
assert case_obj
# WHEN uploading the genotypes
result = cli_runner.invoke(upload_genotypes_cmd, [case_id],
obj=upload_context)
# THEN check that the command exits with success
assert result.exit_code == 0
# THEN assert the correct information is communicated
assert "loading VCF genotypes for sample(s):" in caplog.text
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_populated_compress_context(compress_api: CompressAPI,
populated_compress_store: Store,
cg_config_object: CGConfig) -> CGConfig:
"""Return a compress context populated with a completed analysis"""
# Make sure that there is a case where analysis is completed
cg_config_object.meta_apis["compress_api"] = compress_api
cg_config_object.status_db_ = populated_compress_store
return cg_config_object
def fixture_populated_mip_context(
base_context: CGConfig,
analysis_store: Store,
mip_dna_housekeeper: HousekeeperAPI,
project_dir: Path,
) -> CGConfig:
base_context.housekeeper_api_ = mip_dna_housekeeper
base_context.status_db_ = analysis_store
base_context.delivery_path = str(project_dir)
return base_context
def fixture_upload_genotypes_context(
upload_genotypes_hk_api: HousekeeperAPI,
genotype_api: GenotypeAPI,
analysis_store_trio: Store,
base_context: CGConfig,
) -> CGConfig:
"""Create a upload genotypes context"""
base_context.genotype_api_ = genotype_api
base_context.housekeeper_api_ = upload_genotypes_hk_api
base_context.status_db_ = analysis_store_trio
return base_context
def fixture_base_context(
analysis_store: Store,
housekeeper_api: HousekeeperAPI,
upload_scout_api: UploadScoutAPI,
trailblazer_api: TrailblazerAPI,
cg_context: CGConfig,
) -> CGConfig:
"""context to use in cli"""
cg_context.status_db_ = analysis_store
cg_context.housekeeper_api_ = housekeeper_api
cg_context.trailblazer_api_ = trailblazer_api
cg_context.scout_api_ = MockScoutApi()
cg_context.meta_apis["report_api"] = MockReportApi()
cg_context.meta_apis["scout_upload_api"] = upload_scout_api
cg_context.mip_rd_dna.root = tempdir
return cg_context
def test_delete_flow_cell_housekeeper_only_sample_level(
caplog,
cg_context: CGConfig,
demultiplexed_flowcells_working_directory: Path,
flowcell_full_name: str,
populated_flow_cell_store: Store,
sample_level_housekeeper_api: HousekeeperAPI,
tmp_fastq_paths: List[Path],
):
"""Test function to remove fastqs from Housekeeper when there are only files on sample level
(not on flow cell name)
"""
caplog.set_level(logging.INFO)
cg_context.housekeeper_api_ = sample_level_housekeeper_api
cg_context.status_db_ = populated_flow_cell_store
# GIVEN a DeleteDemuxAPI with a HousekeeperAPI with no files with flow cell name as a tag
sample_level_files: List[Path] = tmp_fastq_paths
wipe_demultiplex_api: DeleteDemuxAPI = DeleteDemuxAPI(
config=cg_context,
demultiplex_base=demultiplexed_flowcells_working_directory,
dry_run=False,
run_path=Path(flowcell_full_name),
)
wipe_demultiplex_api._set_samples_on_flow_cell()
# WHEN wiping files in Housekeeper
wipe_demultiplex_api.delete_flow_cell_housekeeper()
# THEN you should be notified that there are no files on flow cell names
assert (
f"Housekeeper: No files found with tag: {wipe_demultiplex_api.flow_cell_name}"
in caplog.text)
# AND you should be notified that there were fastq files removed on sample level
for file in sample_level_files:
assert f"{file.as_posix()} deleted" in caplog.text
def test_delete_flow_cell_housekeeper_flowcell_name(
caplog,
cg_context: CGConfig,
demultiplexed_flowcells_working_directory: Path,
flow_cell_name_housekeeper_api: HousekeeperAPI,
flowcell_full_name: str,
populated_flow_cell_store: Store,
tmp_fastq_paths: List[Path],
tmp_sample_sheet_path: Path,
):
"""Test function to remove files from Housekeeper using flow cell name as a tag"""
caplog.set_level(logging.INFO)
cg_context.housekeeper_api_ = flow_cell_name_housekeeper_api
cg_context.status_db_ = populated_flow_cell_store
# GIVEN
fastq_files: List[Path] = tmp_fastq_paths
sample_sheet_file: Path = tmp_sample_sheet_path
wipe_demultiplex_api: DeleteDemuxAPI = DeleteDemuxAPI(
config=cg_context,
demultiplex_base=demultiplexed_flowcells_working_directory,
dry_run=False,
run_path=Path(flowcell_full_name),
)
wipe_demultiplex_api._set_samples_on_flow_cell()
# WHEN
wipe_demultiplex_api.delete_flow_cell_housekeeper()
# THEN
assert (
f"Housekeeper: No files found with tag: {wipe_demultiplex_api.flow_cell_name}"
not in caplog.text)
assert f"Deleted {sample_sheet_file.as_posix()} from housekeeper" in caplog.text
for fastq_file in fastq_files:
assert f"{fastq_file.as_posix()} deleted" in caplog.text
def fixture_config_object(cg_context: CGConfig, analysis_store: Store,
real_housekeeper_api: HousekeeperAPI):
cg_context.status_db_ = analysis_store
cg_context.housekeeper_api_ = real_housekeeper_api
return cg_context
def fixture_config_object_no_gisaid_samples(config: dict,
cg_config_object: CGConfig,
base_store: Store):
cg_config_object.status_db_ = base_store
cg_config_object.gisaid = GisaidConfig(**config["gisaid"])
return cg_config_object
def fixture_cg_context(context_config: dict, base_store: Store,
housekeeper_api: HousekeeperAPI) -> CGConfig:
cg_config = CGConfig(**context_config)
cg_config.status_db_ = base_store
cg_config.housekeeper_api_ = housekeeper_api
return cg_config
def base_context(cg_context: CGConfig, analysis_store: Store) -> CGConfig:
"""context to use in cli"""
cg_context.status_db_ = analysis_store
return cg_context
def fixture_base_context(base_store: Store, housekeeper_api: HousekeeperAPI,
cg_config_object: CGConfig) -> CGConfig:
"""context to use in cli"""
cg_config_object.status_db_ = base_store
cg_config_object.housekeeper_api_ = housekeeper_api
return cg_config_object
def fixture_store_fastq_context(compress_api: CompressAPI, store: Store,
cg_config_object: CGConfig) -> CGConfig:
"""Return a compress context"""
cg_config_object.meta_apis["compress_api"] = compress_api
cg_config_object.status_db_ = store
return cg_config_object