def test_add_flowcell_cmd(
cli_runner: CliRunner,
flowcell_object: Flowcell,
demultiplex_context: CGConfig,
demultiplexed_flowcell_finished_working_directory: Path,
demultiplex_ready_flowcell: Path,
):
# GIVEN a cgstats api and a demultiplex api
# GIVEN that there is a flowcell in the run dir
assert demultiplex_ready_flowcell.exists()
# GIVEN that there is a demultiplexed flowcell
assert demultiplexed_flowcell_finished_working_directory.exists()
# GIVEN that the flowcell does not exist in the cgstats database
assert not get_flowcell_id(flowcell_name=flowcell_object.flowcell_id)
# WHEN running the add flowcell command
result = cli_runner.invoke(
add_flowcell_cmd, [flowcell_object.flowcell_full_name], obj=demultiplex_context
)
# THEN assert that the run was success
assert result.exit_code == 0
# THEN assert that the flowcell was added to cgstats
assert get_flowcell_id(flowcell_name=flowcell_object.flowcell_id)
def test_create_flowcell(stats_api: StatsAPI,
bcl2fastq_demux_results: DemuxResults):
# GIVEN a api without a flowcell object
assert not find.get_flowcell_id(
flowcell_name=bcl2fastq_demux_results.flowcell.flowcell_id)
# WHEN creating a new flowcell
create.create_flowcell(manager=stats_api,
demux_results=bcl2fastq_demux_results)
# THEN assert that the flowcell was created
assert find.get_flowcell_id(
flowcell_name=bcl2fastq_demux_results.flowcell.flowcell_id)
def test_create_novaseq_flowcell(stats_api: StatsAPI,
bcl2fastq_demux_results: DemuxResults):
# GIVEN a setup with an existing sample sheet with information
assert bcl2fastq_demux_results.flowcell.sample_sheet_path.read_text()
# GIVEN that the flowcell does not exist in the database
assert not find.get_flowcell_id(
flowcell_name=bcl2fastq_demux_results.flowcell.flowcell_id)
# WHEN creating the novaseq flowcell
create.create_novaseq_flowcell(manager=stats_api,
demux_results=bcl2fastq_demux_results)
# THEN assert that the flowcell was created
assert find.get_flowcell_id(
flowcell_name=bcl2fastq_demux_results.flowcell.flowcell_id)
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 create_novaseq_flowcell(manager: StatsAPI, demux_results: DemuxResults):
"""Add a novaseq flowcell to CG stats"""
LOG.info("Adding flowcell information to cgstats")
support_parameters_id: Optional[int] = find.get_support_parameters_id(
demux_results=demux_results)
if not support_parameters_id:
support_parameters: stats_models.Supportparams = create_support_parameters(
manager=manager, demux_results=demux_results)
support_parameters_id: int = support_parameters.supportparams_id
else:
LOG.info("Support parameters already exists")
datasource_id: Optional[int] = find.get_datasource_id(
demux_results=demux_results)
if not datasource_id:
datasource_object: stats_models.Datasource = create_datasource(
manager=manager,
demux_results=demux_results,
support_parameters_id=support_parameters_id,
)
datasource_id: int = datasource_object.datasource_id
else:
LOG.info("Data source already exists")
flowcell_id: Optional[int] = find.get_flowcell_id(
flowcell_name=demux_results.flowcell.flowcell_id)
if not flowcell_id:
flowcell: stats_models.Flowcell = create_flowcell(
manager=manager, demux_results=demux_results)
flowcell_id: int = flowcell.flowcell_id
else:
LOG.info("Flowcell already exists")
demux_id: Optional[int] = find.get_demux_id(flowcell_object_id=flowcell_id)
if not demux_id:
demux_object: stats_models.Demux = create_demux(
manager=manager,
demux_results=demux_results,
flowcell_id=flowcell_id,
datasource_id=datasource_id,
)
demux_id: int = demux_object.demux_id
else:
LOG.info("Demux object already exists")
project_name_to_id = create_projects(manager=manager,
project_names=demux_results.projects)
create_samples(
manager=manager,
demux_results=demux_results,
project_name_to_id=project_name_to_id,
demux_id=demux_id,
)
manager.commit()
def delete_flowcell(manager: StatsAPI, flowcell_name: str):
flowcell_id: Optional[int] = get_flowcell_id(flowcell_name=flowcell_name)
if flowcell_id:
flowcell: List[models.Flowcell] = manager.Flowcell.query.filter_by(
flowcell_id=flowcell_id).all()
for entry in flowcell:
log.info("Removing entry %s in from cgstats", entry.flowcellname)
manager.delete(flowcell)
manager.commit()
def test_delete_flowcell(populated_stats_api: StatsAPI, flowcell_name: str):
"""Test to delete a flowcell from cg-stats"""
# GIVEN a populated StatsAPI, with an existing flow cell
flow_cell_id = get_flowcell_id(flowcell_name=flowcell_name)
assert flow_cell_id
# WHEN deleting a flow cell from the StatsAPI
delete_flowcell(manager=populated_stats_api, flowcell_name=flowcell_name)
# THEN the flowcell should not exist any longer
results = populated_stats_api.Flowcell.query.filter_by(
flowcell_id=flow_cell_id).all()
assert not results