def start(context: click.Context, dry_run: bool = False):
"""Start all cases that are ready for analysis"""
exit_code = 0
cases = [case_obj.internal_id for case_obj in context.obj["db"].cases_to_mip_analyze()]
for case_id in cases:
case_obj = context.obj["db"].family(case_id)
if AnalysisAPI.is_dna_only_case(case_obj):
LOG.info("%s: start analysis", case_obj.internal_id)
else:
LOG.warning("%s: contains non-dna samples, skipping", case_obj.internal_id)
continue
priority = (
"high" if case_obj.high_priority else ("low" if case_obj.low_priority else "normal")
)
if dry_run:
continue
try:
context.invoke(mip_dna, priority=priority, case_id=case_obj.internal_id)
except tb.MipStartError as error:
LOG.error(error.message)
exit_code = 1
except CgError as error:
LOG.error(error.message)
exit_code = 11
sys.exit(exit_code)
def test_get_latest_data_rank_model_version(analysis_api: AnalysisAPI):
# GIVEN
family_id = "dummy_family_id"
# WHEN
trending_data = analysis_api.get_latest_metadata("dummy_family_id")
# THEN contains rankmodelversion
assert trending_data["rank_model_version"]
def test_get_latest_data_genome_build(analysis_api: AnalysisAPI):
# GIVEN
family_id = "dummy_family_id"
# WHEN
trending_data = analysis_api.get_latest_metadata("dummy_family_id")
# THEN contains genome_build
assert trending_data["genome_build"]
def test_config(analysis_store: Store, analysis_api: AnalysisAPI):
# GIVEN a status db with a family
family_obj = analysis_store.families().first()
assert family_obj is not None
# WHEN generating the MIP config for the family
mip_config = analysis_api.config(family_obj)
# THEN it should fill in values accordingly
assert len(mip_config["samples"]) == len(family_obj.links)
def test_get_latest_metadata_logging(analysis_api: AnalysisAPI):
# GIVEN an initialised report_api and the deliver_api does not have what we want
analysis_api.tb._get_trending_raises_keyerror = True
# WHEN failing to get latest trending data for a family
latest_data = analysis_api.get_latest_metadata(family_id="bluebull")
# THEN there should be a log entry about this
found = False
for warn in analysis_api.log.get_warnings():
if "bluebull" in warn:
found = True
assert found
assert not latest_data
def analysis_api(analysis_store, housekeeper_api, scout_store):
"""Setup an analysis API."""
Path_mock = MockPath("")
tb_mock = MockTB()
deliver_mock = MockDeliver()
deliver_mock.housekeeper = housekeeper_api
_analysis_api = AnalysisAPI(
db=analysis_store,
hk_api=housekeeper_api,
scout_api=scout_store,
tb_api=tb_mock,
lims_api=None,
deliver_api=deliver_mock,
yaml_loader=safe_loader,
path_api=Path_mock,
logger=MockLogger(),
)
yield _analysis_api
def mip_dna(context: click.Context, case_id: str, email: str, priority: str, start_with: str):
"""Rare disease DNA workflow"""
context.obj["db"] = Store(context.obj["database"])
hk_api = hk.HousekeeperAPI(context.obj)
scout_api = scoutapi.ScoutAPI(context.obj)
lims_api = lims.LimsAPI(context.obj)
context.obj["tb"] = tb.TrailblazerAPI(context.obj)
deliver = DeliverAPI(
context.obj, hk_api=hk_api, lims_api=lims_api, case_tags=CASE_TAGS, sample_tags=SAMPLE_TAGS,
)
context.obj["api"] = AnalysisAPI(
db=context.obj["db"],
hk_api=hk_api,
tb_api=context.obj["tb"],
scout_api=scout_api,
lims_api=lims_api,
deliver_api=deliver,
)
if context.invoked_subcommand is None:
if case_id is None:
_suggest_cases_to_analyze(context, show_as_error=True)
context.abort()
# check everything is ok
case_obj = context.obj["db"].family(case_id)
if case_obj is None:
LOG.error("%s: not found", case_id)
context.abort()
is_ok = context.obj["api"].check(case_obj)
if not is_ok:
LOG.warning("%s: not ready to run", case_obj.internal_id)
# commit the updates to request flowcells
context.obj["db"].commit()
else:
# execute the analysis!
context.invoke(config_case, case_id=case_id)
context.invoke(link, case_id=case_id)
context.invoke(panel, case_id=case_id)
context.invoke(
run, case_id=case_id, priority=priority, email=email, start_with=start_with,
)
def upload(context, family_id, force_restart):
"""Upload results from analyses."""
click.echo(click.style("----------------- UPLOAD ----------------------"))
context.obj["status"] = Store(context.obj["database"])
if family_id:
family_obj = context.obj["status"].family(family_id)
if not family_obj:
message = f"family not found: {family_id}"
click.echo(click.style(message, fg="red"))
context.abort()
if not family_obj.analyses:
message = f"no analysis exists for family: {family_id}"
click.echo(click.style(message, fg="red"))
context.abort()
analysis_obj = family_obj.analyses[0]
if analysis_obj.uploaded_at is not None:
message = f"analysis already uploaded: {analysis_obj.uploaded_at.date()}"
click.echo(click.style(message, fg="red"))
context.abort()
if not force_restart and analysis_obj.upload_started_at is not None:
if dt.datetime.now(
) - analysis_obj.upload_started_at > dt.timedelta(hours=24):
raise AnalysisUploadError(
f"The upload started at {analysis_obj.upload_started_at} "
f"something went wrong, restart it with the --restart flag"
)
message = f"analysis upload already started: {analysis_obj.upload_started_at.date()}"
click.echo(click.style(message, fg="yellow"))
return
context.obj["housekeeper_api"] = hk.HousekeeperAPI(context.obj)
context.obj["madeline_api"] = madeline.api.MadelineAPI(context.obj)
context.obj["genotype_api"] = gt.GenotypeAPI(context.obj)
context.obj["lims_api"] = lims.LimsAPI(context.obj)
context.obj["tb_api"] = tb.TrailblazerAPI(context.obj)
context.obj["chanjo_api"] = coverage_app.ChanjoAPI(context.obj)
context.obj["deliver_api"] = DeliverAPI(
context.obj,
hk_api=context.obj["housekeeper_api"],
lims_api=context.obj["lims_api"],
case_tags=CASE_TAGS,
sample_tags=SAMPLE_TAGS,
)
context.obj["scout_api"] = scoutapi.ScoutAPI(context.obj)
context.obj["analysis_api"] = AnalysisAPI(
context.obj,
hk_api=context.obj["housekeeper_api"],
scout_api=context.obj["scout_api"],
tb_api=context.obj["tb_api"],
lims_api=context.obj["lims_api"],
deliver_api=context.obj["deliver_api"],
)
context.obj["report_api"] = ReportAPI(
store=context.obj["status"],
lims_api=context.obj["lims_api"],
chanjo_api=context.obj["chanjo_api"],
analysis_api=context.obj["analysis_api"],
scout_api=context.obj["scout_api"],
)
context.obj["scout_upload_api"] = UploadScoutAPI(
hk_api=context.obj["housekeeper_api"],
scout_api=context.obj["scout_api"],
madeline_api=context.obj["madeline_api"],
analysis_api=context.obj["analysis_api"],
lims_api=context.obj["lims_api"],
)
if context.invoked_subcommand is not None:
return
if not family_id:
_suggest_cases_to_upload(context)
context.abort()
family_obj = context.obj["status"].family(family_id)
analysis_obj = family_obj.analyses[0]
if analysis_obj.uploaded_at is not None:
message = f"analysis already uploaded: {analysis_obj.uploaded_at.date()}"
click.echo(click.style(message, fg="yellow"))
else:
analysis_obj.upload_started_at = dt.datetime.now()
context.obj["status"].commit()
context.invoke(coverage, re_upload=True, family_id=family_id)
context.invoke(validate, family_id=family_id)
context.invoke(genotypes, re_upload=False, family_id=family_id)
context.invoke(observations, case_id=family_id)
context.invoke(scout, case_id=family_id)
analysis_obj.uploaded_at = dt.datetime.now()
context.obj["status"].commit()
click.echo(click.style(f"{family_id}: analysis uploaded!", fg="green"))