def test_render_delivery_report(report_api):
# GIVEN proper qc data from an analysis exist
report_data = report_api._get_delivery_data(case_id="yellowhog")
# WHEN rendering a report from that data
rendered_report = ReportAPI._render_delivery_report(report_data)
# THEN a html report with certain data should have been rendered
assert len(rendered_report) > 0
def test_create_delivery_report_file(report_api: ReportAPI):
# GIVEN initialized ReportAPI
# WHEN rendering a report from that data
created_report_file = report_api.create_delivery_report_file(
case_id="yellowhog", file_path=Path("."))
# THEN a html report with certain data should have been created on disk
assert os.path.isfile(created_report_file.name)
os.unlink(created_report_file.name)
def test_render_delivery_report(report_store, report_api):
# GIVEN proper qc data from an analysis exist
case_id = "yellowhog"
case = report_store.family(case_id)
report_data = report_api._get_delivery_data(
case_id=case_id, analysis_date=case.analyses[0].started_at)
# WHEN rendering a report from that data
rendered_report = ReportAPI._render_delivery_report(report_data)
# THEN a html report with certain data should have been rendered
assert len(rendered_report) > 0
def test_render_non_accredited_delivery_report(report_api):
# GIVEN proper qc data from an analysis exist with non accredited application
report_api.store._application_accreditation = False
case_id = "yellowhog"
analysis_date = report_api.store.family(case_id).analyses[0].started_at
delivery_data = report_api._get_delivery_data(case_id=case_id,
analysis_date=analysis_date)
report_data = report_api._make_data_presentable(delivery_data)
assert report_data["accredited"] is False
# WHEN rendering a report from that data
rendered_report = ReportAPI._render_delivery_report(report_data)
# THEN a html report without swedac logo should have been rendered
assert "SWEDAC logo" not in rendered_report
def test_create_delivery_report_file(report_store, report_api: ReportAPI,
tmp_path):
# GIVEN initialized ReportAPI
case_id = "yellowhog"
anlysis_started_at = report_store.family(case_id).analyses[0].started_at
# WHEN rendering a report from that data
created_report_file = report_api.create_delivery_report_file(
case_id="yellowhog",
analysis_date=anlysis_started_at,
file_path=tmp_path)
# THEN a html report with certain data should have been created on disk
assert os.path.isfile(created_report_file.name)
os.unlink(created_report_file.name)
def report_api(report_store, lims_samples):
db = MockDB(report_store)
lims = MockLimsAPI(samples=lims_samples)
chanjo = MockChanjo()
analysis = MockMipAnalysis()
scout = MockScout()
logger = MockLogger()
path_tool = MockPath()
return ReportAPI(
lims_api=lims,
store=db,
chanjo_api=chanjo,
analysis_api=analysis,
scout_api=scout,
logger=logger,
path_tool=path_tool,
)
def report_api(report_store, lims_samples):
db = MockDB(report_store)
lims = MockLims(lims_samples)
chanjo = MockChanjo()
analysis = MockAnalysis()
scout = MockScout()
logger = MockLogger()
yaml_loader = MockYamlLoader()
path_tool = MockPath()
_report_api = ReportAPI(
lims_api=lims,
store=db,
chanjo_api=chanjo,
analysis_api=analysis,
scout_api=scout,
logger=logger,
yaml_loader=yaml_loader,
path_tool=path_tool,
)
return _report_api
def upload_context(cg_context: CGConfig) -> CGConfig:
analysis_api = MipDNAAnalysisAPI(config=cg_context)
cg_context.meta_apis["analysis_api"] = analysis_api
cg_context.meta_apis["report_api"] = ReportAPI(
store=cg_context.status_db,
lims_api=cg_context.lims_api,
chanjo_api=cg_context.chanjo_api,
analysis_api=analysis_api,
scout_api=cg_context.scout_api,
)
cg_context.meta_apis["scout_upload_api"] = UploadScoutAPI(
hk_api=cg_context.housekeeper_api,
scout_api=cg_context.scout_api,
madeline_api=cg_context.madeline_api,
analysis_api=analysis_api,
lims_api=cg_context.lims_api,
status_db=cg_context.status_db,
)
return cg_context
def upload(context: click.Context, family_id: Optional[str],
force_restart: bool):
"""Upload results from analyses."""
config_object: CGConfig = context.obj
if not config_object.meta_apis.get("analysis_api"):
config_object.meta_apis["analysis_api"] = MipDNAAnalysisAPI(
context.obj)
analysis_api: AnalysisAPI = config_object.meta_apis["analysis_api"]
status_db: Store = config_object.status_db
click.echo(click.style("----------------- UPLOAD ----------------------"))
if family_id:
try:
analysis_api.verify_case_id_in_statusdb(case_id=family_id)
except CgError:
raise click.Abort
case_obj: models.Family = status_db.family(family_id)
if not case_obj.analyses:
message = f"no analysis exists for family: {family_id}"
click.echo(click.style(message, fg="red"))
raise click.Abort
analysis_obj: models.Analysis = case_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"))
raise click.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.meta_apis["report_api"] = ReportAPI(
store=status_db,
lims_api=config_object.lims_api,
chanjo_api=config_object.chanjo_api,
analysis_api=analysis_api,
scout_api=config_object.scout_api,
)
context.obj.meta_apis["scout_upload_api"] = UploadScoutAPI(
hk_api=config_object.housekeeper_api,
scout_api=config_object.scout_api,
madeline_api=config_object.madeline_api,
analysis_api=analysis_api,
lims_api=config_object.lims_api,
status_db=status_db,
)
if context.invoked_subcommand is not None:
return
if not family_id:
suggest_cases_to_upload(status_db=status_db)
raise click.Abort
case_obj: models.Family = status_db.family(family_id)
analysis_obj: models.Analysis = case_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()
status_db.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()
status_db.commit()
click.echo(click.style(f"{family_id}: analysis uploaded!", fg="green"))
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"))