def clean(context):
"""Clean up processes"""
context.obj["db"] = Store(context.obj["database"])
context.obj["tb"] = tb.TrailblazerAPI(context.obj)
context.obj["hk"] = hk.HousekeeperAPI(context.obj)
context.obj["scout"] = scoutapi.ScoutAPI(context.obj)
context.obj["beacon"] = beacon_app.BeaconApi(context.obj)
context.obj["crunchy"] = crunchy.CrunchyAPI(context.obj)
def scout(context, re_upload, print_console, family_id):
"""Upload variants from analysis to Scout."""
scout_api = scoutapi.ScoutAPI(context.obj)
family_obj = context.obj['status'].family(family_id)
api = UploadScoutAPI(
status_api=context.obj['status'],
hk_api=context.obj['housekeeper_api'],
scout_api=scout_api,
madeline_exe=context.obj['madeline_exe'],
)
results = api.data(family_obj.analyses[0])
if print_console:
print(results)
else:
scout_api.upload(results, force=re_upload)
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 analysis(context, priority, email, family_id):
"""Prepare and start a MIP analysis for a FAMILY_ID."""
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)
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,
)
if context.invoked_subcommand is None:
if family_id is None:
LOG.error('provide a family')
context.abort()
# check everything is okey
family_obj = context.obj['db'].family(family_id)
if family_obj is None:
LOG.error(f"{family_id} not found")
context.abort()
is_ok = context.obj['api'].check(family_obj)
if not is_ok:
LOG.warning(f"{family_obj.internal_id}: not ready to start")
# commit the updates to request flowcells
context.obj['db'].commit()
else:
# execute the analysis!
context.invoke(config, family_id=family_id)
context.invoke(link, family_id=family_id)
context.invoke(panel, family_id=family_id)
context.invoke(start,
family_id=family_id,
priority=priority,
email=email)
def _add_delivery_report_to_scout(context, path, case_id):
scout_api = scoutapi.ScoutAPI(context.obj)
scout_api.upload_delivery_report(path, case_id, update=True)
def compress(context):
"""Compress files"""
context.obj["db"] = Store(context.obj["database"])
context.obj["hk"] = hk.HousekeeperAPI(context.obj)
context.obj["scout"] = scoutapi.ScoutAPI(context.obj)
context.obj["crunchy"] = crunchy.CrunchyAPI(context.obj)
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"))