def microsalt(context: click.Context, order_id):
"""Microbial workflow"""
context.obj["db"] = Store(context.obj["database"])
hk_api = hk.HousekeeperAPI(context.obj)
lims_api = lims.LimsAPI(context.obj)
deliver = DeliverAPI(
context.obj,
hk_api=hk_api,
lims_api=lims_api,
case_tags=PROJECT_TAGS,
sample_tags=SAMPLE_TAGS,
)
context.obj["api"] = AnalysisAPI(db=context.obj["db"],
hk_api=hk_api,
lims_api=lims_api)
context.obj["lims_microsalt_api"] = LimsMicrosaltAPI(lims=lims_api)
if context.invoked_subcommand is None:
if order_id is None:
LOG.error("Please provide an order")
context.abort()
else:
# execute the analysis!
context.invoke(config_case, order_id=order_id)
context.invoke(link, order_id=order_id)
context.invoke(run, order_id=order_id)
def balsamic(context, case_id, priority, email, target_bed):
"""Cancer workflow """
context.obj["store_api"] = Store(context.obj["database"])
context.obj["hk_api"] = hk.HousekeeperAPI(context.obj)
context.obj["fastq_handler"] = FastqHandler
context.obj["gzipper"] = gzip
context.obj["lims_api"] = lims.LimsAPI(context.obj)
context.obj["fastq_api"] = FastqAPI
context.obj["analysis_api"] = AnalysisAPI(
hk_api=context.obj["hk_api"], fastq_api=context.obj["fastq_api"])
if context.invoked_subcommand is None:
if case_id is None:
LOG.error("provide a case")
context.abort()
# execute the analysis!
context.invoke(link, case_id=case_id)
context.invoke(config_case, case_id=case_id, target_bed=target_bed)
context.invoke(run,
run_analysis=True,
case_id=case_id,
priority=priority,
email=email)
def pools(context, status):
"""
Update pools with received_at or delivered_at dates from LIMS. Defaults to delivered if no
option is provided.
"""
lims_api = lims_app.LimsAPI(context.obj)
transfer_api = transfer_app.TransferLims(context.obj["db"], lims_api)
transfer_api.transfer_pools(transfer_app.PoolState[status.upper()])
def microbials(context, status):
"""
Update microbial samples with received_at, prepared_at, sequenced_at or delivered_at dates
from LIMS. Defaults to delivered if no option is provided.
"""
lims_api = lims_app.LimsAPI(context.obj)
transfer_api = transfer_app.TransferLims(context.obj["db"], lims_api)
transfer_api.transfer_microbial_samples(
transfer_app.MicrobialState[status.upper()])
def deliver(context):
"""Deliver stuff."""
context.obj["db"] = Store(context.obj["database"])
context.obj["deliver_api"] = DeliverAPI(
db=context.obj["db"],
hk_api=hk.HousekeeperAPI(context.obj),
lims_api=lims.LimsAPI(context.obj),
case_tags=CASE_TAGS,
sample_tags=SAMPLE_TAGS,
)
def transfer(admin, housekeeper, config_file):
"""Transfer stuff from external interfaces."""
config = ruamel.yaml.safe_load(config_file)
admin_api = AdminDatabase(admin)
# ApplicationImporter(config['database'], admin_api).process()
# CustomerImporter(config['database'], admin_api).process()
# UserImporter(config['database'], admin_api).process()
# PanelImporter(config['database'], scoutapi.ScoutAPI(config)).process()
lims_api = lims_app.LimsAPI(config)
SampleImporter(config["database"], lims_api).process()
FamilyImporter(config["database"], lims_api).process()
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 mip_rna(context: click.Context):
"""Rare disease RNA workflow"""
context.obj["db"] = Store(context.obj["database"])
hk_api = hk.HousekeeperAPI(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"],
lims_api=lims_api,
deliver_api=deliver,
)
context.obj["rna_api"] = MipAPI(context.obj["mip-rd-rna"]["script"],
context.obj["mip-rd-rna"]["pipeline"])
def lims(context, status):
"""Check if samples have been updated in LIMS."""
lims_api = lims_app.LimsAPI(context.obj)
transfer_api = transfer_app.TransferLims(context.obj['db'], lims_api)
transfer_api.transfer_samples(transfer_app.SampleState[status.upper()])
def inbox(context, dry, family, version, tag, inbox):
"""Link files from HK to cust inbox."""
db = Store(context.obj['database'])
deliver_api = DeliverAPI(db=db,
hk_api=hk.HousekeeperAPI(context.obj),
lims_api=lims.LimsAPI(context.obj))
family_obj = db.family(family)
if family_obj is None:
LOG.error(f"Family '{family}' not found.")
context.abort()
family_files = deliver_api.get_post_analysis_family_files(family=family,
version=version,
tag=tag)
if not family_files:
LOG.warning(f"No family files found.")
for file_obj in family_files:
out_dir = Path(
inbox.format(family=family_obj.name,
customer=family_obj.customer.internal_id))
out_dir.mkdir(parents=True, exist_ok=True)
# might be fun to name exit files according to tags instead of MIP's long name
#file_name = Path('_'.join([ tag.name for tag in file_obj.tags ]))
#file_ext = ''.join(Path(file_obj.path).suffixes)
out_file_name = Path(file_obj.path).name.replace(
family, family_obj.name)
out_path = Path(f"{out_dir/ out_file_name}")
in_path = Path(file_obj.full_path)
if not out_path.exists():
os.link(in_path, out_path)
LOG.info(f"linked file: {in_path} -> {out_path}")
else:
LOG.info(f"Target file exists: {out_path}")
link_obj = db.family_samples(family)
if not link_obj:
LOG.warning(f"No sample files found.")
for family_sample in link_obj:
sample_obj = family_sample.sample
sample_files = deliver_api.get_post_analysis_sample_files(
family=family,
sample=sample_obj.internal_id,
version=version,
tag=tag)
if not sample_files:
LOG.warning(
f"No sample files found for '{sample_obj.internal_id}'.")
for file_obj in sample_files:
out_dir = Path(
inbox.format(family=family_obj.name,
customer=family_obj.customer.internal_id))
out_dir = out_dir.joinpath(sample_obj.name)
out_dir.mkdir(parents=True, exist_ok=True)
out_file_name = Path(file_obj.path).name.replace(
sample_obj.internal_id, sample_obj.name)
out_path = Path(f"{out_dir / out_file_name}")
in_path = Path(file_obj.full_path)
if not out_path.exists():
os.link(in_path, out_path)
LOG.info(f"linked file: {in_path} -> {out_path}")
else:
LOG.info(f"Target file exists: {out_path}")
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"))