def fillin(context, sample_id):
"""Fill in defaults for a LIMS sample."""
lims_api = api.connect(context.obj)
lims_sample = lims_api.sample(sample_id)
click.echo("filling in defaults...")
set_defaults(lims_sample)
lims_sample.put()
click.echo("saved new defaults")
def get(context, condense, project, external, minimal, raw_identifier, field,
all_samples):
"""Get information from LIMS: either sample or family samples."""
if '--' in raw_identifier:
identifier, ext = raw_identifier.split('--', 1)
else:
identifier, ext = raw_identifier, None
lims = api.connect(context.obj)
if project:
lims_samples = lims.get_samples(projectlimsid=identifier)
elif identifier.startswith('cust'):
# look up samples in a case
lims_samples = lims.case(*identifier.split('-', 1))
elif external:
lims_samples = lims.get_samples(name=identifier)
else:
# look up a single sample
is_cgid = True if identifier[0].isdigit() else False
lims_samples = [lims.sample(identifier, is_cgid=is_cgid)]
if len(lims_samples) > 1 and not all_samples:
# filter out tumor and cancelled samples
lims_samples = relevant_samples(lims_samples)
for lims_sample in lims_samples:
sample_obj = ClinicalSample(lims_sample)
data = sample_obj.to_dict(minimal=minimal)
data['sample_id'] = "{}--{}".format(data['sample_id'],
ext) if ext else data['sample_id']
data['case_id'] = "{}--{}".format(data['case_id'],
ext) if ext else data['case_id']
if field:
if field not in data:
log.error("can't find UDF on sample: %s", field)
context.abort()
elif isinstance(data[field], list):
for item in data[field]:
click.echo(item)
else:
click.echo(data[field])
else:
if condense:
dump = jsonify(data)
else:
raw_dump = yaml.safe_dump(data,
default_flow_style=False,
allow_unicode=True)
dump = fix_dump(raw_dump)
click.echo(click.style('>>> Sample: ', fg='red'), nl=False)
click.echo(click.style(data['id'], bold=True, fg='red'))
if data.get('cancelled') == 'yes':
click.echo(click.style('CANCELLED', bold=True,
fg='yellow'))
click.echo(dump)
def sample(context, delivered, lims_id):
"""Fetch information about a sample."""
lims_api = api.connect(context.obj)
if delivered:
delivery_date = lims_api.is_delivered(lims_id)
if delivery_date:
click.echo(delivery_date)
else:
log.error("sample not yet delivered")
context.abort()
def update(context, lims_id, field_key, new_value):
"""Update a UDF for a sample."""
lims = api.connect(context.obj)
lims_sample = lims.sample(lims_id)
old_value = lims_sample.udf.get(field_key, 'N/A').encode('utf-8')
click.echo("about to update sample: {}".format(lims_sample.id))
message_tmlt = "are you sure you want to change '{}': '{}' -> '{}'"
if click.confirm(message_tmlt.format(field_key, old_value, new_value)):
lims_sample.udf[field_key] = new_value
lims_sample.put()
def samples(context, source, apptags, lims_id):
"""Fetch projects from the database."""
lims = api.connect(context.obj)
if source == 'process':
lims_process = Process(lims, id=lims_id)
lims_samples = process_samples(lims_process)
elif source == 'project':
lims_samples = ({'sample': sample} for sample in
lims.get_samples(projectlimsid=lims_id))
for lims_sample in lims_samples:
click.echo(lims_sample.id)
def export(context, customer_or_case, family_id):
"""Parse out interesting data about a case."""
lims = api.connect(context.obj)
if family_id:
customer = customer_or_case
else:
customer, family_id = customer_or_case.split('-', 1)
lims_samples = lims.case(customer, family_id)
case_data = export_case(lims, lims_samples)
raw_dump = yaml.safe_dump(case_data,
default_flow_style=False,
allow_unicode=True)
click.echo(raw_dump)
def check(context, update, version, force, source, lims_id):
"""Check LIMS sample or all samples in a process."""
lims = api.connect(context.obj)
if source == 'sample':
lims_samples = [{'sample': lims.sample(lims_id)}]
elif source == 'process':
lims_process = Process(lims, id=lims_id)
lims_samples = process_samples(lims_process)
elif source == 'project':
lims_samples = ({'sample': sample} for sample in
lims.get_samples(projectlimsid=lims_id))
for sample in lims_samples:
check_sample(lims, sample['sample'], lims_artifact=sample.get('artifact'),
update=update, version=version, force=force)
def pedigree(context, gene_panel, family_id, samples, customer_family):
"""DEPRECATED: Create pedigree from LIMS."""
lims_api = api.connect(context.obj)
if customer_family:
lims_samples = lims_api.case(*customer_family)
elif samples:
lims_samples = [lims_api.sample(sample_id) for sample_id in samples]
else:
click.echo("you need to provide customer+family or samples")
context.abort()
content = make_pedigree(lims_api,
lims_samples,
family_id=family_id,
gene_panel=gene_panel)
click.echo(content)
def config(context, gene_panel, family_id, samples, capture_kit, force,
raw_case_id):
"""Create pedigree YAML file from LIMS data."""
if '--' in raw_case_id:
case_id, ext = raw_case_id.split('--', 1)
else:
case_id, ext = raw_case_id, None
customer, family = case_id.split('-', 1)
lims_api = api.connect(context.obj)
gene_panels = [gene_panel] if gene_panel else None
if samples:
lims_samples = [lims_api.sample(sample_id) for sample_id in samples]
else:
lims_samples = lims_api.case(customer, family)
included_samples = relevant_samples(lims_samples)
data = make_config(lims_api,
included_samples,
family_id=family_id,
gene_panels=gene_panels,
capture_kit=capture_kit,
force=force)
if ext:
# handle cases with e.g. downsampled data
data['family'] = '--'.join([data['family'], ext])
for sample in data['samples']:
sample['sample_id'] = '--'.join([sample['sample_id'], ext])
# handle single sample cases with 'unknown' phenotype
if len(data['samples']) == 1:
if data['samples'][0]['phenotype'] == 'unknown':
log.info("setting 'unknown' phenotype to 'unaffected'")
data['samples'][0]['phenotype'] = 'unaffected'
dump = yaml.safe_dump(data, default_flow_style=False, allow_unicode=True)
click.echo(fix_dump(dump))