def post(self):
"""Add new spof results to the database."""
read_count = request.form['read_count']
flowcell_id = request.form['flowcell_id']
sample_id = request.form['sample_id']
fastq_files = request.form.getlist('fastq_files')
trimmed_at_str = request.form.get('trimmed_at')
completed_at_str = request.form.get('completed_at')
if trimmed_at_str:
trimmed_at = dateify(trimmed_at_str)
else:
trimmed_at = None
if completed_at_str:
completed_at = dateify(completed_at_str)
else:
completed_at = None
flowcell_obj = Flowcell.query.filter_by(flowcell_id=flowcell_id).one()
sample_obj = Sample.query.filter_by(lims_id=sample_id).one()
logger.debug('create Spof record')
filters = dict(flowcell=flowcell_obj, sample=sample_obj,
read_count=read_count, trimmed_at=trimmed_at,
completed_at=completed_at)
spof_obj, was_created = utils.get_or_create(Spof, **filters)
logger.debug('create related FASTQ file objects')
for fastq_file in fastq_files:
utils.add_fastq_file(fastq_file, sample_obj, spof_obj)
db.session.commit()
new_spof = Spof.query.filter_by(flowcell=flowcell_obj,
sample=sample_obj).one()
return new_spof.to_json()
def test_dateify():
regular_date_str = '2015-02-17T19:31:24'
regular_date = dateify(regular_date_str)
assert regular_date.year == 2015
assert regular_date.month == 2
assert regular_date.day == 17
assert regular_date.hour == 19
assert regular_date.minute == 31
assert regular_date.second == 24
def update_analysis(self, cust_id, case_id, **kwargs):
"""Update info for an existing analysis."""
analysis_obj = self._find_analysis(cust_id, case_id)
for field, value in iteritems(kwargs):
if field == 'finished_at':
analysis_obj.finished_at = dateify(value)
else:
setattr(analysis_obj, field, value)
self.db.save()
return analysis_obj.__json__()
def post(self):
"""Register a new upload to Scout."""
cust_id = request.form['cust_id']
case_id = request.form['case_id']
uploaded_at = request.form['uploaded_at']
analysis_obj = utils.latest_analysis(cust_id, case_id)
upload_date = dateify(uploaded_at)
upload_obj = Upload(uploaded_at=upload_date, analysis=analysis_obj)
utils.commit(upload_obj)
return upload_obj.to_json()
def add_analysis(self, cust_id, case_id, analysis_type, analyzed_at):
"""Add an Analysis to the database."""
logger.debug('fetch related case')
case_obj = self._get_case(cust_id, case_id)
logger.debug('create new Analysis record')
analyzed_date = dateify(analyzed_at)
analysis_obj = Analysis(case=case_obj, type=analysis_type,
started_at=analyzed_date)
logger.debug('commit to database')
self.add_commit(analysis_obj)
def put(self, cust_id, case_id):
"""Update info for an existing analysis."""
analysis_obj = utils.latest_analysis(cust_id, case_id)
for field, value in iteritems(request.form):
if field == 'finished_at':
analysis_obj.finished_at = dateify(value)
elif field == 'was_successful':
value = False if value.lower() == 'false' else True
analysis_obj.was_successful = value
else:
setattr(analysis_obj, field, value)
db.session.commit()
return analysis_obj.to_json()
def post(self):
"""Add an Analysis to the database."""
cust_id = request.form['cust_id']
case_id = request.form['case_id']
analysis_type = request.form['analysis_type']
analyzed_at = request.form['analyzed_at']
logger.debug('fetch related case')
case_obj = utils.get_case(cust_id, case_id)
logger.debug('create new Analysis record')
analyzed_date = dateify(analyzed_at)
analysis_obj = Analysis(case=case_obj, type=analysis_type,
started_at=analyzed_date)
logger.debug('commit to database')
utils.commit(analysis_obj)
new_analysis = Analysis.query.filter_by(case=case_obj,
started_at=analyzed_date).one()
return new_analysis.to_json()
def add_genotyping(self, sample_id, started_at, matches, mismatches,
unknowns, is_failed=False, deviation=None,
dev_category=None):
"""Add genotyping record to database."""
started_date = dateify(started_at)
sample_obj = self.db.query(Sample).filter_by(lims_id=sample_id).one()
analysis_obj = (self.db.query(Analysis)
.filter_by(case=sample_obj.case,
started_at=started_date)).one()
genotyping_obj = Genotyping(sample=sample_obj, matches=matches,
mismatches=mismatches, unknowns=unknowns,
is_failed=is_failed,
deviation_category=dev_category,
deviation_no=deviation,
analysis=analysis_obj)
self.db.add(genotyping_obj)
self.db.save()
return genotyping_obj.__json__()
def post_symlink_spof(demux_root, flowcell_id, sample_id, reason='analysis'):
"""Assemble/symlink files for a sample flowcell directory.
Args:
demux_root (str): root path to demux folder
sample_id (str): globally unique sample id
flowcell_id (str): flowcell id
"""
logger.debug('gather information from LIMS')
sample_res = glue.get('lims', 'samples', sample_id)
analysis_type = sample_res.json['analysis_type']
case_id = sample_res.json['family_id']
cust_id = sample_res.json['customer']
logger.debug('gather information from status db')
spof_res = glue.get('moneypenny', 'spofs', flowcell_id, sample_id)
demux_folder = spof_res.json['flowcell']['demux_folder']
demuxed_at = dateify(spof_res.json['flowcell']['demuxed_at']).date()
spof_dir = build_sampledir(demux_root, demux_folder, sample_id)
fastq_paths = [spof_dir.joinpath(fq_file['file_name'])
for fq_file in spof_res.json['fastq_files']]
logger.debug("symlink FASTQ files for %s/%s", sample_id, flowcell_id)
payload = {'cust_id': cust_id, 'case_id': case_id,
'analysis_type': analysis_type, 'fastq_paths': fastq_paths,
'demuxed_at': demuxed_at.strftime('%y%m%d')}
symlink_res = glue.post('assemble', 'spofs', 'prepare', flowcell_id,
sample_id, data=payload)
for fastq_path, symlink_path in symlink_res.json['symlinks']:
fastq_file = path(fastq_path).basename()
data = {'fastq_file': fastq_file, 'symlink': symlink_path,
'flowcell_id': flowcell_id, 'reason': reason}
glue.post('moneypenny', 'symlinks', data=data)
return symlink_res.json
def post(self):
"""Add genotyping record to database."""
started_at = request.form['started_at']
sample_id = request.form['sample_id']
matches = request.form['matches']
mismatches = request.form['mismatches']
unknowns = request.form['unknowns']
is_failed = True if request.form.get('is_failed') else False
dev_category = request.form.get('dev_category')
deviation = request.form.get('deviation')
started_date = dateify(started_at)
sample_obj = Sample.query.filter_by(lims_id=sample_id).one()
analysis_obj = Analysis.query.filter_by(case=sample_obj.case,
started_at=started_date).one()
genotyping_obj = Genotyping(sample=sample_obj, matches=matches,
mismatches=mismatches, unknowns=unknowns,
is_failed=is_failed,
deviation_category=dev_category,
deviation_no=deviation,
analysis=analysis_obj)
utils.commit(genotyping_obj)
new_genotyping = Genotyping.query.filter_by(sample=sample_obj).one()
return new_genotyping.to_json()
def add_upload(self, cust_id, case_id, uploaded_at=None):
"""Register a new upload to Scout."""
analysis_obj = self._find_analysis(cust_id, case_id)
upload_date = dateify(uploaded_at)
upload_obj = Upload(uploaded_at=upload_date, analysis=analysis_obj)
self.add_commit(upload_obj)