def test_extract_flowcell():
run_dir = 'tests/fixtures/demux/150410_D00134_0189_BHF3GKADXX'
flowcell_id = extract_flowcell(run_dir)
assert flowcell_id == 'HF3GKADXX'
# test with trailing slash
run_dir = 'tests/fixtures/demux/150410_D00134_0189_BHF3GKADXX/'
flowcell_id = extract_flowcell(run_dir)
assert flowcell_id == 'HF3GKADXX'
def add_flowcell(flowcell_dir, samples=None):
"""Create a new instance of a Spof to the database."""
logger.debug('extracting info from run dir')
flowcell_id = extract_flowcell(flowcell_dir)
demux_date = date_from_rundir(flowcell_dir)
run_folder = path(flowcell_dir).realpath().basename()
logger.debug('check of the flowcell already exists')
flowcell_obj = Flowcell.query.filter_by(flowcell_id=flowcell_id).first()
if flowcell_obj is None:
if samples is None:
sample_rundirs = get_sample_rundirs(flowcell_dir)
sample_ids = (sample_from_rundir(sample_dir)
for sample_dir in sample_rundirs)
samples = [Sample.query.filter_by(lims_id=sample_id).one()
for sample_id in sample_ids]
logger.debug('creating new Flowcell record')
flowcell_obj = Flowcell(flowcell_id=flowcell_id,
demux_folder=run_folder,
demuxed_at=demux_date,
samples=samples)
logger.debug('committing to database')
return flowcell_obj
def add_symlink(self, fastq_file, symlink, reason='analysis'):
parts = split_fastq(fastq_file)
# fetch relevant unaligned record
run_dir = get_run_dir(fastq_file)
flowcell_id = extract_flowcell(run_dir)
unaligned_obj = self._get_unaligned(parts['sample'], flowcell_id)
fastq_obj = (self.db.query(FastqFile)
.filter_by(lane=parts['lane'], read=parts['read'],
segment=parts['segment'],
unaligned=unaligned_obj)
.one())
logger.debug('saving symlink to database')
symlink_obj = Symlink(path=symlink, reason=reason, original=fastq_obj)
self.add_commit(symlink_obj)
