def test_build_sampledir():
demux_root = 'tests/fixtures/demux'
run_folder = '150410_D00134_0189_BHF3GKADXX'
true_sample_id = 'ADM992A9'
false_sample_id = 'ADM992A9fake'
# test with existing sample run dir
sample_rundir = build_sampledir(demux_root, run_folder, true_sample_id)
the_rundir = ("tests/fixtures/demux/150410_D00134_0189_BHF3GKADXX/"
"Unaligned2/Project_600597/Sample_ADM992A9_XTA02/")
assert sample_rundir == the_rundir
# test with non-existing sample run dir
with pytest.raises(AttributeError):
build_sampledir(demux_root, run_folder, false_sample_id)
def get_fastq_files(self, flowcell_id, sample_id):
"""Retrive FASTQ files for a sample run directory."""
demux_root = self.config['general']['demux_root']
rundir_path = self.get_rundir(flowcell_id)
run_folder = path(rundir_path).basename()
logger.debug('create related FASTQ-file records')
sample_rundir = build_sampledir(demux_root, run_folder, sample_id)
fastq_files = sample_fastqfiles(sample_rundir, basename=True)
return fastq_files
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
