def reset_charon_records_by_name(project_id, restrict_to_samples=None,
restrict_to_libpreps=None, restrict_to_seqruns=None):
if not restrict_to_samples: restrict_to_samples = []
if not restrict_to_libpreps: restrict_to_libpreps = []
if not restrict_to_seqruns: restrict_to_seqruns = []
charon_session = CharonSession()
LOG.info("Resetting Charon record for project {}".format(project_id))
charon_session.project_reset(projectid=project_id)
LOG.info("Charon record for project {} reset".format(project_id))
for sample in charon_session.project_get_samples(projectid=project_id).get('samples', []):
sample_id = sample['sampleid']
if restrict_to_samples and sample_id not in restrict_to_samples:
LOG.info("Skipping project/sample {}/{}: not in list of samples to use "
"({})".format(project_id, sample_id, ", ".join(restrict_to_samples)))
continue
LOG.info("Resetting Charon record for project/sample {}/{}".format(project_id,
sample_id))
charon_session.sample_reset(projectid=project_id, sampleid=sample_id)
LOG.info("Charon record for project/sample {}/{} reset".format(project_id,
sample_id))
for libprep in charon_session.sample_get_libpreps(projectid=project_id,
sampleid=sample_id).get('libpreps', []):
libprep_id = libprep['libprepid']
if restrict_to_libpreps and libprep_id not in restrict_to_libpreps:
LOG.info("Skipping project/sample/libprep {}/{}/{}: not in list "
"of libpreps to use ({})".format(project_id, sample_id,
libprep_id, ", ".join(restrict_to_libpreps)))
continue
LOG.info("Resetting Charon record for project/sample"
"libprep {}/{}/{}".format(project_id, sample_id, libprep_id))
charon_session.libprep_reset(projectid=project_id, sampleid=sample_id,
libprepid=libprep_id)
LOG.info("Charon record for project/sample/libprep {}/{}/{} "
"reset".format(project_id, sample_id, libprep_id))
for seqrun in charon_session.libprep_get_seqruns(projectid=project_id,
sampleid=sample_id,
libprepid=libprep_id).get('seqruns', []):
seqrun_id = seqrun['seqrunid']
if restrict_to_seqruns and seqrun_id not in restrict_to_seqruns:
LOG.info("Skipping project/sample/libprep/seqrun {}/{}/{}/{}: "
"not in list of seqruns to use ({})".format(project_id,
sample_id,
libprep_id,
seqrun_id,
", ".join(restrict_to_seqruns)))
continue
LOG.info("Resetting Charon record for project/sample/libprep/"
"seqrun {}/{}/{}/{}".format(project_id, sample_id,
libprep_id, seqrun_id))
charon_session.seqrun_reset(projectid=project_id, sampleid=sample_id,
libprepid=libprep_id, seqrunid=seqrun_id)
LOG.info("Charon record for project/sample/libprep/seqrun "
"{}/{}/{}/{} reset".format(project_id, sample_id,
libprep_id, seqrun_id))
def reset_charon_records_by_object(project_obj):
charon_session = CharonSession()
LOG.info("Resetting Charon record for project {}".format(project_obj))
charon_session.project_reset(projectid=project_obj.project_id)
LOG.info("Charon record for project {} reset".format(project_obj))
for sample_obj in project_obj:
LOG.info("Resetting Charon record for project/sample {}/{}".format(project_obj,
sample_obj))
try:
charon_session.sample_reset(projectid=project_obj.project_id,
sampleid=sample_obj.name)
LOG.info("Charon record for project/sample {}/{} reset".format(project_obj,
sample_obj))
except CharonError as e:
LOG.error("Unable to reset Charon record for project/sample {}/{}: "
"{}".format(project_obj, sample_obj, e))
for libprep_obj in sample_obj:
LOG.info("Resetting Charon record for project/sample"
"libprep {}/{}/{}".format(project_obj, sample_obj, libprep_obj))
try:
charon_session.libprep_reset(projectid=project_obj.project_id,
sampleid=sample_obj.name,
libprepid=libprep_obj.name)
LOG.info("Charon record for project/sample/libprep {}/{}/{} "
"reset".format(project_obj, sample_obj, libprep_obj))
except CharonError as e:
LOG.error("Unable to reset Charon record for project/sample/libprep "
"{}/{}/{}: {}".format(project_obj, sample_obj,
libprep_obj, e))
for seqrun_obj in libprep_obj:
LOG.info("Resetting Charon record for project/sample/libprep/"
"seqrun {}/{}/{}/{}".format(project_obj, sample_obj,
libprep_obj, seqrun_obj))
try:
charon_session.seqrun_reset(projectid=project_obj.project_id,
sampleid=sample_obj.name,
libprepid=libprep_obj.name,
seqrunid=seqrun_obj.name)
LOG.info("Charon record for project/sample/libprep/seqrun "
"{}/{}/{}/{} reset".format(project_obj, sample_obj,
libprep_obj, seqrun_obj))
except CharonError as e:
LOG.error("Unable to reset Charon record for project/sample/"
"libprep/seqrun {}/{}/{}/{}: {}".format(project_obj,
sample_obj,
libprep_obj,
seqrun_obj,
e))
