def test_organize_projects_from_flowcell(self, mock_dir_setup,
mock_locate):
mock_dir_setup.return_value = {'some_dir': 'P12345'}
demux_fcid_dirs = ['201103_A00187_0332_AHFCFLDSXX']
expected_projects = ['P12345']
got_projects = organize_projects_from_flowcell(demux_fcid_dirs)
self.assertEqual(expected_projects, got_projects)
restrict_to_samples=args.restrict_to_samples)
if not project.samples:
LOG.info('No samples found for project {} (path {})'.format(
project.project_id, qc_project_dir))
for sample in project:
qc_ngi.launchers.analyze(project, sample, quiet=args.quiet)
## Organize Flowcell
elif 'organize_fc_dirs' in args:
organize_fc_dirs_list = list(set(args.organize_fc_dirs))
LOG.info("Organizing flowcell {} {}".format(
inflector.plural("directory", len(organize_fc_dirs_list)),
", ".join(organize_fc_dirs_list)))
projects_to_analyze = \
organize_projects_from_flowcell(demux_fcid_dirs=organize_fc_dirs_list,
restrict_to_projects=args.restrict_to_projects,
restrict_to_samples=args.restrict_to_samples,
fallback_libprep=args.fallback_libprep,
quiet=args.quiet)
for project in projects_to_analyze:
try:
create_charon_entries_from_project(
project=project,
best_practice_analysis=args.best_practice_analysis,
sequencing_facility=args.sequencing_facility,
force_overwrite=args.force_update)
except Exception as e:
LOG.error(e.message)
print(e, file=sys.stderr)
LOG.info("Done with organization.")
def flowcell_summarize(flowcells, brief=False, verbose=False):
projects_to_analyze = \
organize_projects_from_flowcell(demux_fcid_dirs=flowcells,
quiet=True, create_files=False)
project_summarize(projects_to_analyze, brief=brief, verbose=verbose)
LOG.error(
"Error when resetting Charon records for project " "{}: {}".format(delete_proj_analysis, e)
)
## QC Flowcell
elif "qc_flowcell_dirs" in args:
qc_flowcell_dirs_list = list(set(args.qc_flowcell_dirs))
LOG.info(
"Organizing flowcell {} {}".format(
inflector.plural("directory", len(qc_flowcell_dirs_list)), ", ".join(qc_flowcell_dirs_list)
)
)
projects_to_analyze = organize_projects_from_flowcell(
demux_fcid_dirs=qc_flowcell_dirs_list,
restrict_to_projects=args.restrict_to_projects,
restrict_to_samples=args.restrict_to_samples,
fallback_libprep=args.fallback_libprep,
quiet=args.quiet,
)
for project in projects_to_analyze:
try:
create_charon_entries_from_project(
project=project,
best_practice_analysis=args.best_practice_analysis,
sequencing_facility=args.sequencing_facility,
force_overwrite=args.force_update,
delete_existing=args.delete_existing,
)
except Exception as e:
print(e, file=sys.stderr)
LOG.info("Done with organization.")
def flowcell_summarize(flowcells, brief=False, verbose=False):
projects_to_analyze = \
organize_projects_from_flowcell(demux_fcid_dirs=flowcells,
quiet=True, create_files=False)
project_summarize(projects_to_analyze, brief=brief, verbose=verbose)
