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)