def test_get_project_names(self): """Get the projects from a samplesheet """ # Assert that an empty file returns an empty list fh, ssheet = tempfile.mkstemp(dir=self.rootdir, suffix=".csv") os.close(fh) self.assertListEqual([],HiSeqRun.get_project_names(ssheet), "The list of projects for an empty file is not empty") # Generate artificial samplesheet data data = td.generate_samplesheet_data() projects = {} for d in data: projects[d[-1]] = 1 # Write the data to a samplesheet td._write_samplesheet(data,ssheet) # Assert that the list of projects returned is the same that we generated self.assertListEqual(sorted(projects.keys()),sorted(HiSeqRun.get_project_names(ssheet)), "The list of projects does not match the original list")
def status_query(archive_dir, analysis_dir, flowcell, project, brief): """Get a status report of the progress of flowcells based on a snapshot of the file system """ last_step = 14 status = [] # Process each flowcell in the archive directory for fcdir in IlluminaRun.get_flowcell(archive_dir,flowcell): fc_status = {} fc_status['flowcell'] = os.path.basename(fcdir) # Locate the samplesheet samplesheet = IlluminaRun.get_samplesheet(fcdir) if samplesheet is None: print("{}***ERROR***: Could not locate samplesheet in flowcell directory. Skipping..") continue fc_status['samplesheet'] = samplesheet # Get a list of the projects in the samplesheet projects = HiSeqRun.get_project_names(samplesheet) if len(projects) == 0: print("\t***WARNING***: No projects matched your filter [{}] for flowcell. Skipping..".format(project)) continue fc_status['projects'] = [] # Iterate over the projects in the flowcell for proj in projects: proj = proj.replace("__",".") proj_status = {} proj_status['project'] = proj pdir = bcbio.get_project_analysis_dir(analysis_dir, proj) if not pdir: continue proj_status['project_dir'] = pdir proj_status['samples'] = [] proj_status['no_finished_samples'] = 0 samples = HiSeqRun.get_project_sample_ids(samplesheet, proj) for smpl in samples: smpl = smpl.replace("__",".") sample_status = {} proj_status['samples'].append(sample_status) sample_status['sample_id'] = smpl sdir = bcbio.get_sample_analysis_dir(pdir, smpl) if not sdir: continue sample_status['sample_dir'] = sdir # Match the flowcell we're processing to the sample flowcell directories sample_fc = [d for d in IlluminaRun.get_flowcell(sdir) if d.split("_")[-1] == fcdir.split("_")[-1]] if len(sample_fc) == 0: continue sample_fc = sample_fc[0] sample_status['sample_fc_dir'] = sample_fc fastq_screen = bcbio.get_fastq_screen_folder(sample_fc) if fastq_screen: sample_status['fastq_screen'] = [fastq_screen,bcbio.fastq_screen_finished(fastq_screen)] now = datetime.datetime.now() pipeline_start_indicator = bcbio.get_pipeline_indicator(sample_fc,[1]) if len(pipeline_start_indicator) == 0: continue pipeline_start_indicator = pipeline_start_indicator[0] most_recent, _ = bcbio.get_most_recent_indicator([pipeline_start_indicator]) sample_status['pipeline_started'] = [pipeline_start_indicator,most_recent] most_recent, ifile = bcbio.get_most_recent_indicator(bcbio.get_pipeline_indicator(sample_fc)) sample_status['pipeline_progress'] = [ifile,most_recent] sample_log = bcbio.get_sample_pipeline_log(sample_fc,smpl) if not sample_log: continue st = os.stat(sample_log) sample_status['pipeline_log'] = [sample_log,datetime.datetime.fromtimestamp(st.st_mtime)] jobids = slurm.get_slurm_jobid(smpl) sample_status['slurm_job'] = [] for jobid in jobids: sample_status['slurm_job'].append([jobid,slurm.get_slurm_jobstatus(jobid)]) most_recent, ifile = bcbio.get_most_recent_indicator(bcbio.get_pipeline_indicator(sample_fc,[last_step])) if ifile is not None and sample_status.get('fastq_screen',[None,False])[1]: sample_status['finished'] = True proj_status['no_finished_samples'] += 1 if proj_status['no_finished_samples'] == len(samples): proj_status['finished'] = True fc_status['projects'].append(proj_status) status.append(fc_status) print_status(status,brief)