def test_get_project_samples(self):
"""Test that getting the project samples from a samplesheet behaves as expected
"""
# Generate artificial samplesheet data
data = td.generate_samplesheet_data()
fh, ssheet = tempfile.mkstemp(dir=self.rootdir, suffix=".csv")
os.close(fh)
td._write_samplesheet(data,ssheet)
# Assert that getting samples for a non-existing project returns an empty list
self.assertListEqual([],sq.get_project_samples(ssheet,td.generate_project()),
"Getting samples for a non-existing project returned unexpected output")
# Iterate over the projects and assert that the returned samples are correct
samples = {}
for row in data:
if row[9] not in samples:
samples[row[9]] = []
samples[row[9]].append(row[2])
for proj, sample in samples.items():
self.assertListEqual(sorted(sample),sorted(sq.get_project_samples(ssheet,proj)),
"The returned list of samples did not match the original")
def status_query(archive_dir, analysis_dir, flowcell, project, brief=False):
"""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 bcbio.get_flowcelldirs(archive_dir, flowcell):
fc_status = {}
fc_status['flowcell'] = os.path.basename(fcdir)
# Locate the samplesheet
samplesheet = bcbio.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 = bcbio.get_projects(samplesheet, project)
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 = bcbio.get_project_samples(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 bcbio.get_flowcelldirs(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)
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 bcbio.get_flowcelldirs(archive_dir,flowcell):
fc_status = {}
fc_status['flowcell'] = os.path.basename(fcdir)
# Locate the samplesheet
samplesheet = bcbio.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 = bcbio.get_projects(samplesheet,project)
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 = bcbio.get_project_samples(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 bcbio.get_flowcelldirs(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)