def get_started_outdirs_from_db(testing=True, win=None):
"""FIXME:add-doc"""
connection = mongodb_conn(testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
if win:
epoch_present, epoch_back = generate_window(win)
results = db.find({
"analysis.Status": "STARTED",
"timestamp": {
"$gt": epoch_back,
"$lt": epoch_present
}
})
else:
results = db.find({"analysis.Status": "STARTED"})
# results is a pymongo.cursor.Cursor which works like an iterator i.e. dont use len()
logger.info("Found %d runs", results.count())
for record in results:
logger.debug("record: %s", record)
#run_number = record['run']
# we might have several analysis runs:
for analysis in record['analysis']:
yield analysis["out_dir"]
def instantiate_query(args):
"""
Instantiates MongoDB query dictionary object
"""
instance = {}
if args.status:
instance["analysis.Status"] = args.status
if args.mux:
instance["analysis.per_mux_status.mux_id"] = args.mux
if args.run:
instance["run"] = {"$regex": "^" + args.run}
if args.win:
epoch_present, epoch_initial = generate_window(args.win)
else:
epoch_present, epoch_initial = generate_window(7)
instance["timestamp"] = {"$gt": epoch_initial, "$lt": epoch_present}
return instance
def instantiate_query(args):
"""
Instantiates MongoDB query dictionary object
"""
instance = {}
if args.status:
instance["analysis.Status"] = args.status
if args.mux:
instance["analysis.per_mux_status.mux_id"] = args.mux
if args.run:
instance["run"] = {"$regex": "^" + args.run}
if args.win:
epoch_present, epoch_initial = generate_window(args.win)
else:
epoch_present, epoch_initial = generate_window(7)
instance["timestamp"] = {"$gt": epoch_initial, "$lt": epoch_present}
return instance
def runs_from_db(connection, testing, win=14):
"""Get the runs from pipeline_run collections"""
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(win)
results = db.find({"run" : {"$regex" : "^NG00"},
"timestamp": {"$gt": epoch_back, "$lt": epoch_present}})
logger.info("Found %d runs", results.count())
for record in results:
run_number = record['run']
logger.debug("record: %s", record)
if not record.get('analysis'):
continue
# Check if Novogene run_mode
_, run_id, _ = get_machine_run_flowcell_id(run_number)
if testing:
rest_url = rest_services['run_details']['testing'].replace("run_num", run_id)
else:
rest_url = rest_services['run_details']['production'].replace("run_num", run_id)
response = requests.get(rest_url)
if response.status_code != requests.codes.ok:
response.raise_for_status()
rest_data = response.json()
sg10k_lib_list = get_sg10_lib_list(rest_data)
run_records = {}
for (analysis_count, analysis) in enumerate(record['analysis']):
analysis_id = analysis['analysis_id']
per_mux_status = analysis.get("per_mux_status", None)
if per_mux_status is None:
continue
for (mux_count, mux_status) in enumerate(per_mux_status):
# sanity checks against corrupted DB entries
if mux_status is None or mux_status.get('mux_id') is None:
logger.warning("mux_status is None or incomplete for run %s analysis %s."
" Requires fix in DB. Skipping entry for now.", \
run_number, analysis_id)
continue
if mux_status.get('Status', None) != "SUCCESS":
continue
mux_id = mux_status['mux_id']
out_dir = analysis['out_dir']
if not os.path.exists(out_dir):
logger.warning("Direcotry does not exists %s", out_dir)
continue
downstream_id = "analysis.{}.per_mux_status.{}.DownstreamSubmission".format(
analysis_count, mux_count)
if mux_status.get('Status') == "SUCCESS" and \
mux_status.get('DownstreamSubmission') == "TODO":
mux_info = (run_number, downstream_id, analysis_id, out_dir)
if mux_id in run_records:
logger.info("MUX %s from %s has been analyzed more than 1 time \
succeessfully, please check", mux_id, run_number)
del run_records[mux_id]
elif mux_id in sg10k_lib_list:
run_records[mux_id] = mux_info
if run_records:
yield run_records
def check_mongo():
"""
Instantiates MongoDB database object
For Test Server, testing == True
For Production Server, testing == False
"""
warnings = ""
epoch_present, epoch_window = generate_window(MAX_WINDOW)
epoch_present, epoch_started = generate_window(MAX_RUN)
del epoch_present
query = {}
query["timestamp"] = {"$gte": epoch_window, "$lte": epoch_started}
query["analysis.Status"] = "STARTED"
mongo = mongodb_conn(False).gisds.runcomplete.find(query)
count_warnings = 0
for record in mongo:
# PrettyPrinter(indent=2).pprint(record)
if record["analysis"][-1]["Status"] != "SUCCESS":
warnings += ("[started >= " + str(MAX_RUN) + " days]:\t" +
str(record["run"]) + "\n")
count_warnings += 1
if count_warnings > 0:
warnings += ("[started >= " + str(MAX_RUN) + " days]:\t" +
str(count_warnings) + "\n\n")
query = {}
query["timestamp"] = {"$gte": epoch_window, "$lte": epoch_started}
query["analysis"] = {"$exists": False}
mongo = mongodb_conn(False).gisds.runcomplete.find(query)
count_warnings = 0
for record in mongo:
# PrettyPrinter(indent=2).pprint(record)
warnings += ("[no analysis >= " + str(MAX_RUN) + " days]:\t" +
str(record["run"]) + "\n")
count_warnings += 1
if count_warnings > 0:
warnings += ("[no analysis >= " + str(MAX_RUN) + " days]:\t" +
str(count_warnings) + "\n\n")
return warnings
def check_mongo():
"""
Instantiates MongoDB database object
For Test Server, testing == True
For Production Server, testing == False
"""
warnings = ""
epoch_present, epoch_window = generate_window(MAX_WINDOW)
epoch_present, epoch_started = generate_window(MAX_RUN)
del epoch_present
query = {}
query["timestamp"] = {"$gte": epoch_window, "$lte": epoch_started}
query["analysis.Status"] = "STARTED"
mongo = mongodb_conn(False).gisds.runcomplete.find(query)
count_warnings = 0
for record in mongo:
# PrettyPrinter(indent=2).pprint(record)
if record["analysis"][-1]["Status"] != "SUCCESS":
warnings += ("[started >= " + str(MAX_RUN) + " days]:\t" + str(record["run"]) + "\n")
count_warnings += 1
if count_warnings > 0:
warnings += ("[started >= " + str(MAX_RUN) + " days]:\t" + str(count_warnings) + "\n\n")
query = {}
query["timestamp"] = {"$gte": epoch_window, "$lte": epoch_started}
query["analysis"] = {"$exists": False}
mongo = mongodb_conn(False).gisds.runcomplete.find(query)
count_warnings = 0
for record in mongo:
# PrettyPrinter(indent=2).pprint(record)
warnings += ("[no analysis >= " + str(MAX_RUN) + " days]:\t" + str(record["run"]) + "\n")
count_warnings += 1
if count_warnings > 0:
warnings += ("[no analysis >= " + str(MAX_RUN) + " days]:\t" + str(count_warnings) + "\n\n")
return warnings
def get_sample_info(child, rows, mux_analysis_list, mux_id, fastq_data_dir, \
run_num_flowcell, sample_info):
"""Collects sample info from ELM JOSN
"""
sample_cfg = {}
site = get_site()
ctime, _ = generate_window(1)
_, _, flowcellid = get_machine_run_flowcell_id(run_num_flowcell)
mux_analysis_list.add(mux_id)
sample_id = child['libraryId']
sample_cfg['requestor'] = rows['requestor']
sample_cfg['ctime'] = ctime
sample_cfg['site'] = site
try:
sample_cfg['pipeline_name'] = legacy_mapper['pipeline_mapper'][
child['Analysis']]
except KeyError as e:
sample_cfg['pipeline_name'] = child['Analysis']
logger.warning(str(e) + " Pipeline not mappped to newer version")
return sample_info
pipeline_version = get_pipeline_version(child['pipeline_version'] \
if 'pipeline_version' in rows else None)
sample_cfg['pipeline_version'] = pipeline_version
#sample_cfg['pipeline_params'] = 'params'
ref_info = get_reference_info(child['Analysis'], \
sample_cfg['pipeline_version'], child['genome'])
if not ref_info:
logger.info("ref_info not available")
return sample_info
cmdline_info = get_cmdline_info(child)
sample_cfg['references_cfg'] = ref_info
if cmdline_info:
sample_cfg['cmdline'] = cmdline_info
readunits_dict = {}
status, fq1, fq2 = check_fastq(fastq_data_dir, child['libraryId'],\
rows['laneId'])
if status:
ru = ReadUnit(run_num_flowcell, flowcellid, child['libraryId'],\
rows['laneId'], None, fq1, fq2)
k = key_for_readunit(ru)
readunits_dict[k] = dict(ru._asdict())
sample_cfg['readunits'] = readunits_dict
if sample_info.get(sample_id, {}).get('readunits', {}):
sample_info[sample_id]['readunits'].update(readunits_dict)
else:
sample_info[sample_id] = sample_cfg
return sample_info
def runs_from_db(testing=True, win=34):
"""Get the runs from pipeline_run collections"""
connection = mongodb_conn(testing)
if connection is None:
sys.exit(1)
db = connection.gisds.pipeline_runs
epoch_present, epoch_back = generate_window(win)
results = db.find({"runs": {"$exists": True},
"ctime": {"$gt": 1470127013000, "$lt": 1470127093000}})
# results is a pymongo.cursor.Cursor which works like an iterator i.e. dont use len()
logger.info("Found %d runs for last %s days", results.count(), win)
for record in results:
logger.debug("record: %s", record)
for runs in record['runs']:
if runs["status"] == "STARTED":
test = (record['_id'], record['out_dir'], runs['start_time'])
yield test
def get_outdirs_from_db(testing=True, win=14):
"""FIXME:add-doc"""
connection = mongodb_conn(testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(win)
results = db.find({"analysis": {"$exists": True},
"timestamp": {"$gt": epoch_back, "$lt": epoch_present}})
# results is a pymongo.cursor.Cursor which works like an iterator i.e. dont use len()
logger.info("Found %d runs for last %s days", results.count(), win)
for record in results:
logger.debug("record: %s", record)
#run_number = record['run']
# we might have several analysis runs:
for analysis in record['analysis']:
yield analysis["out_dir"]
def runs_from_db(db, mail_to, ccaddr, win=34):
"""Get the runs from pipeline_run collections"""
epoch_present, epoch_back = generate_window(win)
results = db.find({"analysis" : {"$exists": False},
"timestamp": {"$gt": epoch_back, "$lt": epoch_present}})
logger.info("Found %d runs for last %s days", results.count(), win)
mail = False
subject = "Runs with missing ELM information"
body = "Dear NGSP, " + "\n"
body += subject + " for the following runs. Please include in the ELM." + "\n"
for record in results:
logger.debug("record: %s", record)
_, runid, _ = get_machine_run_flowcell_id(record.get('run'))
rest_data = get_rest_data(runid)
if not rest_data.get('runId'):
body += record.get('run')+ "\n"
mail = True
if mail:
send_mail(subject, body, toaddr=mail_to, ccaddr=ccaddr)
def runs_from_db(db, days=75, win=34):
"""Get the runs from pipeline_run collections"""
epoch_present, epoch_back = generate_window(win)
results = db.find({
"run": {
"$regex": "^NG00"
},
"raw-delete": {
"$exists": False
},
"timestamp": {
"$gt": epoch_back,
"$lt": epoch_present
}
})
LOGGER.info("Found %d runs for last %s days", results.count(), win)
for record in results:
LOGGER.debug("record: %s", record)
if not record.get('run'):
LOGGER.critical("run is missing for DB-id %s", record['_id'])
continue
runid_and_flowcellid = (record['run'])
results = db.find({"run": runid_and_flowcellid})
if not 'analysis' in record:
continue
last_analysis = record['analysis'][-1]
status = last_analysis.get("Status")
end_time = last_analysis.get("end_time")
if not status or not end_time:
continue
analysis_epoch_time = isoformat_to_epoch_time(end_time + "+08:00")
epoch_time_now = isoformat_to_epoch_time(generate_timestamp() +
"+08:00")
rd = relative_epoch_time(epoch_time_now, analysis_epoch_time)
relative_days = rd.months * 30 + rd.days
if status == 'SUCCESS' and relative_days > days:
yield runid_and_flowcellid
def main():
"""main function"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-1', "--break-after-first", action='store_true',
help="Only process first run returned")
parser.add_argument('-n', "--dry-run", action='store_true',
help="Don't run anything")
parser.add_argument('-t', "--testing", action='store_true',
help="Use MongoDB test-server")
default = 14
parser.add_argument('-w', '--win', type=int, default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
#Check if pipeline scripts are available
assert os.path.exists(BWA)
assert os.path.exists(RNA)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
num_triggers = 0
results = db.find({"analysis.Status": "SUCCESS",
"timestamp": {"$gt": epoch_back, "$lt": epoch_present}})
logger.info("Found %s runs", results.count())
for record in results:
run_number = record['run']
analysis = record['analysis']
for analysis in record['analysis']:
out_dir = analysis.get("out_dir")
#Check if bcl2Fastq is completed successfully
if 'Status' in analysis and analysis.get("Status") == "SUCCESS":
if not os.path.exists(out_dir):
logger.critical("Following directory listed in DB doesn't exist: %s", out_dir)
continue
#Check if downstream analysis has been started
if not os.path.exists(os.path.join(out_dir, "config_casava-1.8.2.txt".format())):
logger.info("Start the downstream analysis at %s", out_dir)
os.makedirs(os.path.join(out_dir, LOG_DIR_REL), exist_ok=True)
#generate config file
config_cmd = [CONFIG, '-r', run_number]
try:
f = open(os.path.join(out_dir, "config_casava-1.8.2.txt".format()), "w")
_ = subprocess.call(config_cmd, stderr=subprocess.STDOUT, stdout=f)
except subprocess.CalledProcessError as e:
logger.fatal("The following command failed with return code %s: %s",
e.returncode, ' '.join(config_cmd))
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Exiting")
sys.exit(1)
#Generate and Submit BWA and RNAseq mapping pipeline
if os.path.exists(os.path.join(out_dir, "samplesheet.csv".format())):
dirs = os.path.join(out_dir, "out")
cmd = "cd {} && {} -r {} -f {} -s {} -j 0 -p Production -c 5 >> {}".format(dirs, BWA, run_number, out_dir, os.path.join(out_dir, "samplesheet.csv".format()), os.path.join(out_dir, SUBMISSIONLOG))
cmd += "&& {} -r {} -f {} -s {} -j 0 -p Production -c 5 >> {}".format(RNA, run_number, out_dir, os.path.join(out_dir, "samplesheet.csv".format()), os.path.join(out_dir, SUBMISSIONLOG))
if args.dry_run:
logger.warning("Skipped following run: %s", cmd)
#Remove config txt
os.remove(os.path.join(out_dir, "config_casava-1.8.2.txt".format()))
else:
try:
#ananlysisReport into submission log
with open(os.path.join(out_dir, SUBMISSIONLOG), 'w') as fh:
fh.write(cmd)
_ = subprocess.check_output(cmd, shell=True)
except subprocess.CalledProcessError as e:
logger.fatal("The following command failed with return code %s: %s",
e.returncode, ' '.join(cmd))
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Exiting")
#send_status_mail
send_status_mail(PIPELINE_NAME, False, analysis_id, os.path.join(out_dir, LOG_DIR_REL, "mapping_submission.log"))
sys.exit(1)
num_triggers += 1
if args.break_after_first:
logger.info("Stopping after first sequencing run")
sys.exit(0)
else:
#send_status_mail
logger.info("samplesheet.csv missing for %s under %s", run_number, out_dir)
send_status_mail(PIPELINE_NAME, False, analysis_id, os.path.abspath(out_dir))
elif analysis.get("Status") == "FAILED":
logger.debug("BCL2FASTQ FAILED for %s under %s", run_number, out_dir)
# close the connection to MongoDB
connection.close()
logger.info("%s dirs with triggers", num_triggers)
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-t',
"--testing",
action='store_true',
help="Use MongoDB test server")
parser.add_argument('-n',
"--no-mail",
action='store_true',
help="Don't mail. Just print to console")
default = 14
parser.add_argument(
'-w',
'--win',
type=int,
default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
results = db.find({"timestamp": {"$gt": epoch_back, "$lt": epoch_present}})
runs = {}
extra_text = ""
for record in results:
run_number = record['run']
timestamp = record['timestamp']
runs[timestamp] = run_number
od = collections.OrderedDict(sorted(runs.items()))
logger.info("Found %s runs", results.count())
extra_text = "Found {} runs. \n".format(results.count())
for _, v in od.items(): # v is run
results = db.find({"run": v})
for record in results:
if not 'analysis' in record:
continue
last_analysis = record['analysis'][-1]
status = last_analysis.get("Status")
if not status:
continue
if status == 'SUCCESS':
if last_analysis.get("per_mux_status"):
mux = last_analysis.get("per_mux_status")
for d in mux:
if d is None:
logger.warning("Skipping empty per_mux_status for run %s." \
"Needs fix in DB", v)
continue
if d.get(
'Status'
) == "SUCCESS": # FIXME what if key is missing?
mux_id = d['mux_id']
stats_submission = d['StatsSubmission']
if stats_submission == "FAILED":
extra_text += "StatsSubmission for mux_id {} from run {} " \
"has FAILED and out_dir is {} \n" \
.format(mux_id, v, last_analysis.get("out_dir"))
extra_text += "\n"
archive_submission = d['ArchiveSubmission']
if archive_submission == "FAILED":
extra_text += "ArchiveSubmission for mux_id {} from run {} " \
"has FAILED and out_dir is {} \n" \
.format(mux_id, v, last_analysis.get("out_dir"))
extra_text += "\n"
elif status == 'FAILED':
extra_text += "Analysis for run {} has failed. \n".format(v)
extra_text += "Analysis_id is {} and out_dir is {} \n" \
.format(last_analysis.get("analysis_id"), \
last_analysis.get("out_dir"))
extra_text += "\n"
extra_text += "---------------------------------------------------\n"
logger.info("Analysis for run %s has failed ", v)
elif status == 'STARTED':
analysis_id = last_analysis.get("analysis_id")
analysis_epoch_time = isoformat_to_epoch_time(analysis_id +
"+08:00")
run_completion_time = timestamp / 1000
rd = relative_epoch_time(run_completion_time,
analysis_epoch_time)
if rd.days > 3:
extra_text += "Analysis for run {} was started {} days ago. "\
"Please check. \n".format(v, rd.days)
extra_text += "Analysis_id is {} and out_dir is {} \n" \
.format(last_analysis.get("analysis_id"), \
last_analysis.get("out_dir"))
extra_text += "\n"
extra_text += "---------------------------------------------------\n"
extra_text += "Report generation is completed"
subject = "Report generation for bcl2fastq"
if args.testing:
subject = "Testing:" + subject
if args.no_mail:
print(
"Skipping sending of email with subject '{}' and following body:".
format(subject))
print(extra_text)
else:
send_mail(subject, extra_text)
logger.info("Report generation is completed")
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-n', "--dry-run", action='store_true',
help="Don't run anything")
parser.add_argument('-t', "--testing", action='store_true',
help="Use MongoDB test-server here and when calling bcl2fastq wrapper (-t)")
default = 14
parser.add_argument('-w', '--win', type=int, default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
user_name = getpass.getuser()
if user_name != "userrig":
logger.warning("Not a production user. Skipping MongoDB update")
sys.exit(0)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
results = db.find({"analysis.per_mux_status" : {"$exists": True},
"timestamp": {"$gt": epoch_back, "$lt": epoch_present}})
logger.info("Found %s runs", results.count())
run_list = {}
mongo_db_ref = {}
for record in results:
run_number = record['run']
print(run_number)
mux_list = {}
for (analysis_count, analysis) in enumerate(record['analysis']):
analysis_id = analysis['analysis_id']
per_mux_status = analysis.get("per_mux_status", None)
if per_mux_status is None:
continue
for (mux_count, mux_status) in enumerate(per_mux_status):
# sanity checks against corrupted DB entries
if mux_status is None or mux_status.get('mux_id') is None:
logger.warning("mux_status is None or incomplete for run %s analysis %s."
" Requires fix in DB. Skipping entry for now.", \
run_number, analysis_id)
continue
if mux_status.get('Status', None) != "SUCCESS":
logger.info("MUX %s from %s is not SUCCESS. Skipping downstream analysis",
mux_status['mux_id'], run_number)
continue
mux_id = mux_status['mux_id']
out_dir = analysis['out_dir']
mux_db_id = "analysis.{}.per_mux_status.{}.DownstreamSubmission".format(
analysis_count, mux_count)
if mux_status.get('Status') == "SUCCESS" and \
mux_status.get('DownstreamSubmission', None) == "TODO":
mongo_list = (mux_id, mux_db_id, analysis_id)
mongo_db_ref.setdefault(run_number, []).append(mongo_list)
mux_list.setdefault(mux_id, []).append(out_dir)
for mux_id, out_dir in mux_list.items():
mux_list_success = mux_list[mux_id]
#Check if MUX has been analyzed more then 1 time successfully
if len(mux_list_success) > 1:
body = "{} has been analyzed more than 1 time successfully..".format(mux_id) \
+ "delegator is skipping the downstream analysis under {}. Please" \
"check the results.".format(mux_list_success)
subject = "Downstream delegator skipped job submission for {}".format(mux_id)
if args.testing:
subject += " (testing)"
send_mail(subject, body, toaddr='veeravallil', ccaddr=None)
continue
mux_info = (mux_id, out_dir)
run_list.setdefault(run_number, []).append(mux_info)
for run_num_flowcell, mux_list in run_list.items():
update_status = True
pipeline_params_dict = get_lib_details(run_num_flowcell, mux_list, args.testing)
if not bool(pipeline_params_dict):
logger.warning("pipeline_paramas_dict is empty for run num %s", run_num_flowcell)
continue
for lib, lib_info in pipeline_params_dict.items():
readunits_list = list()
for outer_key in lib_info:
if outer_key == 'readunits':
for inner_key in lib_info[outer_key]:
readunits_list.append(inner_key)
lib_info['samples'] = {}
lib_info['samples'][lib] = readunits_list
if args.dry_run:
logger.warning("Skipping job delegation for %s", \
lib)
continue
res = mongodb_insert_libjob(lib_info, connection)
if not res:
logger.critical("Skipping rest of analysis job submission" \
"for %s from %s", lib, lib_info.run_id)
subject = "Downstream delegator failed job submission for" \
"{}".format(lib)
if args.testing:
subject += " (testing)"
body = "Downstream delegator failed to insert job submission for" \
"{}".format(lib)
send_mail(subject, body, toaddr='veeravallil', ccaddr=None)
update_status = False
logger.warning("Clean up the database for mux %s from run %s and ctime %s", \
lib_info.mux_id, lib_info.run_id, lib_info.ctime)
mongodb_remove_muxjob(lib_info.mux_id, lib_info.run_id, \
lib_info.ctime, connection)
break
if not args.dry_run and update_status:
value = mongo_db_ref[run_num_flowcell]
for mux_id, insert_id, analysis_id in value:
logger.info("Update mongoDb runComplete for %s and runnumber is %s" \
"and id is %s and analysis_id %s", run_num_flowcell, mux_id, \
insert_id, analysis_id)
res = mongodb_update_runcomplete(run_num_flowcell, analysis_id, mux_id, \
insert_id, connection)
if not res:
logger.critical("Skipping rest of analysis job submission for %s" \
"from %s", mux_id, run_num_flowcell)
subject = "Downstream delegator failed job submission for {}" \
.format(mux_id)
if args.testing:
subject += " (testing)"
body = "Downstream delegator failed to insert job submission for" \
"{}".format(mux_id)
send_mail(subject, body, toaddr='veeravallil', ccaddr=None)
update_status = False
break
connection.close()
def main():
"""main function"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-1',
"--break-after-first",
action='store_true',
help="Only process first run returned")
parser.add_argument('-n',
"--dry-run",
action='store_true',
help="Don't run anything")
parser.add_argument(
'-t',
"--testing",
action='store_true',
help=
"Use MongoDB test-server here and when calling bcl2fastq wrapper (-t)")
parser.add_argument('-e',
"--wrapper-args",
nargs="*",
help="Extra arguments for bcl2fastq wrapper"
" (prefix leading dashes with X, e.g. X-n for -n)")
default = 14
parser.add_argument(
'-w',
'--win',
type=int,
default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
bcl2fastq_wrapper = os.path.join(os.path.dirname(sys.argv[0]),
"bcl2fastq.py")
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
# db query for jobs that are yet to be analysed in the epoch window
epoch_present, epoch_back = generate_window(args.win)
results = db.find({
"analysis": {
"$exists": 0
},
"timestamp": {
"$gt": epoch_back,
"$lt": epoch_present
}
})
# results is a pymongo.cursor.Cursor which works like an iterator i.e. dont use len()
logger.info("Found %s runs", results.count())
for record in results:
run_number = record['run']
logger.debug("Processing record %s", record)
cmd = [bcl2fastq_wrapper, "-r", run_number, "-v"]
if args.testing:
cmd.append("-t")
if args.wrapper_args:
cmd.extend([x.lstrip('X') for x in args.wrapper_args])
if args.dry_run:
logger.warning("Skipped following run: %s", ' '.join(cmd))
continue
else:
try:
logger.info("Executing: %s", ' '.join(cmd))
res = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
if res:
logger.info("bcl2fastq wrapper returned:\n%s",
res.decode().rstrip())
except subprocess.CalledProcessError as e:
logger.critical(
"The following command failed with"
" return code %s: %s", e.returncode, ' '.join(cmd))
logger.critical("Full error message was: %s", e.stdout)
if 'commlib error' in e.stdout.decode():
logger.critical(
"Looks like a qmaster problem (commlib error). Exiting"
)
break
else:
logger.critical("Will keep going")
# continue so that a failed run doesn't count,
# i.e. args.break_after_first shouldn't be trigger
continue
if args.break_after_first:
logger.info("Stopping after first sequencing run")
break
# close the connection to MongoDB
connection.close()
logger.info("Successful program exit")
def start_data_transfer(connection, mux, mux_info, site, mail_to):
""" Data transfer from source to destination
"""
run_number, downstream_id, analysis_id, bcl_path = mux_info
fastq_src = os.path.join(bcl_path, "out", "Project_"+mux)
bcl_dir = os.path.basename(bcl_path)
if is_devel_version():
fastq_dest = os.path.join(novogene_conf['FASTQ_DEST'][site]['devel'], \
mux, run_number, bcl_dir)
yaml_dest = os.path.join(novogene_conf['FASTQ_DEST'][site]['devel'], \
mux, mux +"_multisample.yaml")
else:
fastq_dest = os.path.join(novogene_conf['FASTQ_DEST'][site]['production'], \
mux, run_number, bcl_dir)
yaml_dest = os.path.join(novogene_conf['FASTQ_DEST'][site]['production'], \
mux, mux+ "_multisample.yaml")
rsync_cmd = 'rsync -va %s %s' % (fastq_src, fastq_dest)
if not os.path.exists(fastq_dest):
try:
os.makedirs(fastq_dest)
logger.info("data transfer started for %s from %s", mux, run_number)
st_time = generate_timestamp()
update_downstream_mux(connection, run_number, analysis_id, downstream_id, \
"COPYING_" + st_time)
_ = subprocess.check_output(rsync_cmd, shell=True, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError as e:
body = "The following command failed with return code {}: {}". \
format(e.returncode, rsync_cmd)
subject = "{} from {}: SG10K data transfer ({}) failed".format(mux, run_number, site)
logger.fatal(body)
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Exiting")
#Send_mail
send_mail(subject, body, toaddr=mail_to, ccaddr=None)
#Delete the partial info being rsync
update_downstream_mux(connection, run_number, analysis_id, downstream_id, "ERROR")
sys.exit(1)
#Update the mongoDB for successful data transfer
sample_info = get_mux_details(run_number, mux, fastq_dest)
#Touch rsync complete file
with open(os.path.join(fastq_dest, "rsync_complete.txt"), "w") as f:
f.write("")
with open(yaml_dest, 'w') as fh:
yaml.dump(dict(sample_info), fh, default_flow_style=False)
job = {}
job['sample_cfg'] = {}
for outer_key, outer_value in sample_info.items():
ctime, _ = generate_window(1)
job['sample_cfg'].update({outer_key:outer_value})
job['site'] = site
job['pipeline_name'] = 'custom/SG10K'
job['pipeline_version'] = novogene_conf['PIPELINE_VERSION']
job['ctime'] = ctime
job['requestor'] = 'userrig'
if is_devel_version():
novogene_outdir = os.path.join(novogene_conf['NOVOGENE_OUTDIR'][site]['devel'], \
mux)
else:
novogene_outdir = os.path.join(novogene_conf['NOVOGENE_OUTDIR'][site]['production'],
mux)
job['out_dir_override'] = novogene_outdir
logger.info("Data transfer completed successfully for %s from %s", mux, run_number)
job_id = insert_muxjob(connection, mux, job)
update_downstream_mux(connection, run_number, analysis_id, downstream_id, job_id)
subject = "{} from {}: SG10K data transfer ({}) completed".format(mux, run_number, site)
body = "Data transfer successfully completed for {} from {}".format(mux, run_number)
send_mail(subject, body, toaddr=mail_to, ccaddr=None)
return True
else:
logger.critical("Mux %s from %s directory already exists under %s", mux, \
run_number, fastq_dest)
return False
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-n',
"--dry-run",
action='store_true',
help="Don't run anything")
parser.add_argument('-s', "--site", help="site information")
parser.add_argument(
'-t',
"--testing",
action='store_true',
help=
"Use MongoDB test-server here and when calling bcl2fastq wrapper (-t)")
default = 14
parser.add_argument(
'-w',
'--win',
type=int,
default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
if not is_production_user():
logger.warning("Not a production user. Skipping MongoDB update")
sys.exit(1)
if not args.site:
site = 'NSCC'
else:
site = args.site
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.pipeline_runs
epoch_present, epoch_back = generate_window(args.win)
results = db.find({
"run": {
"$exists": False
},
"site": site,
"ctime": {
"$gt": epoch_back,
"$lt": epoch_present
}
})
logger.info("Found %s runs to start analysis", results.count())
for record in results:
start_analysis(record, args.testing, args.dry_run)
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-1',
"--break-after-first",
action='store_true',
help="Only process first run returned")
parser.add_argument('-n',
"--dryrun",
action='store_true',
help="Don't run anything")
default = 84
parser.add_argument(
'-w',
'--win',
type=int,
default=default,
help="Number of days to look back (default {})".format(default))
default = 60
parser.add_argument(
'-d',
'--days',
type=int,
default=default,
help="Bcl analysis not older than days(default {})".format(default))
default = 60
parser.add_argument(
'-r',
'--tardays',
type=int,
default=default,
help="tar ball not older than days(default {})".format(default))
parser.add_argument(
'-t',
"--testing",
action='store_true',
help=
"Use MongoDB test-server here and when calling bcl2fastq wrapper (-t)")
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
LOGGER.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
if not is_production_user():
LOGGER.warning("Not a production user. Skipping archival steps")
sys.exit(1)
if is_devel_version() or args.testing:
mail_to = 'veeravallil' # domain added in mail function
else:
mail_to = 'rpd'
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
results = db.find({
"run": {
"$regex": "^((?!NG00).)*$"
},
"raw-delete": {
"$exists": False
},
"timestamp": {
"$gt": epoch_back,
"$lt": epoch_present
}
})
LOGGER.info("Looping through %s jobs", results.count())
trigger = 0
for record in results:
try:
run_num = record['run']
except KeyError:
run_num = None
if not record.get('deletion'):
#Check run_status
res = check_run_status(record, args.days)
if res:
LOGGER.info("Create tar ball %s ", run_num)
if args.dryrun:
LOGGER.warning("Skipping Create tar ball %s ", run_num)
continue
create_run_tar(db, run_num)
trigger = 1
elif record['deletion'].get('tar'):
res = check_tar_status_and_delete(db,
record,
args.tardays,
dryrun=args.dryrun)
if res:
trigger = 1
if args.break_after_first and trigger == 1:
LOGGER.info("Stopping after first run")
break
def main():
"""main function
"""
stats_upload_script = os.path.abspath(
os.path.join(os.path.dirname(sys.argv[0]), "bcl_stats_upload.py"))
assert os.path.exists(stats_upload_script)
archive_upload_script = os.path.abspath(
os.path.join(os.path.dirname(sys.argv[0]), "sra_fastq_upload.py"))
assert os.path.exists(archive_upload_script)
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-t',
"--testing",
action='store_true',
help="Use MongoDB test server")
default = 14
parser.add_argument(
'-w',
'--win',
type=int,
default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-n', "--dry-run", action='store_true', help="Dry run")
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
if not is_production_user():
logger.warning("Not a production user. Skipping MongoDB update")
sys.exit(1)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
num_triggers = 0
results = db.find({
"analysis": {
"$exists": True
},
"timestamp": {
"$gt": epoch_back,
"$lt": epoch_present
}
})
logger.info("Found %s runs", results.count())
for record in results:
run_number = record['run']
for (analysis_count, analysis) in enumerate(record['analysis']):
analysis_id = analysis['analysis_id']
per_mux_status = analysis.get("per_mux_status", None)
if per_mux_status is None:
continue
for (mux_count, mux_status) in enumerate(per_mux_status):
# sanity checks against corrupted DB entries
if mux_status is None or mux_status.get('mux_id') is None:
logger.warning(
"mux_status is None or incomplete for run %s analysis %s."
" Requires fix in DB. Skipping entry for now.",
run_number, analysis_id)
continue
if mux_status.get('Status', None) != "SUCCESS":
logger.info(
"MUX %s from %s is not SUCCESS. Skipping SRA and STATS uploading",
mux_status['mux_id'], run_number)
continue
mux_id = mux_status['mux_id']
out_dir = analysis['out_dir']
if args.dry_run:
logger.warning(
"Skipping analysis %s run %s MUX %s"
" with StatsSubmission %s and ArchiveSubmission %s",
analysis_id, run_number, mux_status['mux_id'],
mux_status.get('StatsSubmission', None),
mux_status.get('ArchiveSubmission', None))
continue
# Call STATS upload
#
if mux_status.get('StatsSubmission', None) == "TODO":
logger.info(
"Stats upload for %s from %s and analysis_id is %s",
mux_id, run_number, analysis_id)
StatsSubmission = "analysis.{}.per_mux_status.{}.StatsSubmission".format(
analysis_count, mux_count)
stats_upload_script_cmd = [
stats_upload_script, '-o', out_dir, '-m', mux_id
]
if args.testing:
stats_upload_script_cmd.append("-t")
try:
_ = subprocess.check_output(stats_upload_script_cmd,
stderr=subprocess.STDOUT)
StatsSubmission_status = "SUCCESS"
except subprocess.CalledProcessError as e:
logger.fatal(
"The following command failed with return code %s: %s",
e.returncode, ' '.join(stats_upload_script_cmd))
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Resetting to TODO")
StatsSubmission_status = "TODO"
try:
db.update(
{
"run": run_number,
'analysis.analysis_id': analysis_id
}, {
"$set": {
StatsSubmission: StatsSubmission_status,
}
})
except pymongo.errors.OperationFailure:
logger.fatal("MongoDB OperationFailure")
sys.exit(0)
num_triggers += 1
# Call FASTQ upload
#
if mux_status.get('ArchiveSubmission', None) == "TODO":
logger.info(
"SRA upload for %s from %s and analysis_id is %s",
mux_id, run_number, analysis_id)
ArchiveSubmission = "analysis.{}.per_mux_status.{}.ArchiveSubmission".format(
analysis_count, mux_count)
archive_upload_script_cmd = [
archive_upload_script, '-o', out_dir, '-m', mux_id
]
if args.testing:
archive_upload_script_cmd.append("-t")
try:
_ = subprocess.check_output(archive_upload_script_cmd,
stderr=subprocess.STDOUT)
ArchiveSubmission_status = "SUCCESS"
except subprocess.CalledProcessError as e:
logger.fatal(
"The following command failed with return code %s: %s",
e.returncode, ' '.join(archive_upload_script_cmd))
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Resetting to TODO")
ArchiveSubmission_status = "TODO"
#update mongoDB
try:
db.update(
{
"run": run_number,
'analysis.analysis_id': analysis_id
}, {
"$set": {
ArchiveSubmission: ArchiveSubmission_status
}
})
except pymongo.errors.OperationFailure:
logger.fatal("MongoDB OperationFailure")
sys.exit(0)
num_triggers += 1
# close the connection to MongoDB
connection.close()
logger.info("%s dirs with triggers", num_triggers)
def get_lib_details(run_num_flowcell, mux_list, testing):
"""Lib info collection from ELM per run
"""
_, run_num, flowcellid = get_machine_run_flowcell_id(run_num_flowcell)
# Call rest service to get component libraries
if testing:
print(run_num)
rest_url = rest_services['run_details']['testing'].replace("run_num", run_num)
logger.info("development server")
else:
rest_url = rest_services['run_details']['production'].replace("run_num", run_num)
logger.info("production server")
response = requests.get(rest_url)
if response.status_code != requests.codes.ok:
response.raise_for_status()
rest_data = response.json()
logger.debug("rest_data from %s: %s", rest_url, rest_data)
sample_info = {}
if rest_data.get('runId') is None:
logger.info("JSON data is empty for run num %s", run_num)
return sample_info
for mux_id, out_dir in mux_list:
fastq_data_dir = os.path.join(out_dir[0], 'out', "Project_"+mux_id)
if os.path.exists(fastq_data_dir):
for rows in rest_data['lanes']:
if mux_id in rows['libraryId']:
if "MUX" in rows['libraryId']:
for child in rows['Children']:
if child['Analysis'] != "Sequence only":
ctime, _ = generate_window(1)
sample_dict = {}
sample = child['libraryId']
sample_dict['requestor'] = rows['requestor']
sample_dict['ctime'] = ctime
sample_dict['pipeline_name'] = child['Analysis']
if 'pipeline_version' in rows:
sample_dict['pipeline_version'] = child['pipeline_version']
else:
sample_dict['pipeline_version'] = None
sample_dict['pipeline_params'] = 'params'
sample_dict['site'] = get_site()
out_dir = get_downstream_outdir(sample_dict['requestor'], \
sample_dict['pipeline_version'], sample_dict['pipeline_name'])
sample_dict['out_dir'] = out_dir
readunits_dict = {}
status, fq1, fq2 = check_fastq(fastq_data_dir, child['libraryId'],\
rows['laneId'])
if status:
ru = ReadUnit(run_num_flowcell, flowcellid, child['libraryId'],\
rows['laneId'], None, fq1, fq2)
k = key_for_read_unit(ru)
readunits_dict[k] = dict(ru._asdict())
sample_dict['readunits'] = readunits_dict
if sample_info.get(sample, {}).get('readunits'):
sample_info[sample]['readunits'].update(readunits_dict)
else:
sample_info[sample] = sample_dict
else:
if rows['Analysis'] != "Sequence only":
sample = rows['libraryId']
status, fq1, fq2 = check_fastq(fastq_data_dir, rows['libraryId'], \
rows['laneId'])
if status:
ctime, _ = generate_window(1)
sample_dict = {}
readunits_dict = {}
ru = ReadUnit(run_num_flowcell, flowcellid, rows['libraryId'], \
rows['laneId'], None, fq1, fq2)
k = key_for_read_unit(ru)
readunits_dict[k] = dict(ru._asdict())
sample_dict['readunits'] = readunits_dict
sample_info[sample] = sample_dict
return sample_info
def main():
"""main function
"""
stats_upload_script = os.path.abspath(os.path.join(
os.path.dirname(sys.argv[0]), "bcl_stats_upload.py"))
assert os.path.exists(stats_upload_script)
archive_upload_script = os.path.abspath(os.path.join(
os.path.dirname(sys.argv[0]), "sra_fastq_upload.py"))
assert os.path.exists(archive_upload_script)
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-t', "--testing", action='store_true',
help="Use MongoDB test server")
default = 14
parser.add_argument('-w', '--win', type=int, default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-n', "--dry-run", action='store_true',
help="Dry run")
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
user_name = getpass.getuser()
if user_name != "userrig":
logger.warning("Not a production user. Skipping sending of emails")
sys.exit(0)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
num_emails = 0
results = db.find({"analysis" : {"$exists": True},
"timestamp": {"$gt": epoch_back, "$lt": epoch_present}})
logger.info("Found %s runs", results.count())
if is_devel_version() or args.testing:
mail_to = 'veeravallil'# domain added in mail function
else:
#mail_to = '*****@*****.**'
mail_to = '*****@*****.**'
for record in results:
run_number = record['run']
#print(run_number)
for (analysis_count, analysis) in enumerate(record['analysis']):
analysis_id = analysis['analysis_id']
per_mux_status = analysis.get("per_mux_status", None)
if per_mux_status is None:
continue
for (mux_count, mux_status) in enumerate(per_mux_status):
if args.dry_run:
logger.warning("Skipping analysis %s run %s MUX %s"
" with email_sent %s",
analysis_id, run_number, mux_status['mux_id'],
mux_status.get('email_sent', None))
continue
if mux_status.get('email_sent', None):
continue
# for all others: send email and update db
email_sent_query = "analysis.{}.per_mux_status.{}.email_sent".format(
analysis_count, mux_count)
mux_id = mux_status['mux_id']
out_dir = analysis['out_dir']
if mux_status.get('Status', None) == "FAILED":
logger.info("bcl2fastq for MUX %s from %s failed. ",
mux_status['mux_id'], run_number)
subject = 'bcl2fastq: ' + mux_id
body = "bcl2fastq for {} from {} failed.".format(mux_id, run_number)
body += "\n\nPlease check the logs under {}".format(out_dir + "/logs")
send_mail(subject, body, mail_to, ccaddr="rpd")
num_emails += 1
update_mongodb_email(db, run_number, analysis_id, email_sent_query, True)
elif mux_status.get('Status', None) == "SUCCESS":
muxdir = os.path.join(out_dir, 'out', mux_status.get('mux_dir'))
summary = path_to_url(os.path.join(muxdir, 'html/index.html'))
body = "bcl2fastq for {} from {} successfully completed.".format(
mux_id, run_number)
body += "\n\nA summary can be found at {}".format(summary)
body += "\n\nFastQ files are located in {}".format(muxdir)
body += "\n\nData can also be downloaded from GIS-SRA (once archival is complete)"
confinfo = os.path.join(out_dir, 'conf.yaml')
#print(body)
if not os.path.exists(confinfo):
logger.fatal("conf info '%s' does not exist"
" under run directory.", confinfo)
continue
subject = 'bcl2fastq'
if args.testing:
subject += ' testing'
if is_devel_version():
subject += ' devel'
subject += ': ' + mux_id
send_mail(subject, body, mail_to, ccaddr="rpd")# mail_to already set
if not args.testing and not is_devel_version():
requestor = get_requestor(mux_id, confinfo)
if requestor is not None:
#requestor = "rpd"
#subject += " (instead of requestor)"
#send_mail(subject, body, requestor, ccaddr="rpd")
send_mail(subject, body, requestor)
num_emails += 1
update_mongodb_email(db, run_number, analysis_id, email_sent_query, True)
# close the connection to MongoDB
connection.close()
logger.info("%d emails sent", num_emails)
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-t', "--testing", action='store_true',
help="Use MongoDB test server")
parser.add_argument('-n', "--no-mail", action='store_true',
help="Don't mail. Just print to console")
default = 14
parser.add_argument('-w', '--win', type=int, default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
results = db.find({"timestamp": {"$gt": epoch_back, "$lt": epoch_present}})
runs = {}
extra_text = ""
for record in results:
run_number = record['run']
timestamp = record['timestamp']
runs[timestamp] = run_number
od = collections.OrderedDict(sorted(runs.items()))
logger.info("Found %s runs", results.count())
extra_text = "Found {} runs. \n".format(results.count())
for _, v in od.items():# v is run
results = db.find({"run": v})
for record in results:
if not 'analysis' in record:
continue
last_analysis = record['analysis'][-1]
status = last_analysis.get("Status")
if not status:
continue
if status == 'SUCCESS':
if last_analysis.get("per_mux_status"):
mux = last_analysis.get("per_mux_status")
for d in mux:
if d is None:
logger.warning("Skipping empty per_mux_status for run %s." \
"Needs fix in DB", v)
continue
if d.get('Status') == "SUCCESS":# FIXME what if key is missing?
mux_id = d['mux_id']
stats_submission = d['StatsSubmission']
if stats_submission == "FAILED":
extra_text += "StatsSubmission for mux_id {} from run {} " \
"has FAILED and out_dir is {} \n" \
.format(mux_id, v, last_analysis.get("out_dir"))
extra_text += "\n"
archive_submission = d['ArchiveSubmission']
if archive_submission == "FAILED":
extra_text += "ArchiveSubmission for mux_id {} from run {} " \
"has FAILED and out_dir is {} \n" \
.format(mux_id, v, last_analysis.get("out_dir"))
extra_text += "\n"
elif status == 'FAILED':
extra_text += "Analysis for run {} has failed. \n".format(v)
extra_text += "Analysis_id is {} and out_dir is {} \n" \
.format(last_analysis.get("analysis_id"), \
last_analysis.get("out_dir"))
extra_text += "\n"
extra_text += "---------------------------------------------------\n"
logger.info("Analysis for run %s has failed ", v)
elif status == 'STARTED':
analysis_id = last_analysis.get("analysis_id")
analysis_epoch_time = isoformat_to_epoch_time(analysis_id+"+08:00")
run_completion_time = timestamp/1000
dt1 = datetime.datetime.fromtimestamp(run_completion_time)
dt2 = datetime.datetime.fromtimestamp(analysis_epoch_time)
rd = dateutil.relativedelta.relativedelta(dt1, dt2)
if rd.days > 3:
extra_text += "Analysis for run {} was started {} days ago. "\
"Please check. \n".format(v, rd.days)
extra_text += "Analysis_id is {} and out_dir is {} \n" \
.format(last_analysis.get("analysis_id"), \
last_analysis.get("out_dir"))
extra_text += "\n"
extra_text += "---------------------------------------------------\n"
extra_text += "Report generation is completed"
subject = "Report generation for bcl2fastq"
if args.testing:
subject = "Testing:" + subject
if args.no_mail:
print("Skipping sending of email with subject '{}' and following body:".format(subject))
print(extra_text)
else:
send_mail(subject, extra_text)
logger.info("Report generation is completed")
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'-n',
"--dryrun",
action='store_true',
help="Don't actually update DB (best used in conjunction with -v -v)")
parser.add_argument('-t',
"--testing",
action='store_true',
help="Use MongoDB test-server. Don't do anything")
default = 14
parser.add_argument(
'-w',
'--win',
type=int,
default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every
LOGGER.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
if not is_production_user():
LOGGER.warning("Not a production user. Exiting")
sys.exit(1)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
#LOGGER.info("Database connection established")
dbcol = connection.gisds.pipeline_runs
site = get_site()
epoch_now, epoch_then = generate_window(args.win)
cursor = dbcol.find({
"ctime": {
"$gt": epoch_then,
"$lt": epoch_now
},
"site": site
})
LOGGER.info("Looping through {} jobs".format(cursor.count()))
for job in cursor:
dbid = job['_id']
# only set here to avoid code duplication below
try:
out_dir = job['execution']['out_dir']
except KeyError:
out_dir = None
# no execution dict means start a new analysis
if not job.get('execution'):
LOGGER.info('Job {} to be started'.format(dbid))
# determine out_dir and set in DB
# out_dir_override will take precedence over generating out_dir with get_downstream_outdir function
if job.get('out_dir_override'):
out_dir = job.get('out_dir_override')
if os.path.exists(out_dir):
mux = os.path.basename(out_dir)
if not args.dryrun:
LOGGER.critical(
"Analysis for {} already exists under {}. Please start the analysis manually"
.format(mux, out_dir))
res = dbcol.update_one(
{"_id": ObjectId(dbid)},
{"$set": {
"execution.status": "MANUAL"
}})
assert res.modified_count == 1, (
"Modified {} documents instead of 1".format(
res.modified_count))
sys.exit(1)
#assert not os.path.exists(out_dir), ("Direcotry already exists {}").format(out_dir)
else:
out_dir = get_downstream_outdir(job['requestor'],
job['pipeline_name'],
job['pipeline_version'])
# Note, since execution (key) exists, accidental double
# starts are prevented even before start time etc is
# logged via flagfiles. No active logging here so that
# flag files logging just works.
if args.dryrun:
LOGGER.info("Skipping dry run option")
continue
status = start_cmd_execution(job, site, out_dir, args.testing)
if status:
res = dbcol.update_one(
{"_id": ObjectId(dbid)},
{"$set": {
"execution.out_dir": out_dir
}})
assert res.modified_count == 1, (
"Modified {} documents instead of 1".format(
res.modified_count))
else:
LOGGER.warning("Job {} could not be started".format(dbid))
elif job['execution'].get('status') == "MANUAL":
continue
elif list_starterflags(
out_dir
): # out_dir cannot be none because it's part of execution dict
LOGGER.info(
'Job {} in {} started but not yet logged as such in DB'.format(
dbid, out_dir))
matches = list_starterflags(out_dir)
assert len(matches) == 1, (
"Got several starter flags in {}".format(out_dir))
sflag = StarterFlag(matches[0])
assert sflag.dbid == str(dbid)
set_started(dbcol,
sflag.dbid,
str(sflag.timestamp),
dryrun=args.dryrun)
os.unlink(sflag.filename)
elif job['execution'].get('status') in ['STARTED', 'RESTART']:
LOGGER.info(
'Job %s in %s set as re|started so checking on completion',
dbid, out_dir)
set_completion_if(dbcol, dbid, out_dir, dryrun=args.dryrun)
else:
# job complete
LOGGER.debug('Job %s in %s should be completed', dbid, out_dir)
LOGGER.info("Successful program exit")
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-n',
"--dry-run",
action='store_true',
help="Don't run anything")
parser.add_argument(
'-t',
"--testing",
action='store_true',
help=
"Use MongoDB test-server here and when calling bcl2fastq wrapper (-t)")
default = 14
parser.add_argument(
'-w',
'--win',
type=int,
default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
user_name = getpass.getuser()
if user_name != "userrig":
logger.warning("Not a production user. Skipping MongoDB update")
sys.exit(0)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
results = db.find({
"analysis.per_mux_status": {
"$exists": True
},
"timestamp": {
"$gt": epoch_back,
"$lt": epoch_present
}
})
logger.info("Found %s runs", results.count())
run_list = {}
mongo_db_ref = {}
for record in results:
run_number = record['run']
mux_list = {}
for (analysis_count, analysis) in enumerate(record['analysis']):
analysis_id = analysis['analysis_id']
per_mux_status = analysis.get("per_mux_status", None)
if per_mux_status is None:
continue
for (mux_count, mux_status) in enumerate(per_mux_status):
# sanity checks against corrupted DB entries
if mux_status is None or mux_status.get('mux_id') is None:
logger.warning("mux_status is None or incomplete for run %s analysis %s."
" Requires fix in DB. Skipping entry for now.", \
run_number, analysis_id)
continue
if mux_status.get('Status', None) != "SUCCESS":
logger.info(
"MUX %s from %s is not SUCCESS. Skipping downstream analysis",
mux_status['mux_id'], run_number)
continue
mux_id = mux_status['mux_id']
out_dir = analysis['out_dir']
mux_db_id = "analysis.{}.per_mux_status.{}.DownstreamSubmission".format(
analysis_count, mux_count)
if mux_status.get('Status') == "SUCCESS" and \
mux_status.get('DownstreamSubmission') == "TODO":
mongo_list = (mux_id, mux_db_id, analysis_id)
mongo_db_ref.setdefault(run_number, []).append(mongo_list)
mux_list.setdefault(mux_id, []).append(out_dir)
for mux_id, out_dir in mux_list.items():
mux_list_success = mux_list[mux_id]
#Check if MUX has been analyzed more then 1 time successfully
if len(mux_list_success) > 1:
body = "{} has been analyzed more than 1 time successfully..".format(mux_id) \
+ "delegator is skipping the downstream analysis under {}. Please" \
"check the results.".format(mux_list_success)
subject = "Downstream delegator skipped job submission for {}".format(
mux_id)
if args.testing:
subject += " (testing)"
send_mail(subject, body, toaddr='veeravallil', ccaddr=None)
continue
mux_info = (mux_id, out_dir)
run_list.setdefault(run_number, []).append(mux_info)
for run_num_flowcell, mux_list in run_list.items():
update_status = True
pipeline_params_dict, mux_analysis_list = get_lib_details(run_num_flowcell, \
mux_list, args.testing)
if not bool(pipeline_params_dict):
logger.warning("pipeline params is empty for run num %s",
run_num_flowcell)
continue
# Insert jobs into pipeline_runs collection
for lib, lib_info in pipeline_params_dict.items():
job = {}
rd_list = {}
job['sample_cfg'] = {}
job['sample_cfg'] = {}
readunits_list = list()
rd_list['samples'] = {}
for outer_key, outer_value in lib_info.items():
if outer_key == 'readunits':
for inner_key in lib_info[outer_key]:
readunits_list.append(inner_key)
job['sample_cfg'].update({outer_key: outer_value})
if outer_key == 'references_cfg':
job['references_cfg'] = {}
job['references_cfg'] = outer_value
elif outer_key == 'cmdline':
job['cmdline'] = {}
job['cmdline'] = outer_value
elif outer_key != 'readunits':
job.update({outer_key: outer_value})
else:
rd_list['samples'][lib] = readunits_list
job['sample_cfg'].update(rd_list)
if args.dry_run:
logger.warning("Skipping job delegation for %s", \
lib)
continue
res = mongodb_insert_libjob(job, connection)
if not res:
logger.critical("Skipping rest of analysis job submission" \
"for %s from %s", lib, lib_info.run_id)
subject = "Downstream delegator failed job submission for" \
"{}".format(lib)
if args.testing:
subject += " (testing)"
body = "Downstream delegator failed to insert job submission for" \
"{}".format(lib)
send_mail(subject, body, toaddr='veeravallil', ccaddr=None)
update_status = False
logger.warning("Clean up the database for mux %s from run %s and ctime %s", \
lib_info.mux_id, lib_info.run_id, lib_info.ctime)
mongodb_remove_muxjob(lib_info.mux_id, lib_info.run_id, \
lib_info.ctime, connection)
break
# Update runcomplete collection for delegated jobs
if not args.dry_run and update_status:
value = mongo_db_ref[run_num_flowcell]
for mux_id, insert_id, analysis_id in value:
if mux_id in mux_analysis_list:
logger.info("Update mongoDb pipeline_runs for mux_id %s from run number %s" \
"and analysis_id is %s", mux_id, run_num_flowcell, analysis_id)
res = mongodb_update_runcomplete(run_num_flowcell, analysis_id, mux_id, \
insert_id, connection)
if not res:
logger.critical("Skipping rest of analysis job submission for %s" \
"from %s", mux_id, run_num_flowcell)
subject = "Downstream delegator failed job submission for {}" \
.format(mux_id)
if args.testing:
subject += " (testing)"
body = "Downstream delegator failed to insert job submission for" \
"{}".format(mux_id)
send_mail(subject,
body,
toaddr='veeravallil',
ccaddr=None)
update_status = False
break
connection.close()
def main():
"""main function"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-1',
"--break-after-first",
action='store_true',
help="Only process first run returned")
parser.add_argument('-n',
"--dry-run",
action='store_true',
help="Don't run anything")
parser.add_argument('-t',
"--testing",
action='store_true',
help="Use MongoDB test-server")
default = 14
parser.add_argument(
'-w',
'--win',
type=int,
default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
#Check if pipeline scripts are available
assert os.path.exists(BWA)
assert os.path.exists(RNA)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
num_triggers = 0
results = db.find({
"analysis.Status": "SUCCESS",
"timestamp": {
"$gt": epoch_back,
"$lt": epoch_present
}
})
logger.info("Found %s runs", results.count())
for record in results:
run_number = record['run']
analysis = record['analysis']
# Downstream analysis will not be intiated for Novogene (NG00*) runs
if "NG00" in run_number:
continue
for analysis in record['analysis']:
out_dir = analysis.get("out_dir")
#Check if bcl2Fastq is completed successfully
if 'Status' in analysis and analysis.get("Status") == "SUCCESS":
if not os.path.exists(out_dir):
logger.critical(
"Following directory listed in DB doesn't exist: %s",
out_dir)
continue
#Check if downstream analysis has been started
if not os.path.exists(
os.path.join(out_dir,
"config_casava-1.8.2.txt".format())):
logger.info("Start the downstream analysis at %s", out_dir)
os.makedirs(os.path.join(out_dir, LOG_DIR_REL),
exist_ok=True)
#generate config file
config_cmd = [CONFIG, '-r', run_number]
try:
f = open(
os.path.join(out_dir,
"config_casava-1.8.2.txt".format()),
"w")
_ = subprocess.call(config_cmd,
stderr=subprocess.STDOUT,
stdout=f)
except subprocess.CalledProcessError as e:
logger.fatal(
"The following command failed with return code %s: %s",
e.returncode, ' '.join(config_cmd))
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Exiting")
sys.exit(1)
#generic sample sheet
samplesheet_cmd = 'cd {} && {} -r {}'.format(
out_dir, SAMPLESHEET, run_number)
try:
_ = subprocess.check_output(samplesheet_cmd,
shell=True)
except subprocess.CalledProcessError as e:
logger.fatal(
"The following command failed with return code %s: %s",
e.returncode, ' '.join(samplesheet_cmd))
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Exiting")
sys.exit(1)
#Generate and Submit BWA and RNAseq mapping pipeline
_, runid, _ = get_machine_run_flowcell_id(run_number)
generic_samplesheet = (os.path.join(
out_dir, runid + "_SampleSheet.csv"))
if os.path.exists(
os.path.join(out_dir, generic_samplesheet)):
dirs = os.path.join(out_dir, "out")
cmd = "cd {} && {} -r {} -f {} -s {} -j 0 -p Production -c 5 >> {}" \
.format(dirs, BWA, run_number, out_dir, os.path.join(out_dir, \
generic_samplesheet), os.path.join(out_dir, SUBMISSIONLOG))
cmd += "&& {} -r {} -f {} -s {} -j 0 -p Production -c 5 >> {}" \
.format(RNA, run_number, out_dir, os.path.join(out_dir, \
generic_samplesheet), os.path.join(out_dir, SUBMISSIONLOG))
if args.dry_run:
logger.warning("Skipped following run: %s", cmd)
#Remove config txt
os.remove(
os.path.join(
out_dir,
"config_casava-1.8.2.txt".format()))
else:
try:
#ananlysisReport into submission log
with open(os.path.join(out_dir, SUBMISSIONLOG),
'w') as fh:
fh.write(cmd)
_ = subprocess.check_output(cmd, shell=True)
except subprocess.CalledProcessError as e:
logger.fatal(
"The following command failed with return code %s: %s",
e.returncode, cmd)
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Exiting")
#send_status_mail
send_status_mail(PIPELINE_NAME, False, analysis_id, \
os.path.join(out_dir, LOG_DIR_REL, "mapping_submission.log"))
sys.exit(1)
num_triggers += 1
if args.break_after_first:
logger.info("Stopping after first sequencing run")
sys.exit(0)
else:
#send_status_mail
logger.info("samplesheet.csv missing for %s under %s",
run_number, out_dir)
send_status_mail(PIPELINE_NAME, False, analysis_id, \
os.path.abspath(out_dir))
elif analysis.get("Status") == "FAILED":
logger.debug("BCL2FASTQ FAILED for %s under %s", run_number,
out_dir)
# close the connection to MongoDB
connection.close()
logger.info("%s dirs with triggers", num_triggers)
def main():
"""main function
"""
stats_upload_script = os.path.abspath(
os.path.join(os.path.dirname(sys.argv[0]), "bcl_stats_upload.py"))
assert os.path.exists(stats_upload_script)
archive_upload_script = os.path.abspath(
os.path.join(os.path.dirname(sys.argv[0]), "sra_fastq_upload.py"))
assert os.path.exists(archive_upload_script)
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-t',
"--testing",
action='store_true',
help="Use MongoDB test server")
default = 14
parser.add_argument(
'-w',
'--win',
type=int,
default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-n', "--dry-run", action='store_true', help="Dry run")
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
if not is_production_user():
logger.warning("Not a production user. Skipping sending of emails")
sys.exit(1)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
num_emails = 0
results = db.find({
"analysis": {
"$exists": True
},
"timestamp": {
"$gt": epoch_back,
"$lt": epoch_present
}
})
logger.info("Found %s runs", results.count())
if is_devel_version() or args.testing:
mail_to = 'veeravallil' # domain added in mail function
else:
#mail_to = '*****@*****.**'
mail_to = '*****@*****.**'
for record in results:
run_number = record['run']
#print(run_number)
for (analysis_count, analysis) in enumerate(record['analysis']):
analysis_id = analysis['analysis_id']
per_mux_status = analysis.get("per_mux_status", None)
if per_mux_status is None:
continue
for (mux_count, mux_status) in enumerate(per_mux_status):
if args.dry_run:
logger.warning(
"Skipping analysis %s run %s MUX %s"
" with email_sent %s", analysis_id,
run_number, mux_status['mux_id'],
mux_status.get('email_sent', None))
continue
if mux_status.get('email_sent', None):
continue
# for all others: send email and update db
email_sent_query = "analysis.{}.per_mux_status.{}.email_sent".format(
analysis_count, mux_count)
mux_id = mux_status['mux_id']
out_dir = analysis['out_dir']
if mux_status.get('Status', None) == "FAILED":
logger.info("bcl2fastq for MUX %s from %s failed. ",
mux_status['mux_id'], run_number)
subject = 'bcl2fastq: ' + mux_id
body = "bcl2fastq for {} from {} failed.".format(
mux_id, run_number)
body += "\n\nPlease check the logs under {}".format(
out_dir + "/logs")
send_mail(subject, body, mail_to, ccaddr="rpd")
num_emails += 1
update_mongodb_email(db, run_number, analysis_id,
email_sent_query, True)
elif mux_status.get('Status', None) == "SUCCESS":
muxdir = os.path.join(out_dir, 'out',
mux_status.get('mux_dir'))
summary = path_to_url(
os.path.join(muxdir, 'html/index.html'))
body = "bcl2fastq for {} from {} successfully completed.".format(
mux_id, run_number)
body += "\n\nA summary can be found at {}".format(summary)
body += "\n\nFastQ files are located in {}".format(muxdir)
body += "\n\nData can also be downloaded from GIS-SRA (once archival is complete)"
confinfo = os.path.join(out_dir, 'conf.yaml')
#print(body)
if not os.path.exists(confinfo):
logger.fatal(
"conf info '%s' does not exist"
" under run directory.", confinfo)
continue
subject = 'bcl2fastq'
if args.testing:
subject += ' testing'
if is_devel_version():
subject += ' devel'
subject += ': ' + mux_id
send_mail(subject, body, mail_to,
ccaddr="rpd") # mail_to already set
if not args.testing and not is_devel_version():
requestor = get_requestor(mux_id, confinfo)
if requestor is not None:
#requestor = "rpd"
#subject += " (instead of requestor)"
#send_mail(subject, body, requestor, ccaddr="rpd")
send_mail(subject, body, requestor)
num_emails += 1
update_mongodb_email(db, run_number, analysis_id,
email_sent_query, True)
# close the connection to MongoDB
connection.close()
logger.info("%d emails sent", num_emails)
def main():
"""main function
"""
bcl2fastq_qc_script = os.path.abspath(os.path.join(
os.path.dirname(sys.argv[0]), "bcl2fastq_qc.py"))
assert os.path.exists(bcl2fastq_qc_script)
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-t', "--testing", action='store_true',
help="Use MongoDB test server")
default = 14
parser.add_argument('-w', '--win', type=int, default=default,
help="Number of days to look back (default {})".format(default))
parser.add_argument('-n', "--dry-run", action='store_true',
help="Dry run")
parser.add_argument('--no-mail', action='store_true',
help="Don't send email on detected failures")
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
if not is_production_user():
logger.warning("Not a production user. Skipping DB update")
sys.exit(1)
connection = mongodb_conn(args.testing)
if connection is None:
sys.exit(1)
db = connection.gisds.runcomplete
epoch_present, epoch_back = generate_window(args.win)
results = db.find({"analysis.Status": "SUCCESS", "analysis.QC_status" : {"$exists": 0},
"timestamp": {"$gt": epoch_back, "$lt": epoch_present}})
logger.info("Found %s runs", results.count())
for record in results:
run_number = record['run']
analysis = record['analysis']
#for analysis in record['analysis']:
for (analysis_count, analysis) in enumerate(record['analysis']):
out_dir = analysis["out_dir"]
analysis_id = analysis['analysis_id']
status = analysis['Status']
#Check if bcl2Fastq is completed successfully
if analysis['Status'] != "SUCCESS":
logger.info("Analysis is not completed successfully under %s", out_dir)
continue
if not os.path.exists(out_dir):
logger.critical("Following directory listed in DB doesn't exist: %s", out_dir)
continue
if args.testing:
bcl2fastq_qc_out = os.path.join(out_dir, "bcl2fastq_qc.test.txt")
else:
bcl2fastq_qc_out = os.path.join(out_dir, "bcl2fastq_qc.txt")
if os.path.exists(bcl2fastq_qc_out):
logger.critical("Refusing to overwrite existing file %s. Skipping QC check", bcl2fastq_qc_out)
continue
bcl2fastq_qc_cmd = [bcl2fastq_qc_script, '-d', out_dir]
if args.no_mail:
bcl2fastq_qc_cmd.append("--no-mail")
if args.dry_run:
logger.warning("Skipped following run: %s", out_dir)
continue
try:
QC_status = "analysis.{}.QC_status".format(analysis_count)
status = subprocess.check_output(bcl2fastq_qc_cmd, stderr=subprocess.STDOUT)
if "QC_FAILED" in str(status):
db.update({"run": run_number, 'analysis.analysis_id' : analysis_id},
{"$set": {QC_status: "FAILED"}})
logger.info("Demux QC failed for run: %s", run_number)
else:
db.update({"run": run_number, 'analysis.analysis_id' : analysis_id},
{"$set": {QC_status: "SUCCESS"}})
logger.info("Demux QC SUCCESS for run: %s", run_number)
with open(bcl2fastq_qc_out, 'w') as fh:
fh.write(status.decode())
except subprocess.CalledProcessError as e:
logger.fatal("The following command failed with return code %s: %s",
e.returncode, ' '.join(bcl2fastq_qc_cmd))
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Exiting")
connection.close()