def __init__(self, use_dev_lims=True):
self.log = logging.getLogger(__name__)
self.lims_server = glsclient.SERVER
if use_dev_lims:
self.lims_server = glsclient.TEST_SERVER
self.glsutil = glsclient.GlsUtil(server=self.lims_server)
self.log.info('*** CONNECT TO GLS LIMS ********************************************************')
def main():
# get the options
parser = argparse.ArgumentParser()
parser.add_argument("--update", dest="update", action="store_true", default=False, help="use this option to preform the update and not only report action")
parser.add_argument("--limsprod", dest="limsprod", action="store_true", default=False, help="Use the production LIMS url, by default it runs against the dev server.")
parser.add_argument("--logfile", dest="logfile", action="store", default=False, help="File to print logging information")
options = parser.parse_args()
# logging configuration
if options.logfile:
log = logger.get_custom_logger(options.logfile)
else:
log = logger.get_custom_logger()
log.setLevel('INFO')
try:
# connect to lims
if options.limsprod:
lims_server = glsclient.SERVER
else:
lims_server = glsclient.TEST_SERVER
log.info('Connected to ' + lims_server)
glsutil = glsclient.GlsUtil(server=lims_server)
# count number of artifacts to modify
count = 0
# get all artifacts to modify in results
glsutil.db.execute(QUERY)
results = glsutil.db.fetchall()
for row in results:
count += 1
artifact = glsutil.api.load('artifact', row['luid'])
field_name = 'LPS Billable'
field_value = None
for field in artifact.field:
if field.name == field_name:
field_value = field.value()
field_new_value = row['outlpsbillable']
log.info("[%s] Retrieved artifact %s, field '%s' value '%s' will be set to '%s'" % (count, artifact.uri, field_name, field_value, field_new_value))
if options.update:
new_field = glsapi.userdefined.field(row['outlpsbillable'])
new_field.name = field_name
artifact.field.append(new_field)
log.debug(artifact.toxml('utf-8'))
updated_artifact = glsutil.api.update(artifact)
log.info("[%s] '%s' changed from '%s' to '%s' on artifact %s" % (count, field_name, field_value, field_new_value, updated_artifact.uri))
except:
log.exception("Unexpected error")
raise
def main():
# get the options
parser = argparse.ArgumentParser()
parser.add_argument("--update", dest="update", action="store_true", default=False, help="use this option to preform the update and not only report action")
parser.add_argument("--limsprod", dest="limsprod", action="store_true", default=False, help="Use the production LIMS url, by default it runs against the dev server.")
parser.add_argument("--logfile", dest="logfile", action="store", default=False, help="File to print logging information")
options = parser.parse_args()
# logging configuration
if options.logfile:
log = logger.get_custom_logger(options.logfile)
else:
log = logger.get_custom_logger()
log.setLevel('INFO')
try:
# connect to lims
if options.limsprod:
lims_server = glsclient.SERVER
else:
lims_server = glsclient.TEST_SERVER
log.info('Connected to ' + lims_server)
glsutil = glsclient.GlsUtil(server=lims_server)
# count number of accounts to modify
count = 0
# get all accounts
all_accounts = glsutil.api.list('lab')
field_name = 'Email Address for Billing Notifications'
for account in all_accounts.lab:
lab = glsutil.api.load_by_uri('lab', account.uri)
try:
if lab.billing_address.institution == 'University of Cambridge MRC Cancer Unit':
count += 1
log.info(lab.billing_address.institution)
field_value = None
for field in lab.field:
if field.name == field_name:
field_value = field.value()
log.info(field_value)
if options.update:
field_new_value = '[email protected], [email protected]'
new_field = glsapi.userdefined.field(field_new_value)
new_field.name = field_name
lab.field.append(new_field)
log.debug(lab.toxml('utf-8'))
updated_lab = glsutil.api.update(lab)
log.info("[%s] '%s' changed from '%s' to '%s' on account %s" % (count, field_name, field_value, field_new_value, updated_lab.uri))
except AttributeError:
log.error(account.name)
continue
except:
log.exception("Unexpected error")
raise
def main():
# get the options
parser = argparse.ArgumentParser()
parser.add_argument("--update", dest="update", action="store_true", default=False, help="use this option to preform the update and not only report action")
parser.add_argument("--updatesamples", dest="updatesamples", action="store_true", default=False, help="use this option to set the date received on sample and not only report action")
parser.add_argument("--limsdev", dest="limsdev", action="store_true", default=False, help="Use the development LIMS url")
parser.add_argument("--email", dest="email", action="store_true", default=False, help="Send email to genomics on MiSeq Express samples")
parser.add_argument("--logfile", dest="logfile", action="store", default=False, help="File to print logging information")
options = parser.parse_args()
# logging configuration
if options.logfile:
log = logger.get_custom_logger(options.logfile)
else:
log = logger.get_custom_logger()
try:
# connect to lims
lims_server = glsclient.SERVER
if options.limsdev:
lims_server = glsclient.TEST_SERVER
glsutil = glsclient.GlsUtil(server=lims_server)
glsutil.db.execute(glssql.UNASSIGNED_SAMPLES_QUERY)
results = glsutil.db.fetchall()
count = 0
count_miseqexpress = 0
count_nextseqdirect = 0
count_unknownworkflow = 0
report_assignedsamples = ''
report_unassignedsamples = ''
# MiSeq Express report to include: SLXID | username | workflow | entype | seqtype
report_miseqexpresssamples = 'SLX-ID\t| project\t| researcher\t| read length\t| seq. type\n'
# NextSeq Direct report to include: SLXID | username | workflow | entype | seqtype
report_nextseqdirectsamples = 'SLX-ID\t| project\t| researcher\t| read length\t| seq. type\n'
# Unassigned samples report to include: SLXID | username | workflow | entype | seqtype
report_unknownworkflowsamples = 'SLX-ID\t| project\t| researcher\t| read length\t| seq. type\n'
for row in results:
# projectname,researchername,artifactid,samplename,slxid,workflow,readlength,seqtype,seqinfo,submissiondate,email
try:
# update sample date received if empty
if row['submissiondate'] is None or row['submissiondate'] == '':
log.info('No date received on sample %s' % row['samplename'])
if options.updatesamples:
artifact = glsutil.api.load('artifact', row['artifactid'])
sample = glsutil.api.load('sample', artifact.sample[0].limsid)
sample.date_received = str(datetime.date.today())
log.debug(sample.toxml('utf-8'))
updated_sample = glsutil.api.update(sample)
log.info('Date set to %s on sample %s' % (updated_sample.date_received, updated_sample.name))
log.debug(updated_sample.toxml('utf-8'))
# assign samples to workflow
if row['workflow'] in WORKFLOW_MAPPING.keys():
details = "[%s,%s,%s,%s,%s] to be assigned to workflow '%s'" % (row['artifactid'], row['projectname'], row['samplename'], row['slxid'], row['workflow'], WORKFLOW_MAPPING[row['workflow']])
detailed_info_for_report = "%s\t| %s\t| %s\t| %s\t| %s" % (row['slxid'], row['projectname'], row['researcher'], row['readlength'], row['seqtype'])
report_assignedsamples += details + "\n"
log.info(details)
if options.update:
workflows = glsutil.api.list_filter_by_name('workflow', WORKFLOW_MAPPING[row['workflow']])
workflow = workflows.workflow[0]
log.debug(workflow)
artifact = glsutil.api.load('artifact', row['artifactid'])
glsutil.route_each_artifact_to_workflow([artifact.uri], WORKFLOW_MAPPING[row['workflow']])
count += 1
if row['workflow'] == 'MiSeq Express':
log.debug(detailed_info_for_report)
report_miseqexpresssamples += detailed_info_for_report + "\n"
count_miseqexpress += 1
if row['workflow'].startswith('NextSeq Direct') or row['workflow'].startswith('NextSeq Express'):
log.debug(detailed_info_for_report)
report_nextseqdirectsamples += detailed_info_for_report + "\n"
count_nextseqdirect += 1
else:
details = "[%s,%s,%s,%s,%s] not assigned" % (row['artifactid'], row['projectname'], row['samplename'], row['slxid'], row['workflow'])
detailed_info_for_report = "%s\t| %s\t| %s\t| %s\t| %s\t| %s" % (row['slxid'], row['projectname'], row['researcher'], row['readlength'], row['seqtype'], row['workflow'])
report_unassignedsamples += details + "\n"
log.warn(details)
report_unknownworkflowsamples += detailed_info_for_report + "\n"
count_unknownworkflow += 1
except:
log.exception("Unexpected error")
continue
# email sent to genomics for MiSeq Express
report_miseqexpresssamples = "%s samples assigned to MiSeq Express workflow:\n\n" % count_miseqexpress + report_miseqexpresssamples
if options.email and count_miseqexpress > 0:
send_email('MiSeq Express', report_miseqexpresssamples)
log.info('MISEQ EXPRESS REPORT')
log.info(report_miseqexpresssamples)
# email sent to genomics for NextSeq Direct
report_nextseqdirectsamples = "%s samples assigned to NextSeq Express workflow:\n\n" % count_nextseqdirect + report_nextseqdirectsamples
if options.email and count_nextseqdirect > 0:
send_email('NextSeq Express', report_nextseqdirectsamples)
log.info('NEXTSEQ EXPRESS REPORT')
log.info(report_nextseqdirectsamples)
# email sent to genomics for unknown workflow
report_unknownworkflowsamples = "%s samples unassigned to workflow:\n\n" % count_unknownworkflow + report_unknownworkflowsamples
if options.email and count_unknownworkflow > 0:
send_email('Unknown Workflow', report_unknownworkflowsamples)
log.info('UNKNOWN WORKFLOW REPORT')
log.info(report_unknownworkflowsamples)
log.info("%s samples assigned to workflows over %s" % (count, len(results)))
log.info("%s samples assigned to MiSeq Express workflow" % count_miseqexpress)
log.info("%s samples assigned to NextSeq Direct workflow" % count_nextseqdirect)
log.info("%s samples unassigned to any workflow" % count_unknownworkflow)
if not options.update:
log.info('use --update to perform the operation in the lims')
print report_assignedsamples
print report_unassignedsamples
except:
log.exception("Unexpected error")
raise
def main():
# get the options
parser = argparse.ArgumentParser()
parser.add_argument("--stagingdir",
dest="stagingdir",
action="store",
help="staging base directories e.g. '/staging'",
required=True)
parser.add_argument(
"--dry-run",
dest="dry_run",
action="store_true",
default=False,
help=
"use this option to not do any shell command execution, only report actions"
)
parser.add_argument("--dev-lims",
dest="use_limsdev",
action="store_true",
default=False,
help="Use the development LIMS url")
parser.add_argument("--logfile",
dest="logfile",
action="store",
default=False,
help="File to print logging information")
parser.add_argument("--nologemail",
dest="nologemail",
action="store_true",
default=False,
help="turn off sending log emails on error")
options = parser.parse_args()
# logging configuration
log = logger.get_custom_logger(options.logfile, options.nologemail)
# connect to lims
lims_server = glsclient.SERVER
if options.use_limsdev:
lims_server = glsclient.TEST_SERVER
glsutil = glsclient.GlsUtil(server=lims_server)
glsutil.db.execute(glssql.PUBLISHED_RUNS_WITHOUT_FASTQ_ATTACHED)
results = glsutil.db.fetchall()
if results:
for r in results:
run_folder = r['run_id']
if os.path.exists(os.path.join(options.stagingdir, run_folder)):
log.error(
"Published run %s on staging area %s without sample FASTQ files"
% (run_folder, options.stagingdir))
else:
log.warning(
"Published run %s not on staging area %s without sample FASTQ files"
% (run_folder, options.stagingdir))
glsutil.close_db_connection()
def main():
# get the options
parser = argparse.ArgumentParser()
parser.add_argument(
"--mapping",
dest="mapping",
action="store",
help=
"mapping file, tab separated columns with old/new header '/path/to/mapping/file/mapping.txt'",
required=True)
parser.add_argument("--field",
dest="field",
action="store",
help="sample UDF name e.g. 'Billing Information'",
required=True)
parser.add_argument(
"--update",
dest="update",
action="store_true",
default=False,
help="use this option to preform the update and not only report action"
)
parser.add_argument(
"--limsprod",
dest="limsprod",
action="store_true",
default=False,
help=
"Use the production LIMS url, by default it runs against the dev server."
)
parser.add_argument("--logfile",
dest="logfile",
action="store",
default=False,
help="File to print logging information")
options = parser.parse_args()
# logging configuration
if options.logfile:
log = logger.get_custom_logger(options.logfile)
else:
log = logger.get_custom_logger()
log.setLevel('INFO')
try:
# read mapping file
mappings = []
with open(options.mapping, "U") as f:
reader = csv.DictReader(f, delimiter='\t')
for line in reader:
mappings.append(line)
log.info(mappings)
# connect to lims
if options.limsprod:
lims_server = glsclient.SERVER
else:
lims_server = glsclient.TEST_SERVER
log.info('Connected to ' + lims_server)
glsutil = glsclient.GlsUtil(server=lims_server)
# count number of samples to modify
count = 0
# loop over all changes in mapping file
for mapping in mappings:
# get all samples to modify in results
glsutil.db.execute(SAMPLES_QUERY % (options.field, mapping['old']))
results = glsutil.db.fetchall()
for row in results:
count += 1
sample = glsutil.api.load('sample', row['luid'])
log.info(
"[%s] Retrieved sample %s, field '%s' has old value '%s', it will be changed to '%s'"
% (count, sample.uri, options.field, mapping['old'],
mapping['new']))
if options.update:
new_field = glsapi.userdefined.field(mapping['new'])
new_field.name = options.field
sample.field.append(new_field)
log.debug(sample.toxml('utf-8'))
updated_sample = glsutil.api.update(sample)
log.info(
"[%s] '%s' changed from '%s' to '%s' on sample %s" %
(count, options.field, mapping['old'], mapping['new'],
updated_sample.uri))
except:
log.exception("Unexpected error")
raise
def main():
# get the options
parser = argparse.ArgumentParser()
parser.add_argument("--send-email",
dest="send_email",
action="store_true",
default=False,
help="Send email")
parser.add_argument("--logfile",
dest="logfile",
action="store",
default=False,
help="File to print logging information")
options = parser.parse_args()
# logging configuration
if options.logfile:
log = logger.get_custom_logger(options.logfile)
else:
log = logger.get_custom_logger()
log.setLevel('INFO')
try:
# connect to lims
lims_server = glsclient.SERVER
log.info('Connected to ' + lims_server)
glsutil = glsclient.GlsUtil(server=lims_server)
current_group_name = ''
account_list = ''
account_members = ''
report = ''
fail_report = ''
for account in get_group_accounts(glsutil):
if current_group_name != account['group_name']:
if current_group_name and account_list:
log.info('----------')
log.info(current_group_name)
log.info(account['leader_emails'])
log.info(account['approver_emails'])
log.info(account_list)
if account['leader_emails']:
report += 'OK\t%s\t%s\t%s\n' % (
current_group_name, account['leader_emails'],
account_members)
send_email(log, current_group_name,
account['leader_emails'].split(','),
account_list, options.send_email)
else:
log.error('Account without leader')
fail_report += 'FAIL\t%s\t%s\t%s\n' % (
current_group_name, account['leader_emails'],
account_members)
current_group_name = account['group_name']
account_list = ''
account_members = ''
account_list += '- %s <%s>\n' % (account['researcher'],
account['email'])
account_members += '%s <%s>,' % (account['researcher'],
account['email'])
log.info(report)
log.info(fail_report)
except:
log.exception("Unexpected error")
raise
def main():
# get the options
parser = argparse.ArgumentParser()
parser.add_argument(
"--update",
dest="update",
action="store_true",
default=False,
help="use this option to preform the update and not only report action"
)
parser.add_argument("--limsdev",
dest="limsdev",
action="store_true",
default=False,
help="Use the development LIMS url")
parser.add_argument("--logfile",
dest="logfile",
action="store",
default=False,
help="File to print logging information")
options = parser.parse_args()
# logging configuration
if options.logfile:
log = logger.get_custom_logger(options.logfile)
else:
log = logger.get_custom_logger()
try:
# connect to lims
if options.limsdev:
lims_server = 'limsdev'
else:
lims_server = 'lims'
glsutil = glsclient.GlsUtil(server=lims_server)
results = glsutil.db.execute(
glssql.SAMPLES_WITH_NODATE_QUERY).fetchall()
for row in results:
# artifactid,samplename,submissiondate,acceptancedate
try:
# update sample date received if empty
if row.submissiondate is None or row.submissiondate == '':
log.info(
'No date received on sample %s. It will be set to %s.'
% (row.samplename, row.acceptancedate))
if options.update:
artifact = glsutil.api.load('artifact', row.artifactid)
sample = glsutil.api.load('sample',
artifact.sample[0].limsid)
sample.date_received = row.acceptancedate
log.debug(sample.toxml('utf-8'))
updated_sample = glsutil.api.update(sample)
log.info('Date set to %s on sample %s' %
(updated_sample.date_received,
updated_sample.name))
log.debug(updated_sample.toxml('utf-8'))
except:
log.exception("Unexpected error")
continue
except:
log.exception("Unexpected error")
raise