def main(args):
log = setupLog(args)
conf=get_conf(args.conf)
couch = DB.setupServer(conf)
db=couch['x_flowcells']
parser=cl.XTenParser(args.flowcell)
DB.update_doc(db,parser.obj)
def main(args):
log = setupLog(args)
conf = get_conf(args.conf)
couch = DB.setupServer(conf)
db = couch['x_flowcells']
parser = cl.XTenParser(args.flowcell)
DB.update_doc(db, parser.obj)
def upload_to_statusdb(run_dir):
"""
Triggers the upload to statusdb using the dependency flowcell_parser
:param string run_dir: the run directory to upload
"""
couch = fcpdb.setupServer(CONFIG)
db=couch[CONFIG['statusdb']['xten_db']]
parser=XTenParser(run_dir)
fcpdb.update_doc(db,parser.obj)
def _upload_to_statusdb(run):
""" Triggers the upload to statusdb using the dependency flowcell_parser
:param Run run: the object run
"""
couch = fcpdb.setupServer(CONFIG)
db = couch[CONFIG['statusdb']['xten_db']]
parser = run.runParserObj
# Check if I have NoIndex lanes
# This could be refactored and some checks for key exceptions should be added
for element in parser.obj['samplesheet_csv']:
if 'NoIndex' in element['index'] or not element[
'index']: # NoIndex in the case of HiSeq, empty in the case of HiSeqX
lane = element['Lane'] # this is a lane with NoIndex
# in this case PF Cluster is the number of undetermined reads
try:
PFclusters = parser.obj['Undetermined'][lane]['unknown']
except KeyError:
logger.error("While taking extra care of lane {} of NoIndex type " \
"I found out that not all values were available".format(lane))
continue
# In Lanes_stats fix the lane yield
parser.obj['illumina']['Demultiplex_Stats']['Lanes_stats'][
int(lane) - 1]['PF Clusters'] = str(PFclusters)
# Now fix Barcode lane stats
updated = 0 # Check that only one update is made
for sample in parser.obj['illumina']['Demultiplex_Stats'][
'Barcode_lane_statistics']:
if lane in sample['Lane']:
updated += 1
sample['PF Clusters'] = str(PFclusters)
if updated != 1:
logger.error(
"While taking extra care of lane {} of NoIndex type "
"I updated more than once the barcode_lane. "
"This is too much to continue so I will fail.".format(
lane))
os.sys.exit()
# If I am here it means I changed the HTML representation to something
# else to accomodate the wired things we do
# someone told me that in such cases it is better to put a place holder for this
parser.obj['illumina']['Demultiplex_Stats']['NotOriginal'] = "True"
# Update info about bcl2fastq tool
if not parser.obj.get('DemultiplexConfig'):
parser.obj['DemultiplexConfig'] = {
'Setup': {
'Software': run.CONFIG.get('bcl2fastq', {})
}
}
fcpdb.update_doc(db, parser.obj, over_write_db_entry=True)
def _upload_to_statusdb(run):
""" Triggers the upload to statusdb using the dependency flowcell_parser
:param Run run: the object run
"""
couch = fcpdb.setupServer(CONFIG)
db = couch[CONFIG['statusdb']['xten_db']]
parser = run.runParserObj
# Check if I have NoIndex lanes
# This could be refactored and some checks for key exceptions should be added
for element in parser.obj['samplesheet_csv']:
if 'NoIndex' in element['index'] or not element['index']: # NoIndex in the case of HiSeq, empty in the case of HiSeqX
lane = element['Lane'] # this is a lane with NoIndex
# in this case PF Cluster is the number of undetermined reads
try:
PFclusters = parser.obj['Undetermined'][lane]['unknown']
except KeyError:
logger.error("While taking extra care of lane {} of NoIndex type " \
"I found out that not all values were available".format(lane))
continue
# In Lanes_stats fix the lane yield
parser.obj['illumina']['Demultiplex_Stats']['Lanes_stats'][int(lane) - 1]['PF Clusters'] = str(PFclusters)
# Now fix Barcode lane stats
updated = 0 # Check that only one update is made
for sample in parser.obj['illumina']['Demultiplex_Stats']['Barcode_lane_statistics']:
if lane in sample['Lane']:
updated +=1
sample['PF Clusters'] = str(PFclusters)
if updated != 1:
logger.error("While taking extra care of lane {} of NoIndex type "
"I updated more than once the barcode_lane. "
"This is too much to continue so I will fail.".format(lane))
os.sys.exit()
# If I am here it means I changed the HTML representation to something
# else to accomodate the wired things we do
# someone told me that in such cases it is better to put a place holder for this
parser.obj['illumina']['Demultiplex_Stats']['NotOriginal'] = "True"
# Update info about bcl2fastq tool
if not parser.obj.get('DemultiplexConfig'):
parser.obj['DemultiplexConfig'] = {'Setup': {'Software': run.CONFIG.get('bcl2fastq',{})}}
fcpdb.update_doc( db , parser.obj, over_write_db_entry=True)