def xmlrpc_uploadmetrics(
self,
tfmapperstats_outputfile,
procPath,
beadPath,
filterPath,
alignmentSummaryPath,
peakOut,
QualityPath,
BaseCallerJsonPath,
primarykeyPath,
uploadStatusPath,
STATUS,
reportLink,
):
"""Upload Metrics to the database"""
from ion.reports import uploadMetrics
try:
uploadMetrics.writeDbFromFiles(
tfmapperstats_outputfile,
procPath,
beadPath,
filterPath,
alignmentSummaryPath,
STATUS,
peakOut,
QualityPath,
BaseCallerJsonPath,
primarykeyPath,
uploadStatusPath,
)
# this will replace the five progress squares with a re-analysis button
uploadMetrics.updateStatus(primarykeyPath, STATUS, reportLink)
except:
logging.error(traceback.format_exc())
return traceback.format_exc()
return 0
def xmlrpc_uploadmetrics(self,
tfmapperstats_outputfile,
procParams,
beadPath,
filterPath,
alignmentSummaryPath,
STATUS,
peakOut,
QualityPath,
BaseCallerJsonPath,
primarykeyPath,
uploadStatusPath,
message, boolean):
"""Upload Metrics to the database"""
from ion.reports import uploadMetrics
try:
uploadMetrics.writeDbFromFiles(
tfmapperstats_outputfile,
procParams,
beadPath,
filterPath,
alignmentSummaryPath,
STATUS,
peakOut,
QualityPath,
BaseCallerJsonPath,
primarykeyPath,
uploadStatusPath)
# this will replace the five progress squares with a re-analysis button
uploadMetrics.updateStatus(primarykeyPath, message, boolean)
except:
traceback.print_exc()
return 1
return 0
def xmlrpc_uploadmetrics(
self,
tfmapperstats_outputfile,
procPath,
beadPath,
ionstats_alignment_json_path,
ionParamsPath,
peakOut,
ionstats_basecaller_json_path,
BaseCallerJsonPath,
primarykeyPath,
uploadStatusPath,
STATUS,
reportLink,
cwd,
):
"""Upload Metrics to the database"""
from ion.reports import uploadMetrics
try:
return_message = uploadMetrics.writeDbFromFiles(
tfmapperstats_outputfile,
procPath,
beadPath,
ionstats_alignment_json_path,
ionParamsPath,
STATUS,
peakOut,
ionstats_basecaller_json_path,
BaseCallerJsonPath,
primarykeyPath,
uploadStatusPath,
cwd,
)
# this will replace the five progress squares with a re-analysis button
uploadMetrics.updateStatus(primarykeyPath, STATUS, reportLink)
except Exception as err:
logger.error("Upload Analysis Metrics failed: %s", err)
return traceback.format_exc()
return return_message
def xmlrpc_uploadmetrics(self,
tfmapperstats_outputfile,
procPath,
beadPath,
ionstats_alignment_json_path,
ionParamsPath,
peakOut,
ionstats_basecaller_json_path,
BaseCallerJsonPath,
primarykeyPath,
uploadStatusPath,
STATUS,
reportLink,
cwd):
"""Upload Metrics to the database"""
from ion.reports import uploadMetrics
try:
return_message = uploadMetrics.writeDbFromFiles(
tfmapperstats_outputfile,
procPath,
beadPath,
ionstats_alignment_json_path,
ionParamsPath,
STATUS,
peakOut,
ionstats_basecaller_json_path,
BaseCallerJsonPath,
primarykeyPath,
uploadStatusPath,
cwd)
# this will replace the five progress squares with a re-analysis button
uploadMetrics.updateStatus(primarykeyPath, STATUS, reportLink)
except Exception as err:
logger.error("Upload Analysis Metrics failed: %s", err)
return traceback.format_exc()
return return_message
