def addSample(self, newSampleName,newSampleRefType=None):
#
# Imports
#
import sys
import time
#
# open connection to database
#
self.getConnection()
sampleNames = []
sampleIds = []
#
# check if any of the fastqs already in database
#
data = self.c.execute('SELECT sampleId,sampleName,refType FROM samples').fetchall()
if data:
for (sampleId,sampleName,sampleRefType) in data:
#sampleName = sampleName[0]
sampleNames.append(sampleName)
sampleIds.append(sampleId)
if newSampleName in sampleNames:
msg = '#ERROR_MSG#'+time.strftime("%Y-%m-%d:%H:%M:%S",time.localtime())+'#'+str(self.analysispipe.masterPid)+'# SampleName must be uniq, there is already a sample with name '+newSampleName+' , exiting.\n'
self.analysispipe.logfile.write(msg)
sys.stderr.write(msg)
sys.exit(1)
if sampleIds: sampleId = max(sampleIds)+1
else: sampleId = 0
self.analysispipe.logfile.write('#LOGMSG#'+time.strftime("%Y-%m-%d:%H:%M:%S",time.localtime())+'#'+str(self.analysispipe.masterPid)+'# Adding sample '+newSampleName+' to database with id '+str(sampleId)+'.\n')
values = (sampleId,newSampleName,newSampleRefType)
self.c.execute('INSERT INTO samples VALUES (?,?,?)', values)
from sample import Sample
sample = Sample(sampleName=newSampleName, sampleId=sampleId,refType=newSampleRefType, analysispipe=self.analysispipe)
sample.createDirs()
self.commitAndClose()
return 0
