def process(self, f):
from django.conf import settings
dummies = Sequence.objects.filter(user = self.user).filter(name = 'dummy')
if(len(dummies) == 0):
dummySeq = Sequence(seq = '', name = 'dummy', tag = '', user = self.user, submissionDate = time.strftime("%d/%m/%Y"), seqProc = False)
else:
dummySeq = dummies[0]
newJob = Sequence_jobs(seq = dummySeq, user = self.user)
newJob.jobType = 'mass_seq'
newJob.jobTypeVerbose = 'Mass Sequence Submission'
newJob.status = 'submitted'
import os
from extraFuncs import create_path
newJob.outdir = os.path.normpath("%s/%d/%s/%s/" % (settings.DAEMON_OUT_PATH, newJob.user.pk, 'nonseq', newJob.jobType))
newJob.progressFile = os.path.join(newJob.outdir, 'progress.txt')
if(Sequence_jobs.objects.filter(seq = newJob.seq, jobType = newJob.jobType).exists()):
newJob.status = 'ar'
return newJob
#Make input files
inputFileName = "%d_%s_%s" % (newJob.user.pk, 'nonseq', newJob.jobType)
inputFilePath = os.path.normpath("%s/%d/%s/%s/" % (settings.DAEMON_IN_PATH, newJob.user.pk, 'nonseq', newJob.jobType))
create_path(inputFilePath)
#Input File
with open(os.path.join(inputFilePath, inputFileName), 'w') as f:
f.write('User %s\n' % newJob.user.username)
f.write('First %s\n' % newJob.user.first_name)
f.write('Last %s\n' % newJob.user.last_name)
f.write('Email %s\n' % newJob.user.email)
f.write('JobName %s\n' % os.path.splitext(os.path.basename(inputFilePath))[0])
f.write('JobType %s\n' % newJob.jobType)
f.write('JobExe %s\n' % settings.CAMPARI_PATH)
f.write('JobParameters %s\n' % newJob.jobParameters)
f.write('OutDir %s\n' % newJob.outdir)
f.close()
#Progress File
with open(os.path.join(inputFilePath, 'progress.txt'), 'w') as f:
f.write('submitted')
f.close()
#Sequence File
seqFilePath = os.path.join(inputFilePath, 'seqfile.txt')
def handle_uploaded_file(outpath,f):
with open(outpath, 'wb+') as destination:
for chunk in f.chunks():
destination.write(chunk)
handle_uploaded_file(seqFilePath,f)
newJob.jobParameters = '-s %s' % (seqFilePath)
newJob.save()
return newJob
def launchJob(self):
from django.conf import settings
seqchoice = self.cleaned_data['seq']
newJob = Sequence_jobs(seq = seqchoice, user = self.user)
newJob.jobType = 'hetero'
newJob.jobTypeVerbose = 'FRC Trajectory Generation'
newJob.jobParameters = '-k %s' % (settings.HETERO_KEY)
newJob.status = 'submitted'
import os
from extraFuncs import create_path
newJob.outdir = os.path.normpath("%s/%d/%d/%s/" % (settings.DAEMON_OUT_PATH, newJob.user.pk, newJob.seq.pk, newJob.jobType))
newJob.progressFile = os.path.join(newJob.outdir, 'progress.txt')
if(Sequence_jobs.objects.filter(seq = newJob.seq, jobType = newJob.jobType).exists()):
newJob.status = 'ar'
return newJob
#Make input files
inputFileName = "%d_%d_%s" % (newJob.user.pk, newJob.seq.pk, newJob.jobType)
inputFilePath = os.path.normpath("%s/%d/%d/%s/" % (settings.DAEMON_IN_PATH, newJob.user.pk, newJob.seq.pk, newJob.jobType))
create_path(inputFilePath)
#Progress File
with open(os.path.join(inputFilePath, 'progress.txt'), 'w') as f:
f.write('submitted')
f.close()
#Sequence File
seqFilePath = os.path.join(inputFilePath, 'seq.in')
comp.Sequence(seqchoice.seq).makeCampariSeqFile(seqFilePath)
#Input File
with open(os.path.join(inputFilePath, inputFileName), 'w') as f:
f.write('User %s\n' % newJob.user.username)
f.write('First %s\n' % newJob.user.first_name)
f.write('Last %s\n' % newJob.user.last_name)
f.write('Email %s\n' % newJob.user.email)
f.write('JobName %s\n' % os.path.splitext(os.path.basename(inputFilePath))[0])
f.write('JobType %s\n' % newJob.jobType)
f.write('JobExe %s\n' % settings.CAMPARI_PATH)
f.write('JobParameters %s\n' % newJob.jobParameters)
f.write('OutDir %s\n' % newJob.outdir)
f.close()
newJob.save()
return newJob
def launchJob(self):
seqchoice = self.cleaned_data['seq']
newJob = Sequence_jobs(seq = seqchoice, user = self.user)
from django.conf import settings
if(self.cleaned_data['genPermutants']):
newJob.jobType = 'wlp'
newJob.jobTypeVerbose = 'Kappa Permutant Generation'
newJob.jobParameters = '' #these are initialized as empty until input files are generated
else:
newJob.jobType = 'wl'
newJob.jobTypeVerbose = 'Kappa Density of States'
newJob.jobParameters = '' #these are initialized as empty until input files are generated
newJob.status = 'submitted'
import os
from extraFuncs import create_path
newJob.outdir = os.path.normpath("%s/%d/%d/%s/" % (settings.DAEMON_OUT_PATH, newJob.user.pk, newJob.seq.pk, newJob.jobType))
newJob.progressFile = os.path.join(newJob.outdir, 'progress.txt')
if(Sequence_jobs.objects.filter(seq = newJob.seq, jobType = newJob.jobType).exists()):
newJob.status = 'ar'
return newJob
#Make input files
inputFileName = "%d_%d_%s" % (newJob.user.pk, newJob.seq.pk, newJob.jobType)
inputFilePath = os.path.normpath("%s/%d/%d/%s/" % (settings.DAEMON_IN_PATH, newJob.user.pk, newJob.seq.pk, newJob.jobType))
create_path(inputFilePath)
#Progress File
with open(os.path.join(inputFilePath, 'progress.txt'), 'w') as f:
f.write('submitted')
f.close()
#Sequence File
with open(os.path.join(inputFilePath, 'seqfile.txt'), 'w') as f:
f.write(seqchoice)
f.close()
newJob.jobParameters = '-s %s -o %s' % (os.path.join(inputFilePath, 'seqfile.txt'), inputFilePath)
'''
if(not frzfile is None):
newJob.jobParameters += ' -f %s' % (frzfile)
'''
#Input File
with open(os.path.join(inputFilePath, inputFileName), 'w') as f:
f.write('User %s\n' % newJob.user.username)
f.write('First %s\n' % newJob.user.first_name)
f.write('Last %s\n' % newJob.user.last_name)
f.write('Email %s\n' % newJob.user.email)
f.write('JobName %s\n' % os.path.splitext(os.path.basename(inputFilePath))[0])
f.write('JobType %s\n' % newJob.jobType)
f.write('JobExe %s\n' % settings.WL_PATH)
f.write('JobParameters %s\n' % newJob.jobParameters)
f.write('OutDir %s\n' % newJob.outdir)
f.close()
newJob.save()
return newJob