def execute(limit=1):
"""
Executes a job
"""
# no locking here for now, TODO
jobs = models.Job.objects.filter(status=status.WAITING).order_by('id')[0:limit]
for job in jobs:
#logger.info( 'executing %s' % job)
set_status(job, status=status.RUNNING)
else:
logger.info('no jobs are waiting')
# run the selected jobs
for job in jobs:
logger.info( 'executing %s' % job)
jobtype = job.json.get('type')
data = get_data(job)
try:
if jobtype == status.INDEXING_JOB:
jobdefs.indexing_job(data=data)
else:
raise Exception ("unknown jobtype")
job.delete()
except Exception, exc:
logger.error(exc)
set_error(exc, (data, job))
def result_save_trigger(sender, instance, signal, *args, **kwargs):
"""
Post save hook for results, creates the thumbnails
"""
if instance.image:
try:
# requires PIL
size = 300, 300
import Image
img = Image.open(instance.image.path)
img.thumbnail(size, Image.ANTIALIAS)
img.save(instance.thumbpath)
except Exception, exc:
logger.error(exc)
def load_users(fname, options):
"Loads users into the database"
if not os.path.isfile(fname):
logger.error('file not found %s' % fname)
return
if options.flush:
"Resets the database with fresh values"
flush_database()
# alters site settings
fix_site_settings()
# this will be the admin password
passwd = settings.SECRET_KEY
# check the lenght of secret key in non debug modes
if not settings.DEBUG and len(passwd) < 5:
msg = 'The value of the SECRET_KEY setting is too short. Please make it longer!'
logger.error(msg)
sys.exit()
# shorcut to user creatgion
user_get = User.objects.get_or_create
# read the file and create the users based on the data in it
stream = file(fname)
for row in csv.DictReader( stream ):
username, email, first_name, last_name = row['username'], row['email'], row['first_name'], row['last_name']
is_superuser = (row['is_superuser'] == 'yes')
user, flag = user_get(username=username, email=email, first_name=first_name, last_name=last_name, is_superuser=is_superuser, is_staff=is_superuser)
if flag:
logger.debug( 'created user: %s' % user.get_full_name() )
if username in ('admin', 'demo', 'public'):
# admin user will get the secret key as password
user.set_password(passwd)
else:
if options.test_mode:
# in testmode we will set known passwords
# used during functional testing
user.set_password( passwd + 'X')
else:
# all other users will need to reset their passwords
user.set_unusable_password()
user.save()
def stop(text):
"Unrecoverable error"
error(text)
sys.exit()
def transform(inpname, outname, format, shift=0, index=False, options=None):
"""
Transforms reads stored in bedfile to a genetrack input file.
Requires at least 6 bed columns to access the strand.
"""
# detect file formats
if format == "BED":
CHROM, START, END, STRAND = 0, 1, 2, 5
elif format == "GFF":
CHROM, START, END, STRAND = 0, 3, 4, 6
else:
raise Exception('Invalid file format' % format)
# two sanity checks, one day someone will thank me
if format == 'BED' and inpname.endswith('gff'):
raise Exception('BED format on a gff file?')
if format == 'GFF' and inpname.endswith('bed'):
raise Exception('GFF format on a bed file?')
# find the basename of the outputname
basename = os.path.basename(outname)
# two files store intermediate results
flat = conf.tempdata( '%s.flat' % basename )
sorted = conf.tempdata( '%s.sorted' % basename )
# check for track information on first line,
# much faster this way than conditional checking on each line
fp = file(inpname, 'rU')
first = fp.readline()
fp.close()
# create the reader
reader = csv.reader(file(inpname, 'rU'), delimiter='\t')
# skip if trackline exists
if first.startswith == 'track':
reader.next()
# unwind the comments
list(takewhile(lambda x: x[0].startswith('#'), reader))
# copious timing info for those who enjoy these
timer, full = util.Timer(), util.Timer()
logger.debug("parsing '%s'" % inpname)
logger.debug("output to '%s'" % outname)
# create the unsorted output file and apply corrections
logger.debug("unsorted flat file '%s'" % flat)
fp = file(flat, 'wt')
for linec, row in enumerate(reader):
try:
chrom, start, end, strand = row[CHROM], row[START], row[END], row[STRAND]
except Exception, exc:
first = row[0][0]
# may be hitting the end of the file with other comments
if first == '>':
break # hit the sequence content of the gff file
elif first == '#':
continue # hit upon some comments
else:
logger.error(row)
raise Exception(exc)
if strand == '+':
# on forward strand, 5' is at start
idx = int(start) + shift
fwd, rev, val = 1, 0, 1
elif strand == '-':
# on reverse strand, 5' is at end
idx = int(end) - shift
fwd, rev, val = 0, 1, 1
else:
# no strand specified, generate interval centers
idx = (int(start)+int(end))/2
fwd, rev, val = 0, 0, 1
# it is essential be able to sort the index as a string!
fp.write('%s\t%012d\t%s\t%s\t%s\n' % (chrom, idx, fwd, rev, val))
def error500(request):
"Server error page when debug flag is False"
context = RequestContext(request)
exc_type, exc_value, tb = sys.exc_info()
logger.error(exc_value)
return html.template( request, name='500.html', debug=exc_value )
def stop( text ):
"Unrecoverable error"
error ( text )
sys.exit()
