def __init__(self, fname, workdir=None, update=False, nobuild=False, index=None):
"""
Create the PositionalData
"""
self.fname = fname
self.db = None
# split the incoming name to find the real name, and base directory
basedir, basename = os.path.split(self.fname)
# the index may be stored in the workdir if it was specified
basedir = workdir or basedir
# this is the HDF index name that the file operates on
self.index = index or conf.path_join(basedir, "%s.hdf" % basename)
# debug messages
logger.debug("file path %s" % self.fname)
logger.debug("index path %s" % self.index)
# no building permitted
if nobuild and missing(self.index):
raise Exception("No autobuild allowed and no index found at %s" % self.index)
# creating indices if these are missing or an update is forced
if update or missing(self.index):
self.build()
# operates on the HDF file
self.db = openFile(self.index, mode="r")
self.root = self.db.root
# shows the internal labels
logger.debug("index labels -> %s" % self.labels)
def galaxy(request):
"""
Returns a data view based on a galaxy forward
"""
# validates a filename
filename, encoded, hashkey, dataid, galaxy_url = validate_filename(request)
# access the data on the filesystem
# extract the work directory from the filename
path, fname = os.path.split(filename)
name, ext = os.path.splitext(fname)
workdir = conf.path_join(path, name+"_files")
print workdir
index = hdflib.PositionalData(fname='', index=filename, nobuild=True, workdir=workdir)
#url = urlib.urlencode()
url = "/galaxy/?filename=%s&hashkey=%s&input=%s&GALAXY_URL=%s" % (encoded, hashkey, dataid, galaxy_url)
return browser(request=request, index=index, url=url, dataid=dataid, galaxy_url=galaxy_url)
def __init__(self,
fname,
workdir=None,
update=False,
nobuild=False,
index=None):
"""
Create the PositionalData
"""
self.fname = fname
self.db = None
# split the incoming name to find the real name, and base directory
basedir, basename = os.path.split(self.fname)
# the index may be stored in the workdir if it was specified
basedir = workdir or basedir
# this is the HDF index name that the file operates on
self.index = index or conf.path_join(basedir, '%s.hdf' % basename)
# debug messages
logger.debug('file path %s' % self.fname)
logger.debug('index path %s' % self.index)
# no building permitted
if nobuild and missing(self.index):
raise Exception('No autobuild allowed and no index found at %s' %
self.index)
# creating indices if these are missing or an update is forced
if update or missing(self.index):
self.build()
# operates on the HDF file
self.db = openFile(self.index, mode='r')
self.root = self.db.root
# shows the internal labels
logger.debug('index labels -> %s' % self.labels)
# exclusion mode
if options.exclude:
targets = [name for name in all_tests() if name not in targets]
if options.verbosity == 0:
logger.disable('INFO')
elif options.verbosity == 1:
logger.disable('DEBUG')
elif options.verbosity >= 2:
logger.disable(None)
# cleans full entire test directory
if options.reset:
conf.reset_dir(conf.TEMP_DATA_DIR)
# run all the tests
if options.coverage:
coverdir = conf.path_join(conf.TEST_DIR, 'coverage')
good, bad, skip = testutil.generate_coverage(run,
coverdir,
targets=targets,
options=options)
else:
good, bad, skip = run(targets=targets, options=options)
if bad:
sys.exit(-1)
sys.exit(0)
targets = [ t.rstrip(".py") for t in targets ]
# exclusion mode
if options.exclude:
targets = [ name for name in all_tests() if name not in targets ]
if options.verbosity == 0:
logger.disable('INFO')
elif options.verbosity == 1:
logger.disable('DEBUG')
elif options.verbosity >= 2:
logger.disable(None)
# cleans full entire test directory
if options.reset:
conf.reset_dir(conf.TEMP_DATA_DIR)
# run all the tests
if options.coverage:
coverdir = conf.path_join(conf.TEST_DIR, 'coverage')
good, bad, skip = testutil.generate_coverage(run, coverdir,
targets=targets,
options=options)
else:
good, bad, skip = run(targets=targets, options=options)
if bad:
sys.exit(-1)
sys.exit(0)
def thumbpath(self):
"Thumbnail image path"
return conf.path_join(settings.THUMB_IMAGE_DIR, self.thumbname)
