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)