This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tool_util.verify.asserts.hdf5

import io

    import h5py
except ImportError:
    h5py = None

IMPORT_MISSING_MESSAGE = "h5 assertion requires unavailable optional dependency h5py"

def _assert_h5py():
    if h5py is None:
        raise Exception(IMPORT_MISSING_MESSAGE)

[docs]def assert_has_h5_attribute(output_bytes, key, value): """Asserts the specified HDF5 output has a given key-value pair as HDF5 attribute""" _assert_h5py() output_temp = io.BytesIO(output_bytes) local_attrs = h5py.File(output_temp, 'r').attrs assert key in local_attrs and str(local_attrs[key]) == value, ( "Not a HDF5 file or H5 attributes do not match:\n\t%s\n\n\t(%s : %s)" % (local_attrs.items(), key, value))
[docs]def assert_has_h5_keys(output_bytes, keys): """ Asserts the specified HDF5 output has the given keys.""" _assert_h5py() keys = [k.strip() for k in keys.strip().split(',')] h5_keys = sorted(keys) output_temp = io.BytesIO(output_bytes) local_keys = [] def append_keys(key): local_keys.append(key) return None h5py.File(output_temp, 'r').visit(append_keys) missing = 0 for key in h5_keys: if key not in local_keys: missing += 1 assert missing == 0, "Not a HDF5 file or H5 keys missing:\n\t%s\n\t%s" % (local_keys, h5_keys)