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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: bytes, key: str, value: str) -> None: """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 ), f"Not a HDF5 file or H5 attributes do not match:\n\t{list(local_attrs.items())}\n\n\t({key} : {value})"
# TODO the function actually queries groups. so the function and argument name are misleading
[docs]def assert_has_h5_keys(output_bytes: bytes, keys: str) -> None: """Asserts the specified HDF5 output has the given keys.""" _assert_h5py() h5_keys = sorted([k.strip() for k in keys.strip().split(",")]) 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, f"Not a HDF5 file or H5 keys missing:\n\t{local_keys}\n\t{h5_keys}"