Python is_hdf5_file Examples

Example #1

    def run(self, **kwargs):
        is_json = not is_hdf5_file(kwargs['table'])

        if kwargs['format_version'] in [None, 'None']:
            if is_json:
                kwargs['format_version'] = '1.0.0'
            else:
                kwargs['format_version'] = '2.1'
        else:
            if is_json:
                raise ValueError("Only format 1.0.0 is valid for JSON")

            fmt_ver = [int(v) for v in kwargs['format_version'].split('.')]
            if tuple(fmt_ver) not in self.HDF5FormatVersions:
                raise ValueError("Unrecognized format version: %s" %
                                 kwargs['format_version'])

        with biom_open(kwargs['table']) as f:
            if is_json:
                kwargs['table'] = json.load(f)
                return self._validate_json(**kwargs)
            elif HAVE_H5PY:
                import h5py
                kwargs['table'] = f

                if not isinstance(f, h5py.File):
                    print("Attempting to validate an HDF5 BIOM table, but the "
                          "table does not appear to be in HDF5 format!")
                    sys.exit(1)
                return self._validate_hdf5(**kwargs)
            else:
                raise IOError("h5py is not installed, can only validate JSON "
                              "tables")

Example #2

File: table_validator.py Project: MZ-CY-Han1998/biom-format

    def run(self, **kwargs):
        is_json = not is_hdf5_file(kwargs['table'])

        if kwargs['format_version'] in [None, 'None']:
            if is_json:
                kwargs['format_version'] = '1.0.0'
            else:
                kwargs['format_version'] = '2.1'
        elif is_json:
            if kwargs['format_version'] != "1.0.0":
                raise ValueError("Only format 1.0.0 is valid for JSON")
        else:
            fmt_ver = [int(v) for v in kwargs['format_version'].split('.')]
            if tuple(fmt_ver) not in self.HDF5FormatVersions:
                raise ValueError("Unrecognized format version: %s" %
                                 kwargs['format_version'])

        with biom_open(kwargs['table']) as f:
            if is_json:
                kwargs['table'] = json.load(f)
                return self._validate_json(**kwargs)
            elif HAVE_H5PY:
                import h5py
                kwargs['table'] = f

                if not isinstance(f, h5py.File):
                    print("Attempting to validate an HDF5 BIOM table, but the "
                          "table does not appear to be in HDF5 format!")
                    sys.exit(1)
                return self._validate_hdf5(**kwargs)
            else:
                raise IOError("h5py is not installed, can only validate JSON "
                              "tables")

Example #3

File: test_util.py Project: TankMermaid/biom-format

 def test_is_hdf5_file(self):
     self.assertTrue(is_hdf5_file(get_data_path('test.biom')))
     self.assertFalse(is_hdf5_file(get_data_path('test.json')))

Example #4

File: test_util.py Project: antgonza/biom-format

 def test_is_hdf5_file(self):
     self.assertTrue(is_hdf5_file(get_data_path('test.biom')))
     self.assertFalse(is_hdf5_file(get_data_path('test.json')))