Unverified Commit e905161c authored by Nicola Soranzo's avatar Nicola Soranzo Committed by GitHub
Browse files

Merge pull request #12347 from nsoranzo/release_21.01_fix_Loom

parents 72f4531d 8a7ca520

lib/galaxy/datatypes/binary.py

+7 −1
Original line number Diff line number Diff line
@@ -16,6 +16,7 @@ from json import dumps 
from typing import Optional



import h5py

import numpy as np

import pysam

import pysam.bcftools

from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP
@@ -928,7 +929,12 @@ class Loom(H5): 
                dataset.metadata.description = loom_file.attrs.get('description')

                dataset.metadata.url = loom_file.attrs.get('url')

                dataset.metadata.doi = loom_file.attrs.get('doi')

                dataset.metadata.loom_spec_version = loom_file.attrs.get('LOOM_SPEC_VERSION')

                loom_spec_version = loom_file.attrs.get('LOOM_SPEC_VERSION')

                if isinstance(loom_spec_version, np.ndarray):

                    loom_spec_version = loom_spec_version[0]

                    if isinstance(loom_spec_version, bytes):

                        loom_spec_version = loom_spec_version.decode()

                dataset.metadata.loom_spec_version = loom_spec_version

                dataset.creation_date = loom_file.attrs.get('creation_date')

                dataset.metadata.shape = tuple(loom_file['matrix'].shape)

lib/galaxy/datatypes/test/test_binary_loom_spec_version.loom

0 → 100644
+15.5 KiB

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lib/galaxy/model/metadata.py

+4 −1
Original line number Diff line number Diff line
@@ -239,7 +239,10 @@ class MetadataCollection(Mapping): 
            meta_dict['__validated_state__'] = dataset_meta_dict['__validated_state__']

        if '__validated_state_message__' in dataset_meta_dict:

            meta_dict['__validated_state_message__'] = dataset_meta_dict['__validated_state_message__']

        try:

            encoded_meta_dict = galaxy.model.custom_types.json_encoder.encode(meta_dict)

        except Exception as e:

            raise Exception(f"Failed encoding metadata dictionary: {meta_dict}") from e

        if filename is None:

            return encoded_meta_dict

        with open(filename, 'wt+') as fh: