[21.01] Fix setting metadata for some Loom files #12347
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Add the second part in the following traceback:
```
DEBUG galaxy.metadata:__init__.py:93 setting metadata externally failed for HistoryDatasetAssociation 1: Traceback (most recent call last):
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/model/metadata.py", line 246, in to_JSON_dict
encoded_meta_dict = galaxy.model.custom_types.json_encoder.encode(meta_dict)
File "/usr/lib/python3.8/json/encoder.py", line 199, in encode
chunks = self.iterencode(o, _one_shot=True)
File "/usr/lib/python3.8/json/encoder.py", line 257, in iterencode
return _iterencode(o, 0)
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/model/custom_types.py", line 39, in default
return json.JSONEncoder.default(self, obj)
File "/usr/lib/python3.8/json/encoder.py", line 179, in default
raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type ndarray is not JSON serializable
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/metadata/set_metadata.py", line 334, in set_metadata_portable
dataset.metadata.to_JSON_dict(filename_out) # write out results of set_meta
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/model/metadata.py", line 248, in to_JSON_dict
raise Exception(f"Failed encoding metadata dictionary: {meta_dict}") from e
Exception: Failed encoding metadata dictionary: {'dbkey': '?', 'title': None, 'description': None, 'url': None, 'doi': None, 'loom_spec_version': array([b'2.0.1'], dtype='|S6'), 'shape': (5, 10), 'layers
_count': 0, 'layers_names': [], 'row_attrs_count': 1, 'row_attrs_names': ['rownames'], 'col_attrs_count': 2, 'col_attrs_names': ['colnames', 'colnames_factor'], 'col_graphs_count': 0, 'col_graphs_names':
[], 'row_graphs_count': 0, 'row_graphs_names': []}
```
Loom files created by recent versions of LoomExperiment Bioconductor package encode the Loom version in an binary array, which breaks metadata setting in Galaxy.
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nuwang
approved these changes
Sep 7, 2021
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Loom files created by recent versions of LoomExperiment Bioconductor package encode the Loom version in a binary array, which breaks metadata setting in Galaxy.
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