Merge branch 'release_21.01' into release_21.05

galaxyproject · Sep 7, 2021 · fa3828a · fa3828a
2 parents cf5708e + e905161
commit fa3828a
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Showing 3 changed files with 11 additions and 2 deletions.
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
@@ -17,6 +17,7 @@
 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
@@ -962,7 +963,12 @@ def set_meta(self, dataset, overwrite=True, **kwd):
                 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)
 

diff --git a/lib/galaxy/datatypes/test/test_binary_loom_spec_version.loom b/lib/galaxy/datatypes/test/test_binary_loom_spec_version.loom
diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py
@@ -242,7 +242,10 @@ def to_JSON_dict(self, filename=None):
             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__']
-        encoded_meta_dict = galaxy.model.custom_types.json_encoder.encode(meta_dict)
+        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: