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Restore try/except around Biom2 metadata setting

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mvdbeek
2019-08-23 19:28:44 +02:00
parent fa3e09b689
commit 14f6483378
1 changed files with 16 additions and 13 deletions
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lib/galaxy/datatypes/binary.py
+16 -13
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@@ -1010,20 +1010,23 @@ class Biom2(H5):
def set_meta(self, dataset, overwrite=True, **kwd):
super(Biom2, self).set_meta(dataset, overwrite=overwrite, **kwd)
with h5py.File(dataset.file_name, 'r') as f:
attributes = dict(f.attrs.items())
try:
with h5py.File(dataset.file_name, 'r') as f:
attributes = dict(f.attrs.items())
dataset.metadata.id = util.unicodify(attributes['id'])
dataset.metadata.format_url = util.unicodify(attributes['format-url'])
if 'format-version' in attributes: # biom 2.1
dataset.metadata.format_version = '.'.join(str(_) for _ in attributes['format-version'])
elif 'format' in attributes: # biom 2.0
dataset.metadata.format = util.unicodify(attributes['format'])
dataset.metadata.type = util.unicodify(attributes['type'])
dataset.metadata.shape = tuple((int(_) for _ in attributes['shape']))
dataset.metadata.generated_by = util.unicodify(attributes['generated-by'])
dataset.metadata.creation_date = util.unicodify(attributes['creation-date'])
dataset.metadata.nnz = int(attributes['nnz'])
dataset.metadata.id = util.unicodify(attributes['id'])
dataset.metadata.format_url = util.unicodify(attributes['format-url'])
if 'format-version' in attributes: # biom 2.1
dataset.metadata.format_version = '.'.join(str(_) for _ in attributes['format-version'])
elif 'format' in attributes: # biom 2.0
dataset.metadata.format = util.unicodify(attributes['format'])
dataset.metadata.type = util.unicodify(attributes['type'])
dataset.metadata.shape = tuple((int(_) for _ in attributes['shape']))
dataset.metadata.generated_by = util.unicodify(attributes['generated-by'])
dataset.metadata.creation_date = util.unicodify(attributes['creation-date'])
dataset.metadata.nnz = int(attributes['nnz'])
except Exception as e:
log.warning('%s, set_meta Exception: %s', self, util.unicodify(e))
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged: