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[23.1] Skip change_datatype things if we're not actually changing the extension #16931

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merged 2 commits into from
Oct 26, 2023
Merged

[23.1] Skip change_datatype things if we're not actually changing the extension #16931

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ca5132d
Skip change_datatype things if we're not actually changing the extension
mvdbeek Oct 26, 2023
d7beda0
Commit if we've got outstanding MetadataFile instances
mvdbeek Oct 26, 2023
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15 changes: 8 additions & 7 deletions lib/galaxy/datatypes/registry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -590,13 +590,14 @@ def get_datatype_by_extension(self, ext):
return self.datatypes_by_extension.get(ext, None)

def change_datatype(self, data, ext):
data.extension = ext
# call init_meta and copy metadata from itself. The datatype
# being converted *to* will handle any metadata copying and
# initialization.
if data.has_data():
data.set_size()
data.init_meta(copy_from=data)
if data.extension != ext:
data.extension = ext
# call init_meta and copy metadata from itself. The datatype
# being converted *to* will handle any metadata copying and
# initialization.
if data.has_data():
data.set_size()
data.init_meta(copy_from=data)
return data

def load_datatype_converters(self, toolbox, use_cached=False):
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11 changes: 10 additions & 1 deletion lib/galaxy/model/metadata.py
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Expand Up @@ -604,7 +604,16 @@ def wrap(self, value, session):
if isinstance(value, int):
return session.query(galaxy.model.MetadataFile).get(value)
else:
return session.query(galaxy.model.MetadataFile).filter_by(uuid=value).one()
wrapped_value = session.query(galaxy.model.MetadataFile).filter_by(uuid=value).one_or_none()
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if wrapped_value:
return wrapped_value
else:
# If we've simultaneously copied the dataset and we've changed the datatype on the
# copy we may not have committed the MetadataFile yet, so we need to commit the session.
# TODO: It would be great if we can avoid the commit in the future.
with transaction(session):
session.commit()
return session.query(galaxy.model.MetadataFile).filter_by(uuid=value).one_or_none()

def make_copy(self, value, target_context: MetadataCollection, source_context):
session = target_context._object_session(target_context.parent)
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