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Fix via refactor set_metadata so more output metadata pruned properly.

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This commit is contained in:
John Chilton
2018-12-07 10:02:25 -05:00
parent bddfe38890
commit 5c384efb8d
1 changed files with 9 additions and 8 deletions
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lib/galaxy_ext/metadata/set_metadata.py
+9 -8
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@@ -34,7 +34,7 @@ log = logging.getLogger(__name__)
galaxy.model.Job() # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
def set_meta_with_tool_provided(dataset_instance, file_dict, set_meta_kwds, datatypes_registry):
def set_meta_with_tool_provided(dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size):
# This method is somewhat odd, in that we set the metadata attributes from tool,
# then call set_meta, then set metadata attributes from tool again.
# This is intentional due to interplay of overwrite kwd, the fact that some metadata
@@ -62,6 +62,12 @@ def set_meta_with_tool_provided(dataset_instance, file_dict, set_meta_kwds, data
for metadata_name, metadata_value in file_dict.get('metadata', {}).items():
setattr(dataset_instance.metadata, metadata_name, metadata_value)
if max_metadata_value_size:
for k, v in list(dataset_instance.metadata.items()):
if total_size(v) > max_metadata_value_size:
log.info("Key %s too large for metadata, discarding" % k)
dataset_instance.metadata.remove_key(k)
def set_metadata():
# locate galaxy_root for loading datatypes
@@ -140,12 +146,7 @@ def set_metadata():
metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON(metadata_file_override)
setattr(dataset.metadata, metadata_name, metadata_file_override)
file_dict = existing_job_metadata_dict.get(dataset.dataset.id, {})
set_meta_with_tool_provided(dataset, file_dict, set_meta_kwds, datatypes_registry)
if max_metadata_value_size:
for k, v in list(dataset.metadata.items()):
if total_size(v) > max_metadata_value_size:
log.info("Key %s too large for metadata, discarding" % k)
dataset.metadata.remove_key(k)
set_meta_with_tool_provided(dataset, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size)
dataset.metadata.to_JSON_dict(filename_out) # write out results of set_meta
json.dump((True, 'Metadata has been set successfully'), open(filename_results_code, 'wt+')) # setting metadata has succeeded
except Exception as e:
@@ -159,7 +160,7 @@ def set_metadata():
new_dataset._extra_files_path = os.path.join(tool_job_working_directory, "working", extra_files)
new_dataset.state = new_dataset.states.OK
new_dataset_instance = galaxy.model.HistoryDatasetAssociation(id=-i, dataset=new_dataset, extension=file_dict.get('ext', 'data'))
set_meta_with_tool_provided(new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry)
set_meta_with_tool_provided(new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size)
file_dict['metadata'] = json.loads(new_dataset_instance.metadata.to_JSON_dict()) # storing metadata in external form, need to turn back into dict, then later jsonify
if existing_job_metadata_dict or new_job_metadata_dict:
with open(job_metadata, 'wt') as job_metadata_fh: