galaxy.metadata package
Define abstraction for capturing the metadata of job’s output datasets.
- galaxy.metadata.get_metadata_compute_strategy(config, job_id, metadata_strategy_override=None, tool_id=None, tool_type=None)[source]
- class galaxy.metadata.MetadataCollectionStrategy[source]
Bases:
object
Interface describing the abstract process of writing out and collecting output metadata.
- extended = False
- abstract setup_external_metadata(datasets_dict, out_collections, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, output_fnames=None, config_root=None, use_bin=False, config_file=None, datatypes_config=None, job_metadata=None, provided_metadata_style=None, compute_tmp_dir=None, include_command=True, max_metadata_value_size=0, max_discovered_files=None, object_store_conf=None, tool=None, job=None, kwds=None)[source]
Setup files needed for external metadata collection.
If include_command is True, return full Python command to externally compute metadata otherwise just the arguments to galaxy_ext.metadata.set_metadata required to build.
- class galaxy.metadata.PortableDirectoryMetadataGenerator(job_id)[source]
Bases:
MetadataCollectionStrategy
- portable = True
- write_object_store_conf = False
- setup_external_metadata(datasets_dict, out_collections, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, output_fnames=None, config_root=None, use_bin=False, config_file=None, datatypes_config=None, job_metadata=None, provided_metadata_style=None, compute_tmp_dir=None, compute_version_path=None, include_command=True, max_metadata_value_size=0, max_discovered_files=None, validate_outputs=False, object_store_conf=None, tool=None, job=None, link_data_only=False, kwds=None)[source]
Setup files needed for external metadata collection.
If include_command is True, return full Python command to externally compute metadata otherwise just the arguments to galaxy_ext.metadata.set_metadata required to build.
- class galaxy.metadata.ExtendedDirectoryMetadataGenerator(job_id)[source]
Bases:
PortableDirectoryMetadataGenerator
- extended = True
- write_object_store_conf = True
- setup_external_metadata(datasets_dict, out_collections, sa_session, **kwd)[source]
Setup files needed for external metadata collection.
If include_command is True, return full Python command to externally compute metadata otherwise just the arguments to galaxy_ext.metadata.set_metadata required to build.
Submodules
galaxy.metadata.set_metadata module
Execute an external process to set_meta() on a provided list of pickled datasets.
This was formerly scripts/set_metadata.py and expects these arguments:
%prog datatypes_conf.xml job_metadata_file metadata_kwds,metadata_out,metadata_results_code,output_filename_override,metadata_override… max_metadata_value_size
Galaxy should be importable on sys.path and output_filename_override should be set to the path of the dataset on which metadata is being set (output_filename_override could previously be left empty and the path would be constructed automatically).
- galaxy.metadata.set_metadata.reset_external_filename(dataset_instance: DatasetInstance)[source]
- galaxy.metadata.set_metadata.push_if_necessary(object_store: ObjectStore, dataset: DatasetInstance, external_filename)[source]
- galaxy.metadata.set_metadata.set_meta_with_tool_provided(dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size)[source]
- galaxy.metadata.set_metadata.get_object_store(tool_job_working_directory, object_store=None)[source]