Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
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)[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, 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:
galaxy.metadata.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, include_command=True, max_metadata_value_size=0, validate_outputs=False, 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.
ExtendedDirectoryMetadataGenerator
(job_id)[source]¶ Bases:
galaxy.metadata.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).