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galaxy.metadata package

Define abstraction for capturing the metadata of job’s output datasets.

galaxy.metadata.get_metadata_compute_strategy(app, job_id)[source]
class galaxy.metadata.MetadataCollectionStrategy[source]

Bases: object

Interface describing the abstract process of writing out and collecting output metadata.

invalidate_external_metadata(datasets, sa_session)[source]

Invalidate written files.

set_job_runner_external_pid(pid, sa_session)[source]
cleanup_external_metadata(sa_session)[source]
setup_external_metadata(datasets_dict, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, compute_tmp_dir=None, include_command=True, max_metadata_value_size=0, 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.

external_metadata_set_successfully(dataset, name, sa_session, working_directory)[source]

Return boolean indicating if metadata for specified dataset was written properly.

load_metadata(dataset, name, sa_session, working_directory, remote_metadata_directory=None)[source]

Load metadata calculated externally into specified dataset.

class galaxy.metadata.PortableDirectoryMetadataGenerator(job_id)[source]

Bases: galaxy.metadata.MetadataCollectionStrategy

portable = True
__init__(job_id)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

setup_external_metadata(datasets_dict, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, compute_tmp_dir=None, include_command=True, max_metadata_value_size=0, 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.

load_metadata(dataset, name, sa_session, working_directory, remote_metadata_directory=None)[source]

Load metadata calculated externally into specified dataset.

external_metadata_set_successfully(dataset, name, sa_session, working_directory)[source]

Return boolean indicating if metadata for specified dataset was written properly.

class galaxy.metadata.JobExternalOutputMetadataWrapper(job_id)[source]

Bases: galaxy.metadata.MetadataCollectionStrategy

Class with methods allowing set_meta() to be called externally to the Galaxy head. This class allows access to external metadata filenames for all outputs associated with a job. We will use JSON as the medium of exchange of information, except for the DatasetInstance object which will use pickle (in the future this could be JSONified as well)

portable = False
__init__(job_id)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

invalidate_external_metadata(datasets, sa_session)[source]

Invalidate written files.

setup_external_metadata(datasets_dict, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, compute_tmp_dir=None, include_command=True, max_metadata_value_size=0, 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.

external_metadata_set_successfully(dataset, name, sa_session, working_directory)[source]

Return boolean indicating if metadata for specified dataset was written properly.

cleanup_external_metadata(sa_session)[source]
set_job_runner_external_pid(pid, sa_session)[source]
load_metadata(dataset, name, sa_session, working_directory, remote_metadata_directory=None)[source]

Load metadata calculated externally into specified dataset.