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galaxy.tools.imp_exp package

class galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper(app, job_id)

Bases: object, galaxy.model.item_attrs.UsesAnnotations

Class provides support for performing jobs that import a history from an archive.

__init__(app, job_id)

cleanup_after_job()

Set history, datasets, and jobs’ attributes and clean up archive directory.

class galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper(job_id)

Bases: object, galaxy.model.item_attrs.UsesAnnotations

Class provides support for performing jobs that export a history to an archive.

__init__(job_id)

get_history_datasets(trans, history)

Returns history’s datasets.

setup_job(trans, jeha, include_hidden=False, include_deleted=False)

Perform setup for job to export a history into an archive. Method generates attribute files for export, sets the corresponding attributes in the jeha object, and returns a command line for running the job. The command line includes the command, inputs, and options; it does not include the output file because it must be set at runtime.

cleanup_after_job(db_session)

Remove temporary directory and attribute files generated during setup for this job.

Submodules

galaxy.tools.imp_exp.export_history module

Export a history to an archive file using attribute files.

usage: %prog history_attrs dataset_attrs job_attrs out_file

-G, –gzip: gzip archive file

galaxy.tools.imp_exp.export_history.get_dataset_filename(name, ext, hid)

Builds a filename for a dataset using its name an extension.

galaxy.tools.imp_exp.export_history.create_archive(history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False)

Create archive from the given attribute/metadata files and save it to out_file.

galaxy.tools.imp_exp.export_history.main()

galaxy.tools.imp_exp.unpack_tar_gz_archive module

Unpack a tar or tar.gz archive into a directory.

usage: %prog archive_source dest_dir

–[url|file] source type, either a URL or a file.

galaxy.tools.imp_exp.unpack_tar_gz_archive.check_archive(archive_file, dest_dir)

Ensure that a tar archive has no absolute paths or relative paths outside the archive.

galaxy.tools.imp_exp.unpack_tar_gz_archive.main(options, args)

galaxy.tools.imp_exp.unpack_tar_gz_archive.unpack_archive(archive_file, dest_dir)

Unpack a tar and/or gzipped archive into a destination directory.

galaxy.tools.imp_exp.unpack_tar_gz_archive.url_to_file(url, dest_file)

Transfer a file from a remote URL to a temporary file.