galaxy/scripts/tool_shed/api/export.py

#!/usr/bin/env python
"""
Export a specified repository revision and optionally all of its defined repository
dependencies from the tool shed into a compressed archive.

Here is a working example of how to use this script to export a repository from the tool shed.
./export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp
"""

import argparse
import os
import sys
import tempfile
import urllib2

sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
from tool_shed.util import basic_util

from common import display, submit

CAPSULE_FILENAME = 'capsule'
CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies'
CHUNK_SIZE = 2 ** 20  # 1Mb


def generate_repository_archive_filename(tool_shed_url, name, owner, changeset_revision, file_type,
                                         export_repository_dependencies, use_tmp_archive_dir=False):
    tool_shed = remove_protocol_from_tool_shed_url(tool_shed_url)
    file_type_str = basic_util.get_file_type_str(changeset_revision, file_type)
    if export_repository_dependencies:
        repositories_archive_filename = '%s_%s_%s_%s_%s' % (CAPSULE_WITH_DEPENDENCIES_FILENAME,
                                                            tool_shed,
                                                            name,
                                                            owner,
                                                            file_type_str)
    else:
        repositories_archive_filename = '%s_%s_%s_%s_%s' % (CAPSULE_FILENAME,
                                                            tool_shed,
                                                            name,
                                                            owner,
                                                            file_type_str)
    if use_tmp_archive_dir:
        tmp_archive_dir = tempfile.mkdtemp(prefix="tmp-toolshed-arcdir")
        repositories_archive_filename = os.path.join(tmp_archive_dir, repositories_archive_filename)
    return repositories_archive_filename


def remove_protocol_from_tool_shed_url(tool_shed_url):
    protocol, base = tool_shed_url.split('://')
    base = base.replace(':', '_colon_')
    base = base.rstrip('/')
    return base


def string_as_bool(string):
    if str(string).lower() in ('true', 'yes', 'on'):
        return True
    else:
        return False


def main(options):
    """Collect all user data and export the repository via the Tool Shed API."""
    base_tool_shed_url = options.tool_shed_url.rstrip('/')
    repositories_url = '%s/api/repositories' % base_tool_shed_url
    data = {}
    data['tool_shed_url'] = base_tool_shed_url
    data['name'] = options.name
    data['owner'] = options.owner
    data['changeset_revision'] = options.changeset_revision
    data['export_repository_dependencies'] = options.export_repository_dependencies
    repository_id = None
    repositories = display(repositories_url, api_key=None, return_formatted=False)
    for repository in repositories:
        name = str(repository['name'])
        owner = str(repository['owner'])
        if name == options.name and owner == options.owner:
            repository_id = repository['id']
            break
    if repository_id:
        # We'll currently support only gzip-compressed tar archives.
        file_type = 'gz'
        url = '%s%s' % (base_tool_shed_url, '/api/repository_revisions/%s/export' % str(repository_id))
        export_dict = submit(url, data, return_formatted=False)
        error_messages = export_dict['error_messages']
        if error_messages:
            print "Error attempting to export revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner, ":\n", error_messages
        else:
            export_repository_dependencies = string_as_bool(options.export_repository_dependencies)
            repositories_archive_filename = \
                generate_repository_archive_filename(base_tool_shed_url,
                                                     options.name,
                                                     options.owner,
                                                     options.changeset_revision,
                                                     file_type,
                                                     export_repository_dependencies=export_repository_dependencies,
                                                     use_tmp_archive_dir=False)
            download_url = export_dict['download_url']
            download_dir = os.path.abspath(options.download_dir)
            file_path = os.path.join(download_dir, repositories_archive_filename)
            src = None
            dst = None
            try:
                src = urllib2.urlopen(download_url)
                dst = open(file_path, 'wb')
                while True:
                    chunk = src.read(CHUNK_SIZE)
                    if chunk:
                        dst.write(chunk)
                    else:
                        break
            except:
                raise
            finally:
                if src:
                    src.close()
                if dst:
                    dst.close()
            print "Successfully exported revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner
            print "to location ", file_path
    else:
        print "Invalid tool_shed / name / owner ."


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Installation of tool shed repositories via the Galaxy API.')
    parser.add_argument("-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL")
    parser.add_argument("-n", "--name", required=True, help="Repository name.")
    parser.add_argument("-o", "--owner", required=True, help="Repository owner.")
    parser.add_argument("-r", "--revision", dest="changeset_revision", required=True, help="Repository owner.")
    parser.add_argument("-e", "--export_repository_dependencies", dest="export_repository_dependencies", required=False, default='False', help="Export repository dependencies.")
    parser.add_argument("-d", "--download_dir", dest="download_dir", required=False, default='/tmp', help="Download directory.")
    options = parser.parse_args()
    main(options)