Source code for galaxy.tool_shed.util.container_util

import logging

from galaxy.util.tool_shed.common_util import remove_protocol_from_tool_shed_url

log = logging.getLogger(__name__)

# String separator
STRSEP = '__ESEP__'


[docs]def generate_repository_dependencies_key_for_repository(toolshed_base_url, repository_name, repository_owner,
                                                        changeset_revision, prior_installation_required,
                                                        only_if_compiling_contained_td):
    """
    Assumes tool shed is current tool shed since repository dependencies across tool sheds
    is not yet supported.
    """
    # The tool_shed portion of the key must be the value that is stored in the tool_shed_repository.tool_shed column
    # of the Galaxy database for an installed repository.  This value does not include the protocol, but does include
    # the port if there is one.
    tool_shed = remove_protocol_from_tool_shed_url(toolshed_base_url)
    return '{}{}{}{}{}{}{}{}{}{}{}'.format(tool_shed,
                                       STRSEP,
                                       str(repository_name),
                                       STRSEP,
                                       str(repository_owner),
                                       STRSEP,
                                       str(changeset_revision),
                                       STRSEP,
                                       str(prior_installation_required),
                                       STRSEP,
                                       str(only_if_compiling_contained_td))


[docs]def get_components_from_key(key):
    """
    Assumes tool shed is current tool shed since repository dependencies across tool sheds is not
    yet supported.
    """
    items = key.split(STRSEP)
    toolshed_base_url = items[0]
    repository_name = items[1]
    repository_owner = items[2]
    changeset_revision = items[3]
    if len(items) == 5:
        prior_installation_required = items[4]
        return toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required
    elif len(items) == 6:
        prior_installation_required = items[4]
        only_if_compiling_contained_td = items[5]
        return toolshed_base_url, repository_name, repository_owner, \
            changeset_revision, prior_installation_required, \
            only_if_compiling_contained_td
    else:
        # For backward compatibility to the 12/20/12 Galaxy release we have to return the following, and callers
        # must handle exceptions.
        return toolshed_base_url, repository_name, repository_owner, changeset_revision


[docs]def print_folders(pad, folder):
    # For debugging...
    pad_str = ''
    for i in range(1, pad):
        pad_str += ' '
    print('{}id: {} key: {}'.format(pad_str, str(folder.id), folder.key))
    for repository_dependency in folder.repository_dependencies:
        print('    {}{}'.format(pad_str, repository_dependency.listify))
    for sub_folder in folder.folders:
        print_folders(pad + 5, sub_folder)