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galaxy.util.tool_shed package

Submodules

galaxy.util.tool_shed.common_util module

galaxy.util.tool_shed.common_util.accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies)[source]
galaxy.util.tool_shed.common_util.check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number)[source]
galaxy.util.tool_shed.common_util.check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict)[source]
galaxy.util.tool_shed.common_util.generate_clone_url_for_installed_repository(app, repository)[source]

Generate the URL for cloning a repository that has been installed into a Galaxy instance.

galaxy.util.tool_shed.common_util.generate_clone_url_for_repository_in_tool_shed(user, repository)[source]

Generate the URL for cloning a repository that is in the tool shed.

galaxy.util.tool_shed.common_util.generate_clone_url_from_repo_info_tup(app, repo_info_tup)[source]

Generate the URL for cloning a repository given a tuple of toolshed, name, owner, changeset_revision.

galaxy.util.tool_shed.common_util.get_non_shed_tool_panel_configs(app)[source]

Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml.

galaxy.util.tool_shed.common_util.get_repository_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision)[source]
galaxy.util.tool_shed.common_util.get_protocol_from_tool_shed_url(tool_shed_url)[source]

Return the protocol from the received tool_shed_url if it exists.

galaxy.util.tool_shed.common_util.get_tool_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision)[source]
galaxy.util.tool_shed.common_util.get_tool_shed_repository_ids(as_string=False, **kwd)[source]
galaxy.util.tool_shed.common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed)[source]

The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like: http://toolshed.g2.bx.psu.edu/

galaxy.util.tool_shed.common_util.get_tool_shed_repository_url(app, tool_shed, owner, name)[source]
galaxy.util.tool_shed.common_util.get_user_by_username(app, username)[source]

Get a user from the database by username.

galaxy.util.tool_shed.common_util.handle_galaxy_url(trans, **kwd)[source]
galaxy.util.tool_shed.common_util.handle_tool_shed_url_protocol(app, shed_url)[source]

Handle secure and insecure HTTP protocol since they may change over time.

galaxy.util.tool_shed.common_util.parse_repository_dependency_tuple(repository_dependency_tuple, contains_error=False)[source]
galaxy.util.tool_shed.common_util.remove_port_from_tool_shed_url(tool_shed_url)[source]

Return a partial Tool Shed URL, eliminating the port if it exists.

galaxy.util.tool_shed.common_util.remove_protocol_and_port_from_tool_shed_url(tool_shed_url)[source]

Return a partial Tool Shed URL, eliminating the protocol and/or port if either exists.

galaxy.util.tool_shed.common_util.remove_protocol_and_user_from_clone_url(repository_clone_url)[source]

Return a URL that can be used to clone a repository, eliminating the protocol and user if either exists.

galaxy.util.tool_shed.common_util.remove_protocol_from_tool_shed_url(tool_shed_url)[source]

Return a partial Tool Shed URL, eliminating the protocol if it exists.

galaxy.util.tool_shed.encoding_util module

galaxy.util.tool_shed.encoding_util.tool_shed_decode(value)[source]
galaxy.util.tool_shed.encoding_util.tool_shed_encode(val)[source]

galaxy.util.tool_shed.xml_util module

class galaxy.util.tool_shed.xml_util.CommentedTreeBuilder(element_factory=None)[source]

Bases: xml.etree.ElementTree.TreeBuilder

non_comment_seen = False
doctype(*args)[source]
start(tag, attrib)[source]
comment(data)[source]
galaxy.util.tool_shed.xml_util.create_and_write_tmp_file(elem)[source]
galaxy.util.tool_shed.xml_util.create_element(tag, attributes=None, sub_elements=None)[source]

Create a new element whose tag is the value of the received tag, and whose attributes are all key / value pairs in the received attributes and sub_elements.

galaxy.util.tool_shed.xml_util.parse_xml(file_name, check_exists=True)[source]

Returns a parsed xml tree with comments intact.