This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for tool_shed.dependencies.attribute_handlers

import copy
import logging
from typing import (

from galaxy.util import (
from galaxy.web import url_for
from tool_shed.dependencies.tool import tag_attribute_handler
from tool_shed.repository_types.util import (
from tool_shed.util import (

log = logging.getLogger(__name__)

[docs]class RepositoryDependencyAttributeHandler:
[docs] def __init__(self, app, unpopulate): self.app = app self.file_name = REPOSITORY_DEPENDENCY_DEFINITION_FILENAME self.unpopulate = unpopulate
[docs] def check_tag_attributes(self, elem): # <repository name="molecule_datatypes" owner="test" /> error_message = "" name = elem.get("name") if not name: error_message += "The tag is missing the required name attribute. " owner = elem.get("owner") if not owner: error_message += "The tag is missing the required owner attribute. " log.debug(error_message) return error_message
[docs] def handle_complex_dependency_elem(self, parent_elem, elem_index, elem): """ Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag that defines a complex repository dependency. """ # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" /> altered, new_elem, error_message = self.handle_elem(elem) if error_message: error_message += f" The {TOOL_DEPENDENCY_DEFINITION_FILENAME} file contains an invalid <repository> tag." return altered, new_elem, error_message
[docs] def handle_elem(self, elem): """Populate or unpopulate the changeset_revision and toolshed attributes of repository tags.""" # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy"> # <package name="xorg_macros" version="1.17.1" /> # </repository> error_message = "" name = elem.get("name") owner = elem.get("owner") # The name and owner attributes are always required, so if either are missing, return the error message. if not name or not owner: error_message = self.check_tag_attributes(elem) return False, elem, error_message altered = False toolshed = elem.get("toolshed") changeset_revision = elem.get("changeset_revision") # Over a short period of time a bug existed which caused the prior_installation_required attribute # to be set to False and included in the <repository> tag when a repository was exported along with # its dependencies. The following will eliminate this problematic attribute upon import. prior_installation_required = elem.get("prior_installation_required") if prior_installation_required is not None and not asbool(prior_installation_required): del elem.attrib["prior_installation_required"] sub_elems = [child_elem for child_elem in list(elem)] if len(sub_elems) > 0: # At this point, a <repository> tag will point only to a package. # <package name="xorg_macros" version="1.17.1" /> # Coerce the list to dict. sub_elements = {} packages = [] for sub_elem in sub_elems: sub_elem_type = sub_elem.tag sub_elem_name = sub_elem.get("name") sub_elem_version = sub_elem.get("version") if sub_elem_type and sub_elem_name and sub_elem_version: packages.append((sub_elem_name, sub_elem_version)) sub_elements["packages"] = packages else: # Set to None. sub_elements = None if self.unpopulate: # We're exporting the repository, so eliminate all toolshed and changeset_revision attributes # from the <repository> tag. if toolshed or changeset_revision: attributes = {} attributes["name"] = name attributes["owner"] = owner prior_installation_required = elem.get("prior_installation_required") if asbool(prior_installation_required): attributes["prior_installation_required"] = "True" new_elem = _create_element("repository", attributes=attributes, sub_elements=sub_elements) altered = True return altered, new_elem, error_message # From here on we're populating the toolshed and changeset_revision attributes if necessary. if not toolshed: # Default the setting to the current tool shed. toolshed = str(url_for("/", qualified=True)).rstrip("/") elem.attrib["toolshed"] = toolshed altered = True if not changeset_revision: # Populate the changeset_revision attribute with the latest installable metadata revision for # the defined repository. We use the latest installable revision instead of the latest metadata # revision to ensure that the contents of the revision are valid. repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner) if repository: lastest_installable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision( self.app, repository ) if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH: elem.attrib["changeset_revision"] = lastest_installable_changeset_revision altered = True else: error_message = "Invalid latest installable changeset_revision %s " % str( lastest_installable_changeset_revision ) error_message += f"retrieved for repository {name} owned by {owner}. " else: error_message = f"Unable to locate repository with name {name} and owner {owner}. " return altered, elem, error_message
[docs] def handle_sub_elem(self, parent_elem, elem_index, elem): """ Populate or unpopulate the toolshed and changeset_revision attributes for each of the following tag sets. <action type="set_environment_for_install"> <action type="setup_r_environment"> <action type="setup_ruby_environment"> """ sub_elem_altered = False error_message = "" for sub_index, sub_elem in enumerate(elem): # Make sure to skip comments and tags that are not <repository>. if sub_elem.tag == "repository": altered, new_sub_elem, message = self.handle_elem(sub_elem) if message: error_message += f"The {TOOL_DEPENDENCY_DEFINITION_FILENAME} file contains an invalid <repository> tag. {message}" if altered: if not sub_elem_altered: sub_elem_altered = True elem[sub_index] = new_sub_elem if sub_elem_altered: parent_elem[elem_index] = elem return sub_elem_altered, parent_elem, error_message
[docs] def handle_tag_attributes(self, config): """ Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag. Populating will occur when a dependency definition file is being uploaded to the repository, while unpopulating will occur when the repository is being exported. """ # Make sure we're looking at a valid repository_dependencies.xml file. tree, error_message = xml_util.parse_xml(config) if tree is None: return False, None, error_message root = tree.getroot() root_altered = False new_root = copy.deepcopy(root) for index, elem in enumerate(root): if elem.tag == "repository": # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> altered, new_elem, error_message = self.handle_elem(elem) if error_message: error_message = f"The {self.file_name} file contains an invalid <repository> tag. {error_message}" return False, None, error_message if altered: if not root_altered: root_altered = True new_root[index] = new_elem return root_altered, new_root, error_message
[docs]class ToolDependencyAttributeHandler:
[docs] def __init__(self, app, unpopulate): self.app = app self.file_name = TOOL_DEPENDENCY_DEFINITION_FILENAME self.unpopulate = unpopulate
[docs] def handle_tag_attributes(self, tool_dependencies_config): """ Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> tag defined within a tool_dependencies.xml file. """ rdah = RepositoryDependencyAttributeHandler(self.app, self.unpopulate) tah = tag_attribute_handler.TagAttributeHandler(self.app, rdah, self.unpopulate) altered = False error_message = "" # Make sure we're looking at a valid tool_dependencies.xml file. tree, error_message = xml_util.parse_xml(tool_dependencies_config) if tree is None: return False, None, error_message root = tree.getroot() altered, new_root, error_message = tah.process_config(root, skip_actions_tags=False) return altered, new_root, error_message
def _create_element( tag: str, attributes: Optional[Dict[str, str]] = None, sub_elements: Optional[Dict[str, List[Tuple[str, str]]]] = None, ) -> Optional[etree.Element]: """ 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. """ if tag: elem = etree.Element(tag) if attributes: # The received attributes is an odict to preserve ordering. for k, attribute_value in attributes.items(): elem.set(k, attribute_value) if sub_elements: # The received attributes is an odict. These handle information that tends to be # long text including paragraphs (e.g., description and long_description. for k, v in sub_elements.items(): # Don't include fields that are blank. if v: if k == "packages": # The received sub_elements is an odict whose key is 'packages' and whose # value is a list of ( name, version ) tuples. for v_tuple in v: sub_elem = etree.SubElement(elem, "package") sub_elem_name, sub_elem_version = v_tuple sub_elem.set("name", sub_elem_name) sub_elem.set("version", sub_elem_version) elif isinstance(v, list): sub_elem = etree.SubElement(elem, k) # If v is a list, then it must be a list of tuples where the first # item is the tag and the second item is the text value. for v_tuple in v: if len(v_tuple) == 2: v_tag = v_tuple[0] v_text = v_tuple[1] # Don't include fields that are blank. if v_text: v_elem = etree.SubElement(sub_elem, v_tag) v_elem.text = v_text else: sub_elem = etree.SubElement(elem, k) sub_elem.text = v return elem return None