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Source code for galaxy.tool_shed.util.tool_dependency_util

import logging
import os
import shutil

from sqlalchemy import and_

from galaxy import util
from galaxy.model.base import transaction

log = logging.getLogger(__name__)

[docs]def get_tool_dependency(app, id): """Get a tool_dependency from the database via id""" return app.install_model.context.query(app.install_model.ToolDependency).get(app.security.decode_id(id))
[docs]def get_tool_dependency_by_name_type_repository(app, repository, name, type): context = app.install_model.context return ( context.query(app.install_model.ToolDependency) .filter( and_( app.install_model.ToolDependency.table.c.tool_shed_repository_id == repository.id, app.install_model.ToolDependency.table.c.name == name, app.install_model.ToolDependency.table.c.type == type, ) ) .first() )
[docs]def get_tool_dependency_by_name_version_type(app, name, version, type): context = app.install_model.context return ( context.query(app.install_model.ToolDependency) .filter( and_( app.install_model.ToolDependency.table.c.name == name, app.install_model.ToolDependency.table.c.version == version, app.install_model.ToolDependency.table.c.type == type, ) ) .first() )
[docs]def get_tool_dependency_by_name_version_type_repository(app, repository, name, version, type): context = app.install_model.context return ( context.query(app.install_model.ToolDependency) .filter( and_( app.install_model.ToolDependency.table.c.tool_shed_repository_id == repository.id, app.install_model.ToolDependency.table.c.name == name, app.install_model.ToolDependency.table.c.version == version, app.install_model.ToolDependency.table.c.type == type, ) ) .first() )
[docs]def get_tool_dependency_ids(as_string=False, **kwd): tool_dependency_id = kwd.get("tool_dependency_id", None) if "tool_dependency_ids" in kwd: tool_dependency_ids = util.listify(kwd["tool_dependency_ids"]) elif "id" in kwd: tool_dependency_ids = util.listify(kwd["id"]) elif "inst_td_ids" in kwd: tool_dependency_ids = util.listify(kwd["inst_td_ids"]) elif "uninstalled_tool_dependency_ids" in kwd: tool_dependency_ids = util.listify(kwd["uninstalled_tool_dependency_ids"]) else: tool_dependency_ids = [] if tool_dependency_id and tool_dependency_id not in tool_dependency_ids: tool_dependency_ids.append(tool_dependency_id) if as_string: return ",".join(tool_dependency_ids) return tool_dependency_ids
[docs]def parse_package_elem(package_elem, platform_info_dict=None, include_after_install_actions=True): """ Parse a <package> element within a tool dependency definition and return a list of action tuples. This method is called when setting metadata on a repository that includes a tool_dependencies.xml file or when installing a repository that includes a tool_dependencies.xml file. If installing, platform_info_dict must be a valid dictionary and include_after_install_actions must be True. """ # The actions_elem_tuples list contains <actions> tag sets (possibly inside of an <actions_group> # tag set) to be processed in the order they are defined in the tool_dependencies.xml file. actions_elem_tuples = [] # The tag sets that will go into the actions_elem_list are those that install a compiled binary if # the architecture and operating system match its defined attributes. If compiled binary is not # installed, the first <actions> tag set [following those that have the os and architecture attributes] # that does not have os or architecture attributes will be processed. This tag set must contain the # recipe for downloading and compiling source. actions_elem_list = [] for elem in package_elem: if elem.tag == "actions": # We have an <actions> tag that should not be matched against a specific combination of # architecture and operating system. in_actions_group = False actions_elem_tuples.append((in_actions_group, elem)) elif elem.tag == "actions_group": # We have an actions_group element, and its child <actions> elements should therefore be compared # with the current operating system # and processor architecture. in_actions_group = True # Record the number of <actions> elements so we can filter out any <action> elements that precede # <actions> elements. actions_elem_count = len(elem.findall("actions")) # Record the number of <actions> elements that have both architecture and os specified, in order # to filter out any platform-independent <actions> elements that come before platform-specific # <actions> elements. platform_actions_elements = [] for actions_elem in elem.findall("actions"): if actions_elem.get("architecture") is not None and actions_elem.get("os") is not None: platform_actions_elements.append(actions_elem) platform_actions_element_count = len(platform_actions_elements) platform_actions_elements_processed = 0 actions_elems_processed = 0 # The tag sets that will go into the after_install_actions list are <action> tags instead of <actions> # tags. These will be processed only if they are at the very end of the <actions_group> tag set (after # all <actions> tag sets). See below for details. after_install_actions = [] # Inspect the <actions_group> element and build the actions_elem_list and the after_install_actions list. for child_element in elem: if child_element.tag == "actions": actions_elems_processed += 1 system = child_element.get("os") architecture = child_element.get("architecture") # Skip <actions> tags that have only one of architecture or os specified, in order for the # count in platform_actions_elements_processed to remain accurate. if (system and not architecture) or (architecture and not system): log.debug("Error: Both architecture and os attributes must be specified in an <actions> tag.") continue # Since we are inside an <actions_group> tag set, compare it with our current platform information # and filter the <actions> tag sets that don't match. Require both the os and architecture attributes # to be defined in order to find a match. if system and architecture: platform_actions_elements_processed += 1 # If either the os or architecture do not match the platform, this <actions> tag will not be # considered a match. Skip it and proceed with checking the next one. if platform_info_dict: if platform_info_dict["os"] != system or platform_info_dict["architecture"] != architecture: continue else: # We must not be installing a repository into Galaxy, so determining if we can install a # binary is not necessary. continue else: # <actions> tags without both os and architecture attributes are only allowed to be specified # after platform-specific <actions> tags. If we find a platform-independent <actions> tag before # all platform-specific <actions> tags have been processed. if platform_actions_elements_processed < platform_actions_element_count: debug_msg = "Error: <actions> tags without os and architecture attributes are only allowed " debug_msg += ( "after all <actions> tags with os and architecture attributes have been defined. " ) debug_msg += ( "Skipping the <actions> tag set with no os or architecture attributes that has " ) debug_msg += ( "been defined between two <actions> tag sets that have these attributes defined. " ) log.debug(debug_msg) continue # If we reach this point, it means one of two things: 1) The system and architecture attributes are # not defined in this <actions> tag, or 2) The system and architecture attributes are defined, and # they are an exact match for the current platform. Append the child element to the list of elements # to process. actions_elem_list.append(child_element) elif child_element.tag == "action": # Any <action> tags within an <actions_group> tag set must come after all <actions> tags. if actions_elems_processed == actions_elem_count: # If all <actions> elements have been processed, then this <action> element can be appended to the # list of actions to execute within this group. after_install_actions.append(child_element) else: # If any <actions> elements remain to be processed, then log a message stating that <action> # elements are not allowed to precede any <actions> elements within an <actions_group> tag set. debug_msg = ( "Error: <action> tags are only allowed at the end of an <actions_group> tag set after " ) debug_msg += f"all <actions> tags. Skipping <{child_element.tag}> element with type {child_element.get('type', 'unknown')}." log.debug(debug_msg) continue if platform_info_dict is None and not include_after_install_actions: # We must be setting metadata on a repository. if len(actions_elem_list) >= 1: actions_elem_tuples.append((in_actions_group, actions_elem_list[0])) else: # We are processing a recipe that contains only an <actions_group> tag set for installing a binary, # but does not include an additional recipe for installing and compiling from source. actions_elem_tuples.append((in_actions_group, [])) elif platform_info_dict is not None and include_after_install_actions: # We must be installing a repository. if after_install_actions: actions_elem_list.extend(after_install_actions) actions_elem_tuples.append((in_actions_group, actions_elem_list)) else: # Skip any element that is not <actions> or <actions_group> - this will skip comments, <repository> tags # and <readme> tags. in_actions_group = False continue return actions_elem_tuples
[docs]def remove_tool_dependency(app, tool_dependency): """The received tool_dependency must be in an error state.""" context = app.install_model.context dependency_install_dir = tool_dependency.installation_directory(app) removed, error_message = remove_tool_dependency_installation_directory(dependency_install_dir) if removed: tool_dependency.status = app.install_model.ToolDependency.installation_status.UNINSTALLED tool_dependency.error_message = None context.add(tool_dependency) with transaction(context): context.commit() # Since the received tool_dependency is in an error state, nothing will need to be changed in any # of the in-memory dictionaries in the installed_repository_manager because changing the state from # error to uninstalled requires no in-memory changes.. return removed, error_message
[docs]def remove_tool_dependency_installation_directory(dependency_install_dir): if os.path.exists(dependency_install_dir): try: shutil.rmtree(dependency_install_dir) removed = True error_message = "" log.debug(f"Removed tool dependency installation directory: {dependency_install_dir}") except Exception as e: removed = False error_message = f"Error removing tool dependency installation directory {dependency_install_dir}: {e}" log.warning(error_message) else: removed = True error_message = "" return removed, error_message