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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.tool_shed.util.hg_util import get_config_from_disk
from galaxy.util.tool_shed.xml_util import parse_xml
from galaxy.web.form_builder import SelectField

log = logging.getLogger(__name__)

[docs]def build_tool_dependencies_select_field(app, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled_only=False): """ Generate a SelectField consisting of the current list of tool dependency ids for an installed tool shed repository. """ tool_dependencies_select_field = SelectField(name=name, multiple=multiple, display=display) for tool_dependency in tool_shed_repository.tool_dependencies: if uninstalled_only: if tool_dependency.status not in [app.install_model.ToolDependency.installation_status.NEVER_INSTALLED, app.install_model.ToolDependency.installation_status.UNINSTALLED]: continue else: if tool_dependency.status in [app.install_model.ToolDependency.installation_status.NEVER_INSTALLED, app.install_model.ToolDependency.installation_status.UNINSTALLED]: continue option_label = '{} version {}'.format(str(tool_dependency.name), str(tool_dependency.version)) option_value = app.security.encode_id(tool_dependency.id) tool_dependencies_select_field.add_option(option_label, option_value) return tool_dependencies_select_field
[docs]def create_or_update_tool_dependency(app, tool_shed_repository, name, version, type, status, set_status=True): """Create or update a tool_dependency record in the Galaxy database.""" # Called from Galaxy (never the tool shed) when a new repository is being installed or when an uninstalled # repository is being reinstalled. context = app.install_model.context # First see if an appropriate tool_dependency record exists for the received tool_shed_repository. if version: tool_dependency = get_tool_dependency_by_name_version_type_repository(app, tool_shed_repository, name, version, type) else: tool_dependency = get_tool_dependency_by_name_type_repository(app, tool_shed_repository, name, type) if tool_dependency: # In some cases we should not override the current status of an existing tool_dependency, so do so only # if set_status is True. if set_status: set_tool_dependency_attributes(app, tool_dependency=tool_dependency, status=status) else: # Create a new tool_dependency record for the tool_shed_repository. debug_msg = 'Creating a new record for version %s of tool dependency %s for revision %s of repository %s. ' % \ (str(version), str(name), str(tool_shed_repository.changeset_revision), str(tool_shed_repository.name)) debug_msg += 'The status is being set to %s.' % str(status) log.debug(debug_msg) tool_dependency = app.install_model.ToolDependency(tool_shed_repository.id, name, version, type, status) context.add(tool_dependency) context.flush() return tool_dependency
[docs]def create_tool_dependency_objects(app, tool_shed_repository, relative_install_dir, set_status=True): """ Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when installing a new tool_shed_repository. """ tool_dependency_objects = [] shed_config_dict = tool_shed_repository.get_shed_config_dict(app) if shed_config_dict.get('tool_path'): relative_install_dir = os.path.join(shed_config_dict.get('tool_path'), relative_install_dir) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = get_config_from_disk('tool_dependencies.xml', relative_install_dir) tree, error_message = parse_xml(tool_dependencies_config) if tree is None: return tool_dependency_objects root = tree.getroot() for elem in root: tool_dependency_type = elem.tag if tool_dependency_type == 'package': name = elem.get('name', None) version = elem.get('version', None) if name and version: status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED tool_dependency = create_or_update_tool_dependency(app, tool_shed_repository, name=name, version=version, type=tool_dependency_type, status=status, set_status=set_status) tool_dependency_objects.append(tool_dependency) elif tool_dependency_type == 'set_environment': for env_elem in elem: # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> name = env_elem.get('name', None) action = env_elem.get('action', None) if name and action: status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED tool_dependency = create_or_update_tool_dependency(app, tool_shed_repository, name=name, version=None, type=tool_dependency_type, status=status, set_status=set_status) tool_dependency_objects.append(tool_dependency) return tool_dependency_objects
[docs]def get_download_url_for_platform(url_templates, platform_info_dict): ''' Compare the dict returned by get_platform_info() with the values specified in the url_template element. Return true if and only if all defined attributes match the corresponding dict entries. If an entry is not defined in the url_template element, it is assumed to be irrelevant at this stage. For example, <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/faToTwoBit</url_template> where the OS must be 'darwin', but the architecture is filled in later using string.Template. ''' os_ok = False architecture_ok = False for url_template in url_templates: os_name = url_template.get('os', None) architecture = url_template.get('architecture', None) if os_name: if os_name.lower() == platform_info_dict['os']: os_ok = True else: os_ok = False else: os_ok = True if architecture: if architecture.lower() == platform_info_dict['architecture']: architecture_ok = True else: architecture_ok = False else: architecture_ok = True if os_ok and architecture_ok: return url_template return None
[docs]def get_platform_info_dict(): '''Return a dict with information about the current platform.''' platform_dict = {} sysname, nodename, release, version, machine = os.uname() platform_dict['os'] = sysname.lower() platform_dict['architecture'] = machine.lower() return platform_dict
[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 get_tool_dependency_install_dir(app, repository_name, repository_owner, repository_changeset_revision, tool_dependency_type, tool_dependency_name, tool_dependency_version): if tool_dependency_type == 'package': return os.path.abspath(os.path.join(app.tool_dependency_dir, tool_dependency_name, tool_dependency_version, repository_owner, repository_name, repository_changeset_revision)) if tool_dependency_type == 'set_environment': return os.path.abspath(os.path.join(app.tool_dependency_dir, 'environment_settings', tool_dependency_name, repository_owner, repository_name, repository_changeset_revision))
[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 += 'all <actions> tags. Skipping <%s> element with type %s.' % \ (child_element.tag, 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) context.flush() # 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("Removed tool dependency installation directory: %s" % str(dependency_install_dir)) except Exception as e: removed = False error_message = "Error removing tool dependency installation directory {}: {}".format(str(dependency_install_dir), str(e)) log.warning(error_message) else: removed = True error_message = '' return removed, error_message
[docs]def set_tool_dependency_attributes(app, tool_dependency, status, error_message=None): sa_session = app.install_model.context if status == app.install_model.ToolDependency.installation_status.UNINSTALLED: installation_directory = tool_dependency.installation_directory(app) remove_tool_dependency_installation_directory(installation_directory) tool_dependency.error_message = error_message if str(tool_dependency.status) != str(status): tool_shed_repository = tool_dependency.tool_shed_repository debug_msg = 'Updating an existing record for version %s of tool dependency %s for revision %s of repository %s ' % \ (str(tool_dependency.version), str(tool_dependency.name), str(tool_shed_repository.changeset_revision), str(tool_shed_repository.name)) debug_msg += 'by updating the status from {} to {}.'.format(str(tool_dependency.status), str(status)) log.debug(debug_msg) tool_dependency.status = status sa_session.add(tool_dependency) sa_session.flush() app.tool_shed_repository_cache.rebuild() return tool_dependency