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Source code for galaxy.tool_shed.util.shed_util_common

import logging
import re

from galaxy import util
from galaxy.tool_shed.util import repository_util
from galaxy.util.tool_shed import common_util
from galaxy.web import url_for

log = logging.getLogger(__name__)

DATATYPES_CONFIG_FILENAME = 'datatypes_conf.xml'

[docs]def can_eliminate_repository_dependency(metadata_dict, tool_shed_url, name, owner): """ Determine if the relationship between a repository_dependency record associated with a tool_shed_repository record on the Galaxy side can be eliminated. """ rd_dict = metadata_dict.get('repository_dependencies', {}) rd_tups = rd_dict.get('repository_dependencies', []) for rd_tup in rd_tups: tsu, n, o, none1, none2, none3 = common_util.parse_repository_dependency_tuple(rd_tup) if tsu == tool_shed_url and n == name and o == owner: # The repository dependency is current, so keep it. return False return True
[docs]def can_eliminate_tool_dependency(metadata_dict, name, dependency_type, version): """ Determine if the relationship between a tool_dependency record associated with a tool_shed_repository record on the Galaxy side can be eliminated. """ td_dict = metadata_dict.get('tool_dependencies', {}) for td_key, td_val in td_dict.items(): if td_key == 'set_environment': for td in td_val: n = td.get('name', None) t = td.get('type', None) if n == name and t == dependency_type: # The tool dependency is current, so keep it. return False else: n = td_val.get('name', None) t = td_val.get('type', None) v = td_val.get('version', None) if n == name and t == dependency_type and v == version: # The tool dependency is current, so keep it. return False return True
[docs]def clean_dependency_relationships(trans, metadata_dict, tool_shed_repository, tool_shed_url): """ Repositories of type tool_dependency_definition allow for defining a package dependency at some point in the change log and then removing the dependency later in the change log. This function keeps the dependency relationships on the Galaxy side current by deleting database records that defined the now-broken relationships. """ for rrda in tool_shed_repository.required_repositories: rd = rrda.repository_dependency r = rd.repository if can_eliminate_repository_dependency(metadata_dict, tool_shed_url, r.name, r.owner): message = "Repository dependency %s by owner %s is not required by repository %s, owner %s, " message += "removing from list of repository dependencies." log.debug(message % (r.name, r.owner, tool_shed_repository.name, tool_shed_repository.owner)) trans.install_model.context.delete(rrda) trans.install_model.context.flush() for td in tool_shed_repository.tool_dependencies: if can_eliminate_tool_dependency(metadata_dict, td.name, td.type, td.version): message = "Tool dependency %s, version %s is not required by repository %s, owner %s, " message += "removing from list of tool dependencies." log.debug(message % (td.name, td.version, tool_shed_repository.name, tool_shed_repository.owner)) trans.install_model.context.delete(td) trans.install_model.context.flush()
[docs]def generate_tool_guid(repository_clone_url, tool): """ Generate a guid for the installed tool. It is critical that this guid matches the guid for the tool in the Galaxy tool shed from which it is being installed. The form of the guid is <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version> """ tmp_url = common_util.remove_protocol_and_user_from_clone_url(repository_clone_url) return f'{tmp_url}/{tool.id}/{tool.version}'
[docs]def get_ctx_rev(app, tool_shed_url, name, owner, changeset_revision): """ Send a request to the tool shed to retrieve the ctx_rev for a repository defined by the combination of a name, owner and changeset revision. """ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url) params = dict(name=name, owner=owner, changeset_revision=changeset_revision) pathspec = ['repository', 'get_ctx_rev'] ctx_rev = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) return ctx_rev
[docs]def get_next_prior_import_or_install_required_dict_entry(prior_required_dict, processed_tsr_ids): """ This method is used in the Tool Shed when exporting a repository and its dependencies, and in Galaxy when a repository and its dependencies are being installed. The order in which the prior_required_dict is processed is critical in order to ensure that the ultimate repository import or installation order is correctly defined. This method determines the next key / value pair from the received prior_required_dict that should be processed. """ # Return the first key / value pair that is not yet processed and whose value is an empty list. for key, value in prior_required_dict.items(): if key in processed_tsr_ids: continue if not value: return key # Return the first key / value pair that is not yet processed and whose ids in value are all included # in processed_tsr_ids. for key, value in prior_required_dict.items(): if key in processed_tsr_ids: continue all_contained = True for required_repository_id in value: if required_repository_id not in processed_tsr_ids: all_contained = False break if all_contained: return key # Return the first key / value pair that is not yet processed. Hopefully this is all that is necessary # at this point. for key in prior_required_dict.keys(): if key in processed_tsr_ids: continue return key
[docs]def get_tool_panel_config_tool_path_install_dir(app, repository): """ Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the repository is installed. This method assumes all repository tools are defined in a single shed-related tool panel config. """ tool_shed = common_util.remove_port_from_tool_shed_url(str(repository.tool_shed)) relative_install_dir = '{}/repos/{}/{}/{}'.format(tool_shed, str(repository.owner), str(repository.name), str(repository.installed_changeset_revision)) # Get the relative tool installation paths from each of the shed tool configs. shed_config_dict = repository.get_shed_config_dict(app) shed_tool_conf = shed_config_dict['config_filename'] tool_path = shed_config_dict['tool_path'] return shed_tool_conf, tool_path, relative_install_dir
[docs]def get_user(app, id): """Get a user from the database by id.""" sa_session = app.model.context.current return sa_session.query(app.model.User).get(app.security.decode_id(id))
[docs]def have_shed_tool_conf_for_install(app): return bool(app.toolbox.dynamic_confs(include_migrated_tool_conf=False))
[docs]def set_image_paths(app, text, encoded_repository_id=None, tool_shed_repository=None, tool_id=None, tool_version=None): """ Handle tool help image display for tools that are contained in repositories in the tool shed or installed into Galaxy as well as image display in repository README files. This method will determine the location of the image file and return the path to it that will enable the caller to open the file. """ if text: if repository_util.is_tool_shed_client(app) and encoded_repository_id: route_to_images = 'admin_toolshed/static/images/%s' % encoded_repository_id elif encoded_repository_id: # We're in the tool shed. route_to_images = '/repository/static/images/%s' % encoded_repository_id elif tool_shed_repository and tool_id and tool_version: route_to_images = 'shed_tool_static/{shed}/{owner}/{repo}/{tool}/{version}'.format( shed=tool_shed_repository.tool_shed, owner=tool_shed_repository.owner, repo=tool_shed_repository.name, tool=tool_id, version=tool_version, ) else: raise Exception("encoded_repository_id or tool_shed_repository and tool_id and tool_version must be provided") # We used to require $PATH_TO_IMAGES and ${static_path}, but # we now eliminate it if it's used. text = text.replace('$PATH_TO_IMAGES', '') text = text.replace('${static_path}', '') # Use regex to instantiate routes into the defined image paths, but replace # paths that start with neither http:// nor https://, which will allow for # settings like .. images:: http_files/images/help.png for match in re.findall('.. image:: (?!http)/?(.+)', text): text = text.replace(match, match.replace('/', '%2F')) text = re.sub(r'\.\. image:: (?!https?://)/?(.+)', r'.. image:: %s/\1' % route_to_images, text) return text
[docs]def tool_shed_is_this_tool_shed(toolshed_base_url): """Determine if a tool shed is the current tool shed.""" cleaned_toolshed_base_url = common_util.remove_protocol_from_tool_shed_url(toolshed_base_url) cleaned_tool_shed = common_util.remove_protocol_from_tool_shed_url(str(url_for('/', qualified=True))) return cleaned_toolshed_base_url == cleaned_tool_shed
__all__ = ( 'can_eliminate_repository_dependency', 'can_eliminate_tool_dependency', 'clean_dependency_relationships', 'DATATYPES_CONFIG_FILENAME', 'generate_tool_guid', 'get_ctx_rev', 'get_next_prior_import_or_install_required_dict_entry', 'get_tool_panel_config_tool_path_install_dir', 'get_user', 'have_shed_tool_conf_for_install', 'set_image_paths', 'tool_shed_is_this_tool_shed', )