Source code for galaxy.webapps.galaxy.api.tool_dependencies

"""
API operations allowing clients to manage tool dependencies.
"""
import logging

from galaxy.tool_util.deps import views
from galaxy.web import (
    expose_api,
    require_admin
)
from galaxy.webapps.base.controller import BaseAPIController

log = logging.getLogger(__name__)


[docs]class ToolDependenciesAPIController(BaseAPIController):
[docs] def __init__(self, app): super(ToolDependenciesAPIController, self).__init__(app) self._view = views.DependencyResolversView(app)
[docs] @require_admin @expose_api def index(self, trans, **kwd): """ GET /api/dependency_resolvers """ return self._view.index()
[docs] @require_admin @expose_api def show(self, trans, id): """ GET /api/dependency_resolvers/<id> """ return self._view.show(id)
[docs] @require_admin @expose_api def update(self, trans): """ PUT /api/dependency_resolvers Reload tool dependency resolution configuration. """ return self._view.reload()
[docs] @require_admin @expose_api def resolver_dependency(self, trans, id, **kwds): """ GET /api/dependency_resolvers/{index}/dependency Resolve described requirement against specified dependency resolver. :type index: int :param index: index of the dependency resolver :type kwds: dict :param kwds: dictionary structure containing extra parameters :type name: str :param name: name of the requirement to find a dependency for (required) :type version: str :param version: version of the requirement to find a dependency for (required) :type exact: bool :param exact: require an exact match to specify requirement (do not discard version information to resolve dependency). :rtype: dict :returns: a dictified description of the dependency, with attribute ``dependency_type: None`` if no match was found. """ return self._view.resolver_dependency(id, **kwds)
[docs] @require_admin @expose_api def install_dependency(self, trans, id=None, **kwds): """ POST /api/dependency_resolvers/{index}/dependency POST /api/dependency_resolvers/dependency Install described requirement against specified dependency resolver. :type index: int :param index: index of the dependency resolver :type kwds: dict :param kwds: dictionary structure containing extra parameters :type name: str :param name: name of the requirement to find a dependency for (required) :type version: str :param version: version of the requirement to find a dependency for (required) :type exact: bool :param exact: require an exact match to specify requirement (do not discard version information to resolve dependency). :type tool_id: str :param tool_id: tool_id to install requirements for :rtype: dict :returns: a dictified description of the dependency, with attribute ``dependency_type: None`` if no match was found. """ self._view.install_dependency(id, **kwds) return self._view.manager_dependency(**kwds)
[docs] @require_admin @expose_api def manager_dependency(self, trans, **kwds): """ GET /api/dependency_resolvers/dependency Resolve described requirement against all dependency resolvers, returning the match with highest priority. :type index: int :param index: index of the dependency resolver :type kwds: dict :param kwds: dictionary structure containing extra parameters :type name: str :param name: name of the requirement to find a dependency for (required) :type version: str :param version: version of the requirement to find a dependency for (required) :type exact: bool :param exact: require an exact match to specify requirement (do not discard version information to resolve dependency). :rtype: dict :returns: a dictified description of the dependency, with type: None if no match was found. """ return self._view.manager_dependency(**kwds)
[docs] @require_admin @expose_api def resolver_requirements(self, trans, id, **kwds): """ GET /api/dependency_resolvers/{index}/requirements Find all "simple" requirements that could be resolved "exactly" by this dependency resolver. The dependency resolver must implement ListDependencyResolver. :type index: int :param index: index of the dependency resolver :rtype: dict :returns: a dictified description of the requirement that could be resolved. """ return self._view.resolver_requirements(id)
[docs] @require_admin @expose_api def manager_requirements(self, trans, **kwds): """ GET /api/dependency_resolvers/requirements Find all "simple" requirements that could be resolved "exactly" by all dependency resolvers that support this operation. :type index: int :param index: index of the dependency resolver :rtype: dict :returns: a dictified description of the requirement that could be resolved (keyed on 'requirement') and the index of the corresponding resolver (keyed on 'index'). """ return self._view.manager_requirements()
[docs] @require_admin @expose_api def clean(self, trans, id=None, **kwds): """ POST /api/dependency_resolvers/{index}/clean Cleans up intermediate files created by resolvers during the dependency installation. :type index: int :param index: index of the dependency resolver :rtype: dict :returns: a dictified description of the requirement that could be resolved (keyed on 'requirement') and the index of the corresponding resolver (keyed on 'index'). """ return self._view.clean(id, **kwds)
[docs] @expose_api @require_admin def summarize_toolbox(self, trans, **kwds): """ GET /api/dependency_resolvers/toolbox Summarize requirements across toolbox (for Tool Management grid). This is an experiemental API particularly tied to the GUI - expect breaking changes until this notice is removed. Container resolution via this API is especially experimental and the container resolution API should be used to summarize this information instead in most cases. :type index: int :param index: index of the dependency resolver :type tool_ids: str :param tool_ids: tool_id to install dependency for :type resolver_type: str :param resolver_type: restrict to uninstall to specified resolver type :type include_containers: bool :param include_containers: include container resolvers in resolution :type container_type: str :param container_type: restrict to uninstall to specified container type :type index_by: str :param index_by: By default consider only context of requirements, group tools by requirements. Set this to 'tools' to summarize across all tools though. Tools may provide additional context for container resolution for instance. :rtype: list :returns: dictified descriptions of the dependencies, with attribute ``dependency_type: None`` if no match was found. """ kwds["for_json"] = True index_by = kwds.get("index_by", "requirements") if index_by == "requirements": return self._view.summarize_requirements(**kwds) else: return self._view.summarize_tools(**kwds)
[docs] @expose_api @require_admin def toolbox_install(self, trans, payload, index=None, **kwds): """ POST /api/dependency_resolvers/{index}/toolbox/install POST /api/dependency_resolvers/toolbox/install Install described requirement against specified dependency resolver(s). This is an experiemental API particularly tied to the GUI - expect breaking changes until this notice is removed. :type index: int :param index: index of the dependency resolver :type tool_ids: str :param tool_ids: tool_id to install dependency for :type resolver_type: str :param resolver_type: restrict to uninstall to specified resolver type :type include_containers: bool :param include_containers: include container resolvers in resolution :type container_type: str :param container_type: restrict to uninstall to specified container type """ tools_by_id = trans.app.toolbox.tools_by_id.copy() tool_ids = payload.get("tool_ids") requirements = {tools_by_id[tid].tool_requirements for tid in tool_ids} install_kwds = {} for source in [payload, kwds]: if 'include_containers' in source: install_kwds['include_containers'] = source['container_type'] if 'container_type' in kwds: install_kwds['container_type'] = source['container_type'] if 'resolver_type' in source: install_kwds['resolver_type'] = source['resolver_type'] [self._view.install_dependencies(requirements=r, index=index, **install_kwds) for r in requirements]
[docs] @expose_api @require_admin def toolbox_uninstall(self, trans, payload, index=None, **kwds): """ POST /api/dependency_resolvers/{index}/toolbox/uninstall POST /api/dependency_resolvers/toolbox/uninstall Uninstall described requirement against specified dependency resolver(s). This is an experiemental API particularly tied to the GUI - expect breaking changes until this notice is removed. :type index: int :param index: index of the dependency resolver :type tool_ids: str :param tool_ids: tool_id to install dependency for :type include_containers: bool :param include_containers: include container resolvers in resolution :type container_type: str :param container_type: restrict to uninstall to specified container type :type resolver_type: str :param resolver_type: restrict to uninstall to specified resolver type """ tools_by_id = trans.app.toolbox.tools_by_id.copy() tool_ids = payload.get("tool_ids") requirements = {tools_by_id[tid].tool_requirements for tid in tool_ids} install_kwds = {} for source in [payload, kwds]: if 'include_containers' in source: install_kwds['include_containers'] = source['container_type'] if 'container_type' in kwds: install_kwds['container_type'] = source['container_type'] if 'resolver_type' in source: install_kwds['resolver_type'] = source['resolver_type'] [self._view.uninstall_dependencies(index=index, requirements=r, **install_kwds) for r in requirements]
[docs] @expose_api @require_admin def unused_dependency_paths(self, trans, **kwds): """ GET /api/dependency_resolvers/unused_paths """ return list(self._view.unused_dependency_paths)
[docs] @expose_api @require_admin def delete_unused_dependency_paths(self, trans, payload, **kwds): """ PUT /api/dependency_resolvers/unused_paths """ paths = payload.get("paths") self._view.remove_unused_dependency_paths(paths)