Warning

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.webapp.controllers.admin

import logging

import tool_shed.grids.admin_grids as admin_grids
from galaxy import (
    util,
    web,
)
from galaxy.model.base import transaction
from galaxy.util import inflector
from galaxy.web.legacy_framework import grids
from galaxy.webapps.base.controller import BaseUIController
from tool_shed.metadata import repository_metadata_manager
from tool_shed.util import (
    metadata_util,
    repository_util,
    shed_util_common as suc,
)
from tool_shed.util.admin_util import Admin
from tool_shed.util.web_util import escape

log = logging.getLogger(__name__)


[docs]class AdminController(BaseUIController, Admin): user_list_grid = admin_grids.UserGrid() role_list_grid = admin_grids.RoleGrid() group_list_grid = admin_grids.GroupGrid() manage_category_grid = admin_grids.ManageCategoryGrid() repository_grid = admin_grids.AdminRepositoryGrid() repository_metadata_grid = admin_grids.RepositoryMetadataGrid() delete_operation = grids.GridOperation("Delete", condition=(lambda item: not item.deleted), allow_multiple=True) undelete_operation = grids.GridOperation( "Undelete", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True ) purge_operation = grids.GridOperation( "Purge", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True )
[docs] @web.expose @web.require_admin def browse_repositories(self, trans, **kwd): # We add parameters to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have # to take this approach because the "-" character is illegal in HTTP requests. if "operation" in kwd: operation = kwd["operation"].lower() if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for(controller="repository", action="browse_repositories", **kwd) ) elif operation == "edit_repository": return trans.response.send_redirect( web.url_for(controller="repository", action="edit_repository", **kwd) ) elif operation == "repositories_by_user": # Eliminate the current filters if any exist. for k in list(kwd.keys()): if k.startswith("f-"): del kwd[k] if "user_id" in kwd: user = suc.get_user(trans.app, kwd["user_id"]) kwd["f-email"] = user.email del kwd["user_id"] else: # The received id is the repository id, so we need to get the id of the user # that uploaded the repository. repository_id = kwd.get("id", None) repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id) kwd["f-email"] = repository.user.email elif operation == "repositories_by_category": # Eliminate the current filters if any exist. for k in list(kwd.keys()): if k.startswith("f-"): del kwd[k] category_id = kwd.get("id", None) category = suc.get_category(trans.app, category_id) kwd["f-Category.name"] = category.name elif operation == "receive email alerts": if kwd["id"]: kwd["caller"] = "browse_repositories" return trans.response.send_redirect( web.url_for(controller="repository", action="set_email_alerts", **kwd) ) else: del kwd["operation"] elif operation == "delete": return self.delete_repository(trans, **kwd) elif operation == "undelete": return self.undelete_repository(trans, **kwd) # The changeset_revision_select_field in the RepositoryGrid performs a refresh_on_change # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One # of the many select fields on the grid performed the refresh_on_change, so we loop through # all of the received values to see which value is not the repository tip. If we find it, we # know the refresh_on_change occurred, and we have the necessary repository id and change set # revision to pass on. for k, v in kwd.items(): changeset_revision_str = "changeset_revision_" if k.startswith(changeset_revision_str): repository_id = trans.security.encode_id(int(k.lstrip(changeset_revision_str))) repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id) if repository.tip() != v: return trans.response.send_redirect( web.url_for( controller="repository", action="browse_repositories", operation="view_or_manage_repository", id=trans.security.encode_id(repository.id), changeset_revision=v, ) ) # Render the list view return self.repository_grid(trans, **kwd)
[docs] @web.expose @web.require_admin def browse_repository_metadata(self, trans, **kwd): if "operation" in kwd: operation = kwd["operation"].lower() if operation == "delete": return self.delete_repository_metadata(trans, **kwd) if operation == "view_or_manage_repository_revision": # The received id is a RepositoryMetadata object id, so we need to get the # associated Repository and redirect to view_or_manage_repository with the # changeset_revision. repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, kwd["id"]) repository = repository_metadata.repository kwd["id"] = trans.security.encode_id(repository.id) kwd["changeset_revision"] = repository_metadata.changeset_revision kwd["operation"] = "view_or_manage_repository" return trans.response.send_redirect( web.url_for(controller="repository", action="browse_repositories", **kwd) ) return self.repository_metadata_grid(trans, **kwd)
[docs] @web.expose @web.require_admin def create_category(self, trans, **kwd): message = escape(kwd.get("message", "")) status = kwd.get("status", "done") name = kwd.get("name", "").strip() description = kwd.get("description", "").strip() if kwd.get("create_category_button", False): if not name or not description: message = "Enter a valid name and a description" status = "error" elif suc.get_category_by_name(trans.app, name): message = "A category with that name already exists" status = "error" else: # Create the category category = trans.app.model.Category(name=name, description=description) trans.sa_session.add(category) with transaction(trans.sa_session): trans.sa_session.commit() # Update the Tool Shed's repository registry. trans.app.repository_registry.add_category_entry(category) message = f"Category '{escape(category.name)}' has been created" status = "done" trans.response.send_redirect( web.url_for(controller="admin", action="manage_categories", message=message, status=status) ) return trans.fill_template( "/webapps/tool_shed/category/create_category.mako", name=name, description=description, message=message, status=status, )
[docs] @web.expose @web.require_admin def delete_repository(self, trans, **kwd): message = escape(kwd.get("message", "")) status = kwd.get("status", "done") id = kwd.get("id", None) if id: # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. ids = util.listify(id) count = 0 deleted_repositories = "" for repository_id in ids: repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id) if repository: if not repository.deleted: # Mark all installable repository_metadata records as not installable. for repository_metadata in repository.downloadable_revisions: repository_metadata.downloadable = False trans.sa_session.add(repository_metadata) # Mark the repository admin role as deleted. repository_admin_role = repository.admin_role if repository_admin_role is not None: repository_admin_role.deleted = True trans.sa_session.add(repository_admin_role) repository.deleted = True trans.sa_session.add(repository) with transaction(trans.sa_session): trans.sa_session.commit() # Update the repository registry. trans.app.repository_registry.remove_entry(repository) count += 1 deleted_repositories += f" {repository.name} " if count: message = "Deleted %d %s: %s" % ( count, inflector.cond_plural(len(ids), "repository"), escape(deleted_repositories), ) else: message = "All selected repositories were already marked deleted." else: message = "No repository ids received for deleting." status = "error" trans.response.send_redirect( web.url_for( controller="admin", action="browse_repositories", message=util.sanitize_text(message), status=status ) )
[docs] @web.expose @web.require_admin def delete_repository_metadata(self, trans, **kwd): message = escape(kwd.get("message", "")) status = kwd.get("status", "done") id = kwd.get("id", None) if id: ids = util.listify(id) count = 0 for repository_metadata_id in ids: repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id) trans.sa_session.delete(repository_metadata) with transaction(trans.sa_session): trans.sa_session.commit() count += 1 if count: message = "Deleted %d repository metadata %s" % (count, inflector.cond_plural(len(ids), "record")) else: message = "No repository metadata ids received for deleting." status = "error" trans.response.send_redirect( web.url_for( controller="admin", action="browse_repository_metadata", message=util.sanitize_text(message), status=status, ) )
[docs] @web.expose @web.require_admin def edit_category(self, trans, **kwd): """Handle requests to edit TS category name or description""" message = escape(kwd.get("message", "")) status = kwd.get("status", "done") id = kwd.get("id", None) if not id: message = "No category ids received for editing" trans.response.send_redirect( web.url_for(controller="admin", action="manage_categories", message=message, status="error") ) category = suc.get_category(trans.app, id) original_category_name = str(category.name) original_category_description = str(category.description) if kwd.get("edit_category_button", False): flush_needed = False new_name = kwd.get("name", "").strip() new_description = kwd.get("description", "").strip() if original_category_name != new_name: if not new_name: message = "Enter a valid name" status = "error" elif original_category_name != new_name and suc.get_category_by_name(trans.app, new_name): message = "A category with that name already exists" status = "error" else: category.name = new_name flush_needed = True if original_category_description != new_description: category.description = new_description if not flush_needed: flush_needed = True if flush_needed: trans.sa_session.add(category) with transaction(trans.sa_session): trans.sa_session.commit() if original_category_name != new_name: # Update the Tool Shed's repository registry. trans.app.repository_registry.edit_category_entry(original_category_name, new_name) message = f"The information has been saved for category '{escape(category.name)}'" status = "done" return trans.response.send_redirect( web.url_for(controller="admin", action="manage_categories", message=message, status=status) ) return trans.fill_template( "/webapps/tool_shed/category/edit_category.mako", category=category, message=message, status=status )
[docs] @web.expose @web.require_admin def manage_categories(self, trans, **kwd): if "f-free-text-search" in kwd: # Trick to enable searching repository name, description from the CategoryGrid. # What we've done is rendered the search box for the RepositoryGrid on the grid.mako # template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako. # Since we are searching repositories and not categories, redirect to browse_repositories(). return trans.response.send_redirect(web.url_for(controller="admin", action="browse_repositories", **kwd)) if "operation" in kwd: operation = kwd["operation"].lower() if operation == "create": return trans.response.send_redirect(web.url_for(controller="admin", action="create_category", **kwd)) elif operation == "delete": return trans.response.send_redirect( web.url_for(controller="admin", action="mark_category_deleted", **kwd) ) elif operation == "undelete": return trans.response.send_redirect(web.url_for(controller="admin", action="undelete_category", **kwd)) elif operation == "purge": return trans.response.send_redirect(web.url_for(controller="admin", action="purge_category", **kwd)) elif operation == "edit": return trans.response.send_redirect(web.url_for(controller="admin", action="edit_category", **kwd)) return self.manage_category_grid(trans, **kwd)
[docs] @web.expose @web.require_admin def regenerate_statistics(self, trans, **kwd): message = escape(kwd.get("message", "")) status = kwd.get("status", "done") if "regenerate_statistics_button" in kwd: trans.app.shed_counter.generate_statistics() message = "Successfully regenerated statistics" return trans.fill_template("/webapps/tool_shed/admin/statistics.mako", message=message, status=status)
[docs] @web.expose @web.require_admin def manage_role_associations(self, trans, **kwd): """Manage users, groups and repositories associated with a role.""" role_id = kwd.get("id", None) role = repository_util.get_role_by_id(trans.app, role_id) # We currently only have a single role associated with a repository, the repository admin role. repository_role_association = role.repositories[0] repository = repository_role_association.repository associations_dict = repository_util.handle_role_associations(trans.app, role, repository, **kwd) in_users = associations_dict.get("in_users", []) out_users = associations_dict.get("out_users", []) in_groups = associations_dict.get("in_groups", []) out_groups = associations_dict.get("out_groups", []) message = associations_dict.get("message", "") status = associations_dict.get("status", "done") return trans.fill_template( "/webapps/tool_shed/role/role.mako", in_admin_controller=True, repository=repository, role=role, in_users=in_users, out_users=out_users, in_groups=in_groups, out_groups=out_groups, message=message, status=status, )
[docs] @web.expose @web.require_admin def reset_metadata_on_selected_repositories_in_tool_shed(self, trans, **kwd): rmm = repository_metadata_manager.RepositoryMetadataManager(trans.app, trans.user) if "reset_metadata_on_selected_repositories_button" in kwd: message, status = rmm.reset_metadata_on_selected_repositories(**kwd) else: message = escape(util.restore_text(kwd.get("message", ""))) status = kwd.get("status", "done") repositories_select_field = rmm.build_repository_ids_select_field( name="repository_ids", multiple=True, display="checkboxes", my_writable=False ) return trans.fill_template( "/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako", repositories_select_field=repositories_select_field, message=message, status=status, )
[docs] @web.expose @web.require_admin def undelete_repository(self, trans, **kwd): message = escape(kwd.get("message", "")) id = kwd.get("id", None) if id: # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. ids = util.listify(id) count = 0 undeleted_repositories = "" for repository_id in ids: repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id) if repository: if repository.deleted: # Inspect all repository_metadata records to determine those that are installable, and mark # them accordingly. for repository_metadata in repository.metadata_revisions: metadata = repository_metadata.metadata if metadata: if metadata_util.is_downloadable(metadata): repository_metadata.downloadable = True trans.sa_session.add(repository_metadata) # Mark the repository admin role as not deleted. repository_admin_role = repository.admin_role if repository_admin_role is not None: repository_admin_role.deleted = False trans.sa_session.add(repository_admin_role) repository.deleted = False trans.sa_session.add(repository) with transaction(trans.sa_session): trans.sa_session.commit() if not repository.deprecated: # Update the repository registry. trans.app.repository_registry.add_entry(repository) count += 1 undeleted_repositories += f" {repository.name}" if count: message = "Undeleted %d %s: %s" % ( count, inflector.cond_plural(count, "repository"), undeleted_repositories, ) else: message = "No selected repositories were marked deleted, so they could not be undeleted." else: message = "No repository ids received for undeleting." trans.response.send_redirect( web.url_for( controller="admin", action="browse_repositories", message=util.sanitize_text(message), status="done" ) )
[docs] @web.expose @web.require_admin def mark_category_deleted(self, trans, **kwd): # TODO: We should probably eliminate the Category.deleted column since it really makes no # sense to mark a category as deleted (category names and descriptions can be changed instead). # If we do this, and the following 2 methods can be eliminated. message = escape(kwd.get("message", "")) id = kwd.get("id", None) if id: ids = util.listify(id) message = "Deleted %d categories: " % len(ids) for category_id in ids: category = suc.get_category(trans.app, category_id) category.deleted = True trans.sa_session.add(category) with transaction(trans.sa_session): trans.sa_session.commit() # Update the Tool Shed's repository registry. trans.app.repository_registry.remove_category_entry(category) message += f" {escape(category.name)} " else: message = "No category ids received for deleting." trans.response.send_redirect( web.url_for( controller="admin", action="manage_categories", message=util.sanitize_text(message), status="done" ) )
[docs] @web.expose @web.require_admin def purge_category(self, trans, **kwd): # This method should only be called for a Category that has previously been deleted. # Purging a deleted Category deletes all of the following from the database: # - RepoitoryCategoryAssociations where category_id == Category.id message = escape(kwd.get("message", "")) id = kwd.get("id", None) if id: ids = util.listify(id) count = 0 purged_categories = "" message = "Purged %d categories: " % len(ids) for category_id in ids: category = suc.get_category(trans.app, category_id) if category.deleted: # Delete RepositoryCategoryAssociations for rca in category.repositories: trans.sa_session.delete(rca) with transaction(trans.sa_session): trans.sa_session.commit() purged_categories += f" {category.name} " message = "Purged %d categories: %s" % (count, escape(purged_categories)) else: message = "No category ids received for purging." trans.response.send_redirect( web.url_for( controller="admin", action="manage_categories", message=util.sanitize_text(message), status="done" ) )
[docs] @web.expose @web.require_admin def undelete_category(self, trans, **kwd): message = escape(kwd.get("message", "")) id = kwd.get("id", None) if id: ids = util.listify(id) count = 0 undeleted_categories = "" for category_id in ids: category = suc.get_category(trans.app, category_id) if category.deleted: category.deleted = False trans.sa_session.add(category) with transaction(trans.sa_session): trans.sa_session.commit() # Update the Tool Shed's repository registry. trans.app.repository_registry.add_category_entry(category) count += 1 undeleted_categories += f" {category.name}" message = "Undeleted %d categories: %s" % (count, escape(undeleted_categories)) else: message = "No category ids received for undeleting." trans.response.send_redirect( web.url_for( controller="admin", action="manage_categories", message=util.sanitize_text(message), status="done" ) )