Source code for galaxy.webapps.tool_shed.controllers.admin

import logging

import tool_shed.grids.admin_grids as admin_grids
from galaxy import (
    util,
    web
)
from galaxy.util import inflector
from galaxy.web.base.controller import BaseUIController
from galaxy.web.framework.helpers import grids
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, v in list(kwd.items()): 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, v in list(kwd.items()): 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(trans.app) != 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) trans.sa_session.flush() # Update the Tool Shed's repository registry. trans.app.repository_registry.add_category_entry(category) message = "Category '%s' has been created" % escape(category.name) 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) trans.sa_session.flush() # Update the repository registry. trans.app.repository_registry.remove_entry(repository) count += 1 deleted_repositories += " %s " % 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) trans.sa_session.flush() 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) trans.sa_session.flush() 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 = "The information has been saved for category '%s'" % 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) trans.sa_session.flush() if not repository.deprecated: # Update the repository registry. trans.app.repository_registry.add_entry(repository) count += 1 undeleted_repositories += " %s" % 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) trans.sa_session.flush() # Update the Tool Shed's repository registry. trans.app.repository_registry.remove_category_entry(category) message += " %s " % 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) trans.sa_session.flush() purged_categories += " %s " % 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) trans.sa_session.flush() # Update the Tool Shed's repository registry. trans.app.repository_registry.add_category_entry(category) count += 1 undeleted_categories += " %s" % 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'))