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

import imp
import logging
import os
from datetime import datetime, timedelta
import six
from string import punctuation as PUNCTUATION
from sqlalchemy import and_, false, func, or_

import galaxy.queue_worker
from galaxy import util
from galaxy import model
from galaxy import web
from galaxy.actions.admin import AdminActions
from galaxy.exceptions import ActionInputError, MessageException
from galaxy.model import tool_shed_install as install_model
from galaxy.util import nice_size, sanitize_text, url_get
from galaxy.util.odict import odict
from galaxy.web import url_for
from galaxy.web.base import controller
from galaxy.web.base.controller import UsesQuotaMixin
from galaxy.web.framework.helpers import grids, time_ago
from galaxy.web.params import QuotaParamParser
from galaxy.tools import global_tool_errors
from tool_shed.util import common_util
from tool_shed.util import encoding_util
from tool_shed.util import repository_util
from tool_shed.util.web_util import escape


log = logging.getLogger(__name__)


[docs]class UserListGrid(grids.Grid):
[docs] class EmailColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, user): return escape(user.email)
[docs] class UserNameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, user): if user.username: return escape(user.username) return 'not set'
[docs] class StatusColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, user): if user.purged: return "purged" elif user.deleted: return "deleted" return ""
[docs] class GroupsColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, user): if user.groups: return len(user.groups) return 0
[docs] class RolesColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, user): if user.roles: return len(user.roles) return 0
[docs] class ExternalColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, user): if user.external: return 'yes' return 'no'
[docs] class LastLoginColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, user): if user.galaxy_sessions: return self.format(user.galaxy_sessions[0].update_time) return 'never'
[docs] class TimeCreatedColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, user): return user.create_time.strftime('%x')
[docs] class ActivatedColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, user): if user.active: return 'Y' else: return 'N'
# Grid definition title = "Users" model_class = model.User default_sort_key = "email" columns = [ EmailColumn("Email", key="email", model_class=model.User, link=(lambda item: dict(controller="user", action="information", id=item.id, webapp="galaxy")), attach_popup=True, filterable="advanced", target="top"), UserNameColumn("User Name", key="username", model_class=model.User, attach_popup=False, filterable="advanced"), GroupsColumn("Groups", attach_popup=False), RolesColumn("Roles", attach_popup=False), ExternalColumn("External", attach_popup=False), LastLoginColumn("Last Login", format=time_ago), StatusColumn("Status", attach_popup=False), TimeCreatedColumn("Created", attach_popup=False), ActivatedColumn("Activated", attach_popup=False), # Columns that are valid for filtering but are not visible. grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced") ] columns.append(grids.MulticolFilterColumn("Search", cols_to_filter=[columns[0], columns[1]], key="free-text-search", visible=False, filterable="standard")) global_actions = [ grids.GridAction("Create new user", url_args=dict(webapp="galaxy", action="create_new_user")) ] operations = [ grids.GridOperation("Manage Roles and Groups", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="forms/manage_roles_and_groups_for_user")), grids.GridOperation("Reset Password", condition=(lambda item: not item.deleted), allow_multiple=True, url_args=dict(action="forms/reset_user_password"), target="top"), grids.GridOperation("Recalculate Disk Usage", condition=(lambda item: not item.deleted), allow_multiple=False) ] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True, purged=False)), grids.GridColumnFilter("Purged", args=dict(purged=True)), grids.GridColumnFilter("All", args=dict(deleted='All')) ] num_rows_per_page = 50 preserve_state = False use_paging = True
[docs] def get_current_item(self, trans, **kwargs): return trans.user
[docs]class RoleListGrid(grids.Grid):
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, role): return escape(role.name)
[docs] class DescriptionColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, role): if role.description: return escape(role.description) return ''
[docs] class TypeColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, role): return role.type
[docs] class StatusColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, role): if role.deleted: return "deleted" return ""
[docs] class GroupsColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, role): if role.groups: return len(role.groups) return 0
[docs] class UsersColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, role): if role.users: return len(role.users) return 0
# Grid definition title = "Roles" model_class = model.Role default_sort_key = "name" columns = [ NameColumn("Name", key="name", link=(lambda item: dict(action="forms/manage_users_and_groups_for_role", id=item.id, webapp="galaxy")), model_class=model.Role, attach_popup=True, filterable="advanced", target="top"), DescriptionColumn("Description", key='description', model_class=model.Role, attach_popup=False, filterable="advanced"), TypeColumn("Type", key='type', model_class=model.Role, attach_popup=False, filterable="advanced"), GroupsColumn("Groups", attach_popup=False), UsersColumn("Users", attach_popup=False), StatusColumn("Status", attach_popup=False), # Columns that are valid for filtering but are not visible. grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced") ] columns.append(grids.MulticolFilterColumn("Search", cols_to_filter=[columns[0], columns[1], columns[2]], key="free-text-search", visible=False, filterable="standard")) global_actions = [ grids.GridAction("Add new role", url_args=dict(action="forms/create_role")) ] operations = [grids.GridOperation("Edit", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="forms/rename_role")), grids.GridOperation("Delete", condition=(lambda item: not item.deleted), allow_multiple=True), grids.GridOperation("Undelete", condition=(lambda item: item.deleted), allow_multiple=True), grids.GridOperation("Purge", condition=(lambda item: item.deleted), allow_multiple=True)] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True)), grids.GridColumnFilter("All", args=dict(deleted='All')) ] num_rows_per_page = 50 preserve_state = False use_paging = True
[docs] def apply_query_filter(self, trans, query, **kwargs): return query.filter(model.Role.type != model.Role.types.PRIVATE)
[docs]class GroupListGrid(grids.Grid):
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, group): return escape(group.name)
[docs] class StatusColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, group): if group.deleted: return "deleted" return ""
[docs] class RolesColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, group): if group.roles: return len(group.roles) return 0
[docs] class UsersColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, group): if group.members: return len(group.members) return 0
# Grid definition title = "Groups" model_class = model.Group default_sort_key = "name" columns = [ NameColumn("Name", key="name", link=(lambda item: dict(action="forms/manage_users_and_roles_for_group", id=item.id, webapp="galaxy")), model_class=model.Group, attach_popup=True, filterable="advanced"), UsersColumn("Users", attach_popup=False), RolesColumn("Roles", attach_popup=False), StatusColumn("Status", attach_popup=False), # Columns that are valid for filtering but are not visible. grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced") ] columns.append(grids.MulticolFilterColumn("Search", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard")) global_actions = [ grids.GridAction("Add new group", url_args=dict(action="forms/create_group")) ] operations = [grids.GridOperation("Rename", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="forms/rename_group")), grids.GridOperation("Delete", condition=(lambda item: not item.deleted), allow_multiple=True), grids.GridOperation("Undelete", condition=(lambda item: item.deleted), allow_multiple=True), grids.GridOperation("Purge", condition=(lambda item: item.deleted), allow_multiple=True)] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True)), grids.GridColumnFilter("All", args=dict(deleted='All')) ] num_rows_per_page = 50 preserve_state = False use_paging = True
[docs]class QuotaListGrid(grids.Grid):
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, quota): return escape(quota.name)
[docs] class DescriptionColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, quota): if quota.description: return escape(quota.description) return ''
[docs] class AmountColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, quota): return quota.operation + quota.display_amount
[docs] class StatusColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, quota): if quota.deleted: return "deleted" elif quota.default: return "<strong>default for %s users</strong>" % quota.default[0].type return ""
[docs] class UsersColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, quota): if quota.users: return len(quota.users) return 0
[docs] class GroupsColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, quota): if quota.groups: return len(quota.groups) return 0
# Grid definition title = "Quotas" model_class = model.Quota default_sort_key = "name" columns = [ NameColumn("Name", key="name", link=(lambda item: dict(action="forms/edit_quota", id=item.id)), model_class=model.Quota, attach_popup=True, filterable="advanced"), DescriptionColumn("Description", key='description', model_class=model.Quota, attach_popup=False, filterable="advanced"), AmountColumn("Amount", key='amount', model_class=model.Quota, attach_popup=False), UsersColumn("Users", attach_popup=False), GroupsColumn("Groups", attach_popup=False), StatusColumn("Status", attach_popup=False), # Columns that are valid for filtering but are not visible. grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced") ] columns.append(grids.MulticolFilterColumn("Search", cols_to_filter=[columns[0], columns[1]], key="free-text-search", visible=False, filterable="standard")) global_actions = [ grids.GridAction("Add new quota", dict(action='forms/create_quota')) ] operations = [grids.GridOperation("Rename", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="forms/rename_quota")), grids.GridOperation("Change amount", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="forms/edit_quota")), grids.GridOperation("Manage users and groups", condition=(lambda item: not item.default and not item.deleted), allow_multiple=False, url_args=dict(action="forms/manage_users_and_groups_for_quota")), grids.GridOperation("Set as different type of default", condition=(lambda item: item.default), allow_multiple=False, url_args=dict(action="forms/set_quota_default")), grids.GridOperation("Set as default", condition=(lambda item: not item.default and not item.deleted), allow_multiple=False, url_args=dict(action="forms/set_quota_default")), grids.GridOperation("Unset as default", condition=(lambda item: item.default and not item.deleted), allow_multiple=False), grids.GridOperation("Delete", condition=(lambda item: not item.deleted and not item.default), allow_multiple=True), grids.GridOperation("Undelete", condition=(lambda item: item.deleted), allow_multiple=True), grids.GridOperation("Purge", condition=(lambda item: item.deleted), allow_multiple=True)] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True)), grids.GridColumnFilter("All", args=dict(deleted='All')) ] num_rows_per_page = 50 preserve_state = False use_paging = True
[docs]class ToolVersionListGrid(grids.Grid):
[docs] class ToolIdColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, tool_version): toolbox = trans.app.toolbox if toolbox.has_tool(tool_version.tool_id, exact=True): link = url_for(controller='tool_runner', tool_id=tool_version.tool_id) link_str = '<a target="_blank" href="%s">' % link return '<div class="count-box state-color-ok">%s%s</a></div>' % (link_str, tool_version.tool_id) return tool_version.tool_id
[docs] class ToolVersionsColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, tool_version): tool_ids_str = '' toolbox = trans.app.toolbox tool = toolbox._tools_by_id.get(tool_version.tool_id) if tool: for tool_id in tool.lineage.tool_ids: if toolbox.has_tool(tool_id, exact=True): link = url_for(controller='tool_runner', tool_id=tool_id) link_str = '<a target="_blank" href="%s">' % link tool_ids_str += '<div class="count-box state-color-ok">%s%s</a></div><br/>' % (link_str, tool_id) else: tool_ids_str += '%s<br/>' % tool_version.tool_id else: tool_ids_str += '%s<br/>' % tool_version.tool_id return tool_ids_str
# Grid definition title = "Tool versions" model_class = install_model.ToolVersion default_sort_key = "tool_id" columns = [ ToolIdColumn("Tool id", key='tool_id', attach_popup=False), ToolVersionsColumn("Version lineage by tool id (parent/child ordered)") ] columns.append(grids.MulticolFilterColumn("Search tool id", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard")) global_actions = [] operations = [] standard_filters = [] default_filter = {} num_rows_per_page = 50 preserve_state = False use_paging = True
[docs] def build_initial_query(self, trans, **kwd): return trans.install_model.context.query(self.model_class)
[docs]class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaParamParser): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() group_list_grid = GroupListGrid() quota_list_grid = QuotaListGrid() tool_version_list_grid = ToolVersionListGrid() 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 index(self, trans, **kwd): message = escape(kwd.get('message', '')) status = kwd.get('status', 'done') settings = { 'is_repo_installed' : trans.install_model.context.query(trans.install_model.ToolShedRepository).first() is not None, 'installing_repository_ids' : repository_util.get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True), 'is_tool_shed_installed' : bool(trans.app.tool_shed_registry and trans.app.tool_shed_registry.tool_sheds) } return self.template(trans, 'admin', settings=settings, message=message, status=status)
[docs] @web.expose @web.json @web.require_admin def users_list(self, trans, **kwd): message = kwd.get('message', '') status = kwd.get('status', '') if 'operation' in kwd: id = kwd.get('id') if not id: message, status = ('Invalid user id (%s) received.' % str(id), 'error') ids = util.listify(id) operation = kwd['operation'].lower() if operation == 'delete': message, status = self._delete_user(trans, ids) elif operation == 'undelete': message, status = self._undelete_user(trans, ids) elif operation == 'purge': message, status = self._purge_user(trans, ids) elif operation == 'recalculate disk usage': message, status = self._recalculate_user(trans, id) if trans.app.config.allow_user_deletion: if self.delete_operation not in self.user_list_grid.operations: self.user_list_grid.operations.append(self.delete_operation) if self.undelete_operation not in self.user_list_grid.operations: self.user_list_grid.operations.append(self.undelete_operation) if self.purge_operation not in self.user_list_grid.operations: self.user_list_grid.operations.append(self.purge_operation) if message and status: kwd['message'] = util.sanitize_text(message) kwd['status'] = status kwd['dict_format'] = True return self.user_list_grid(trans, **kwd)
[docs] @web.expose_api @web.require_admin def quotas_list(self, trans, payload=None, **kwargs): message = kwargs.get('message', '') status = kwargs.get('status', '') if 'operation' in kwargs: id = kwargs.get('id') if not id: return message_exception(trans, 'Invalid quota id (%s) received.' % str(id)) quotas = [] for quota_id in util.listify(id): try: quotas.append(get_quota(trans, quota_id)) except MessageException as e: return message_exception(trans, str(e)) operation = kwargs.pop('operation').lower() try: if operation == 'delete': message = self._delete_quota(quotas) elif operation == 'undelete': message = self._undelete_quota(quotas) elif operation == 'purge': message = self._purge_quota(quotas) elif operation == 'unset as default': message = self._unset_quota_default(quotas[0]) except ActionInputError as e: message, status = (e.err_msg, 'error') if message: kwargs['message'] = util.sanitize_text(message) kwargs['status'] = status or 'done' kwargs['dict_format'] = True return self.quota_list_grid(trans, **kwargs)
[docs] @web.expose_api @web.require_admin def create_quota(self, trans, payload=None, **kwd): if trans.request.method == 'GET': all_users = [] all_groups = [] for user in trans.sa_session.query(trans.app.model.User) \ .filter(trans.app.model.User.table.c.deleted == false()) \ .order_by(trans.app.model.User.table.c.email): all_users.append((user.email, trans.security.encode_id(user.id))) for group in trans.sa_session.query(trans.app.model.Group) \ .filter(trans.app.model.Group.table.c.deleted == false()) \ .order_by(trans.app.model.Group.table.c.name): all_groups.append((group.name, trans.security.encode_id(group.id))) default_options = [('No', 'no')] for typ in trans.app.model.DefaultQuotaAssociation.types.__dict__.values(): default_options.append(('Yes, ' + typ, typ)) return {'title' : 'Create Quota', 'inputs' : [ { 'name' : 'name', 'label' : 'Name' }, { 'name' : 'description', 'label' : 'Description' }, { 'name' : 'amount', 'label' : 'Amount', 'help' : 'Examples: "10000MB", "99 gb", "0.2T", "unlimited"' }, { 'name' : 'operation', 'label' : 'Assign, increase by amount, or decrease by amount?', 'options' : [('=', '='), ('+', '+'), ('-', '-')] }, { 'name' : 'default', 'label' : 'Is this quota a default for a class of users (if yes, what type)?', 'options' : default_options, 'help' : 'Warning: Any users or groups associated with this quota will be disassociated.' }, build_select_input('in_groups', 'Groups', all_groups, []), build_select_input('in_users', 'Users', all_users, [])]} else: try: quota, message = self._create_quota(util.Params(payload), decode_id=trans.security.decode_id) return {'message': message} except ActionInputError as e: return message_exception(trans, e.err_msg)
[docs] @web.expose_api @web.require_admin def rename_quota(self, trans, payload=None, **kwd): id = kwd.get('id') if not id: return message_exception(trans, 'No quota id received for renaming.') quota = get_quota(trans, id) if trans.request.method == 'GET': return { 'title' : 'Change quota name and description for \'%s\'' % util.sanitize_text(quota.name), 'inputs' : [{ 'name' : 'name', 'label' : 'Name', 'value' : quota.name }, { 'name' : 'description', 'label' : 'Description', 'value' : quota.description }] } else: try: return {'message': self._rename_quota(quota, util.Params(payload))} except ActionInputError as e: return message_exception(trans, e.err_msg)
[docs] @web.expose_api @web.require_admin def manage_users_and_groups_for_quota(self, trans, payload=None, **kwd): quota_id = kwd.get('id') if not quota_id: return message_exception(trans, 'Invalid quota id (%s) received' % str(quota_id)) quota = get_quota(trans, quota_id) if trans.request.method == 'GET': in_users = [] all_users = [] in_groups = [] all_groups = [] for user in trans.sa_session.query(trans.app.model.User) \ .filter(trans.app.model.User.table.c.deleted == false()) \ .order_by(trans.app.model.User.table.c.email): if user in [x.user for x in quota.users]: in_users.append(trans.security.encode_id(user.id)) all_users.append((user.email, trans.security.encode_id(user.id))) for group in trans.sa_session.query(trans.app.model.Group) \ .filter(trans.app.model.Group.table.c.deleted == false()) \ .order_by(trans.app.model.Group.table.c.name): if group in [x.group for x in quota.groups]: in_groups.append(trans.security.encode_id(group.id)) all_groups.append((group.name, trans.security.encode_id(group.id))) return {'title' : 'Quota \'%s\'' % quota.name, 'message': 'Quota \'%s\' is currently associated with %d user(s) and %d group(s).' % (quota.name, len(in_users), len(in_groups)), 'status' : 'info', 'inputs' : [build_select_input('in_groups', 'Groups', all_groups, in_groups), build_select_input('in_users', 'Users', all_users, in_users)]} else: try: return {'message': self._manage_users_and_groups_for_quota(quota, util.Params(payload), decode_id=trans.security.decode_id)} except ActionInputError as e: return message_exception(trans, e.err_msg)
[docs] @web.expose_api @web.require_admin def edit_quota(self, trans, payload=None, **kwd): id = kwd.get('id') if not id: return message_exception(trans, 'No quota id received for renaming.') quota = get_quota(trans, id) if trans.request.method == 'GET': return { 'title' : 'Edit quota size for \'%s\'' % util.sanitize_text(quota.name), 'inputs' : [{ 'name' : 'amount', 'label' : 'Amount', 'value' : quota.display_amount, 'help' : 'Examples: "10000MB", "99 gb", "0.2T", "unlimited"' }, { 'name' : 'operation', 'label' : 'Assign, increase by amount, or decrease by amount?', 'options' : [('=', '='), ('+', '+'), ('-', '-')], 'value' : quota.operation }] } else: try: return {'message': self._edit_quota(quota, util.Params(payload))} except ActionInputError as e: return message_exception(trans, e.err_msg)
[docs] @web.expose_api @web.require_admin def set_quota_default(self, trans, payload=None, **kwd): id = kwd.get('id') if not id: return message_exception(trans, 'No quota id received for renaming.') quota = get_quota(trans, id) if trans.request.method == 'GET': default_value = quota.default[0].type if quota.default else 'no' default_options = [('No', 'no')] for typ in trans.app.model.DefaultQuotaAssociation.types.__dict__.values(): default_options.append(('Yes, ' + typ, typ)) return { 'title' : 'Set quota default for \'%s\'' % util.sanitize_text(quota.name), 'inputs' : [{ 'name' : 'default', 'label' : 'Assign, increase by amount, or decrease by amount?', 'options' : default_options, 'value' : default_value, 'help' : 'Warning: Any users or groups associated with this quota will be disassociated.' }] } else: try: return {'message': self._set_quota_default(quota, util.Params(payload))} except ActionInputError as e: return message_exception(trans, e.err_msg)
[docs] @web.expose @web.require_admin def impersonate(self, trans, email=None, **kwd): if not trans.app.config.allow_user_impersonation: return trans.show_error_message("User impersonation is not enabled in this instance of Galaxy.") message = '' status = 'done' emails = None if email is not None: user = trans.sa_session.query(trans.app.model.User).filter_by(email=email).first() if user: trans.handle_user_logout() trans.handle_user_login(user) message = 'You are now logged in as %s, <a target="_top" href="%s">return to the home page</a>' % (email, url_for(controller='root')) emails = [] else: message = 'Invalid user selected' status = 'error' if emails is None: emails = [u.email for u in trans.sa_session.query(trans.app.model.User).enable_eagerloads(False).all()] return trans.fill_template('admin/impersonate.mako', emails=emails, message=message, status=status)
[docs] def check_for_tool_dependencies(self, trans, migration_stage): # Get the 000x_tools.xml file associated with migration_stage. tools_xml_file_path = os.path.abspath(os.path.join(trans.app.config.root, 'scripts', 'migrate_tools', '%04d_tools.xml' % migration_stage)) tree = util.parse_xml(tools_xml_file_path) root = tree.getroot() tool_shed = root.get('name') shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed) repo_name_dependency_tups = [] if shed_url: for elem in root: if elem.tag == 'repository': tool_dependencies = [] tool_dependencies_dict = {} repository_name = elem.get('name') changeset_revision = elem.get('changeset_revision') params = dict(name=repository_name, owner='devteam', changeset_revision=changeset_revision) pathspec = ['repository', 'get_tool_dependencies'] text = url_get(shed_url, password_mgr=self.app.tool_shed_registry.url_auth(shed_url), pathspec=pathspec, params=params) if text: tool_dependencies_dict = encoding_util.tool_shed_decode(text) for dependency_key, requirements_dict in tool_dependencies_dict.items(): tool_dependency_name = requirements_dict['name'] tool_dependency_version = requirements_dict['version'] tool_dependency_type = requirements_dict['type'] tool_dependency_readme = requirements_dict.get('readme', '') tool_dependencies.append((tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme)) repo_name_dependency_tups.append((repository_name, tool_dependencies)) return repo_name_dependency_tups
[docs] @web.expose @web.require_admin def review_tool_migration_stages(self, trans, **kwd): message = escape(util.restore_text(kwd.get('message', ''))) status = util.restore_text(kwd.get('status', 'done')) migration_stages_dict = odict() migration_modules = [] migration_scripts_dir = os.path.abspath(os.path.join(trans.app.config.root, 'lib', 'tool_shed', 'galaxy_install', 'migrate', 'versions')) migration_scripts_dir_contents = os.listdir(migration_scripts_dir) for item in migration_scripts_dir_contents: if os.path.isfile(os.path.join(migration_scripts_dir, item)) and item.endswith('.py'): module = item.replace('.py', '') migration_modules.append(module) if migration_modules: migration_modules.sort() # Remove the 0001_tools.py script since it is the seed. migration_modules = migration_modules[1:] # Reverse the list so viewing will be newest to oldest. migration_modules.reverse() for migration_module in migration_modules: migration_stage = int(migration_module.replace('_tools', '')) repo_name_dependency_tups = self.check_for_tool_dependencies(trans, migration_stage) open_file_obj, file_name, description = imp.find_module(migration_module, [migration_scripts_dir]) imported_module = imp.load_module('upgrade', open_file_obj, file_name, description) migration_info = imported_module.__doc__ open_file_obj.close() migration_stages_dict[migration_stage] = (migration_info, repo_name_dependency_tups) return trans.fill_template('admin/review_tool_migration_stages.mako', migration_stages_dict=migration_stages_dict, message=message, status=status)
[docs] @web.expose @web.require_admin def tool_errors(self, trans, **kwd): return trans.fill_template('admin/tool_errors.mako', tool_errors=global_tool_errors.error_stack)
[docs] @web.expose @web.require_admin def view_datatypes_registry(self, trans, **kwd): message = escape(util.restore_text(kwd.get('message', ''))) status = util.restore_text(kwd.get('status', 'done')) return trans.fill_template('admin/view_datatypes_registry.mako', message=message, status=status)
[docs] @web.expose @web.require_admin def view_tool_data_tables(self, trans, **kwd): message = escape(util.restore_text(kwd.get('message', ''))) status = util.restore_text(kwd.get('status', 'done')) return trans.fill_template('admin/view_data_tables_registry.mako', message=message, status=status)
[docs] @web.expose @web.require_admin def display_applications(self, trans, **kwd): return trans.fill_template('admin/view_display_applications.mako', display_applications=trans.app.datatypes_registry.display_applications)
[docs] @web.expose @web.require_admin def reload_display_application(self, trans, **kwd): galaxy.queue_worker.send_control_task(trans.app, 'reload_display_application', noop_self=True, kwargs={'display_application_ids': kwd.get('id')}) reloaded, failed = trans.app.datatypes_registry.reload_display_applications(kwd.get('id')) if not reloaded and failed: return trans.show_error_message('Unable to reload any of the %i requested display applications ("%s").' % (len(failed), '", "'.join(failed))) if failed: return trans.show_warn_message('Reloaded %i display applications ("%s"), but failed to reload %i display applications ("%s").' % (len(reloaded), '", "'.join(reloaded), len(failed), '", "'.join(failed))) if not reloaded: return trans.show_warn_message('You need to request at least one display application to reload.') return trans.show_ok_message('Reloaded %i requested display applications ("%s").' % (len(reloaded), '", "'.join(reloaded)))
[docs] @web.expose @web.require_admin def center(self, trans, **kwd): message = escape(kwd.get('message', '')) status = kwd.get('status', 'done') is_repo_installed = trans.install_model.context.query(trans.install_model.ToolShedRepository).first() is not None installing_repository_ids = repository_util.get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True) return trans.fill_template('/webapps/galaxy/admin/center.mako', is_repo_installed=is_repo_installed, installing_repository_ids=installing_repository_ids, message=message, status=status)
[docs] @web.expose @web.require_admin def package_tool(self, trans, **kwd): params = util.Params(kwd) message = util.restore_text(params.get('message', '')) toolbox = self.app.toolbox tool_id = None if params.get('package_tool_button', False): tool_id = params.get('tool_id', None) try: tool_tarball = trans.app.toolbox.package_tool(trans, tool_id) trans.response.set_content_type('application/x-gzip') download_file = open(tool_tarball) os.unlink(tool_tarball) tarball_path, filename = os.path.split(tool_tarball) trans.response.headers["Content-Disposition"] = 'attachment; filename="%s.tgz"' % (tool_id) return download_file except Exception: return trans.fill_template('/admin/package_tool.mako', tool_id=tool_id, toolbox=toolbox, message=message, status='error')
[docs] @web.expose @web.require_admin def reload_tool(self, trans, **kwd): params = util.Params(kwd) message = util.restore_text(params.get('message', '')) status = params.get('status', 'done') toolbox = self.app.toolbox tool_id = None if params.get('reload_tool_button', False): tool_id = kwd.get('tool_id', None) galaxy.queue_worker.send_control_task(trans.app, 'reload_tool', noop_self=True, kwargs={'tool_id': tool_id}) message, status = trans.app.toolbox.reload_tool_by_id(tool_id) return trans.fill_template('/admin/reload_tool.mako', tool_id=tool_id, toolbox=toolbox, message=message, status=status)
[docs] @web.expose_api @web.require_admin def tool_versions_list(self, trans, **kwd): kwd['dict_format'] = True return self.tool_version_list_grid(trans, **kwd)
[docs] @web.expose @web.json @web.require_admin def roles_list(self, trans, **kwargs): message = kwargs.get('message') status = kwargs.get('status') if 'operation' in kwargs: id = kwargs.get('id', None) if not id: message, status = ('Invalid role id (%s) received.' % str(id), 'error') ids = util.listify(id) operation = kwargs['operation'].lower().replace('+', ' ') if operation == 'delete': message, status = self._delete_role(trans, ids) elif operation == 'undelete': message, status = self._undelete_role(trans, ids) elif operation == 'purge': message, status = self._purge_role(trans, ids) kwargs['dict_format'] = True if message and status: kwargs['message'] = util.sanitize_text(message) kwargs['status'] = status return self.role_list_grid(trans, **kwargs)
[docs] @web.expose_api @web.require_admin def create_role(self, trans, payload=None, **kwd): if trans.request.method == 'GET': all_users = [] all_groups = [] for user in trans.sa_session.query(trans.app.model.User) \ .filter(trans.app.model.User.table.c.deleted == false()) \ .order_by(trans.app.model.User.table.c.email): all_users.append((user.email, trans.security.encode_id(user.id))) for group in trans.sa_session.query(trans.app.model.Group) \ .filter(trans.app.model.Group.table.c.deleted == false()) \ .order_by(trans.app.model.Group.table.c.name): all_groups.append((group.name, trans.security.encode_id(group.id))) return { 'title' : 'Create Role', 'inputs' : [{ 'name' : 'name', 'label' : 'Name' }, { 'name' : 'description', 'label' : 'Description' }, build_select_input('in_groups', 'Groups', all_groups, []), build_select_input('in_users', 'Users', all_users, []), { 'name' : 'auto_create', 'label' : 'Create a new group of the same name for this role:', 'type' : 'boolean' }]} else: name = util.restore_text(payload.get('name', '')) description = util.restore_text(payload.get('description', '')) auto_create_checked = payload.get('auto_create') == 'true' in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))] in_groups = [trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_groups'))] if not name or not description: return message_exception(trans, 'Enter a valid name and a description.') elif trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == name).first(): return message_exception(trans, 'Role names must be unique and a role with that name already exists, so choose another name.') elif None in in_users or None in in_groups: return message_exception(trans, 'One or more invalid user/group id has been provided.') else: # Create the role role = trans.app.model.Role(name=name, description=description, type=trans.app.model.Role.types.ADMIN) trans.sa_session.add(role) # Create the UserRoleAssociations for user in in_users: ura = trans.app.model.UserRoleAssociation(user, role) trans.sa_session.add(ura) # Create the GroupRoleAssociations for group in in_groups: gra = trans.app.model.GroupRoleAssociation(group, role) trans.sa_session.add(gra) if auto_create_checked: # Check if role with same name already exists if trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name).first(): return message_exception(trans, 'A group with that name already exists, so choose another name or disable group creation.') # Create the group group = trans.app.model.Group(name=name) trans.sa_session.add(group) # Associate the group with the role gra = trans.model.GroupRoleAssociation(group, role) trans.sa_session.add(gra) num_in_groups = len(in_groups) + 1 else: num_in_groups = len(in_groups) trans.sa_session.flush() message = 'Role \'%s\' has been created with %d associated users and %d associated groups.' % (role.name, len(in_users), num_in_groups) if auto_create_checked: message += 'One of the groups associated with this role is the newly created group with the same name.' return {'message' : message}
[docs] @web.expose_api @web.require_admin def rename_role(self, trans, payload=None, **kwd): id = kwd.get('id') if not id: return message_exception(trans, 'No role id received for renaming.') role = get_role(trans, id) if trans.request.method == 'GET': return { 'title' : 'Change role name and description for \'%s\'' % util.sanitize_text(role.name), 'inputs' : [{ 'name' : 'name', 'label' : 'Name', 'value' : role.name }, { 'name' : 'description', 'label' : 'Description', 'value' : role.description }] } else: old_name = role.name new_name = util.restore_text(payload.get('name')) new_description = util.restore_text(payload.get('description')) if not new_name: return message_exception(trans, 'Enter a valid role name.') else: existing_role = trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == new_name).first() if existing_role and existing_role.id != role.id: return message_exception(trans, 'A role with that name already exists.') else: if not (role.name == new_name and role.description == new_description): role.name = new_name role.description = new_description trans.sa_session.add(role) trans.sa_session.flush() return {'message': 'Role \'%s\' has been renamed to \'%s\'.' % (old_name, new_name)}
[docs] @web.expose_api @web.require_admin def manage_users_and_groups_for_role(self, trans, payload=None, **kwd): role_id = kwd.get('id') if not role_id: return message_exception(trans, 'Invalid role id (%s) received' % str(role_id)) role = get_role(trans, role_id) if trans.request.method == 'GET': in_users = [] all_users = [] in_groups = [] all_groups = [] for user in trans.sa_session.query(trans.app.model.User) \ .filter(trans.app.model.User.table.c.deleted == false()) \ .order_by(trans.app.model.User.table.c.email): if user in [x.user for x in role.users]: in_users.append(trans.security.encode_id(user.id)) all_users.append((user.email, trans.security.encode_id(user.id))) for group in trans.sa_session.query(trans.app.model.Group) \ .filter(trans.app.model.Group.table.c.deleted == false()) \ .order_by(trans.app.model.Group.table.c.name): if group in [x.group for x in role.groups]: in_groups.append(trans.security.encode_id(group.id)) all_groups.append((group.name, trans.security.encode_id(group.id))) return {'title' : 'Role \'%s\'' % role.name, 'message': 'Role \'%s\' is currently associated with %d user(s) and %d group(s).' % (role.name, len(in_users), len(in_groups)), 'status' : 'info', 'inputs' : [build_select_input('in_groups', 'Groups', all_groups, in_groups), build_select_input('in_users', 'Users', all_users, in_users)]} else: in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))] in_groups = [trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_groups'))] if None in in_users or None in in_groups: return message_exception(trans, 'One or more invalid user/group id has been provided.') for ura in role.users: user = trans.sa_session.query(trans.app.model.User).get(ura.user_id) if user not in in_users: # Delete DefaultUserPermissions for previously associated users that have been removed from the role for dup in user.default_permissions: if role == dup.role: trans.sa_session.delete(dup) # Delete DefaultHistoryPermissions for previously associated users that have been removed from the role for history in user.histories: for dhp in history.default_permissions: if role == dhp.role: trans.sa_session.delete(dhp) trans.sa_session.flush() trans.app.security_agent.set_entity_role_associations(roles=[role], users=in_users, groups=in_groups) trans.sa_session.refresh(role) return {'message' : 'Role \'%s\' has been updated with %d associated users and %d associated groups.' % (role.name, len(in_users), len(in_groups))}
def _delete_role(self, trans, ids): message = 'Deleted %d roles: ' % len(ids) for role_id in ids: role = get_role(trans, role_id) role.deleted = True trans.sa_session.add(role) trans.sa_session.flush() message += ' %s ' % role.name return (message, 'done') def _undelete_role(self, trans, ids): count = 0 undeleted_roles = "" for role_id in ids: role = get_role(trans, role_id) if not role.deleted: return ("Role '%s' has not been deleted, so it cannot be undeleted." % role.name, "error") role.deleted = False trans.sa_session.add(role) trans.sa_session.flush() count += 1 undeleted_roles += " %s" % role.name return ("Undeleted %d roles: %s" % (count, undeleted_roles), "done") def _purge_role(self, trans, ids): # This method should only be called for a Role that has previously been deleted. # Purging a deleted Role deletes all of the following from the database: # - UserRoleAssociations where role_id == Role.id # - DefaultUserPermissions where role_id == Role.id # - DefaultHistoryPermissions where role_id == Role.id # - GroupRoleAssociations where role_id == Role.id # - DatasetPermissionss where role_id == Role.id message = "Purged %d roles: " % len(ids) for role_id in ids: role = get_role(trans, role_id) if not role.deleted: return ("Role '%s' has not been deleted, so it cannot be purged." % role.name, "error") # Delete UserRoleAssociations for ura in role.users: user = trans.sa_session.query(trans.app.model.User).get(ura.user_id) # Delete DefaultUserPermissions for associated users for dup in user.default_permissions: if role == dup.role: trans.sa_session.delete(dup) # Delete DefaultHistoryPermissions for associated users for history in user.histories: for dhp in history.default_permissions: if role == dhp.role: trans.sa_session.delete(dhp) trans.sa_session.delete(ura) # Delete GroupRoleAssociations for gra in role.groups: trans.sa_session.delete(gra) # Delete DatasetPermissionss for dp in role.dataset_actions: trans.sa_session.delete(dp) trans.sa_session.flush() message += " %s " % role.name return (message, "done")
[docs] @web.expose_api @web.require_admin def groups_list(self, trans, **kwargs): message = kwargs.get('message') status = kwargs.get('status') if 'operation' in kwargs: id = kwargs.get('id') if not id: return message_exception(trans, 'Invalid group id (%s) received.' % str(id)) ids = util.listify(id) operation = kwargs['operation'].lower().replace('+', ' ') if operation == 'delete': message, status = self._delete_group(trans, ids) elif operation == 'undelete': message, status = self._undelete_group(trans, ids) elif operation == 'purge': message, status = self._purge_group(trans, ids) kwargs['dict_format'] = True if message and status: kwargs['message'] = util.sanitize_text(message) kwargs['status'] = status return self.group_list_grid(trans, **kwargs)
[docs] @web.expose_api @web.require_admin def rename_group(self, trans, payload=None, **kwd): id = kwd.get('id') if not id: return message_exception(trans, 'No group id received for renaming.') group = get_group(trans, id) if trans.request.method == 'GET': return { 'title' : 'Change group name for \'%s\'' % util.sanitize_text(group.name), 'inputs' : [{ 'name' : 'name', 'label' : 'Name', 'value' : group.name }] } else: old_name = group.name new_name = util.restore_text(payload.get('name')) if not new_name: return message_exception(trans, 'Enter a valid group name.') else: existing_group = trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == new_name).first() if existing_group and existing_group.id != group.id: return message_exception(trans, 'A group with that name already exists.') else: if not (group.name == new_name): group.name = new_name trans.sa_session.add(group) trans.sa_session.flush() return {'message': 'Group \'%s\' has been renamed to \'%s\'.' % (old_name, new_name)}
[docs] @web.expose_api @web.require_admin def manage_users_and_roles_for_group(self, trans, payload=None, **kwd): group_id = kwd.get('id') if not group_id: return message_exception(trans, 'Invalid group id (%s) received' % str(group_id)) group = get_group(trans, group_id) if trans.request.method == 'GET': in_users = [] all_users = [] in_roles = [] all_roles = [] for user in trans.sa_session.query(trans.app.model.User) \ .filter(trans.app.model.User.table.c.deleted == false()) \ .order_by(trans.app.model.User.table.c.email): if user in [x.user for x in group.users]: in_users.append(trans.security.encode_id(user.id)) all_users.append((user.email, trans.security.encode_id(user.id))) for role in trans.sa_session.query(trans.app.model.Role) \ .filter(trans.app.model.Role.table.c.deleted == false()) \ .order_by(trans.app.model.Role.table.c.name): if role in [x.role for x in group.roles]: in_roles.append(trans.security.encode_id(role.id)) all_roles.append((role.name, trans.security.encode_id(role.id))) return {'title' : 'Group \'%s\'' % group.name, 'message': 'Group \'%s\' is currently associated with %d user(s) and %d role(s).' % (group.name, len(in_users), len(in_roles)), 'status' : 'info', 'inputs' : [build_select_input('in_roles', 'Roles', all_roles, in_roles), build_select_input('in_users', 'Users', all_users, in_users)]} else: in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))] in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))] if None in in_users or None in in_roles: return message_exception(trans, 'One or more invalid user/role id has been provided.') trans.app.security_agent.set_entity_group_associations(groups=[group], users=in_users, roles=in_roles) trans.sa_session.refresh(group) return {'message' : 'Group \'%s\' has been updated with %d associated users and %d associated roles.' % (group.name, len(in_users), len(in_roles))}
[docs] @web.expose_api @web.require_admin def create_group(self, trans, payload=None, **kwd): if trans.request.method == 'GET': all_users = [] all_roles = [] for user in trans.sa_session.query(trans.app.model.User) \ .filter(trans.app.model.User.table.c.deleted == false()) \ .order_by(trans.app.model.User.table.c.email): all_users.append((user.email, trans.security.encode_id(user.id))) for role in trans.sa_session.query(trans.app.model.Role) \ .filter(trans.app.model.Role.table.c.deleted == false()) \ .order_by(trans.app.model.Role.table.c.name): all_roles.append((role.name, trans.security.encode_id(role.id))) return { 'title' : 'Create Group', 'inputs' : [{ 'name' : 'name', 'label' : 'Name' }, build_select_input('in_roles', 'Roles', all_roles, []), build_select_input('in_users', 'Users', all_users, []), { 'name' : 'auto_create', 'label' : 'Create a new role of the same name for this group:', 'type' : 'boolean' }] } else: name = util.restore_text(payload.get('name', '')) auto_create_checked = payload.get('auto_create') == 'true' in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))] in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))] if not name: return message_exception(trans, 'Enter a valid name.') elif trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name).first(): return message_exception(trans, 'Group names must be unique and a group with that name already exists, so choose another name.') elif None in in_users or None in in_roles: return message_exception(trans, 'One or more invalid user/role id has been provided.') else: # Create the role group = trans.app.model.Group(name=name) trans.sa_session.add(group) # Create the UserRoleAssociations for user in in_users: uga = trans.app.model.UserGroupAssociation(user, group) trans.sa_session.add(uga) # Create the GroupRoleAssociations for role in in_roles: gra = trans.app.model.GroupRoleAssociation(group, role) trans.sa_session.add(gra) if auto_create_checked: # Check if role with same name already exists if trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == name).first(): return message_exception(trans, 'A role with that name already exists, so choose another name or disable role creation.') # Create the role role = trans.app.model.Role(name=name, description='Role for group %s' % name) trans.sa_session.add(role) # Associate the group with the role gra = trans.model.GroupRoleAssociation(group, role) trans.sa_session.add(gra) num_in_roles = len(in_roles) + 1 else: num_in_roles = len(in_roles) trans.sa_session.flush() message = 'Group \'%s\' has been created with %d associated users and %d associated roles.' % (group.name, len(in_users), num_in_roles) if auto_create_checked: message += 'One of the roles associated with this group is the newly created role with the same name.' return {'message' : message}
def _delete_group(self, trans, ids): message = 'Deleted %d groups: ' % len(ids) for group_id in ids: group = get_group(trans, group_id) group.deleted = True trans.sa_session.add(group) trans.sa_session.flush() message += ' %s ' % group.name return (message, 'done') def _undelete_group(self, trans, ids): count = 0 undeleted_groups = "" for group_id in ids: group = get_group(trans, group_id) if not group.deleted: return ("Group '%s' has not been deleted, so it cannot be undeleted." % group.name, "error") group.deleted = False trans.sa_session.add(group) trans.sa_session.flush() count += 1 undeleted_groups += " %s" % group.name return ("Undeleted %d groups: %s" % (count, undeleted_groups), "done") def _purge_group(self, trans, ids): message = "Purged %d groups: " % len(ids) for group_id in ids: group = get_group(trans, group_id) if not group.deleted: return ("Group '%s' has not been deleted, so it cannot be purged." % group.name, "error") # Delete UserGroupAssociations for uga in group.users: trans.sa_session.delete(uga) # Delete GroupRoleAssociations for gra in group.roles: trans.sa_session.delete(gra) trans.sa_session.flush() message += " %s " % group.name return (message, "done")
[docs] @web.expose @web.require_admin def create_new_user(self, trans, **kwd): return trans.response.send_redirect(web.url_for(controller='user', action='create', cntrller='admin'))
[docs] @web.expose_api @web.require_admin def reset_user_password(self, trans, payload=None, **kwd): users = {user_id: get_user(trans, user_id) for user_id in util.listify(kwd.get('id'))} if users: if trans.request.method == 'GET': return { 'message': 'Changes password(s) for: %s.' % ', '.join([user.email for user in users.itervalues()]), 'status' : 'info', 'inputs' : [{'name' : 'password', 'label' : 'New password', 'type' : 'password'}, {'name' : 'confirm', 'label' : 'Confirm password', 'type' : 'password'}] } else: password = payload.get('password') confirm = payload.get('confirm') if len(password) < 6: return message_exception(trans, 'Use a password of at least 6 characters.') elif password != confirm: return message_exception(trans, 'Passwords do not match.') for user in users.itervalues(): user.set_password_cleartext(password) trans.sa_session.add(user) trans.sa_session.flush() return {'message': 'Passwords reset for %d user(s).' % len(users)} else: return message_exception(trans, 'Please specify user ids.')
def _delete_user(self, trans, ids): message = 'Deleted %d users: ' % len(ids) for user_id in ids: user = get_user(trans, user_id) user.deleted = True trans.sa_session.add(user) trans.sa_session.flush() message += ' %s ' % user.email return (message, 'done') def _undelete_user(self, trans, ids): count = 0 undeleted_users = "" for user_id in ids: user = get_user(trans, user_id) if not user.deleted: message = 'User \'%s\' has not been deleted, so it cannot be undeleted.' % user.email return (message, 'error') user.deleted = False trans.sa_session.add(user) trans.sa_session.flush() count += 1 undeleted_users += ' %s' % user.email message = 'Undeleted %d users: %s' % (count, undeleted_users) return (message, 'done') def _purge_user(self, trans, ids): # This method should only be called for a User that has previously been deleted. # We keep the User in the database ( marked as purged ), and stuff associated # with the user's private role in case we want the ability to unpurge the user # some time in the future. # Purging a deleted User deletes all of the following: # - History where user_id = User.id # - HistoryDatasetAssociation where history_id = History.id # - Dataset where HistoryDatasetAssociation.dataset_id = Dataset.id # - UserGroupAssociation where user_id == User.id # - UserRoleAssociation where user_id == User.id EXCEPT FOR THE PRIVATE ROLE # - UserAddress where user_id == User.id # Purging Histories and Datasets must be handled via the cleanup_datasets.py script message = 'Purged %d users: ' % len(ids) for user_id in ids: user = get_user(trans, user_id) if not user.deleted: return ('User \'%s\' has not been deleted, so it cannot be purged.' % user.email, 'error') private_role = trans.app.security_agent.get_private_user_role(user) # Delete History for h in user.active_histories: trans.sa_session.refresh(h) for hda in h.active_datasets: # Delete HistoryDatasetAssociation d = trans.sa_session.query(trans.app.model.Dataset).get(hda.dataset_id) # Delete Dataset if not d.deleted: d.deleted = True trans.sa_session.add(d) hda.deleted = True trans.sa_session.add(hda) h.deleted = True trans.sa_session.add(h) # Delete UserGroupAssociations for uga in user.groups: trans.sa_session.delete(uga) # Delete UserRoleAssociations EXCEPT FOR THE PRIVATE ROLE for ura in user.roles: if ura.role_id != private_role.id: trans.sa_session.delete(ura) # Delete UserAddresses for address in user.addresses: trans.sa_session.delete(address) # Purge the user user.purged = True trans.sa_session.add(user) trans.sa_session.flush() message += '%s ' % user.email return (message, 'done') def _recalculate_user(self, trans, user_id): user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id)) if not user: return ('User not found for id (%s)' % sanitize_text(str(user_id)), 'error') current = user.get_disk_usage() user.calculate_and_set_disk_usage() new = user.get_disk_usage() if new in (current, None): message = 'Usage is unchanged at %s.' % nice_size(current) else: message = 'Usage has changed by %s to %s.' % (nice_size(new - current), nice_size(new)) return (message, 'done')
[docs] @web.expose @web.require_admin def name_autocomplete_data(self, trans, q=None, limit=None, timestamp=None): """Return autocomplete data for user emails""" ac_data = "" for user in trans.sa_session.query(trans.app.model.User).filter_by(deleted=False).filter(func.lower(trans.app.model.User.email).like(q.lower() + "%")): ac_data = ac_data + user.email + "\n" return ac_data
[docs] @web.expose_api @web.require_admin def manage_roles_and_groups_for_user(self, trans, payload=None, **kwd): user_id = kwd.get('id') if not user_id: return message_exception(trans, 'Invalid user id (%s) received' % str(user_id)) user = get_user(trans, user_id) if trans.request.method == 'GET': in_roles = [] all_roles = [] in_groups = [] all_groups = [] for role in trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.deleted == false()) \ .order_by(trans.app.model.Role.table.c.name): if role in [x.role for x in user.roles]: in_roles.append(trans.security.encode_id(role.id)) if role.type != trans.app.model.Role.types.PRIVATE: # There is a 1 to 1 mapping between a user and a PRIVATE role, so private roles should # not be listed in the roles form fields, except for the currently selected user's private # role, which should always be in in_roles. The check above is added as an additional # precaution, since for a period of time we were including private roles in the form fields. all_roles.append((role.name, trans.security.encode_id(role.id))) for group in trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.deleted == false()) \ .order_by(trans.app.model.Group.table.c.name): if group in [x.group for x in user.groups]: in_groups.append(trans.security.encode_id(group.id)) all_groups.append((group.name, trans.security.encode_id(group.id))) return {'title' : 'Roles and groups for \'%s\'' % user.email, 'message': 'User \'%s\' is currently associated with %d role(s) and is a member of %d group(s).' % (user.email, len(in_roles) - 1, len(in_groups)), 'status' : 'info', 'inputs' : [build_select_input('in_roles', 'Roles', all_roles, in_roles), build_select_input('in_groups', 'Groups', all_groups, in_groups)]} else: in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))] in_groups = [trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_groups'))] if None in in_groups or None in in_roles: return message_exception(trans, 'One or more invalid role/group id has been provided.') # make sure the user is not dis-associating himself from his private role private_role = trans.app.security_agent.get_private_user_role(user) if private_role not in in_roles: in_roles.append(private_role) trans.app.security_agent.set_entity_user_associations(users=[user], roles=in_roles, groups=in_groups) trans.sa_session.refresh(user) return {'message' : 'User \'%s\' has been updated with %d associated roles and %d associated groups (private roles are not displayed).' % (user.email, len(in_roles) - 1, len(in_groups))}
[docs] @web.expose @web.require_admin def jobs(self, trans, stop=[], stop_msg=None, cutoff=180, job_lock=None, ajl_submit=None, **kwd): deleted = [] msg = None status = None job_ids = util.listify(stop) if job_ids and stop_msg in [None, '']: msg = 'Please enter an error message to display to the user describing why the job was terminated' status = 'error' elif job_ids: if stop_msg[-1] not in PUNCTUATION: stop_msg += '.' for job_id in job_ids: error_msg = "This job was stopped by an administrator: %s <a href='%s' target='_blank'>Contact support</a> for additional help." \ % (stop_msg, self.app.config.get("support_url", "https://galaxyproject.org/support/")) if trans.app.config.track_jobs_in_database: job = trans.sa_session.query(trans.app.model.Job).get(job_id) job.stderr = error_msg job.set_state(trans.app.model.Job.states.DELETED_NEW) trans.sa_session.add(job) else: trans.app.job_manager.job_stop_queue.put(job_id, error_msg=error_msg) deleted.append(str(job_id)) if deleted: msg = 'Queued job' if len(deleted) > 1: msg += 's' msg += ' for deletion: ' msg += ', '.join(deleted) status = 'done' trans.sa_session.flush() if ajl_submit: if job_lock == 'on': galaxy.queue_worker.send_control_task(trans.app, 'admin_job_lock', kwargs={'job_lock': True}) job_lock = True else: galaxy.queue_worker.send_control_task(trans.app, 'admin_job_lock', kwargs={'job_lock': False}) job_lock = False else: job_lock = trans.app.job_manager.job_lock cutoff_time = datetime.utcnow() - timedelta(seconds=int(cutoff)) jobs = trans.sa_session.query(trans.app.model.Job) \ .filter(and_(trans.app.model.Job.table.c.update_time < cutoff_time, or_(trans.app.model.Job.state == trans.app.model.Job.states.NEW, trans.app.model.Job.state == trans.app.model.Job.states.QUEUED, trans.app.model.Job.state == trans.app.model.Job.states.RUNNING, trans.app.model.Job.state == trans.app.model.Job.states.UPLOAD))) \ .order_by(trans.app.model.Job.table.c.update_time.desc()).all() recent_jobs = trans.sa_session.query(trans.app.model.Job) \ .filter(and_(trans.app.model.Job.table.c.update_time > cutoff_time, or_(trans.app.model.Job.state == trans.app.model.Job.states.ERROR, trans.app.model.Job.state == trans.app.model.Job.states.OK))) \ .order_by(trans.app.model.Job.table.c.update_time.desc()).all() last_updated = {} for job in jobs: delta = datetime.utcnow() - job.update_time if delta.days > 0: last_updated[job.id] = '%s hours' % (delta.days * 24 + int(delta.seconds / 60 / 60)) elif delta > timedelta(minutes=59): last_updated[job.id] = '%s hours' % int(delta.seconds / 60 / 60) else: last_updated[job.id] = '%s minutes' % int(delta.seconds / 60) finished = {} for job in recent_jobs: delta = datetime.utcnow() - job.update_time if delta.days > 0: finished[job.id] = '%s hours' % (delta.days * 24 + int(delta.seconds / 60 / 60)) elif delta > timedelta(minutes=59): finished[job.id] = '%s hours' % int(delta.seconds / 60 / 60) else: finished[job.id] = '%s minutes' % int(delta.seconds / 60) return trans.fill_template('/admin/jobs.mako', jobs=jobs, recent_jobs=recent_jobs, last_updated=last_updated, finished=finished, cutoff=cutoff, msg=msg, status=status, job_lock=job_lock)
[docs] @web.expose @web.require_admin def job_info(self, trans, jobid=None): job = None if jobid is not None: job = trans.sa_session.query(trans.app.model.Job).get(jobid) return trans.fill_template('/webapps/reports/job_info.mako', job=job, message="<a href='jobs'>Back</a>")
[docs] @web.expose @web.require_admin def manage_tool_dependencies(self, trans, install_dependencies=False, uninstall_dependencies=False, remove_unused_dependencies=False, selected_tool_ids=None, selected_environments_to_uninstall=None, viewkey='View tool-centric dependencies'): if not selected_tool_ids: selected_tool_ids = [] if not selected_environments_to_uninstall: selected_environments_to_uninstall = [] tools_by_id = trans.app.toolbox.tools_by_id view = six.next(six.itervalues(trans.app.toolbox.tools_by_id))._view if selected_tool_ids: # install the dependencies for the tools in the selected_tool_ids list if not isinstance(selected_tool_ids, list): selected_tool_ids = [selected_tool_ids] requirements = set([tools_by_id[tid].tool_requirements for tid in selected_tool_ids]) if install_dependencies: [view.install_dependencies(r) for r in requirements] elif uninstall_dependencies: [view.uninstall_dependencies(index=None, requirements=r) for r in requirements] if selected_environments_to_uninstall and remove_unused_dependencies: if not isinstance(selected_environments_to_uninstall, list): selected_environments_to_uninstall = [selected_environments_to_uninstall] view.remove_unused_dependency_paths(selected_environments_to_uninstall) return trans.fill_template('/webapps/galaxy/admin/manage_dependencies.mako', tools=tools_by_id, requirements_status=view.toolbox_requirements_status, tool_ids_by_requirements=view.tool_ids_by_requirements, unused_environments=view.unused_dependency_paths, viewkey=viewkey)
[docs] @web.expose @web.require_admin def sanitize_whitelist(self, trans, submit_whitelist=False, tools_to_whitelist=[]): if submit_whitelist: # write the configured sanitize_whitelist_file with new whitelist # and update in-memory list. with open(trans.app.config.sanitize_whitelist_file, 'wt') as f: if isinstance(tools_to_whitelist, six.string_types): tools_to_whitelist = [tools_to_whitelist] new_whitelist = sorted([tid for tid in tools_to_whitelist if tid in trans.app.toolbox.tools_by_id]) f.write("\n".join(new_whitelist)) trans.app.config.sanitize_whitelist = new_whitelist galaxy.queue_worker.send_control_task(trans.app, 'reload_sanitize_whitelist', noop_self=True) # dispatch a message to reload list for other processes return trans.fill_template('/webapps/galaxy/admin/sanitize_whitelist.mako', sanitize_all=trans.app.config.sanitize_all_html, tools=trans.app.toolbox.tools_by_id)
# ---- Utility methods -------------------------------------------------------
[docs]def build_select_input(name, label, options, value): return {'type' : 'select', 'multiple' : True, 'optional' : True, 'individual': True, 'name' : name, 'label' : label, 'options' : options, 'value' : value}
[docs]def message_exception(trans, message): trans.response.status = 400 return {'err_msg': sanitize_text(message)}
[docs]def get_user(trans, user_id): """Get a User from the database by id.""" user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id)) if not user: return trans.show_error_message("User not found for id (%s)" % str(user_id)) return user
[docs]def get_role(trans, id): """Get a Role from the database by id.""" # Load user from database id = trans.security.decode_id(id) role = trans.sa_session.query(trans.model.Role).get(id) if not role: return trans.show_error_message("Role not found for id (%s)" % str(id)) return role
[docs]def get_group(trans, id): """Get a Group from the database by id.""" # Load user from database id = trans.security.decode_id(id) group = trans.sa_session.query(trans.model.Group).get(id) if not group: return trans.show_error_message("Group not found for id (%s)" % str(id)) return group
[docs]def get_quota(trans, id): """Get a Quota from the database by id.""" # Load user from database id = trans.security.decode_id(id) quota = trans.sa_session.query(trans.model.Quota).get(id) return quota