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Source code for tool_shed.grids.admin_grids

import logging

from markupsafe import escape
from sqlalchemy import and_

from galaxy.web.framework.helpers import grids, time_ago
from galaxy.webapps.tool_shed import model
from tool_shed.grids.repository_grids import CategoryGrid, RepositoryGrid
from tool_shed.util import hg_util

log = logging.getLogger(__name__)


[docs]class UserGrid(grids.Grid):
[docs] class UserLoginColumn(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 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 StatusColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, user): if user.purged: return "purged" elif user.deleted: return "deleted" return ""
[docs] class EmailColumn(grids.GridColumn):
[docs] def filter(self, trans, user, query, column_filter): if column_filter == 'All': return query return query.filter(and_(model.Tool.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter))
title = "Users" model_class = model.User default_sort_key = "email" columns = [ UserLoginColumn("Email", key="email", link=(lambda item: dict(operation="information", id=item.id)), attach_popup=True, filterable="advanced"), UserNameColumn("User Name", key="username", 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), # Columns that are valid for filtering but are not visible. EmailColumn("Email", key="email", visible=False) ] 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", dict(controller='admin', action='users', operation='create')) ] operations = [ grids.GridOperation("Manage Roles and Groups", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="manage_roles_and_groups_for_user")), grids.GridOperation("Reset Password", condition=(lambda item: not item.deleted), allow_multiple=True, allow_popup=False, url_args=dict(action="reset_user_password")) ] 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')) ] use_paging = False
[docs] def get_current_item(self, trans, **kwargs): return trans.user
[docs]class RoleGrid(grids.Grid):
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, role): return escape(str(role.name))
[docs] class DescriptionColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, role): if role.description: return str(role.description) return ''
[docs] class TypeColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, role): return str(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 RepositoriesColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, role): if role.repositories: return len(role.repositories) return 0
[docs] class UsersColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, role): if role.users: return len(role.users) return 0
title = "Roles" model_class = model.Role default_sort_key = "name" columns = [ NameColumn("Name", key="name", link=(lambda item: dict(operation="Manage role associations", id=item.id)), attach_popup=True, filterable="advanced"), DescriptionColumn("Description", key='description', attach_popup=False, filterable="advanced"), GroupsColumn("Groups", attach_popup=False), RepositoriesColumn("Repositories", attach_popup=False), UsersColumn("Users", 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 role", dict(controller='admin', action='roles', operation='create')) ] # Repository admin roles currently do not have any operations since they are managed automatically based # on other events. For example, if a repository is renamed, its associated admin role is automatically # renamed accordingly and if a repository is deleted its associated admin role is automatically deleted. operations = [grids.GridOperation("Rename", condition=(lambda item: not item.deleted and not item.is_repository_admin_role), allow_multiple=False, url_args=dict(action="rename_role")), grids.GridOperation("Delete", condition=(lambda item: not item.deleted and not item.is_repository_admin_role), allow_multiple=True, url_args=dict(action="mark_role_deleted")), grids.GridOperation("Undelete", condition=(lambda item: item.deleted and not item.is_repository_admin_role), allow_multiple=True, url_args=dict(action="undelete_role")), grids.GridOperation("Purge", condition=(lambda item: item.deleted and not item.is_repository_admin_role), allow_multiple=True, url_args=dict(action="purge_role"))] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True)), grids.GridColumnFilter("All", args=dict(deleted='All')) ] use_paging = False
[docs] def apply_query_filter(self, trans, query, **kwd): return query.filter(model.Role.type != model.Role.types.PRIVATE)
[docs]class GroupGrid(grids.Grid):
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, group): return str(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
title = "Groups" model_class = model.Group default_sort_key = "name" columns = [ NameColumn("Name", key="name", link=(lambda item: dict(operation="Manage users and roles", id=item.id)), attach_popup=True), 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", dict(controller='admin', action='groups', operation='create')) ] operations = [grids.GridOperation("Rename", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="rename_group")), grids.GridOperation("Delete", condition=(lambda item: not item.deleted), allow_multiple=True, url_args=dict(action="mark_group_deleted")), grids.GridOperation("Undelete", condition=(lambda item: item.deleted), allow_multiple=True, url_args=dict(action="undelete_group")), grids.GridOperation("Purge", condition=(lambda item: item.deleted), allow_multiple=True, url_args=dict(action="purge_group"))] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True)), grids.GridColumnFilter("All", args=dict(deleted='All')) ] use_paging = False
[docs]class ManageCategoryGrid(CategoryGrid): columns = [col for col in CategoryGrid.columns] # Override the NameColumn to include an Edit link columns[0] = CategoryGrid.NameColumn("Name", key="Category.name", link=(lambda item: dict(operation="Edit", id=item.id)), model_class=model.Category, attach_popup=False) global_actions = [ grids.GridAction("Add new category", dict(controller='admin', action='manage_categories', operation='create')) ]
[docs]class AdminRepositoryGrid(RepositoryGrid):
[docs] class DeletedColumn(grids.BooleanColumn):
[docs] def get_value(self, trans, grid, repository): if repository.deleted: return 'yes' return ''
columns = [RepositoryGrid.NameColumn("Name", key="name", link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)), attach_popup=True), RepositoryGrid.HeadsColumn("Heads"), RepositoryGrid.UserColumn("Owner", model_class=model.User, link=(lambda item: dict(operation="repositories_by_user", id=item.id)), attach_popup=False, key="User.username"), RepositoryGrid.DeprecatedColumn("Deprecated", key="deprecated", attach_popup=False), # Columns that are valid for filtering but are not visible. DeletedColumn("Deleted", key="deleted", attach_popup=False)] columns.append(grids.MulticolFilterColumn("Search repository name", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard")) operations = [operation for operation in RepositoryGrid.operations] operations.append(grids.GridOperation("Delete", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False)) operations.append(grids.GridOperation("Undelete", allow_multiple=False, condition=(lambda item: item.deleted), async_compatible=False)) standard_filters = [] default_filter = {}
[docs] def build_initial_query(self, trans, **kwd): return trans.sa_session.query(model.Repository) \ .join(model.User.table)
[docs]class RepositoryMetadataGrid(grids.Grid):
[docs] class IdColumn(grids.IntegerColumn):
[docs] def get_value(self, trans, grid, repository_metadata): return repository_metadata.id
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, repository_metadata): return escape(repository_metadata.repository.name)
[docs] class OwnerColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, repository_metadata): return escape(repository_metadata.repository.user.username)
[docs] class RevisionColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, repository_metadata): repository = repository_metadata.repository return hg_util.get_revision_label(trans.app, repository, repository_metadata.changeset_revision, include_date=True, include_hash=True)
[docs] class ToolsColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, repository_metadata): tools_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: # We used to display the following, but grid was too cluttered. # for tool_metadata_dict in metadata[ 'tools' ]: # tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) return '%d' % len(metadata['tools']) return tools_str
[docs] class DatatypesColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, repository_metadata): datatypes_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'datatypes' in metadata: # We used to display the following, but grid was too cluttered. # for datatype_metadata_dict in metadata[ 'datatypes' ]: # datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] return '%d' % len(metadata['datatypes']) return datatypes_str
[docs] class WorkflowsColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, repository_metadata): workflows_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'workflows' in metadata: # We used to display the following, but grid was too cluttered. # workflows_str += '<b>Workflows:</b><br/>' # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] # workflow_tups = metadata[ 'workflows' ] # workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] # for workflow_metadata_dict in workflow_metadata_dicts: # workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] return '%d' % len(metadata['workflows']) return workflows_str
[docs] class DeletedColumn(grids.BooleanColumn):
[docs] def get_value(self, trans, grid, repository_metadata): if repository_metadata.repository.deleted: return 'yes' return ''
[docs] class DeprecatedColumn(grids.BooleanColumn):
[docs] def get_value(self, trans, grid, repository_metadata): if repository_metadata.repository.deprecated: return 'yes' return ''
[docs] class MaliciousColumn(grids.BooleanColumn):
[docs] def get_value(self, trans, grid, repository_metadata): if repository_metadata.malicious: return 'yes' return ''
# Grid definition title = "Repository Metadata" model_class = model.RepositoryMetadata default_sort_key = "name" use_hide_message = False columns = [ IdColumn("Id", visible=False, attach_popup=False), NameColumn("Name", key="name", model_class=model.Repository, link=(lambda item: dict(operation="view_or_manage_repository_revision", id=item.id)), attach_popup=True), OwnerColumn("Owner", attach_popup=False), RevisionColumn("Revision", attach_popup=False), ToolsColumn("Tools", attach_popup=False), DatatypesColumn("Datatypes", attach_popup=False), WorkflowsColumn("Workflows", attach_popup=False), DeletedColumn("Deleted", attach_popup=False), DeprecatedColumn("Deprecated", attach_popup=False), MaliciousColumn("Malicious", attach_popup=False) ] columns.append(grids.MulticolFilterColumn("Search repository name", cols_to_filter=[columns[1]], key="free-text-search", visible=False, filterable="standard")) operations = [grids.GridOperation("Delete", allow_multiple=False, allow_popup=True, async_compatible=False, confirm="Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items.")] standard_filters = [] default_filter = {} use_paging = False
[docs] def build_initial_query(self, trans, **kwd): return trans.sa_session.query(model.RepositoryMetadata) \ .join(model.Repository.table)