mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 23:49:37 +08:00
550 lines
22 KiB
Python
550 lines
22 KiB
Python
import logging
|
|
import os
|
|
from galaxy.web.framework.helpers import grids
|
|
from galaxy.web.framework.helpers import time_ago
|
|
from galaxy.webapps.tool_shed import model
|
|
from galaxy.model.orm import and_
|
|
import tool_shed.util.shed_util_common as suc
|
|
from tool_shed.util import hg_util
|
|
from tool_shed.grids.repository_grids import CategoryGrid
|
|
from tool_shed.grids.repository_grids import RepositoryGrid
|
|
|
|
from galaxy import eggs
|
|
eggs.require( 'mercurial' )
|
|
|
|
from mercurial import commands
|
|
from mercurial import hg
|
|
from mercurial import ui
|
|
|
|
log = logging.getLogger( __name__ )
|
|
|
|
|
|
class UserGrid( grids.Grid ):
|
|
|
|
|
|
class UserLoginColumn( grids.TextColumn ):
|
|
|
|
def get_value( self, trans, grid, user ):
|
|
return user.email
|
|
|
|
|
|
class UserNameColumn( grids.TextColumn ):
|
|
|
|
def get_value( self, trans, grid, user ):
|
|
if user.username:
|
|
return user.username
|
|
return 'not set'
|
|
|
|
|
|
class GroupsColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, user ):
|
|
if user.groups:
|
|
return len( user.groups )
|
|
return 0
|
|
|
|
|
|
class RolesColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, user ):
|
|
if user.roles:
|
|
return len( user.roles )
|
|
return 0
|
|
|
|
|
|
class ExternalColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, user ):
|
|
if user.external:
|
|
return 'yes'
|
|
return 'no'
|
|
|
|
|
|
class LastLoginColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, user ):
|
|
if user.galaxy_sessions:
|
|
return self.format( user.galaxy_sessions[ 0 ].update_time )
|
|
return 'never'
|
|
|
|
|
|
class StatusColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, user ):
|
|
if user.purged:
|
|
return "purged"
|
|
elif user.deleted:
|
|
return "deleted"
|
|
return ""
|
|
|
|
|
|
class EmailColumn( grids.GridColumn ):
|
|
|
|
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
|
|
template='/admin/user/grid.mako'
|
|
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
|
|
|
|
def get_current_item( self, trans, **kwargs ):
|
|
return trans.user
|
|
|
|
|
|
class RoleGrid( grids.Grid ):
|
|
|
|
|
|
class NameColumn( grids.TextColumn ):
|
|
|
|
def get_value( self, trans, grid, role ):
|
|
return str( role.name )
|
|
|
|
|
|
class DescriptionColumn( grids.TextColumn ):
|
|
|
|
def get_value( self, trans, grid, role ):
|
|
if role.description:
|
|
return str( role.description )
|
|
return ''
|
|
|
|
|
|
class TypeColumn( grids.TextColumn ):
|
|
def get_value( self, trans, grid, role ):
|
|
return str( role.type )
|
|
|
|
|
|
class StatusColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, role ):
|
|
if role.deleted:
|
|
return "deleted"
|
|
return ""
|
|
|
|
|
|
class GroupsColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, role ):
|
|
if role.groups:
|
|
return len( role.groups )
|
|
return 0
|
|
|
|
|
|
class RepositoriesColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, role ):
|
|
if role.repositories:
|
|
return len( role.repositories )
|
|
return 0
|
|
|
|
|
|
class UsersColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, role ):
|
|
if role.users:
|
|
return len( role.users )
|
|
return 0
|
|
|
|
title = "Roles"
|
|
model_class = model.Role
|
|
template='/admin/dataset_security/role/grid.mako'
|
|
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
|
|
|
|
def apply_query_filter( self, trans, query, **kwd ):
|
|
return query.filter( model.Role.type != model.Role.types.PRIVATE )
|
|
|
|
|
|
class GroupGrid( grids.Grid ):
|
|
|
|
|
|
class NameColumn( grids.TextColumn ):
|
|
|
|
def get_value( self, trans, grid, group ):
|
|
return str( group.name )
|
|
|
|
|
|
class StatusColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, group ):
|
|
if group.deleted:
|
|
return "deleted"
|
|
return ""
|
|
|
|
|
|
class RolesColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, group ):
|
|
if group.roles:
|
|
return len( group.roles )
|
|
return 0
|
|
|
|
|
|
class UsersColumn( grids.GridColumn ):
|
|
|
|
def get_value( self, trans, grid, group ):
|
|
if group.members:
|
|
return len( group.members )
|
|
return 0
|
|
|
|
title = "Groups"
|
|
model_class = model.Group
|
|
template='/admin/dataset_security/group/grid.mako'
|
|
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
|
|
|
|
|
|
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' ) )
|
|
]
|
|
|
|
|
|
class AdminRepositoryGrid( RepositoryGrid ):
|
|
|
|
|
|
class DeletedColumn( grids.BooleanColumn ):
|
|
|
|
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 = {}
|
|
|
|
def build_initial_query( self, trans, **kwd ):
|
|
return trans.sa_session.query( model.Repository ) \
|
|
.join( model.User.table )
|
|
|
|
|
|
class RepositoryMetadataGrid( grids.Grid ):
|
|
|
|
|
|
class IdColumn( grids.IntegerColumn ):
|
|
|
|
def get_value( self, trans, grid, repository_metadata ):
|
|
return repository_metadata.id
|
|
|
|
|
|
class NameColumn( grids.TextColumn ):
|
|
|
|
def get_value( self, trans, grid, repository_metadata ):
|
|
return repository_metadata.repository.name
|
|
|
|
|
|
class OwnerColumn( grids.TextColumn ):
|
|
|
|
def get_value( self, trans, grid, repository_metadata ):
|
|
return repository_metadata.repository.user.username
|
|
|
|
class RevisionColumn( grids.TextColumn ):
|
|
|
|
def get_value( self, trans, grid, repository_metadata ):
|
|
repository = repository_metadata.repository
|
|
return hg_util.get_revision_label( trans,
|
|
repository,
|
|
repository_metadata.changeset_revision,
|
|
include_date=True,
|
|
include_hash=True )
|
|
|
|
|
|
class ToolsColumn( grids.TextColumn ):
|
|
|
|
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
|
|
|
|
|
|
class DatatypesColumn( grids.TextColumn ):
|
|
|
|
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
|
|
|
|
|
|
class WorkflowsColumn( grids.TextColumn ):
|
|
|
|
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
|
|
|
|
|
|
class DeletedColumn( grids.BooleanColumn ):
|
|
|
|
def get_value( self, trans, grid, repository_metadata ):
|
|
if repository_metadata.repository.deleted:
|
|
return 'yes'
|
|
return ''
|
|
|
|
|
|
class DeprecatedColumn( grids.BooleanColumn ):
|
|
|
|
def get_value( self, trans, grid, repository_metadata ):
|
|
if repository_metadata.repository.deprecated:
|
|
return 'yes'
|
|
return ''
|
|
|
|
|
|
class MaliciousColumn( grids.BooleanColumn ):
|
|
|
|
def get_value( self, trans, grid, repository_metadata ):
|
|
if repository_metadata.malicious:
|
|
return 'yes'
|
|
return ''
|
|
|
|
# Grid definition
|
|
title = "Repository Metadata"
|
|
model_class = model.RepositoryMetadata
|
|
template='/webapps/tool_shed/repository/grid.mako'
|
|
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
|
|
|
|
def build_initial_query( self, trans, **kwd ):
|
|
return trans.sa_session.query( model.RepositoryMetadata ) \
|
|
.join( model.Repository.table )
|