Source code for tool_shed.grids.admin_grids

import logging

from markupsafe import escape
from sqlalchemy import and_

from galaxy.web.framework.helpers import time_ago
from galaxy.webapps.reports.framework import grids
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)