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Merge pull request #11412 from davelopez/refactor_api_groups
Refactor groups API logic into GroupsManager
This commit is contained in:
John Chilton
@@ -0,0 +1,116 @@
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from typing import (
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Any,
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Dict,
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List,
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)
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from sqlalchemy import false
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from galaxy import model
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from galaxy.app import StructuredApp
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from galaxy.exceptions import (
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Conflict,
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ObjectAttributeMissingException,
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ObjectNotFound,
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)
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from galaxy.managers.base import decode_id
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from galaxy.managers.context import ProvidesAppContext
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from galaxy.schema.fields import EncodedDatabaseIdField
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from galaxy.web import url_for
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class GroupsManager:
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"""Interface/service object shared by controllers for interacting with groups."""
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def __init__(self, app: StructuredApp) -> None:
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self._app = app
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def index(self, trans: ProvidesAppContext):
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"""
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Displays a collection (list) of groups.
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"""
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rval = []
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for group in trans.sa_session.query(model.Group).filter(model.Group.table.c.deleted == false()):
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item = group.to_dict(value_mapper={'id': trans.security.encode_id})
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encoded_id = trans.security.encode_id(group.id)
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item['url'] = url_for('group', id=encoded_id)
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rval.append(item)
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return rval
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def create(self, trans: ProvidesAppContext, payload: Dict[str, Any]):
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"""
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Creates a new group.
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"""
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name = payload.get('name', None)
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if name is None:
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raise ObjectAttributeMissingException("Missing required name")
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self._check_duplicated_group_name(trans, name)
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group = model.Group(name=name)
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trans.sa_session.add(group)
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encoded_user_ids = payload.get('user_ids', [])
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users = self._get_users_by_encoded_ids(trans, encoded_user_ids)
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encoded_role_ids = payload.get('role_ids', [])
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roles = self._get_roles_by_encoded_ids(trans, encoded_role_ids)
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trans.app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users)
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trans.sa_session.flush()
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encoded_id = trans.security.encode_id(group.id)
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item = group.to_dict(view='element', value_mapper={'id': trans.security.encode_id})
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item['url'] = url_for('group', id=encoded_id)
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return [item]
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def show(self, trans: ProvidesAppContext, encoded_id: EncodedDatabaseIdField):
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"""
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Displays information about a group.
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"""
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group = self._get_group(trans, encoded_id)
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item = group.to_dict(view='element', value_mapper={'id': trans.security.encode_id})
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item['url'] = url_for('group', id=encoded_id)
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item['users_url'] = url_for('group_users', group_id=encoded_id)
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item['roles_url'] = url_for('group_roles', group_id=encoded_id)
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return item
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def update(self, trans: ProvidesAppContext, encoded_id: EncodedDatabaseIdField, payload: Dict[str, Any]):
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"""
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Modifies a group.
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"""
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group = self._get_group(trans, encoded_id)
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name = payload.get('name', None)
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if name:
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self._check_duplicated_group_name(trans, name)
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group.name = name
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trans.sa_session.add(group)
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encoded_user_ids = payload.get('user_ids', [])
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users = self._get_users_by_encoded_ids(trans, encoded_user_ids)
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encoded_role_ids = payload.get('role_ids', [])
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roles = self._get_roles_by_encoded_ids(trans, encoded_role_ids)
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trans.app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users, delete_existing_assocs=False)
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trans.sa_session.flush()
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def _decode_id(self, encoded_id: EncodedDatabaseIdField) -> int:
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return decode_id(self._app, encoded_id)
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def _decode_ids(self, encoded_ids: List[EncodedDatabaseIdField]) -> List[int]:
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return [self._decode_id(encoded_id) for encoded_id in encoded_ids]
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def _check_duplicated_group_name(self, trans: ProvidesAppContext, group_name: str) -> None:
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if trans.sa_session.query(model.Group).filter(model.Group.table.c.name == group_name).first():
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raise Conflict(f"A group with name '{group_name}' already exists")
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def _get_group(self, trans: ProvidesAppContext, encoded_id: EncodedDatabaseIdField) -> model.Group:
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decoded_group_id = self._decode_id(encoded_id)
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group = trans.sa_session.query(model.Group).get(decoded_group_id)
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if group is None:
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raise ObjectNotFound(f"Group with id {encoded_id} was not found.")
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return group
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def _get_users_by_encoded_ids(self, trans: ProvidesAppContext, encoded_user_ids: List[EncodedDatabaseIdField]) -> List[model.User]:
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decoded_user_ids = self._decode_ids(encoded_user_ids)
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users = trans.sa_session.query(model.User).filter(model.User.table.c.id.in_(decoded_user_ids)).all()
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return users
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def _get_roles_by_encoded_ids(self, trans: ProvidesAppContext, encoded_role_ids: List[EncodedDatabaseIdField]) -> List[model.Role]:
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decoded_role_ids = self._decode_ids(encoded_role_ids)
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roles = trans.sa_session.query(model.Role).filter(model.Role.table.c.id.in_(decoded_role_ids)).all()
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return roles
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@@ -2,128 +2,62 @@
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API operations on Group objects.
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"""
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import logging
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from typing import (
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Any,
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Dict,
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)
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from sqlalchemy import false
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from galaxy import web
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from galaxy.webapps.base.controller import BaseAPIController, url_for
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from galaxy.app import StructuredApp
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from galaxy.managers.context import ProvidesAppContext
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from galaxy.managers.groups import GroupsManager
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from galaxy.schema.fields import EncodedDatabaseIdField
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from galaxy.web import (
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expose_api,
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require_admin,
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)
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from galaxy.webapps.base.controller import BaseAPIController
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log = logging.getLogger(__name__)
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class GroupAPIController(BaseAPIController):
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@web.require_admin
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@web.legacy_expose_api
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def index(self, trans, **kwd):
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def __init__(self, app: StructuredApp):
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super().__init__(app)
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self.manager = GroupsManager(app)
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@expose_api
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@require_admin
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def index(self, trans: ProvidesAppContext, **kwd):
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"""
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GET /api/groups
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Displays a collection (list) of groups.
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"""
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rval = []
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for group in trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.deleted == false()):
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if trans.user_is_admin:
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item = group.to_dict(value_mapper={'id': trans.security.encode_id})
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encoded_id = trans.security.encode_id(group.id)
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item['url'] = url_for('group', id=encoded_id)
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rval.append(item)
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return rval
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return self.manager.index(trans)
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@web.legacy_expose_api
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def create(self, trans, payload, **kwd):
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@expose_api
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@require_admin
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def create(self, trans: ProvidesAppContext, payload: Dict[str, Any], **kwd):
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"""
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POST /api/groups
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Creates a new group.
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"""
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log.info("groups payload%s\n" % (payload))
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if not trans.user_is_admin:
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trans.response.status = 403
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return "You are not authorized to create a new group."
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name = payload.get('name', None)
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if not name:
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trans.response.status = 400
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return "Enter a valid name"
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if trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name).first():
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trans.response.status = 400
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return "A group with that name already exists"
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return self.manager.create(trans, payload)
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group = trans.app.model.Group(name=name)
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trans.sa_session.add(group)
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user_ids = payload.get('user_ids', [])
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for i in user_ids:
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log.info("user_id: %s\n" % (i))
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log.info("{} {}\n".format(i, trans.security.decode_id(i)))
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users = [trans.sa_session.query(trans.model.User).get(trans.security.decode_id(i)) for i in user_ids]
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role_ids = payload.get('role_ids', [])
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roles = [trans.sa_session.query(trans.model.Role).get(trans.security.decode_id(i)) for i in role_ids]
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trans.app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users)
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"""
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# Create the UserGroupAssociations
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for user in users:
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trans.app.security_agent.associate_user_group( user, group )
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# Create the GroupRoleAssociations
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for role in roles:
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trans.app.security_agent.associate_group_role( group, role )
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"""
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trans.sa_session.flush()
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encoded_id = trans.security.encode_id(group.id)
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item = group.to_dict(view='element', value_mapper={'id': trans.security.encode_id})
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item['url'] = url_for('group', id=encoded_id)
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return [item]
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@web.require_admin
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@web.legacy_expose_api
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def show(self, trans, id, **kwd):
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@expose_api
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@require_admin
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def show(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, **kwd):
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"""
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GET /api/groups/{encoded_group_id}
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Displays information about a group.
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"""
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group_id = id
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try:
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decoded_group_id = trans.security.decode_id(group_id)
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except TypeError:
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trans.response.status = 400
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return "Malformed group id ( %s ) specified, unable to decode." % str(group_id)
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try:
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group = trans.sa_session.query(trans.app.model.Group).get(decoded_group_id)
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except Exception:
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group = None
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if not group:
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trans.response.status = 400
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return "Invalid group id ( %s ) specified." % str(group_id)
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item = group.to_dict(view='element', value_mapper={'id': trans.security.encode_id})
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item['url'] = url_for('group', id=group_id)
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item['users_url'] = url_for('group_users', group_id=group_id)
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item['roles_url'] = url_for('group_roles', group_id=group_id)
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return item
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return self.manager.show(trans, id)
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@web.require_admin
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@web.legacy_expose_api
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def update(self, trans, id, payload, **kwd):
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@expose_api
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@require_admin
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def update(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, payload: Dict[str, Any], **kwd):
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"""
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PUT /api/groups/{encoded_group_id}
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Modifies a group.
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"""
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group_id = id
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try:
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decoded_group_id = trans.security.decode_id(group_id)
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except TypeError:
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trans.response.status = 400
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return "Malformed group id ( %s ) specified, unable to decode." % str(group_id)
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try:
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group = trans.sa_session.query(trans.app.model.Group).get(decoded_group_id)
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except Exception:
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group = None
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if not group:
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trans.response.status = 400
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return "Invalid group id ( %s ) specified." % str(group_id)
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name = payload.get('name', None)
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if name:
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group.name = name
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trans.sa_session.add(group)
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user_ids = payload.get('user_ids', [])
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users = [trans.sa_session.query(trans.model.User).get(trans.security.decode_id(i)) for i in user_ids]
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role_ids = payload.get('role_ids', [])
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roles = [trans.sa_session.query(trans.model.Role).get(trans.security.decode_id(i)) for i in role_ids]
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trans.app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users, delete_existing_assocs=False)
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trans.sa_session.flush()
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self.manager.update(trans, id, payload)
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@@ -0,0 +1,117 @@
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import json
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from galaxy_test.base.populators import DatasetPopulator
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from ._framework import ApiTestCase
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class GroupsApiTestCase(ApiTestCase):
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def setUp(self):
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super().setUp()
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self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
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def test_create_valid(self, group_name: str = None):
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payload = self._build_valid_group_payload(group_name)
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response = self._post("groups", payload, admin=True, json=True)
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self._assert_status_code_is(response, 200)
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group = response.json()[0] # POST /api/groups returns a list
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self._assert_valid_group(group)
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return group
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def test_create_only_admin(self):
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response = self._post("groups", json=True)
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self._assert_status_code_is(response, 403)
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def test_create_invalid_params_raises_400(self):
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payload = self._build_valid_group_payload()
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payload["name"] = None
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response = self._post("groups", payload, admin=True, json=True)
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self._assert_status_code_is(response, 400)
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def test_create_duplicated_name_raises_409(self):
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payload = self._build_valid_group_payload()
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response = self._post("groups", payload, admin=True, json=True)
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self._assert_status_code_is(response, 200)
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response = self._post("groups", payload, admin=True, json=True)
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self._assert_status_code_is(response, 409)
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def test_index(self):
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self.test_create_valid()
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response = self._get("groups", admin=True)
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self._assert_status_code_is(response, 200)
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groups = response.json()
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assert isinstance(groups, list)
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assert len(groups) > 0
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for group in groups:
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self._assert_valid_group(group)
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def test_index_only_admin(self):
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response = self._get("groups")
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self._assert_status_code_is(response, 403)
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def test_show(self):
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group = self.test_create_valid()
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group_id = group["id"]
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response = self._get(f"groups/{group_id}", admin=True)
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self._assert_status_code_is(response, 200)
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response_group = response.json()
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self._assert_valid_group(response_group)
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self._assert_has_keys(response_group, "users_url", "roles_url")
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def test_show_only_admin(self):
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group = self.test_create_valid()
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group_id = group["id"]
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response = self._get(f"groups/{group_id}")
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self._assert_status_code_is(response, 403)
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def test_show_unknown_raises_400(self):
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group_id = "invalid-group-id"
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response = self._get(f"groups/{group_id}", admin=True)
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self._assert_status_code_is(response, 400)
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def test_update(self):
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group = self.test_create_valid(group_name="group-test")
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group_id = group["id"]
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updated_name = "group-test-updated"
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update_payload = json.dumps({
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"name": updated_name,
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})
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update_response = self._put(f"groups/{group_id}", data=update_payload, admin=True)
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self._assert_status_code_is_ok(update_response)
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def test_update_only_admin(self):
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group = self.test_create_valid()
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group_id = group["id"]
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response = self._put(f"groups/{group_id}")
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self._assert_status_code_is(response, 403)
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def test_update_duplicating_name_raises_409(self):
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group_a = self.test_create_valid()
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group_b = self.test_create_valid()
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# Update group_b with the same name as group_a
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group_b_id = group_b["id"]
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updated_name = group_a["name"]
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update_payload = json.dumps({
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"name": updated_name,
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})
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update_response = self._put(f"groups/{group_b_id}", data=update_payload, admin=True)
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self._assert_status_code_is(update_response, 409)
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def _assert_valid_group(self, group, assert_id=None):
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self._assert_has_keys(group, "id", "name", "model_class", "url")
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if assert_id is not None:
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assert group["id"] == assert_id
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def _build_valid_group_payload(self, name: str = None):
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name = name or self.dataset_populator.get_random_name()
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user_id = self.dataset_populator.user_id()
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role_id = self.dataset_populator.user_private_role_id()
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payload = {
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"name": name,
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"user_ids": [user_id],
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"role_ids": [role_id],
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}
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return payload
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