Merge pull request galaxyproject#17051 from arash77/migrate_groups_fa…

…stapi

Migrate groups API to fastAPI

client/src/api/schema/schema.ts

@@ -381,9 +381,21 @@ export interface paths {
         /** Return raw sequence data */
         get: operations["sequences_api_genomes__id__sequences_get"];
     };
+    "/api/groups": {
+        /** Displays a collection (list) of groups. */
+        get: operations["index_api_groups_get"];
+        /** Creates a new group. */
+        post: operations["create_api_groups_post"];
+    };
+    "/api/groups/{group_id}": {
+        /** Displays information about a group. */
+        get: operations["show_group_api_groups__group_id__get"];
+        /** Modifies a group. */
+        put: operations["update_api_groups__group_id__put"];
+    };
     "/api/groups/{group_id}/roles": {
         /** Displays a collection (list) of groups. */
-        get: operations["index_api_groups__group_id__roles_get"];
+        get: operations["group_roles_api_groups__group_id__roles_get"];
     };
     "/api/groups/{group_id}/roles/{role_id}": {
         /** Displays information about a group role. */
@@ -418,7 +430,7 @@ export interface paths {
          * @description GET /api/groups/{encoded_group_id}/users
          * Displays a collection (list) of groups.
          */
-        get: operations["index_api_groups__group_id__users_get"];
+        get: operations["group_users_api_groups__group_id__users_get"];
     };
     "/api/groups/{group_id}/users/{user_id}": {
         /**
@@ -4626,6 +4638,29 @@ export interface components {
             /** Tags */
             tags?: string[];
         };
+        /**
+         * GroupCreatePayload
+         * @description Payload schema for creating a group.
+         */
+        GroupCreatePayload: {
+            /** name of the group */
+            name: string;
+            /**
+             * role IDs
+             * @default []
+             */
+            role_ids?: string[];
+            /**
+             * user IDs
+             * @default []
+             */
+            user_ids?: string[];
+        };
+        /**
+         * GroupListResponse
+         * @description Response schema for listing groups.
+         */
+        GroupListResponse: components["schemas"]["GroupResponse"][];
         /**
          * GroupModel
          * @description User group model
@@ -4665,6 +4700,32 @@ export interface components {
              */
             model_class: "GroupQuotaAssociation";
         };
+        /**
+         * GroupResponse
+         * @description Response schema for a group.
+         */
+        GroupResponse: {
+            /**
+             * group ID
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @default Group
+             * @enum {string}
+             */
+            model_class: "Group";
+            /** name of the group */
+            name: string;
+            /** URL for the roles of the group */
+            roles_url?: string;
+            /** URL for the group */
+            url: string;
+            /** URL for the users of the group */
+            users_url?: string;
+        };
         /** GroupRoleListResponse */
         GroupRoleListResponse: components["schemas"]["GroupRoleResponse"][];
         /** GroupRoleResponse */
@@ -11538,7 +11599,115 @@ export interface operations {
             };
         };
     };
-    index_api_groups__group_id__roles_get: {
+    index_api_groups_get: {
+        /** Displays a collection (list) of groups. */
+        parameters?: {
+            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            header?: {
+                "run-as"?: string;
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                content: {
+                    "application/json": components["schemas"]["GroupListResponse"];
+                };
+            };
+            /** @description Validation Error */
+            422: {
+                content: {
+                    "application/json": components["schemas"]["HTTPValidationError"];
+                };
+            };
+        };
+    };
+    create_api_groups_post: {
+        /** Creates a new group. */
+        parameters?: {
+            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            header?: {
+                "run-as"?: string;
+            };
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["GroupCreatePayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                content: {
+                    "application/json": components["schemas"]["GroupListResponse"];
+                };
+            };
+            /** @description Validation Error */
+            422: {
+                content: {
+                    "application/json": components["schemas"]["HTTPValidationError"];
+                };
+            };
+        };
+    };
+    show_group_api_groups__group_id__get: {
+        /** Displays information about a group. */
+        parameters: {
+            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            header?: {
+                "run-as"?: string;
+            };
+            path: {
+                group_id: string;
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                content: {
+                    "application/json": components["schemas"]["GroupResponse"];
+                };
+            };
+            /** @description Validation Error */
+            422: {
+                content: {
+                    "application/json": components["schemas"]["HTTPValidationError"];
+                };
+            };
+        };
+    };
+    update_api_groups__group_id__put: {
+        /** Modifies a group. */
+        parameters: {
+            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            header?: {
+                "run-as"?: string;
+            };
+            path: {
+                group_id: string;
+            };
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["GroupCreatePayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                content: {
+                    "application/json": components["schemas"]["GroupResponse"];
+                };
+            };
+            /** @description Validation Error */
+            422: {
+                content: {
+                    "application/json": components["schemas"]["HTTPValidationError"];
+                };
+            };
+        };
+    };
+    group_roles_api_groups__group_id__roles_get: {
         /** Displays a collection (list) of groups. */
         parameters: {
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
@@ -11750,7 +11919,7 @@ export interface operations {
             };
         };
     };
-    index_api_groups__group_id__users_get: {
+    group_users_api_groups__group_id__users_get: {
         /**
          * Displays a collection (list) of groups.
          * @description GET /api/groups/{encoded_group_id}/users

lib/galaxy/managers/groups.py

@@ -1,9 +1,3 @@
-from typing import (
-    Any,
-    Dict,
-    List,
-)
-
 from sqlalchemy import (
     false,
     select,
@@ -16,21 +10,15 @@
     ObjectAttributeMissingException,
     ObjectNotFound,
 )
-from galaxy.managers.base import decode_id
 from galaxy.managers.context import ProvidesAppContext
+from galaxy.managers.roles import get_roles_by_ids
 from galaxy.managers.users import get_users_by_ids
-from galaxy.model import (
-    Group,
-    Role,
-)
+from galaxy.model import Group
 from galaxy.model.base import transaction
 from galaxy.model.scoped_session import galaxy_scoped_session
-from galaxy.schema.fields import (
-    DecodedDatabaseIdField,
-    EncodedDatabaseIdField,
-)
+from galaxy.schema.fields import DecodedDatabaseIdField
+from galaxy.schema.groups import GroupCreatePayload
 from galaxy.structured_app import MinimalManagerApp
-from galaxy.web import url_for
 
 
 class GroupsManager:
@@ -47,33 +35,33 @@ def index(self, trans: ProvidesAppContext):
         for group in get_not_deleted_groups(trans.sa_session):
             item = group.to_dict(value_mapper={"id": DecodedDatabaseIdField.encode})
             encoded_id = DecodedDatabaseIdField.encode(group.id)
-            item["url"] = url_for("group", id=encoded_id)
+            item["url"] = self._url_for(trans, "show_group", group_id=encoded_id)
             rval.append(item)
         return rval
 
-    def create(self, trans: ProvidesAppContext, payload: Dict[str, Any]):
+    def create(self, trans: ProvidesAppContext, payload: GroupCreatePayload):
         """
         Creates a new group.
         """
         sa_session = trans.sa_session
-        name = payload.get("name", None)
+        name = payload.name
         if name is None:
             raise ObjectAttributeMissingException("Missing required name")
         self._check_duplicated_group_name(sa_session, name)
 
         group = model.Group(name=name)
         sa_session.add(group)
-        encoded_user_ids = payload.get("user_ids", [])
-        users = self._get_users_by_encoded_ids(sa_session, encoded_user_ids)
-        encoded_role_ids = payload.get("role_ids", [])
-        roles = self._get_roles_by_encoded_ids(sa_session, encoded_role_ids)
+        user_ids = payload.user_ids
+        users = get_users_by_ids(sa_session, user_ids)
+        role_ids = payload.role_ids
+        roles = get_roles_by_ids(sa_session, role_ids)
         trans.app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users)
         with transaction(sa_session):
             sa_session.commit()
 
         encoded_id = DecodedDatabaseIdField.encode(group.id)
         item = group.to_dict(view="element", value_mapper={"id": DecodedDatabaseIdField.encode})
-        item["url"] = url_for("group", id=encoded_id)
+        item["url"] = self._url_for(trans, "show_group", group_id=encoded_id)
         return [item]
 
     def show(self, trans: ProvidesAppContext, group_id: int):
@@ -83,32 +71,40 @@ def show(self, trans: ProvidesAppContext, group_id: int):
         encoded_id = DecodedDatabaseIdField.encode(group_id)
         group = self._get_group(trans.sa_session, group_id)
         item = group.to_dict(view="element", value_mapper={"id": DecodedDatabaseIdField.encode})
-        item["url"] = url_for("group", id=encoded_id)
-        item["users_url"] = url_for("group_users", group_id=encoded_id)
-        item["roles_url"] = url_for("group_roles", group_id=encoded_id)
+        item["url"] = self._url_for(trans, "show_group", group_id=encoded_id)
+        item["users_url"] = self._url_for(trans, "group_users", group_id=encoded_id)
+        item["roles_url"] = self._url_for(trans, "group_roles", group_id=encoded_id)
         return item
 
-    def update(self, trans: ProvidesAppContext, group_id: int, payload: Dict[str, Any]):
+    def update(self, trans: ProvidesAppContext, group_id: int, payload: GroupCreatePayload):
         """
         Modifies a group.
         """
         sa_session = trans.sa_session
         group = self._get_group(sa_session, group_id)
-        name = payload.get("name", None)
+        name = payload.name
         if name:
             self._check_duplicated_group_name(sa_session, name)
             group.name = name
             sa_session.add(group)
-        encoded_user_ids = payload.get("user_ids", [])
-        users = self._get_users_by_encoded_ids(sa_session, encoded_user_ids)
-        encoded_role_ids = payload.get("role_ids", [])
-        roles = self._get_roles_by_encoded_ids(sa_session, encoded_role_ids)
+        user_ids = payload.user_ids
+        users = get_users_by_ids(sa_session, user_ids)
+        role_ids = payload.role_ids
+        roles = get_roles_by_ids(sa_session, role_ids)
         self._app.security_agent.set_entity_group_associations(
             groups=[group], roles=roles, users=users, delete_existing_assocs=False
         )
         with transaction(sa_session):
             sa_session.commit()
 
+        encoded_id = DecodedDatabaseIdField.encode(group.id)
+        item = group.to_dict(view="element", value_mapper={"id": DecodedDatabaseIdField.encode})
+        item["url"] = self._url_for(trans, "show_group", group_id=encoded_id)
+        return item
+
+    def _url_for(self, trans, name, **kwargs):
+        return trans.url_builder(name, **kwargs)
+
     def _check_duplicated_group_name(self, sa_session: galaxy_scoped_session, group_name: str) -> None:
         if get_group_by_name(sa_session, group_name):
             raise Conflict(f"A group with name '{group_name}' already exists")
@@ -119,25 +115,6 @@ def _get_group(self, sa_session: galaxy_scoped_session, group_id: int) -> model.
             raise ObjectNotFound("Group with the provided id was not found.")
         return group
 
-    def _get_users_by_encoded_ids(
-        self, sa_session: galaxy_scoped_session, encoded_user_ids: List[EncodedDatabaseIdField]
-    ) -> List[model.User]:
-        user_ids = self._decode_ids(encoded_user_ids)
-        return get_users_by_ids(sa_session, user_ids)
-
-    def _get_roles_by_encoded_ids(
-        self, sa_session: galaxy_scoped_session, encoded_role_ids: List[EncodedDatabaseIdField]
-    ) -> List[model.Role]:
-        role_ids = self._decode_ids(encoded_role_ids)
-        stmt = select(Role).where(Role.id.in_(role_ids))
-        return sa_session.scalars(stmt).all()
-
-    def _decode_id(self, encoded_id: EncodedDatabaseIdField) -> int:
-        return decode_id(self._app, encoded_id)
-
-    def _decode_ids(self, encoded_ids: List[EncodedDatabaseIdField]) -> List[int]:
-        return [self._decode_id(encoded_id) for encoded_id in encoded_ids]
-
 
 def get_group_by_name(session: Session, name: str):
     stmt = select(Group).filter(Group.name == name).limit(1)

lib/galaxy/managers/roles.py

@@ -8,7 +8,10 @@
     false,
     select,
 )
-from sqlalchemy.orm import exc as sqlalchemy_exceptions
+from sqlalchemy.orm import (
+    exc as sqlalchemy_exceptions,
+    Session,
+)
 
 import galaxy.exceptions
 from galaxy import model
@@ -97,3 +100,8 @@ def create_role(self, trans: ProvidesUserContext, role_definition_model: RoleDef
         with transaction(trans.sa_session):
             trans.sa_session.commit()
         return role
+
+
+def get_roles_by_ids(session: Session, role_ids):
+    stmt = select(Role).where(Role.id.in_(role_ids))
+    return session.scalars(stmt).all()