Merge pull request #15189 from mvdbeek/openapi_python_client

Tweak OpenAPI schema
galaxyproject · Dec 14, 2022 · 0d76b26 · 0d76b26
2 parents 35bf24a + 22962f4
commit 0d76b26
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Showing 6 changed files with 33 additions and 102 deletions.
diff --git a/.redocly.lint-ignore.yaml b/.redocly.lint-ignore.yaml
@@ -3,15 +3,7 @@
 _schema.yaml:
   no-empty-servers:
     - '#/openapi'
-  no-identical-paths:
-    - '#/paths/~1api~1groups~1{group_id}~1roles~1{role_id}'
-    - '#/paths/~1api~1groups~1{group_id}~1user~1{user_id}'
-    - '#/paths/~1api~1groups~1{group_id}~1users~1{user_id}'
   no-ambiguous-paths:
-    - '#/paths/~1api~1groups~1{group_id}~1roles~1{role_id}'
-    - '#/paths/~1api~1groups~1{group_id}~1user~1{user_id}'
-    - '#/paths/~1api~1groups~1{group_id}~1users~1{user_id}'
-    - '#/paths/~1api~1histories~1{history_id}~1contents~1archive~1{id}'
     - >-
       #/paths/~1api~1histories~1{history_id}~1contents~1{dataset_id}~1permissions
     - >-
@@ -22,8 +14,3 @@ _schema.yaml:
       #/paths/~1api~1histories~1{history_id}~1contents~1{history_content_id}~1metadata_file
     - '#/paths/~1api~1histories~1{history_id}~1contents~1{id}~1validate'
     - '#/paths/~1api~1histories~1{history_id}~1contents~1{type}s~1{id}'
-  path-parameters-defined:
-    - >-
-      #/paths/~1api~1dataset_collections~1{id}~1prepare_download/post/parameters/0/name
-    - >-
-      #/paths/~1api~1histories~1{history_id}~1contents~1archive~1{id}/get/parameters
diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
@@ -319,25 +319,20 @@ export interface paths {
         /** Displays a collection (list) of groups. */
         get: operations["index_api_groups__group_id__roles_get"];
     };
-    "/api/groups/{group_id}/roles/{id}": {
-        /** Displays information about a group role. */
-        get: operations["group_role_api_groups__group_id__roles__id__get"];
-    };
     "/api/groups/{group_id}/roles/{role_id}": {
+        /** Displays information about a group role. */
+        get: operations["group_role_api_groups__group_id__roles__role_id__get"];
         /** Adds a role to a group */
         put: operations["update_api_groups__group_id__roles__role_id__put"];
         /** Removes a role from a group */
         delete: operations["delete_api_groups__group_id__roles__role_id__delete"];
     };
-    "/api/groups/{group_id}/user/{id}": {
+    "/api/groups/{group_id}/user/{user_id}": {
         /**
          * Displays information about a group user.
-         * @description GET /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Displays information about a group user.
+         * @description Displays information about a group user.
          */
-        get: operations["group_user_api_groups__group_id__user__id__get"];
-    };
-    "/api/groups/{group_id}/user/{user_id}": {
+        get: operations["group_user_api_groups__group_id__user__user_id__get"];
         /**
          * Adds a user to a group
          * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id}
@@ -359,15 +354,12 @@ export interface paths {
          */
         get: operations["index_api_groups__group_id__users_get"];
     };
-    "/api/groups/{group_id}/users/{id}": {
+    "/api/groups/{group_id}/users/{user_id}": {
         /**
          * Displays information about a group user.
-         * @description GET /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Displays information about a group user.
+         * @description Displays information about a group user.
          */
-        get: operations["group_user_api_groups__group_id__users__id__get"];
-    };
-    "/api/groups/{group_id}/users/{user_id}": {
+        get: operations["group_user_api_groups__group_id__users__user_id__get"];
         /**
          * Adds a user to a group
          * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id}
@@ -491,15 +483,6 @@ export interface paths {
          */
         get: operations["download_dataset_collection_api_histories__history_id__contents_dataset_collections__id__download_get"];
     };
-    "/api/histories/{history_id}/contents/dataset_collections/{id}/prepare_download": {
-        /**
-         * Prepare an short term storage object that the collection will be downloaded to.
-         * @description The history dataset collection will be written as a `zip` archive to the
-         * returned short term storage object. Progress tracking this file's creation
-         * can be tracked with the short_term_storage API.
-         */
-        post: operations["prepare_collection_download_api_histories__history_id__contents_dataset_collections__id__prepare_download_post"];
-    };
     "/api/histories/{history_id}/contents/datasets/{id}/materialize": {
         /** Materialize a deferred dataset into real, usable dataset. */
         post: operations["materialize_dataset_api_histories__history_id__contents_datasets__id__materialize_post"];
@@ -7831,15 +7814,13 @@ export interface operations {
             header?: {
                 "run-as"?: string;
             };
-            /** @description The ID of the History. */
             /** @description The ID of the `HDCA` contained in the history. */
             path: {
-                history_id: string;
                 id: string;
             };
         };
         responses: {
-            /** @description Successful Response */
+            /** @description Short term storage reference for async monitoring of this download. */
             200: {
                 content: {
                     "application/json": components["schemas"]["AsyncFile"];
@@ -7851,6 +7832,8 @@ export interface operations {
                     "application/json": components["schemas"]["HTTPValidationError"];
                 };
             };
+            /** @description Required asynchronous tasks required for this operation not available. */
+            501: never;
         };
     };
     suitable_converters_api_dataset_collections__id__suitable_converters_get: {
@@ -9086,7 +9069,7 @@ export interface operations {
             };
         };
     };
-    group_role_api_groups__group_id__roles__id__get: {
+    group_role_api_groups__group_id__roles__role_id__get: {
         /** Displays information about a group role. */
         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. */
@@ -9097,7 +9080,7 @@ export interface operations {
             /** @description The ID of the role */
             path: {
                 group_id: string;
-                id: string;
+                role_id: string;
             };
         };
         responses: {
@@ -9173,11 +9156,10 @@ export interface operations {
             };
         };
     };
-    group_user_api_groups__group_id__user__id__get: {
+    group_user_api_groups__group_id__user__user_id__get: {
         /**
          * Displays information about a group user.
-         * @description GET /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Displays information about a group user.
+         * @description Displays information about a group user.
          */
         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. */
@@ -9188,7 +9170,7 @@ export interface operations {
             /** @description The ID of the user */
             path: {
                 group_id: string;
-                id: string;
+                user_id: string;
             };
         };
         responses: {
@@ -9303,11 +9285,10 @@ export interface operations {
             };
         };
     };
-    group_user_api_groups__group_id__users__id__get: {
+    group_user_api_groups__group_id__users__user_id__get: {
         /**
          * Displays information about a group user.
-         * @description GET /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Displays information about a group user.
+         * @description Displays information about a group user.
          */
         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. */
@@ -9318,7 +9299,7 @@ export interface operations {
             /** @description The ID of the user */
             path: {
                 group_id: string;
-                id: string;
+                user_id: string;
             };
         };
         responses: {
@@ -10329,42 +10310,6 @@ export interface operations {
             };
         };
     };
-    prepare_collection_download_api_histories__history_id__contents_dataset_collections__id__prepare_download_post: {
-        /**
-         * Prepare an short term storage object that the collection will be downloaded to.
-         * @description The history dataset collection will be written as a `zip` archive to the
-         * returned short term storage object. Progress tracking this file's creation
-         * can be tracked with the short_term_storage API.
-         */
-        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;
-            };
-            /** @description The ID of the History. */
-            /** @description The ID of the `HDCA` contained in the history. */
-            path: {
-                history_id: string;
-                id: string;
-            };
-        };
-        responses: {
-            /** @description Short term storage reference for async monitoring of this download. */
-            200: {
-                content: {
-                    "application/json": components["schemas"]["AsyncFile"];
-                };
-            };
-            /** @description Validation Error */
-            422: {
-                content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
-                };
-            };
-            /** @description Required asynchronous tasks required for this operation not available. */
-            501: never;
-        };
-    };
     materialize_dataset_api_histories__history_id__contents_datasets__id__materialize_post: {
         /** Materialize a deferred dataset into real, usable dataset. */
         parameters: {

diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -31,7 +31,7 @@
 def group_role_to_model(trans, group_id: int, role) -> GroupRoleModel:
     encoded_group_id = DecodedDatabaseIdField.encode(group_id)
     encoded_role_id = DecodedDatabaseIdField.encode(role.id)
-    url = trans.url_builder("group_role", group_id=encoded_group_id, id=encoded_role_id)
+    url = trans.url_builder("group_role", group_id=encoded_group_id, role_id=encoded_role_id)
     return GroupRoleModel.construct(id=encoded_role_id, name=role.name, url=url)
 
 
@@ -49,7 +49,7 @@ def index(
         )
 
     @router.get(
-        "/api/groups/{group_id}/roles/{id}",
+        "/api/groups/{group_id}/roles/{role_id}",
         name="group_role",
         require_admin=True,
         summary="Displays information about a group role.",
@@ -58,9 +58,9 @@ def show(
         self,
         trans: ProvidesAppContext = DependsOnTrans,
         group_id: DecodedDatabaseIdField = GroupIDParam,
-        id: DecodedDatabaseIdField = RoleIDParam,
+        role_id: DecodedDatabaseIdField = RoleIDParam,
     ) -> GroupRoleModel:
-        role = self.manager.show(trans, id, group_id)
+        role = self.manager.show(trans, role_id, group_id)
         return group_role_to_model(trans, group_id, role)
 
     @router.put("/api/groups/{group_id}/roles/{role_id}", require_admin=True, summary="Adds a role to a group")

diff --git a/lib/galaxy/webapps/galaxy/api/group_users.py b/lib/galaxy/webapps/galaxy/api/group_users.py
@@ -50,8 +50,8 @@ def index(
         return GroupUserListModel(__root__=[group_user_to_model(trans, group_id, gr) for gr in group_users])
 
     @router.get(
-        "/api/groups/{group_id}/user/{id}",
-        alias="/api/groups/{group_id}/users/{id}",
+        "/api/groups/{group_id}/user/{user_id}",
+        alias="/api/groups/{group_id}/users/{user_id}",
         name="group_user",
         require_admin=True,
         summary="Displays information about a group user.",
@@ -60,13 +60,12 @@ def show(
         self,
         trans: ProvidesAppContext = DependsOnTrans,
         group_id: DecodedDatabaseIdField = GroupIDParam,
-        id: DecodedDatabaseIdField = UserIDParam,
+        user_id: DecodedDatabaseIdField = UserIDParam,
     ) -> GroupUserModel:
         """
-        GET /api/groups/{encoded_group_id}/users/{encoded_user_id}
         Displays information about a group user.
         """
-        user = self.manager.show(trans, id, group_id)
+        user = self.manager.show(trans, user_id, group_id)
         return group_user_to_model(trans, group_id, user)
 
     @router.put(

diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -511,22 +511,22 @@ def download_dataset_collection(
     @router.post(
         "/api/histories/{history_id}/contents/dataset_collections/{id}/prepare_download",
         summary="Prepare an short term storage object that the collection will be downloaded to.",
+        include_in_schema=False,
+    )
+    @router.post(
+        "/api/dataset_collections/{id}/prepare_download",
+        summary="Prepare an short term storage object that the collection will be downloaded to.",
         responses={
             200: {
                 "description": "Short term storage reference for async monitoring of this download.",
             },
             501: {"description": "Required asynchronous tasks required for this operation not available."},
         },
-    )
-    @router.post(
-        "/api/dataset_collections/{id}/prepare_download",
-        summary="Prepare an short term storage object that the collection will be downloaded to.",
         tags=["dataset collections"],
     )
     def prepare_collection_download(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
-        history_id: DecodedDatabaseIdField = HistoryIDPathParam,
         id: DecodedDatabaseIdField = HistoryHDCAIDPathParam,
     ) -> AsyncFile:
         """The history dataset collection will be written as a `zip` archive to the

diff --git a/lib/galaxy/webapps/openapi/utils.py b/lib/galaxy/webapps/openapi/utils.py
@@ -185,7 +185,7 @@ def generate_operation_summary(*, route: routing.APIRoute, method: str) -> str:
 def get_openapi_operation_metadata(*, route: routing.APIRoute, method: str, operation_ids: Set[str]) -> Dict[str, Any]:
     operation: Dict[str, Any] = {}
     if route.tags:
-        operation["tags"] = route.tags
+        operation["tags"] = list(set(route.tags))
     operation["summary"] = generate_operation_summary(route=route, method=method)
     if route.description:
         operation["description"] = route.description