From 92869fc9a938bd5c0754ba4e85550d959d8a2c93 Mon Sep 17 00:00:00 2001
From: Sean-DNAstack <sean@dnastack.com>
Date: Mon, 23 Oct 2023 10:57:36 -0400
Subject: [PATCH] Clean up wes swagger yaml

---
 .../wes/cromwell/CromwellService.java         |  4 +-
 workflow_execution_service.swagger.yaml       | 83 +++++++++++++------
 2 files changed, 60 insertions(+), 27 deletions(-)

diff --git a/src/main/java/com/dnastack/wes/cromwell/CromwellService.java b/src/main/java/com/dnastack/wes/cromwell/CromwellService.java
index 7d6a935..b065521 100644
--- a/src/main/java/com/dnastack/wes/cromwell/CromwellService.java
+++ b/src/main/java/com/dnastack/wes/cromwell/CromwellService.java
@@ -231,7 +231,7 @@ public RunId cancel(String runId) {
      *
      * @return a list of generated files for the run
      */
-    public RunFiles getRunFiles(String runId) throws NotFoundException {
+    public RunFiles getRunFiles(String runId) {
         CromwellMetadataResponse metadataResponse = getMetadata(runId);
         Set<String> finalFileSet = new HashSet<>();
         Set<String> secondaryFileSet = new HashSet<>();
@@ -554,7 +554,7 @@ private void extractSecondaryLogFilesFromCall(Set<String> secondaryFileSet, Set<
         }
         CromwellMetadataResponse subWorkflowMetadata = call.getSubWorkflowMetadata();
         if (subWorkflowMetadata != null) {
-            extractSecondaryLogFiles(secondaryFileSet,logFileSet,subWorkflowMetadata);
+            extractSecondaryLogFiles(secondaryFileSet, logFileSet, subWorkflowMetadata);
         }
     }
 
diff --git a/workflow_execution_service.swagger.yaml b/workflow_execution_service.swagger.yaml
index b8244e9..a2e297f 100644
--- a/workflow_execution_service.swagger.yaml
+++ b/workflow_execution_service.swagger.yaml
@@ -383,7 +383,7 @@ paths:
       description: >-
         This endpoint provides all the generated files from the associated storage 
         client for a workflow run. The returned result has information about the 
-        files of the given run and the type of the given file.
+        files of the given run, including the path and the type of the given file.
       x-swagger-router-controller: ga4gh.wes.server
       operationId: GetRunFiles
       responses:
@@ -434,12 +434,12 @@ paths:
         files are cleaned up. When true the delete operation will be done asynchronously
         with faster execution but higher risk of not doing a "clean" cleanup.
       x-swagger-router-controller: ga4gh.wes.server
-      operationId: GetRunFiles
+      operationId: DeleteRunFiles
       responses:
         '200':
           description: ''
           schema:
-            $ref: '#/definitions/RunId'
+            $ref: '#/definitions/RunFileDeletions'
         '401':
           description: The request is unauthorized.
           schema:
@@ -653,27 +653,21 @@ definitions:
 
 
         - CANCELING: The task was canceled by the user, and is in the process of stopping.       
-  File:
-    type: object
-    properties:
-      type:
-        type: string
-        enum:
-          - FINAL
-          - SECONDARY
-          - LOG
-        default: FINAL
-        description: >-
-          - FINAL: The file exists directly as an output of the metadata response for the specified run.
-          
-          - SECONDARY: The file exists as a part of a task call output or a sub-workflow metadata 
-          response for the specified run
-          
-          - LOG: The file exists as a part of the backend logs or stderr and stdout for the workflow or 
-          sub-workflow metadata for the specified run.
-      path:
-        type: string
-        description: The path of the file.
+  FileType:
+    type: string
+    enum:
+      - FINAL
+      - SECONDARY
+      - LOG
+    default: FINAL
+    description: >-
+      - FINAL: The file exists directly as an output of the metadata response for the specified run.
+
+      - SECONDARY: The file exists as a part of a task call output or a sub-workflow metadata 
+      response for the specified run
+
+      - LOG: The file exists as a part of the backend logs or stderr and stdout for the workflow or 
+      sub-workflow metadata for the specified run.
   RunListResponse:
     type: object
     properties:
@@ -782,7 +776,46 @@ definitions:
       files:
         type: array
         items:
-          $ref: '#/definitions/File'
+          $ref: '#/definitions/RunFile'
+  RunFile:
+    type: object
+    properties:
+      file_type:
+        $ref: '#/definitions/FileType'
+      path:
+        type: string
+        description: The path of the file.
+  RunFileDeletions:
+    type: object
+    required:
+      - run_id
+    properties:
+      deletions:
+        type: array
+        items:
+          $ref: '#/definitions/RunFileDeletion'
+  RunFileDeletion:
+    type: object
+    properties:
+      path:
+        type: string
+        description: The path of the file.
+      file_type:
+        $ref: '#/definitions/FileType'
+      state:
+        type: string
+        enum:
+          - DELETED
+          - ASYNC
+          - FAILED
+        description: >-
+          - DELETED: The file has been successfully deleted from storage.
+
+
+          - ASYNC: The file is being deleted asynchronously.
+
+
+          - FAILED: An error occurred during the process of deleting the file.
   WorkflowTypeVersion:
     type: object
     properties: