adding ability to pass in tokens for accessing inputs

Author: briandoconnor

openapi/workflow_execution_service.openapi.yaml

@@ -1138,6 +1138,9 @@ components:
                       last_modified:
                         type: string
                         description: Last modification time in ISO 8601 format
+                      credential_id:
+                        type: string
+                        description: Reference to a credential ID defined in the 'credentials' section of the RunRequest. This credential will be used to authenticate and authorize access to this File or Directory resource.
                   description:
                     type: string
                     description: Human-readable parameter description
@@ -1238,6 +1241,17 @@ components:
             OPTIONAL
 
             Additional workflow files required for execution (e.g., imported workflows, subworkflows, or dependencies). Each entry specifies both the source URL and target file path for precise file placement.
+        credentials:
+          type: object
+          description: >-
+            OPTIONAL
+            
+            Named credentials that can be referenced by input parameters that require authentication to access File or Directory resources. Each credential is identified by a unique key and can be referenced multiple times by different parameters to avoid duplicating large authentication tokens.
+          additionalProperties:
+            oneOf:
+              - $ref: '#/components/schemas/PassportCredential'
+              - $ref: '#/components/schemas/BearerTokenCredential'
+              - $ref: '#/components/schemas/ApiKeyCredential'
       description: >-
         To execute a workflow, send a run request including all the details needed to begin downloading
 
@@ -1581,6 +1595,59 @@ components:
             page_token:
               type: string
               description: OPTIONAL Token to use to indicate where to start getting results.
+    PassportCredential:
+      title: PassportCredential
+      type: object
+      description: GA4GH passport-based credential for accessing restricted resources
+      properties:
+        type:
+          type: string
+          enum: ["passport"]
+          description: Credential type identifier
+        passport:
+          type: array
+          items:
+            type: string
+            format: jwt
+          description: Array of GA4GH passport JWTs for authentication and authorization
+          minItems: 1
+      required:
+        - type
+        - passport
+    BearerTokenCredential:
+      title: BearerTokenCredential
+      type: object
+      description: Bearer token credential for accessing resources
+      properties:
+        type:
+          type: string
+          enum: ["bearer_token"]
+          description: Credential type identifier
+        token:
+          type: string
+          description: Bearer token for authentication
+      required:
+        - type
+        - token
+    ApiKeyCredential:
+      title: ApiKeyCredential
+      type: object
+      description: API key credential for accessing resources
+      properties:
+        type:
+          type: string
+          enum: ["api_key"]
+          description: Credential type identifier
+        key:
+          type: string
+          description: API key for authentication
+        header_name:
+          type: string
+          description: Header name for the API key (defaults to X-API-Key if not specified)
+          default: "X-API-Key"
+      required:
+        - type
+        - key