Optional DRS upload and delete extensions

openapi/components/requestBodies/AccessMethodUpdateBody.yaml

@@ -0,0 +1,6 @@
+description: Request body for updating access methods of a DRS object
+required: true
+content:
+  application/json:
+    schema:
+      $ref: '../schemas/AccessMethodUpdateRequest.yaml'

openapi/components/requestBodies/BulkAccessMethodUpdateBody.yaml

@@ -0,0 +1,6 @@
+description: Request body for bulk updating access methods of multiple DRS objects
+required: true
+content:
+  application/json:
+    schema:
+      $ref: '../schemas/BulkAccessMethodUpdateRequest.yaml'

openapi/components/requestBodies/BulkDeleteBody.yaml

@@ -0,0 +1,72 @@
+required: true
+content:
+  application/json:
+    schema:
+      $ref: '../schemas/BulkDeleteRequest.yaml'
+    examples:
+      bulk_metadata_delete:
+        summary: Bulk delete metadata only
+        description: Delete multiple DRS objects metadata while preserving underlying storage data (default and safest option)
+        value:
+          bulk_object_ids:
+            - "drs_object_123456"
+            - "drs_object_789012"
+            - "drs_object_345678"
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+          delete_storage_data: false
+      bulk_full_delete:
+        summary: Bulk delete metadata and storage data
+        description: Delete both metadata and storage data for multiple objects (requires server support via deleteStorageDataSupported)
+        value:
+          bulk_object_ids:
+            - "drs_object_123456"
+            - "drs_object_789012"
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+          delete_storage_data: true
+      bulk_no_auth_delete:
+        summary: Bulk delete without authentication
+        description: Bulk delete operation without GA4GH Passport authentication (for public objects or when using Bearer token in headers)
+        value:
+          bulk_object_ids:
+            - "drs_object_123456"
+            - "drs_object_789012"
+          delete_storage_data: false
+      large_bulk_delete:
+        summary: Large bulk delete operation
+        description: Delete many objects in a single request (check maxBulkDeleteLength in service-info for limits)
+        value:
+          bulk_object_ids:
+            - "drs_object_001"
+            - "drs_object_002"
+            - "drs_object_003"
+            - "drs_object_004"
+            - "drs_object_005"
+            - "drs_object_006"
+            - "drs_object_007"
+            - "drs_object_008"
+            - "drs_object_009"
+            - "drs_object_010"
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+          delete_storage_data: false
+      mixed_object_types:
+        summary: Mixed object types deletion
+        description: Delete objects with different ID formats and types in a single request
+        value:
+          bulk_object_ids:
+            - "drs://example.org/123456"
+            - "local_object_789"
+            - "uuid:550e8400-e29b-41d4-a716-446655440000"
+            - "compact:prefix:identifier"
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+          delete_storage_data: false
+      minimal_bulk_request:
+        summary: Minimal bulk delete request
+        description: Simplest bulk delete request with required fields only
+        value:
+          bulk_object_ids:
+            - "drs_object_123456"
+            - "drs_object_789012"

openapi/components/requestBodies/BulkObjectBody.yaml

@@ -0,0 +1,38 @@
+required: true
+content:
+  application/json:
+    schema:
+      type: object
+      required:
+        - bulk_object_ids
+      properties:
+        passports:
+          type: array
+          items:
+            type: string
+            example: eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM
+          description: the encoded JWT GA4GH Passport that contains embedded Visas.  The overall JWT is signed as are the individual Passport Visas.
+        bulk_object_ids:
+          type: array
+          items:
+            type: string
+          minItems: 1
+          description: An array of ObjectIDs to retrieve metadata for
+    examples:
+      bulk_retrieve:
+        summary: Bulk retrieve objects
+        description: Retrieve metadata for multiple existing DRS objects using their IDs
+        value:
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+          bulk_object_ids:
+            - "drs_object_123456"
+            - "drs_object_789012"
+            - "drs_object_345678"
+      bulk_retrieve_no_auth:
+        summary: Bulk retrieve without authentication
+        description: Retrieve metadata for public DRS objects
+        value:
+          bulk_object_ids:
+            - "drs_object_public_123"
+            - "drs_object_public_456"

openapi/components/requestBodies/DeleteBody.yaml

@@ -0,0 +1,44 @@
+required: false
+content:
+  application/json:
+    schema:
+      $ref: '../schemas/DeleteRequest.yaml'
+    examples:
+      metadata_only_delete:
+        summary: Delete metadata only (default)
+        description: Delete DRS object metadata while preserving underlying storage data. This is the default and safest option.
+        value:
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+          delete_storage_data: false
+      full_delete:
+        summary: Delete metadata and storage data
+        description: Delete both DRS object metadata and underlying storage data (requires server support via deleteStorageDataSupported)
+        value:
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+          delete_storage_data: true
+      no_auth_delete:
+        summary: Delete without authentication
+        description: Delete operation without GA4GH Passport authentication (for public objects or when using Bearer token in headers)
+        value:
+          delete_storage_data: false
+      minimal_request:
+        summary: Minimal delete request
+        description: Simplest delete request with no authentication and default behavior (metadata only)
+        value: {}
+      multiple_passports:
+        summary: Multiple GA4GH Passports
+        description: Delete request with multiple GA4GH Passports for complex authorization scenarios
+        value:
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+            - "eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.AbCdEfGhIjKlMnOpQrStUvWxYz"
+          delete_storage_data: false
+      update_workflow:
+        summary: Safe update workflow
+        description: Delete metadata only to enable safe update pattern (delete metadata, then re-register with new metadata)
+        value:
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+          delete_storage_data: false

openapi/components/requestBodies/PostObjectBody.yaml

@@ -25,3 +25,21 @@ content:
             type: string
             example: eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM
           description: the encoded JWT GA4GH Passport that contains embedded Visas.  The overall JWT is signed as are the individual Passport Visas.
+
+    examples:
+      retrieve_with_auth:
+        summary: Retrieve object with authentication
+        description: Request object metadata with passport authentication
+        value:
+          expand: false
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+      retrieve_expanded_bundle:
+        summary: Retrieve expanded bundle with authentication
+        description: Request expanded bundle contents with passport authentication
+        value:
+          expand: true
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+            - "eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.additional_passport_signature"
+

openapi/components/requestBodies/RegisterObjectsBody.yaml

@@ -0,0 +1,66 @@
+description: Request body for registering DRS objects after upload
+required: true
+content:
+  application/json:
+    schema:
+      type: object
+      required:
+        - candidates
+      properties:
+        candidates:
+          type: array
+          items:
+            $ref: '../schemas/DrsObjectCandidate.yaml'
+          minItems: 1
+          description: Array of DRS object candidates to register (server will mint IDs and timestamps)
+        passports:
+          type: array
+          items:
+            type: string
+          description: Optional array of GA4GH Passport JWTs for authorization
+    examples:
+      single_object_registration:
+        summary: Register a single object
+        description: Register one DRS object after upload
+        value:
+          candidates:
+            - name: "sample_data.vcf"
+              size: 1048576
+              mime_type: "text/plain"
+              checksums:
+                - checksum: "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"
+                  type: "sha-256"
+              description: "Variant call format file for sample analysis"
+              access_methods:
+                - type: "s3"
+                  access_url:
+                    url: "s3://my-bucket/uploads/sample_data.vcf"
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9..."
+      bulk_object_registration:
+        summary: Register multiple objects
+        description: Register multiple DRS objects in a single request
+        value:
+          candidates:
+            - name: "genome_assembly.fasta"
+              size: 3221225472
+              mime_type: "text/plain"
+              checksums:
+                - checksum: "a665a45920422f9d417e4867efdc4fb8a04a1f3fff1fa07e998e86f7f7a27ae3"
+                  type: "sha-256"
+              description: "Human genome reference assembly"
+              access_methods:
+                - type: "s3"
+                  access_url:
+                    url: "s3://genomics-bucket/assemblies/hg38.fasta"
+            - name: "annotations.gff3"
+              size: 524288000
+              mime_type: "text/plain"
+              checksums:
+                - checksum: "b94d27b9934d3e08a52e52d7da7dabfac484efe37a5380ee9088f7ace2efcde9"
+                  type: "sha-256"
+              description: "Gene annotations in GFF3 format"
+              access_methods:
+                - type: "https"
+                  access_url:
+                    url: "https://data.example.org/files/annotations.gff3"

openapi/components/requestBodies/UploadRequestBody.yaml

@@ -0,0 +1,65 @@
+required: true
+content:
+  application/json:
+    schema:
+      $ref: '../schemas/UploadRequest.yaml'
+    examples:
+      single_file:
+        summary: Single file upload request
+        description: Request upload methods for a single file
+        value:
+          requests:
+            - name: "sample_data.vcf"
+              size: 1048576
+              mime_type: "text/plain"
+              checksums:
+                - checksum: "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"
+                  type: "sha-256"
+              description: "Variant call format file for sample analysis"
+              aliases:
+                - "sample_001_variants"
+                - "vcf_batch_2024"
+          passports:
+            - "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJnYTRnaF9wYXNzcG9ydF92MSI6W119.JJ5rN0ktP0qwyZmIPpxmF_p7JsxAZH6L6brUxtad3CM"
+      multiple_files:
+        summary: Multiple files upload request
+        description: Request upload methods for multiple files with different types
+        value:
+          requests:
+            - name: "genome_assembly.fasta"
+              size: 3221225472
+              mime_type: "text/plain"
+              checksums:
+                - checksum: "a665a45920422f9d417e4867efdc4fb8a04a1f3fff1fa07e998e86f7f7a27ae3"
+                  type: "sha-256"
+                - checksum: "098f6bcd4621d373cade4e832627b4f6"
+                  type: "md5"
+              description: "Human genome reference assembly"
+              aliases:
+                - "hg38_reference"
+            - name: "annotations.gff3"
+              size: 524288000
+              mime_type: "text/plain"
+              checksums:
+                - checksum: "b94d27b9934d3e08a52e52d7da7dabfac484efe37a5380ee9088f7ace2efcde9"
+                  type: "sha-256"
+              description: "Gene annotations in GFF3 format"
+            - name: "metadata.json"
+              size: 2048
+              mime_type: "application/json"
+              checksums:
+                - checksum: "c89e4c5c7f2c8c8e8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c8c"
+                  type: "sha-256"
+              description: "Sample metadata and experimental conditions"
+      no_passports:
+        summary: Upload request without authentication
+        description: Request for public upload endpoints that don't require authentication
+        value:
+          requests:
+            - name: "public_dataset.csv"
+              size: 10240
+              mime_type: "text/csv"
+              checksums:
+                - checksum: "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35"
+                  type: "sha-256"
+              description: "Public research dataset"

openapi/components/responses/200AccessMethodUpdate.yaml

@@ -0,0 +1,7 @@
+description: >-
+  Access methods successfully updated. Returns the updated DRS object with new access methods
+  and updated timestamp.
+content:
+  application/json:
+    schema:
+      $ref: '../schemas/DrsObject.yaml'

openapi/components/responses/200BulkAccessMethodUpdate.yaml

@@ -0,0 +1,15 @@
+description: >-
+  Access methods successfully updated for all objects. Returns updated DRS objects with 
+  new access methods and updated timestamps.
+content:
+  application/json:
+    schema:
+      type: object
+      required:
+        - objects
+      properties:
+        objects:
+          type: array
+          items:
+            $ref: '../schemas/DrsObject.yaml'
+          description: Array of updated DRS objects