Fix payload for adding file references (#128)

* Fix file reference payload

When adding file references via
the ingest API, the payload needs
to nest the file schema under a
"content" key.

* Update docker version for testing

* Update logging

* Update docker image versions

Author: samanehsan

adapter_pipelines/Optimus/adapter.wdl

@@ -139,7 +139,7 @@ workflow AdapterOptimus {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.48.0"
+  String pipeline_tools_version = "v0.48.1"
 
   call GetInputs as prep {
     input:

adapter_pipelines/cellranger/adapter.wdl

@@ -150,7 +150,7 @@ workflow Adapter10xCount {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.48.0"
+  String pipeline_tools_version = "v0.48.1"
 
   call GetInputs {
     input:

adapter_pipelines/ss2_single_sample/adapter.wdl

@@ -82,7 +82,7 @@ workflow AdapterSmartSeq2SingleCell{
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.48.0"
+  String pipeline_tools_version = "v0.48.1"
 
   call GetInputs as prep {
     input:

pipeline_tools/create_envelope.py

@@ -312,8 +312,13 @@ def add_file_reference(file_ref, file_refs_url, auth_headers, http_requests):
     Raises:
         requests.HTTPError: For 4xx errors or 5xx errors beyond timeout.
     """
-    print('Adding file: {0} to the file reference.'.format(file_ref['file_core']['file_name']))
-    response = http_requests.put(file_refs_url, headers=auth_headers, json=file_ref)
+    # Format payload for ingest file reference API endpoint
+    file_payload = {
+        'fileName': file_ref['file_core']['file_name'],
+        'content': file_ref
+    }
+    print('Adding file reference: {}'.format(file_payload))
+    response = http_requests.put(file_refs_url, headers=auth_headers, json=file_payload)
     return response.json()