Fix arvados-cwl-runner tests, refs #9766

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index a796b2abdf7ab4b7fbdd87ac16da7ce3498c13c2..e6d0cba65fa00b6c0a185861d3dde89db2c3e4e9 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -250,6 +250,7 @@ class RunnerTemplate(object):
     type_to_dataclass = {
         'boolean': 'boolean',
         'File': 'File',
+        'Directory': 'Collection',
         'float': 'number',
         'int': 'number',
         'string': 'text',
@@ -316,8 +317,8 @@ class RunnerTemplate(object):
                 pass
             elif not isinstance(value, dict):
                 param['value'] = value
-            elif param.get('dataclass') == 'File' and value.get('location'):
-                param['value'] = value['location']
+            elif param.get('dataclass') in ('File', 'Collection') and value.get('location'):
+                param['value'] = value['location'][5:]
 
             spec['script_parameters'][param_id] = param
         spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 37a054089f881c7097792940fd07478f65141f6d..8e45890a8d6226d9387524e1dc330effe900e163 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -25,7 +25,7 @@ def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
 
     name = os.path.basename(tool.tool["id"])
     upload_dependencies(arvRunner, name, document_loader,
-                        packed, uri, "keep:", False)
+                        packed, uri, False)
 
     body = {
         "workflow": {

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index b8d2a55fa8ce98033a6e12d4e0a9603c20692aee..200f95433b1127535a151726941b9b2179875ab8 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -85,7 +85,7 @@ def stubs(func):
             'script_parameters': {
                 'x': {
                     'basename': 'blorp.txt',
-                    'location': '99999999999999999999999999999994+99/blorp.txt',
+                    'location': 'keep:99999999999999999999999999999994+99/blorp.txt',
                     'class': 'File'
                 },
                 'cwl:tool':