19385: Fixing tests WIP

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index e151dbf7bb428683d329f2109f1ab5e7ced2a1ab..c3d8dc3aeb2d1e4177f17bbbb7fc90e363a1d29e 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -381,7 +381,7 @@ def main(args=sys.argv[1:],
         # unit tests.
         stdout = None
 
-    if arvargs.workflow.startswith("arvwf:") or workflow_uuid_pattern.match(arvargs.workflow):
+    if arvargs.workflow.startswith("arvwf:") or workflow_uuid_pattern.match(arvargs.workflow) or arvargs.workflow.startswith("keep:"):
         executor.loadingContext.do_validate = False
         executor.fast_submit = True
 

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 7e9840db6f4b007755703d3f0c84cc1d5f96a9d3..053983b0110abf328bc611ccfa250d8b0df54df0 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -36,7 +36,7 @@ import arvados_cwl.util
 from .arvcontainer import RunnerContainer, cleanup_name_for_collection
 from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder
 from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
-from .arvworkflow import ArvadosWorkflow, upload_workflow, new_upload_workflow
+from .arvworkflow import ArvadosWorkflow, upload_workflow, new_upload_workflow, make_workflow_record
 from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
 from .perf import Perf
 from .pathmapper import NoFollowPathMapper

diff --git a/sdk/cwl/tests/collection_per_tool/collection_per_tool.cwl b/sdk/cwl/tests/collection_per_tool/collection_per_tool.cwl
index f864f49206c4a891ed4cfe799d71b426d3cfce22..a7159e3f8a534047a2a60c38ad25a28a5958a067 100644 (file)
--- a/sdk/cwl/tests/collection_per_tool/collection_per_tool.cwl
+++ b/sdk/cwl/tests/collection_per_tool/collection_per_tool.cwl
@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 inputs: []
 outputs: []
@@ -14,4 +14,4 @@ steps:
   step2:
     in: []
     out: []
-    run: step2.cwl
\ No newline at end of file
+    run: step2.cwl

diff --git a/sdk/cwl/tests/collection_per_tool/collection_per_tool_wrapper.cwl b/sdk/cwl/tests/collection_per_tool/collection_per_tool_wrapper.cwl
index fda566c88016b4962ebada51c910ed95d8747bda..e43e1af0f3897e02f0d084334ef49cbfdb57e953 100644 (file)
--- a/sdk/cwl/tests/collection_per_tool/collection_per_tool_wrapper.cwl
+++ b/sdk/cwl/tests/collection_per_tool/collection_per_tool_wrapper.cwl
@@ -26,7 +26,7 @@
                     "in": [],
                     "label": "collection_per_tool.cwl",
                     "out": [],
-                    "run": "keep:92045991f69a417f2f26660db67911ef+61/workflow.json#main"
+                    "run": "keep:473135c3f4af514f85027e9e348cea45+179/collection_per_tool.cwl"
                 }
             ]
         }

diff --git a/sdk/cwl/tests/wf/expect_upload_wrapper.cwl b/sdk/cwl/tests/wf/expect_upload_wrapper.cwl
index 3821527bb2565b979668dc7be8b1e1113e1d9c93..a7a30e68aff4b5edeca43e016586ba0fb7eb1f2f 100644 (file)
--- a/sdk/cwl/tests/wf/expect_upload_wrapper.cwl
+++ b/sdk/cwl/tests/wf/expect_upload_wrapper.cwl
@@ -48,8 +48,7 @@
                                 "nameroot": "renamed",
                                 "size": 0
                             }
-                        ],
-                        "location": "_:df80736f-f14d-4b10-b2e3-03aa27f034b2"
+                        ]
                     },
                     "id": "#main/z",
                     "type": "Directory"
@@ -80,7 +79,7 @@
                     ],
                     "label": "submit_wf.cwl",
                     "out": [],
-                    "run": "keep:f1c2b0c514a5fb9b2a8b5b38a31bab66+61/workflow.json#main"
+                    "run": "keep:62bd293aa703ddb1897c94711dead399+128/wf/submit_wf.cwl"
                 }
             ]
         }

diff --git a/sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl b/sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl
index d486e5a76037904b0bfea1db7f7546271590219d..3edb66d66a6b9d89b0f87f4b0ced1f9887c62efb 100644 (file)
--- a/sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl
+++ b/sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl
@@ -48,8 +48,7 @@
                                 "nameroot": "renamed",
                                 "size": 0
                             }
-                        ],
-                        "location": "_:df80736f-f14d-4b10-b2e3-03aa27f034b2"
+                        ]
                     },
                     "id": "#main/z",
                     "type": "Directory"
@@ -80,7 +79,7 @@
                     ],
                     "label": "testing 123",
                     "out": [],
-                    "run": "keep:f1c2b0c514a5fb9b2a8b5b38a31bab66+61/workflow.json#main"
+                    "run": "keep:62bd293aa703ddb1897c94711dead399+128/wf/submit_wf.cwl"
                 }
             ]
         }