19385: Fix tests because wrapper collection now includes original files

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

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 3703fc62173e42058b6032441c6e792b00518370..ceae0dc02e9fffd93bb55046bc6757b7804f9000 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -544,6 +544,8 @@ class RunnerContainer(Runner):
             container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
         else:
             main = self.loadingContext.loader.idx["_:main"]
+            if main.get("id") == "_:main":
+                del main["id"]
             #print(json.dumps(main, indent=2))
             workflowpath = "/var/lib/cwl/workflow.json#main"
             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 7b10c15af752ba895454fe9cbb85283f32294ba7..2bc823222441e6481296edaf0bb40cda7c7a6169 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -329,7 +329,7 @@ def new_upload_workflow(arvRunner, tool, job_order, project_uuid,
         update_refs(result, w, tool.doc_loader.expand_url, merged_map, jobmapper, set_block_style, runtimeContext, "", "")
 
         with col.open(w[n+1:], "wt") as f:
-            #print(yamlloader.dump(result, stream=sys.stdout))
+            # yamlloader.dump(result, stream=sys.stdout)
             yamlloader.dump(result, stream=f)
 
         with col.open(os.path.join("original", w[n+1:]), "wt") as f:

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 e43e1af0f3897e02f0d084334ef49cbfdb57e953..847c80945ebd61029b8d76251abb8e5c62714885 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:473135c3f4af514f85027e9e348cea45+179/collection_per_tool.cwl"
+                    "run": "keep:177002db236f41230905621862cc4230+367/collection_per_tool.cwl"
                 }
             ]
         }

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index bb0485d8b0685a9fd7f774340d939b971e1dd257..f828347019454ec758ef83f3e100952bc2c1e77f 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -70,7 +70,8 @@ def stubs(wfdetails=('submit_wf.cwl', None)):
             uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1",
                                  "df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3",
                                  "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5",
-                                 "df80736f-f14d-4b10-b2e3-03aa27f034b6"]
+                                 "df80736f-f14d-4b10-b2e3-03aa27f034b6", "df80736f-f14d-4b10-b2e3-03aa27f034b7",
+                                 "df80736f-f14d-4b10-b2e3-03aa27f034b8", "df80736f-f14d-4b10-b2e3-03aa27f034b9"]
 
             determine_image_id.return_value = None
 
@@ -403,7 +404,7 @@ class TestSubmit(unittest.TestCase):
                     "class": "http://arvados.org/cwl#WorkflowRunnerResources"
                 }
         ]
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:af64a47741bcc401f230eee99c6e80ff+137/wf/submit_wf_no_reuse.cwl"
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:fa5fbf21deb74f9f239daa3f5bb4b902+292/wf/submit_wf_no_reuse.cwl"
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
@@ -1023,7 +1024,7 @@ class TestSubmit(unittest.TestCase):
         #    "arv": "http://arvados.org/cwl#",
         #}
         expect_container["command"] = ["--collection-cache-size=512" if v == "--collection-cache-size=256" else v for v in expect_container["command"]]
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:10f1d17b8c4aad888e1dc2a93a95ceab+145/wf/submit_wf_runner_resources.cwl"
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:80b60e39456505b91d3989a1f5058b98+308/wf/submit_wf_runner_resources.cwl"
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
@@ -1180,7 +1181,7 @@ class TestSubmit(unittest.TestCase):
                                         "out": [
                                             {"id": "#main/step/out"}
                                         ],
-                                        "run": "keep:702edbfca88e907b62234556089dbce7+119/secret_wf.cwl"
+                                        "run": "keep:7628e49da34b93de9f4baf08a6212817+247/secret_wf.cwl"
                                     }
                                 ]
                             }
@@ -1423,7 +1424,7 @@ class TestSubmit(unittest.TestCase):
         #    "arv": "http://arvados.org/cwl#"
         #}
 
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:743a5bcaef0604899e4f4706ac525d83+147/wf/submit_wf_process_properties.cwl"
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:df44f9dd4b9467159f210f967e45417f+312/wf/submit_wf_process_properties.cwl"
 
         expect_container["properties"].update({
             "baz": "blorp.txt",

diff --git a/sdk/cwl/tests/wf/expect_upload_wrapper.cwl b/sdk/cwl/tests/wf/expect_upload_wrapper.cwl
index a7a30e68aff4b5edeca43e016586ba0fb7eb1f2f..05599b652d5df74a487e4a7875ff238fa6c3cc45 100644 (file)
--- a/sdk/cwl/tests/wf/expect_upload_wrapper.cwl
+++ b/sdk/cwl/tests/wf/expect_upload_wrapper.cwl
@@ -79,7 +79,7 @@
                     ],
                     "label": "submit_wf.cwl",
                     "out": [],
-                    "run": "keep:62bd293aa703ddb1897c94711dead399+128/wf/submit_wf.cwl"
+                    "run": "keep:5b4cf4181c65ad292ccba5b142d758a4+274/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 3edb66d66a6b9d89b0f87f4b0ced1f9887c62efb..63031110cd048e6321d43531241394f7269a281b 100644 (file)
--- a/sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl
+++ b/sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl
@@ -79,7 +79,7 @@
                     ],
                     "label": "testing 123",
                     "out": [],
-                    "run": "keep:62bd293aa703ddb1897c94711dead399+128/wf/submit_wf.cwl"
+                    "run": "keep:5b4cf4181c65ad292ccba5b142d758a4+274/wf/submit_wf.cwl"
                 }
             ]
         }

diff --git a/sdk/cwl/tests/wf/submit_wf_wrapper.cwl b/sdk/cwl/tests/wf/submit_wf_wrapper.cwl
index 53df05efc1abbc8bd0761eb085657e666a458f6f..3e015d65df426671909e3d74665532d93d579883 100644 (file)
--- a/sdk/cwl/tests/wf/submit_wf_wrapper.cwl
+++ b/sdk/cwl/tests/wf/submit_wf_wrapper.cwl
@@ -52,7 +52,7 @@
                     ],
                     "label": "submit_wf.cwl",
                     "out": [],
-                    "run": "keep:62bd293aa703ddb1897c94711dead399+128/wf/submit_wf.cwl"
+                    "run": "keep:5b4cf4181c65ad292ccba5b142d758a4+274/wf/submit_wf.cwl"
                 }
             ]
         }