[ARVADOS] created: 1.3.0-1482-g03ac6650c

[Git user]

        at  03ac6650c846556e8607e5a3379d03b7d44e62f9 (commit)


commit 03ac6650c846556e8607e5a3379d03b7d44e62f9
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Aug 13 17:06:07 2019 -0400

    15361: Add tests for --create-workflow bugfixes
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 4c9838580..ccbce3ed3 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -336,4 +336,5 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
                              logger_handler=arvados.log_handler,
                              custom_schema_callback=add_arv_hints,
                              loadingContext=executor.loadingContext,
-                             runtimeContext=executor.runtimeContext)
+                             runtimeContext=executor.runtimeContext,
+                             input_required=not (arvargs.create_workflow or arvargs.update_workflow))
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index d215cba7f..d6ef665fb 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -1465,3 +1465,39 @@ class TestCreateWorkflow(unittest.TestCase):
         self.assertEqual(stubs.capture_stdout.getvalue(),
                          stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
+
+    @stubs
+    def test_create_with_imports(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+        exited = arvados_cwl.main(
+            ["--create-workflow", "--debug",
+             "--api=containers",
+             "--project-uuid", project_uuid,
+             "tests/wf/feddemo/feddemo.cwl"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+
+        stubs.api.pipeline_templates().create.refute_called()
+        stubs.api.container_requests().create.refute_called()
+
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_workflow_uuid + '\n')
+        self.assertEqual(exited, 0)
+
+    @stubs
+    def test_create_with_no_input(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+        exited = arvados_cwl.main(
+            ["--create-workflow", "--debug",
+             "--api=containers",
+             "--project-uuid", project_uuid,
+             "tests/wf/revsort/revsort.cwl"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+
+        stubs.api.pipeline_templates().create.refute_called()
+        stubs.api.container_requests().create.refute_called()
+
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_workflow_uuid + '\n')
+        self.assertEqual(exited, 0)

commit 3d9b68358f757f1d3c94a63b641522735c387074
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Aug 13 12:27:01 2019 -0400

    15361: handling imports wip
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 5e42df624..4ca010bab 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -334,7 +334,8 @@ def upload_dependencies(arvrunner, name, document_loader,
                                  builder_job_order,
                                  discovered)
 
-    visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
+    copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri)
+    visit_class(copied, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
 
     for d in list(discovered):
         # Only interested in discovered secondaryFiles which are local

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