16139: Fix secondaryFile errors when running --submit --no-wait

[arvados.git] / sdk / cwl / arvados_cwl / executor.py

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 406ebfd2da064df383105b8e0a7c8f4e7b19a529..99d4c4e9a10a883abc54ce0fe1cbc476af7c7692 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -521,10 +521,10 @@ The 'jobs' API is no longer supported.
             for req in job_reqs:
                 tool.requirements.append(req)
 
-    def arv_executor(self, tool, job_order, runtimeContext, logger=None):
+    def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
         self.debug = runtimeContext.debug
 
-        tool.visit(self.check_features)
+        updated_tool.visit(self.check_features)
 
         self.project_uuid = runtimeContext.project_uuid
         self.pipeline = None
@@ -545,16 +545,20 @@ The 'jobs' API is no longer supported.
             raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api))
 
         if not runtimeContext.name:
-            runtimeContext.name = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
+            runtimeContext.name = self.name = updated_tool.tool.get("label") or updated_tool.metadata.get("label") or os.path.basename(updated_tool.tool["id"])
 
         # Upload local file references in the job order.
         job_order = upload_job_order(self, "%s input" % runtimeContext.name,
-                                     tool, job_order)
+                                     updated_tool, job_order)
+
+        # the last clause means: if it is a command line tool, and we
+        # are going to wait for the result, and always_submit_runner
+        # is false, then we don't submit a runner process.
 
         submitting = (runtimeContext.update_workflow or
                       runtimeContext.create_workflow or
                       (runtimeContext.submit and not
-                       (tool.tool["class"] == "CommandLineTool" and
+                       (updated_tool.tool["class"] == "CommandLineTool" and
                         runtimeContext.wait and
                         not runtimeContext.always_submit_runner)))
 
@@ -564,8 +568,11 @@ The 'jobs' API is no longer supported.
         if submitting:
             # Document may have been auto-updated. Reload the original
             # document with updating disabled because we want to
-            # submit the original document, not the auto-updated one.
-            tool = load_tool(tool.tool["id"], loadingContext)
+            # submit the document with its original CWL version, not
+            # the auto-updated one.
+            tool = load_tool(updated_tool.tool["id"], loadingContext)
+        else:
+            tool = updated_tool
 
         # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
         # Also uploads docker images.
@@ -632,22 +639,23 @@ The 'jobs' API is no longer supported.
         if runtimeContext.submit:
             # Submit a runner job to run the workflow for us.
             if self.work_api == "containers":
-                if tool.tool["class"] == "CommandLineTool" and runtimeContext.wait and (not runtimeContext.always_submit_runner):
-                    runtimeContext.runnerjob = tool.tool["id"]
+                if submitting:
+                    tool = RunnerContainer(self, updated_tool,
+                                           tool, loadingContext, runtimeContext.enable_reuse,
+                                           self.output_name,
+                                           self.output_tags,
+                                           submit_runner_ram=runtimeContext.submit_runner_ram,
+                                           name=runtimeContext.name,
+                                           on_error=runtimeContext.on_error,
+                                           submit_runner_image=runtimeContext.submit_runner_image,
+                                           intermediate_output_ttl=runtimeContext.intermediate_output_ttl,
+                                           merged_map=merged_map,
+                                           priority=runtimeContext.priority,
+                                           secret_store=self.secret_store,
+                                           collection_cache_size=runtimeContext.collection_cache_size,
+                                           collection_cache_is_default=self.should_estimate_cache_size)
                 else:
-                    tool = RunnerContainer(self, tool, loadingContext, runtimeContext.enable_reuse,
-                                                self.output_name,
-                                                self.output_tags,
-                                                submit_runner_ram=runtimeContext.submit_runner_ram,
-                                                name=runtimeContext.name,
-                                                on_error=runtimeContext.on_error,
-                                                submit_runner_image=runtimeContext.submit_runner_image,
-                                                intermediate_output_ttl=runtimeContext.intermediate_output_ttl,
-                                                merged_map=merged_map,
-                                                priority=runtimeContext.priority,
-                                                secret_store=self.secret_store,
-                                                collection_cache_size=runtimeContext.collection_cache_size,
-                                                collection_cache_is_default=self.should_estimate_cache_size)
+                    runtimeContext.runnerjob = tool.tool["id"]
 
         if runtimeContext.cwl_runner_job is not None:
             self.uuid = runtimeContext.cwl_runner_job.get('uuid')