13111: Add spying client for testing deferred loading.

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

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index d15acf767fc90cc3e594be1fca0e67ae96f034ec..e82fd9feef1f3d88c4068e7d0d6cbfee6232c3f2 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -22,7 +22,6 @@ from cwltool.errors import WorkflowException
 import cwltool.main
 import cwltool.workflow
 import cwltool.process
-import schema_salad
 from schema_salad.sourceline import SourceLine
 
 import arvados
@@ -111,8 +110,7 @@ class ArvCwlRunner(object):
         kwargs["fetcher_constructor"] = partial(CollectionFetcher,
                                                 api_client=self.api,
                                                 fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
-                                                num_retries=self.num_retries,
-                                                overrides=kwargs.get("override_tools"))
+                                                num_retries=self.num_retries)
         kwargs["resolver"] = partial(collectionResolver, self.api, num_retries=self.num_retries)
         if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
             return ArvadosCommandTool(self, toolpath_object, **kwargs)
@@ -367,8 +365,7 @@ class ArvCwlRunner(object):
 
         # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
         # Also uploads docker images.
-        override_tools = {}
-        upload_workflow_deps(self, tool, override_tools)
+        merged_map = upload_workflow_deps(self, tool)
 
         # Reload tool object which may have been updated by
         # upload_workflow_deps
@@ -376,8 +373,7 @@ class ArvCwlRunner(object):
                                   makeTool=self.arv_make_tool,
                                   loader=tool.doc_loader,
                                   avsc_names=tool.doc_schema,
-                                  metadata=tool.metadata,
-                                  override_tools=override_tools)
+                                  metadata=tool.metadata)
 
         # Upload local file references in the job order.
         job_order = upload_job_order(self, "%s input" % kwargs["name"],
@@ -391,7 +387,8 @@ class ArvCwlRunner(object):
                                       kwargs.get("enable_reuse"),
                                       uuid=existing_uuid,
                                       submit_runner_ram=kwargs.get("submit_runner_ram"),
-                                      name=kwargs["name"])
+                                      name=kwargs["name"],
+                                      merged_map=merged_map)
                 tmpl.save()
                 # cwltool.main will write our return value to stdout.
                 return (tmpl.uuid, "success")
@@ -400,7 +397,8 @@ class ArvCwlRunner(object):
                                         self.project_uuid,
                                         uuid=existing_uuid,
                                         submit_runner_ram=kwargs.get("submit_runner_ram"),
-                                        name=kwargs["name"]),
+                                        name=kwargs["name"],
+                                        merged_map=merged_map),
                         "success")
 
         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
@@ -438,7 +436,8 @@ class ArvCwlRunner(object):
                                                 name=kwargs.get("name"),
                                                 on_error=kwargs.get("on_error"),
                                                 submit_runner_image=kwargs.get("submit_runner_image"),
-                                                intermediate_output_ttl=kwargs.get("intermediate_output_ttl"))
+                                                intermediate_output_ttl=kwargs.get("intermediate_output_ttl"),
+                                                merged_map=merged_map)
             elif self.work_api == "jobs":
                 runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"),
                                       self.output_name,
@@ -446,7 +445,8 @@ class ArvCwlRunner(object):
                                       submit_runner_ram=kwargs.get("submit_runner_ram"),
                                       name=kwargs.get("name"),
                                       on_error=kwargs.get("on_error"),
-                                      submit_runner_image=kwargs.get("submit_runner_image"))
+                                      submit_runner_image=kwargs.get("submit_runner_image"),
+                                      merged_map=merged_map)
         elif "cwl_runner_job" not in kwargs and self.work_api == "jobs":
             # Create pipeline for local run
             self.pipeline = self.api.pipeline_instances().create(
@@ -554,7 +554,7 @@ def versionstring():
     arvpkg = pkg_resources.require("arvados-python-client")
     cwlpkg = pkg_resources.require("cwltool")
 
-    return "%s %s %s, %s %s, %s %s" % (sys.argv[0], __version__, arvcwlpkg[0].version,
+    return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
                                     "arvados-python-client", arvpkg[0].version,
                                     "cwltool", cwlpkg[0].version)