Merge master to output-tags branch and resolve conflict

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

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 2b5d186843fc8b3162ffaf0f21ad2b07b68dfb86..5cc447e9a3bad9202d9e77fb53919dcc66b804c8 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -9,9 +9,11 @@ from cStringIO import StringIO
 import cwltool.draft2tool
 from cwltool.draft2tool import CommandLineTool
 import cwltool.workflow
-from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs
+from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname
 from cwltool.load_tool import fetch_document
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.utils import aslist
+from cwltool.builder import substitute
 
 import arvados.collection
 import ruamel.yaml as yaml
@@ -108,6 +110,9 @@ def upload_docker(arvrunner, tool):
     if isinstance(tool, CommandLineTool):
         (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
         if docker_req:
+            if docker_req.get("dockerOutputDirectory"):
+                # TODO: can be supported by containers API, but not jobs API.
+                raise UnsupportedRequirement("Option 'dockerOutputDirectory' of DockerRequirement not supported.")
             arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid)
     elif isinstance(tool, cwltool.workflow.Workflow):
         for s in tool.steps:
@@ -116,6 +121,19 @@ def upload_docker(arvrunner, tool):
 def upload_instance(arvrunner, name, tool, job_order):
         upload_docker(arvrunner, tool)
 
+        for t in tool.tool["inputs"]:
+            def setSecondary(fileobj):
+                if isinstance(fileobj, dict) and fileobj.get("class") == "File":
+                    if "secondaryFiles" not in fileobj:
+                        fileobj["secondaryFiles"] = [{"location": substitute(fileobj["location"], sf), "class": "File"} for sf in t["secondaryFiles"]]
+
+                if isinstance(fileobj, list):
+                    for e in fileobj:
+                        setSecondary(e)
+
+            if shortname(t["id"]) in job_order and t.get("secondaryFiles"):
+                setSecondary(job_order[shortname(t["id"])])
+
         workflowmapper = upload_dependencies(arvrunner,
                                              name,
                                              tool.doc_loader,