X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d6e4e65cf3aae701c3e02a814329757e869a1d6d..5c274cd1249ce0f5e0048f8e0974e36deee8c9cc:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 6d382450e2..fd150d7457 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -9,15 +9,18 @@ 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
 
 from .arvdocker import arv_docker_get_image
 from .pathmapper import ArvPathMapper
+from ._version import __version__
 
 logger = logging.getLogger('arvados.cwl-runner')
 
@@ -115,13 +118,23 @@ 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 "__norecurse" in fileobj:
+                    del fileobj["__norecurse"]
+                    return
+                if "secondaryFiles" not in fileobj:
+                    fileobj["secondaryFiles"] = [{"location": substitute(fileobj["location"], sf), "class": "File", "__norecurse": True} for sf in t["secondaryFiles"]]
+
+            if shortname(t["id"]) in job_order and t.get("secondaryFiles"):
+                adjustFileObjs(job_order, setSecondary)
+
         workflowmapper = upload_dependencies(arvrunner,
                                              name,
                                              tool.doc_loader,
                                              tool.tool,
                                              tool.tool["id"],
                                              True)
-
         jobmapper = upload_dependencies(arvrunner,
                                         os.path.basename(job_order.get("id", "#")),
                                         tool.doc_loader,
@@ -134,6 +147,13 @@ def upload_instance(arvrunner, name, tool, job_order):
 
         return workflowmapper
 
+def arvados_jobs_image(arvrunner):
+    img = "arvados/jobs:"+__version__
+    try:
+        arv_docker_get_image(arvrunner.api, {"dockerPull": img}, True, arvrunner.project_uuid)
+    except Exception as e:
+        raise Exception("Docker image %s is not available\n%s" % (img, e) )
+    return img
 
 class Runner(object):
     def __init__(self, runner, tool, job_order, enable_reuse, output_name):