X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e68177bfa8de36bd54f705e16e5c4854eafb29a2..3af6db5dc4e2f08b2ebb49a82109c4325ad7fcc4:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index e5b4e006e8..a1142544f5 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')
 
@@ -107,11 +110,55 @@ 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:
             upload_docker(arvrunner, s.embedded_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,
+                                             tool.tool,
+                                             tool.tool["id"],
+                                             True)
+        jobmapper = upload_dependencies(arvrunner,
+                                        os.path.basename(job_order.get("id", "#")),
+                                        tool.doc_loader,
+                                        job_order,
+                                        job_order.get("id", "#"),
+                                        False)
+
+        if "id" in job_order:
+            del job_order["id"]
+
+        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):
@@ -128,32 +175,11 @@ class Runner(object):
         pass
 
     def arvados_job_spec(self, *args, **kwargs):
-        upload_docker(self.arvrunner, self.tool)
-
         self.name = os.path.basename(self.tool.tool["id"])
-
-        workflowmapper = upload_dependencies(self.arvrunner,
-                                             self.name,
-                                             self.tool.doc_loader,
-                                             self.tool.tool,
-                                             self.tool.tool["id"],
-                                             True)
-
-        jobmapper = upload_dependencies(self.arvrunner,
-                                        os.path.basename(self.job_order.get("id", "#")),
-                                        self.tool.doc_loader,
-                                        self.job_order,
-                                        self.job_order.get("id", "#"),
-                                        False)
-
+        workflowmapper = upload_instance(self.arvrunner, self.name, self.tool, self.job_order)
         adjustDirObjs(self.job_order, trim_listing)
-
-        if "id" in self.job_order:
-            del self.job_order["id"]
-
         return workflowmapper
 
-
     def done(self, record):
         if record["state"] == "Complete":
             if record.get("exit_code") is not None: