X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/91dc5f1d7f5ad9eb2640f6089e2d0476cbf87c8e..2eaa77dc327c024f2faa3fbd322e7054454b6442:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 6d382450e2..3bbcb8b091 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')
 
@@ -107,6 +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:
@@ -115,13 +121,25 @@ 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,
                                              tool.tool,
                                              tool.tool["id"],
                                              True)
-
         jobmapper = upload_dependencies(arvrunner,
                                         os.path.basename(job_order.get("id", "#")),
                                         tool.doc_loader,
@@ -134,9 +152,16 @@ 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):
+    def __init__(self, runner, tool, job_order, enable_reuse, output_name, output_tags):
         self.arvrunner = runner
         self.tool = tool
         self.job_order = job_order
@@ -145,6 +170,7 @@ class Runner(object):
         self.uuid = None
         self.final_output = None
         self.output_name = output_name
+        self.output_tags = output_tags
 
     def update_pipeline_component(self, record):
         pass
@@ -169,7 +195,7 @@ class Runner(object):
         else:
             processStatus = "permanentFail"
 
-        outputs = None
+        outputs = {}
         try:
             try:
                 self.final_output = record["output"]
@@ -186,7 +212,7 @@ class Runner(object):
                 adjustFileObjs(outputs, keepify)
                 adjustDirObjs(outputs, keepify)
             except Exception as e:
-                logger.error("While getting final output object: %s", e)
+                logger.exception("While getting final output object: %s", e)
             self.arvrunner.output_callback(outputs, processStatus)
         finally:
             del self.arvrunner.processes[record["uuid"]]