Merge branch '10700-dispatch'

[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 6978b5469ab00b1096430667e5e35304d3aeb7a8..49047fa14328271106608721c9fa22099dfcb5ae 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -6,7 +6,7 @@ import json
 import re
 import subprocess
 
-from cStringIO import StringIO
+from StringIO import StringIO
 
 from schema_salad.sourceline import SourceLine
 
@@ -98,6 +98,10 @@ def upload_dependencies(arvrunner, name, document_loader,
     if include_primary and "id" in workflowobj:
         sc.append({"class": "File", "location": workflowobj["id"]})
 
+    if "$schemas" in workflowobj:
+        for s in workflowobj["$schemas"]:
+            sc.append({"class": "File", "location": s})
+
     mapper = ArvPathMapper(arvrunner, sc, "",
                            "keep:%s",
                            "keep:%s/%s",
@@ -109,11 +113,18 @@ def upload_dependencies(arvrunner, name, document_loader,
     adjustFileObjs(workflowobj, setloc)
     adjustDirObjs(workflowobj, setloc)
 
+    if "$schemas" in workflowobj:
+        sch = []
+        for s in workflowobj["$schemas"]:
+            sch.append(mapper.mapper(s).resolved)
+        workflowobj["$schemas"] = sch
+
     return mapper
 
 
 def upload_docker(arvrunner, tool):
-    """Visitor which uploads Docker images referenced in CommandLineTool objects."""
+    """Uploads Docker images used in CommandLineTool objects."""
+
     if isinstance(tool, CommandLineTool):
         (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
         if docker_req:
@@ -122,6 +133,9 @@ def upload_docker(arvrunner, tool):
                 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
                     "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 packed_workflow(arvrunner, tool):
     """Create a packed workflow.
@@ -179,7 +193,8 @@ def upload_job_order(arvrunner, name, tool, job_order):
 
 def upload_workflow_deps(arvrunner, tool):
     # Ensure that Docker images needed by this workflow are available
-    tool.visit(partial(upload_docker, arvrunner))
+
+    upload_docker(arvrunner, tool)
 
     document_loader = tool.doc_loader
 
@@ -205,6 +220,31 @@ def arvados_jobs_image(arvrunner, img):
         raise Exception("Docker image %s is not available\n%s" % (img, e) )
     return img
 
+def upload_workflow_collection(arvrunner, name, packed):
+    collection = arvados.collection.Collection(api_client=arvrunner.api,
+                                               keep_client=arvrunner.keep_client,
+                                               num_retries=arvrunner.num_retries)
+    with collection.open("workflow.cwl", "w") as f:
+        f.write(json.dumps(packed, indent=2, sort_keys=True, separators=(',',': ')))
+
+    filters = [["portable_data_hash", "=", collection.portable_data_hash()],
+               ["name", "like", name+"%"]]
+    if arvrunner.project_uuid:
+        filters.append(["owner_uuid", "=", arvrunner.project_uuid])
+    exists = arvrunner.api.collections().list(filters=filters).execute(num_retries=arvrunner.num_retries)
+
+    if exists["items"]:
+        logger.info("Using collection %s", exists["items"][0]["uuid"])
+    else:
+        collection.save_new(name=name,
+                            owner_uuid=arvrunner.project_uuid,
+                            ensure_unique_name=True,
+                            num_retries=arvrunner.num_retries)
+        logger.info("Uploaded to %s", collection.manifest_locator())
+
+    return collection.portable_data_hash()
+
+
 class Runner(object):
     """Base class for runner processes, which submit an instance of
     arvados-cwl-runner and wait for the final result."""