X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b8de9b3e62e82b806576b237be5f317bf378169f..8de338d1178abb71addc344382657d3826d7f0bb:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index d3e0a0e107..69e4f5bd7b 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -3,7 +3,6 @@ import urlparse
 from functools import partial
 import logging
 import json
-import re
 import subprocess
 
 from StringIO import StringIO
@@ -24,26 +23,22 @@ import arvados.collection
 import ruamel.yaml as yaml
 
 from .arvdocker import arv_docker_get_image
-from .pathmapper import ArvPathMapper
+from .pathmapper import ArvPathMapper, trim_listing
 from ._version import __version__
 from . import done
 
 logger = logging.getLogger('arvados.cwl-runner')
 
-cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r".*")
+def trim_anonymous_location(obj):
+    """Remove 'location' field from File and Directory literals.
 
-def trim_listing(obj):
-    """Remove 'listing' field from Directory objects that are keep references.
+    To make internal handling easier, literals are assigned a random id for
+    'location'.  However, when writing the record back out, this can break
+    reproducibility.  Since it is valid for literals not have a 'location'
+    field, remove it.
 
-    When Directory objects represent Keep references, it redundant and
-    potentially very expensive to pass fully enumerated Directory objects
-    between instances of cwl-runner (e.g. a submitting a job, or using the
-    RunInSingleContainer feature), so delete the 'listing' field when it is
-    safe to do so.
     """
 
-    if obj.get("location", "").startswith("keep:") and "listing" in obj:
-        del obj["listing"]
     if obj.get("location", "").startswith("_:"):
         del obj["location"]
 
@@ -123,7 +118,8 @@ def upload_dependencies(arvrunner, name, document_loader,
 
 
 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:
@@ -132,6 +128,9 @@ 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.
@@ -189,7 +188,8 @@ 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
 
@@ -215,6 +215,31 @@ 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."""
@@ -238,7 +263,7 @@ class Runner(object):
         if submit_runner_ram:
             self.submit_runner_ram = submit_runner_ram
         else:
-            self.submit_runner_ram = 1024
+            self.submit_runner_ram = 3000
 
         if self.submit_runner_ram <= 0:
             raise Exception("Value of --submit-runner-ram must be greater than zero")