[ARVADOS] updated: 8539a6c20fecc7bed02f1c7f81d3d2a1c0974e1f

Git user git at public.curoverse.com
Mon Mar 21 17:06:07 EDT 2016


Summary of changes:
 Makefile                                           |  17 +
 backports/python-llfuse/fpm-info.sh                |   3 -
 build/create-plot-data-from-log.sh                 |  59 ++
 build/libcloud-pin                                 |   1 +
 build/package-build-dockerfiles/.gitignore         |   2 +
 build/package-build-dockerfiles/Makefile           |  29 +
 build/package-build-dockerfiles/README             |  13 +
 .../build-all-build-containers.sh                  |  16 +
 build/package-build-dockerfiles/centos6/Dockerfile |  31 +
 build/package-build-dockerfiles/debian7/Dockerfile |  19 +
 build/package-build-dockerfiles/debian8/Dockerfile |  19 +
 .../ubuntu1204/Dockerfile                          |  19 +
 .../ubuntu1404/Dockerfile                          |  19 +
 build/package-test-dockerfiles/centos6/Dockerfile  |  20 +
 .../centos6/localrepo.repo                         |   5 +
 build/package-test-dockerfiles/debian7/Dockerfile  |  14 +
 build/package-test-dockerfiles/debian8/Dockerfile  |  14 +
 .../package-test-dockerfiles/ubuntu1204/Dockerfile |  14 +
 .../package-test-dockerfiles/ubuntu1404/Dockerfile |  14 +
 build/package-testing/common-test-packages.sh      |  28 +
 build/package-testing/deb-common-test-packages.sh  |  37 +
 .../test-package-arvados-api-server.sh             |  20 +
 .../test-package-arvados-node-manager.sh           |   7 +
 .../test-package-arvados-sso-server.sh             | 172 +++++
 .../test-package-arvados-workbench.sh              |  20 +
 .../test-package-python27-python-arvados-fuse.sh   |   6 +
 ...ackage-python27-python-arvados-python-client.sh |   6 +
 build/package-testing/test-packages-centos6.sh     |  44 ++
 build/package-testing/test-packages-debian7.sh     |   1 +
 build/package-testing/test-packages-debian8.sh     |   1 +
 build/package-testing/test-packages-ubuntu1204.sh  |   1 +
 build/package-testing/test-packages-ubuntu1404.sh  |   1 +
 build/rails-package-scripts/README.md              |  14 +
 build/rails-package-scripts/arvados-api-server.sh  |  32 +
 build/rails-package-scripts/arvados-sso-server.sh  |   9 +
 build/rails-package-scripts/arvados-workbench.sh   |   7 +
 build/rails-package-scripts/postinst.sh            | 251 +++++++
 build/rails-package-scripts/postrm.sh              |  23 +
 build/rails-package-scripts/prerm.sh               |  22 +
 build/rails-package-scripts/step2.sh               |  28 +
 build/run-build-docker-images.sh                   | 167 +++++
 build/run-build-docker-jobs-image.sh               | 164 +++++
 build/run-build-packages-all-targets.sh            |  98 +++
 build/run-build-packages-one-target.sh             | 203 ++++++
 build/run-build-packages-sso.sh                    | 161 ++++
 build/run-build-packages.sh                        | 567 +++++++++++++++
 build/run-build-test-packages-one-target.sh        | 111 +++
 build/run-library.sh                               | 385 ++++++++++
 build/run-tests.sh                                 | 806 +++++++++++++++++++++
 crunch_scripts/cwl-runner                          |  12 +-
 docker/compute/Dockerfile                          |   2 +-
 docker/shell/Dockerfile                            |   2 +-
 sdk/cli/bin/crunch-job                             |   4 +-
 sdk/cwl/arvados_cwl/__init__.py                    | 112 ++-
 sdk/cwl/setup.py                                   |   2 +
 .../cwl/tests/__init__.py                          |   0
 sdk/cwl/tests/test_job.py                          |  81 +++
 sdk/go/httpserver/responsewriter.go                |   6 +-
 sdk/python/arvados/arvfile.py                      |   2 +
 sdk/python/arvados/commands/run.py                 |   7 +-
 sdk/python/tests/test_keep_client.py               |   1 +
 sdk/python/tests/test_stream.py                    |  13 +
 sdk/ruby/arvados.gemspec                           |   5 +-
 .../v1/api_client_authorizations_controller.rb     |  65 +-
 .../api/app/models/api_client_authorization.rb     |   5 +-
 .../api_client_authorizations_controller_test.rb   |  92 ++-
 .../arvados/v1/repositories_controller_test.rb     |  14 +-
 .../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 300 ++++++++
 .../crunch-dispatch-slurm_test.go}                 |  88 +--
 .../crunch-dispatch-slurm/crunch-finish-slurm.sh   |  20 +
 services/datamanager/collection/collection.go      |  14 +-
 services/dockercleaner/arvados_docker/cleaner.py   |   2 +-
 services/dockercleaner/tests/test_cleaner.py       |  16 +-
 services/keepstore/azure_blob_volume.go            |   6 +
 services/keepstore/keepstore.go                    |  37 +-
 services/keepstore/s3_volume.go                    |   7 +
 services/keepstore/volume.go                       |   4 +
 services/keepstore/volume_generic_test.go          | 181 ++++-
 services/keepstore/volume_test.go                  |   3 +
 services/keepstore/volume_unix.go                  | 106 ++-
 .../arvnodeman/computenode/dispatch/__init__.py    |   8 +-
 .../arvnodeman/computenode/driver/__init__.py      |  11 +-
 .../arvnodeman/computenode/driver/azure.py         |   6 +-
 .../arvnodeman/computenode/driver/ec2.py           |   4 +
 .../arvnodeman/computenode/driver/gce.py           |   4 +
 services/nodemanager/arvnodeman/daemon.py          |   6 +-
 .../nodemanager/tests/test_computenode_dispatch.py |   1 +
 .../tests/test_computenode_driver_azure.py         |  10 +
 services/nodemanager/tests/test_daemon.py          |   3 +-
 services/nodemanager/tests/testutil.py             |   2 +-
 90 files changed, 4800 insertions(+), 184 deletions(-)
 create mode 100644 Makefile
 create mode 100755 build/create-plot-data-from-log.sh
 create mode 100644 build/libcloud-pin
 create mode 100644 build/package-build-dockerfiles/.gitignore
 create mode 100644 build/package-build-dockerfiles/Makefile
 create mode 100644 build/package-build-dockerfiles/README
 create mode 100755 build/package-build-dockerfiles/build-all-build-containers.sh
 create mode 100644 build/package-build-dockerfiles/centos6/Dockerfile
 create mode 100644 build/package-build-dockerfiles/debian7/Dockerfile
 create mode 100644 build/package-build-dockerfiles/debian8/Dockerfile
 create mode 100644 build/package-build-dockerfiles/ubuntu1204/Dockerfile
 create mode 100644 build/package-build-dockerfiles/ubuntu1404/Dockerfile
 create mode 100644 build/package-test-dockerfiles/centos6/Dockerfile
 create mode 100644 build/package-test-dockerfiles/centos6/localrepo.repo
 create mode 100644 build/package-test-dockerfiles/debian7/Dockerfile
 create mode 100644 build/package-test-dockerfiles/debian8/Dockerfile
 create mode 100644 build/package-test-dockerfiles/ubuntu1204/Dockerfile
 create mode 100644 build/package-test-dockerfiles/ubuntu1404/Dockerfile
 create mode 100755 build/package-testing/common-test-packages.sh
 create mode 100755 build/package-testing/deb-common-test-packages.sh
 create mode 100755 build/package-testing/test-package-arvados-api-server.sh
 create mode 100755 build/package-testing/test-package-arvados-node-manager.sh
 create mode 100755 build/package-testing/test-package-arvados-sso-server.sh
 create mode 100755 build/package-testing/test-package-arvados-workbench.sh
 create mode 100755 build/package-testing/test-package-python27-python-arvados-fuse.sh
 create mode 100755 build/package-testing/test-package-python27-python-arvados-python-client.sh
 create mode 100755 build/package-testing/test-packages-centos6.sh
 create mode 120000 build/package-testing/test-packages-debian7.sh
 create mode 120000 build/package-testing/test-packages-debian8.sh
 create mode 120000 build/package-testing/test-packages-ubuntu1204.sh
 create mode 120000 build/package-testing/test-packages-ubuntu1404.sh
 create mode 100644 build/rails-package-scripts/README.md
 create mode 100644 build/rails-package-scripts/arvados-api-server.sh
 create mode 100644 build/rails-package-scripts/arvados-sso-server.sh
 create mode 100644 build/rails-package-scripts/arvados-workbench.sh
 create mode 100644 build/rails-package-scripts/postinst.sh
 create mode 100644 build/rails-package-scripts/postrm.sh
 create mode 100644 build/rails-package-scripts/prerm.sh
 create mode 100644 build/rails-package-scripts/step2.sh
 create mode 100755 build/run-build-docker-images.sh
 create mode 100755 build/run-build-docker-jobs-image.sh
 create mode 100755 build/run-build-packages-all-targets.sh
 create mode 100755 build/run-build-packages-one-target.sh
 create mode 100755 build/run-build-packages-sso.sh
 create mode 100755 build/run-build-packages.sh
 create mode 100755 build/run-build-test-packages-one-target.sh
 create mode 100755 build/run-library.sh
 create mode 100755 build/run-tests.sh
 copy apps/workbench/app/views/application/_breadcrumb_page_name.html.erb => sdk/cwl/tests/__init__.py (100%)
 create mode 100644 sdk/cwl/tests/test_job.py
 create mode 100644 services/crunch-dispatch-slurm/crunch-dispatch-slurm.go
 copy services/{crunch-dispatch-local/crunch-dispatch-local_test.go => crunch-dispatch-slurm/crunch-dispatch-slurm_test.go} (58%)
 create mode 100755 services/crunch-dispatch-slurm/crunch-finish-slurm.sh

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Those revisions listed above that are new to this repository have
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revisions in full, below.


commit 8539a6c20fecc7bed02f1c7f81d3d2a1c0974e1f
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Mar 21 17:05:08 2016 -0400

    8654: Job has uuid and state fields

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 05be46a..80995f3 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -37,7 +37,7 @@ try:
     np.enable_reuse = True
     np.submit = False
     np.debug = True
-    outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job=arvados.current_job())
+    outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]})
 
     files = {}
     def capture(path):

commit cb6d05e27e37f29ea99cf6e474ee09a1479252e1
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Mar 21 17:02:51 2016 -0400

    8654: Add args.debug = True to get backtraces on errors

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index fbcb873..05be46a 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -36,6 +36,7 @@ try:
     np.project_uuid = arvados.current_job()["owner_uuid"]
     np.enable_reuse = True
     np.submit = False
+    np.debug = True
     outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job=arvados.current_job())
 
     files = {}

commit 46f5721a767f8e012b3e3183412bb8f9c5ff0ac6
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Mar 21 17:01:15 2016 -0400

    8654: Set args.submit = False

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 7fb14ab..fbcb873 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -35,6 +35,7 @@ try:
     np = argparse.Namespace()
     np.project_uuid = arvados.current_job()["owner_uuid"]
     np.enable_reuse = True
+    np.submit = False
     outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job=arvados.current_job())
 
     files = {}

commit 8f46e1564dd7c4f42fdccc6e5c8222ce8955405e
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Mar 21 16:55:12 2016 -0400

    8654: Add runner job to pipeline instance.

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 2b52557..7fb14ab 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -35,7 +35,7 @@ try:
     np = argparse.Namespace()
     np.project_uuid = arvados.current_job()["owner_uuid"]
     np.enable_reuse = True
-    outputObj = runner.arvExecutor(t, job_order_object, "", np)
+    outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job=arvados.current_job())
 
     files = {}
     def capture(path):
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index d4c0b64..e170648 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -460,11 +460,15 @@ class ArvCwlRunner(object):
         if kwargs.get("conformance_test"):
             return cwltool.main.single_job_executor(tool, job_order, input_basedir, args, **kwargs)
         else:
+            components = {}
+            if "cwl_runner_job" in kwargs:
+                components[os.path.basename(tool.tool["id"])] = {"job": kwargs["cwl_runner_job"]}
+
             self.pipeline = self.api.pipeline_instances().create(
                 body={
                     "owner_uuid": self.project_uuid,
                     "name": shortname(tool.tool["id"]),
-                    "components": {},
+                    "components": components,
                     "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
 
             logger.info("Pipeline instance %s", self.pipeline["uuid"])

commit 76c7406f60319da7011ac9797ae32eb22f574d4c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Mar 21 16:46:26 2016 -0400

    8654: Update cwl:tool entry

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 003e418..2b52557 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -24,6 +24,8 @@ try:
         if arvados.util.keep_locator_pattern.match(v):
             return "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
 
+    job_order_object["cwl:tool"] = keeppath(job_order_object["cwl:tool"])
+
     adjustFiles(job_order_object, keeppath)
 
     runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))

commit 785a877a46f0c6580d46dac179ea2d4c4a6e7de3
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Mar 21 16:44:31 2016 -0400

    8654: Fix keeppath and add ensure_unique_name to upload.

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 81755b8..003e418 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -22,7 +22,7 @@ try:
 
     def keeppath(v):
         if arvados.util.keep_locator_pattern.match(v):
-            job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+            return "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
 
     adjustFiles(job_order_object, keeppath)
 
diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index 046f706..643d3f5 100644
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -151,7 +151,7 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPatter
         body = {"owner_uuid": project, "manifest_text": collection.manifest_text()}
         if name is not None:
             body["name"] = name
-        item = api.collections().create(body=body).execute()
+        item = api.collections().create(body=body, ensure_unique_name=True).execute()
         pdh = item["portable_data_hash"]
         logger.info("Uploaded to %s", item["uuid"])
 

commit 4fecea55bd6dd5befd82bf7ec5dd4fe93bd93cea
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Mar 21 16:24:06 2016 -0400

    8654: Scanning for and uploading dependencies for submit works.  Add test for
    --submit.  Fix cwl-runner to handle CWL File objects in script_parameters.

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index d042426..81755b8 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -20,10 +20,12 @@ try:
 
     print job_order_object
 
-    for k,v in job_order_object.items():
+    def keeppath(v):
         if arvados.util.keep_locator_pattern.match(v):
             job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
 
+    adjustFiles(job_order_object, keeppath)
+
     runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
 
     t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index c0adb33..d4c0b64 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -19,8 +19,9 @@ import logging
 import re
 import os
 import sys
+import functools
 
-from cwltool.process import get_feature
+from cwltool.process import get_feature, adjustFiles, scandeps
 from arvados.api import OrderedJsonModel
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -249,7 +250,7 @@ class ArvadosJob(object):
 
 class ArvPathMapper(cwltool.pathmapper.PathMapper):
     def __init__(self, arvrunner, referenced_files, basedir,
-                 collection_pattern, file_pattern, **kwargs):
+                 collection_pattern, file_pattern, name=None, **kwargs):
         self._pathmap = arvrunner.get_uploaded()
         uploadfiles = []
 
@@ -276,6 +277,7 @@ class ArvPathMapper(cwltool.pathmapper.PathMapper):
                                              dry_run=kwargs.get("dry_run"),
                                              num_retries=3,
                                              fnPattern=file_pattern,
+                                             name=name,
                                              project=arvrunner.project_uuid)
 
         for src, ab, st in uploadfiles:
@@ -368,22 +370,43 @@ class ArvCwlRunner(object):
         pass
 
     def submit(self, tool, job_order, input_basedir, args, **kwargs):
-        files = set()
-        def visitFiles(self, path):
+        workflowfiles = set()
+        jobfiles = set()
+        workflowfiles.add(tool.tool["id"])
+
+        def visitFiles(files, path):
             files.add(path)
+            return path
 
-        adjustFiles(process.scandeps("", tool.tool,
-                                     set(("run")),
-                                     set(("$schemas", "path"))),
-                    visitFiles)
-        adjustFiles(job_order, visitFiles)
+        document_loader, _, _ = cwltool.process.get_schema()
+        def loadref(b, u):
+            return document_loader.resolve_ref(u, base_url=b)[0]
 
-        mapper = ArvPathMapper(self, files, "",
-                               "$(task.keep)/%s",
-                               "$(task.keep)/%s/%s",
-                               **kwargs)
+        adjustFiles(scandeps("", tool.tool,
+                             set(("run",)),
+                             set(("$schemas", "path")),
+                             loadref),
+                    functools.partial(visitFiles, workflowfiles))
+        adjustFiles(job_order, functools.partial(visitFiles, jobfiles))
+
+        workflowmapper = ArvPathMapper(self, workflowfiles, "",
+                                       "%s",
+                                       "%s/%s",
+                                       name=os.path.basename(tool.tool["id"]),
+                                       **kwargs)
+
+        jobmapper = ArvPathMapper(self, jobfiles, "",
+                                  "%s",
+                                  "%s/%s",
+                                  name=os.path.basename(job_order.get("id", "#")),
+                                  **kwargs)
 
-        job_order = adjustFiles(job_order, lambda p: mapper.mapper(p))
+        adjustFiles(job_order, lambda p: jobmapper.mapper(p)[1])
+
+        if "id" in job_order:
+            del job_order["id"]
+
+        job_order["cwl:tool"] = workflowmapper.mapper(tool.tool["id"])[1]
 
         response = self.api.jobs().create(body={
             "script": "cwl-runner",
@@ -394,14 +417,18 @@ class ArvCwlRunner(object):
                 "docker_image": "arvados/jobs"
             }
         }, find_or_create=args.enable_reuse).execute(num_retries=self.num_retries)
-        print response["uuid"]
-        return None
+
+        logger.info("Submitted job %s", response["uuid"])
+
+        return
 
 
     def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
+        useruuid = self.api.users().current().execute()["uuid"]
+        self.project_uuid = args.project_uuid if args.project_uuid else useruuid
+
         if args.submit:
-            self.submit(tool, job_order, input_basedir, args, **kwargs)
-            return
+            return self.submit(tool, job_order, input_basedir, args, **kwargs)
 
         events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
 
@@ -430,9 +457,6 @@ class ArvCwlRunner(object):
         kwargs["outdir"] = "$(task.outdir)"
         kwargs["tmpdir"] = "$(task.tmpdir)"
 
-        useruuid = self.api.users().current().execute()["uuid"]
-        self.project_uuid = args.project_uuid if args.project_uuid else useruuid
-
         if kwargs.get("conformance_test"):
             return cwltool.main.single_job_executor(tool, job_order, input_basedir, args, **kwargs)
         else:
@@ -500,12 +524,20 @@ def main(args, stdout, stderr, api_client=None):
                         default=True, dest="enable_reuse",
                         help="")
     parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
-    parser.add_argument("--submit", type=str, help="Submit job and print job uuid.")
+    parser.add_argument("--submit", action="store_true", help="Submit job and print job uuid.",
+                        default=False)
 
     try:
-        runner = ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
+        if api_client is None:
+            api_client=arvados.api('v1', model=OrderedJsonModel())
+        runner = ArvCwlRunner(api_client)
     except Exception as e:
         logger.error(e)
         return 1
 
-    return cwltool.main.main(args, executor=runner.arvExecutor, makeTool=runner.arvMakeTool, parser=parser)
+    return cwltool.main.main(args,
+                             stdout=stdout,
+                             stderr=stderr,
+                             executor=runner.arvExecutor,
+                             makeTool=runner.arvMakeTool,
+                             parser=parser)
diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index ef39be8..046f706 100644
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -101,7 +101,7 @@ def statfile(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
 
     return prefix+fn
 
-def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)"):
+def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None):
     # Find the smallest path prefix that includes all the files that need to be uploaded.
     # This starts at the root and iteratively removes common parent directory prefixes
     # until all file pathes no longer have a common parent.
@@ -148,7 +148,10 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPatter
                 stream = sp[0]
                 collection.start_new_stream(stream)
             collection.write_file(f.fn, sp[1])
-        item = api.collections().create(body={"owner_uuid": project, "manifest_text": collection.manifest_text()}).execute()
+        body = {"owner_uuid": project, "manifest_text": collection.manifest_text()}
+        if name is not None:
+            body["name"] = name
+        item = api.collections().create(body=body).execute()
         pdh = item["portable_data_hash"]
         logger.info("Uploaded to %s", item["uuid"])
 

commit f04cfcce18c6e4bd1faf3140ccbc835328580024
Merge: 8e6e328 9c65985
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Mar 21 12:37:38 2016 -0400

    Merge branch 'master' into 8654-arv-jobs-cwl-runner

diff --cc sdk/cwl/arvados_cwl/__init__.py
index 480d18e,5ed83ab..c0adb33
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@@ -348,47 -360,11 +364,49 @@@ class ArvCwlRunner(object)
      def add_uploaded(self, src, pair):
          self.uploaded[src] = pair
  
 +    def upload_docker(self, tool):
 +        pass
 +
 +    def submit(self, tool, job_order, input_basedir, args, **kwargs):
 +        files = set()
 +        def visitFiles(self, path):
 +            files.add(path)
 +
 +        adjustFiles(process.scandeps("", tool.tool,
 +                                     set(("run")),
 +                                     set(("$schemas", "path"))),
 +                    visitFiles)
 +        adjustFiles(job_order, visitFiles)
 +
 +        mapper = ArvPathMapper(self, files, "",
 +                               "$(task.keep)/%s",
 +                               "$(task.keep)/%s/%s",
 +                               **kwargs)
 +
 +        job_order = adjustFiles(job_order, lambda p: mapper.mapper(p))
 +
 +        response = self.api.jobs().create(body={
 +            "script": "cwl-runner",
 +            "script_version": "8654-arv-jobs-cwl-runner",
 +            "repository": "arvados",
 +            "script_parameters": job_order,
 +            "runtime_constraints": {
 +                "docker_image": "arvados/jobs"
 +            }
 +        }, find_or_create=args.enable_reuse).execute(num_retries=self.num_retries)
 +        print response["uuid"]
 +        return None
 +
 +
      def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
 +        if args.submit:
 +            self.submit(tool, job_order, input_basedir, args, **kwargs)
 +            return
 +
          events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
  
+         self.debug = args.debug
+ 
          try:
              self.api.collections().get(uuid=crunchrunner_pdh).execute()
          except arvados.errors.ApiError as e:

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