[ARVADOS] updated: c14246b9a21d038fc6fa850f4032659a98397784
Git user
git at public.curoverse.com
Tue Nov 15 15:00:13 EST 2016
Summary of changes:
.../app/controllers/application_controller.rb | 24 ++-
.../app/controllers/collections_controller.rb | 13 +-
.../app/controllers/projects_controller.rb | 23 ++-
.../controllers/work_unit_templates_controller.rb | 6 +-
.../app/controllers/work_units_controller.rb | 12 +-
apps/workbench/app/models/arvados_base.rb | 6 +-
.../app/views/projects/_show_workflows.html.erb | 5 +
.../test/controllers/disabled_api_test.rb | 63 ++++++++
apps/workbench/test/unit/disabled_api_test.rb | 15 ++
build/run-build-packages.sh | 4 +-
build/run-tests.sh | 8 +-
sdk/cli/bin/arv-run-pipeline-instance | 2 +
sdk/cwl/arvados_cwl/__init__.py | 36 ++++-
sdk/cwl/arvados_cwl/arvcontainer.py | 4 +-
sdk/cwl/arvados_cwl/arvjob.py | 2 +
sdk/cwl/arvados_cwl/arvworkflow.py | 2 +
sdk/cwl/arvados_cwl/pathmapper.py | 33 ++--
sdk/cwl/arvados_cwl/runner.py | 20 ++-
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/test_container.py | 23 ++-
sdk/cwl/tests/test_make_output.py | 11 +-
sdk/go/arvados/container.go | 38 +++--
.../arvados/v1/collections_controller.rb | 2 +-
services/api/app/models/container.rb | 11 +-
services/api/app/models/container_request.rb | 20 ++-
services/api/app/models/node.rb | 30 ++--
...43147_add_scheduling_parameters_to_container.rb | 6 +
services/api/db/structure.sql | 10 +-
services/api/test/fixtures/nodes.yml | 6 +-
.../arvados/v1/collections_controller_test.rb | 43 +++++
services/api/test/unit/container_request_test.rb | 32 ++++
services/api/test/unit/node_test.rb | 27 ++++
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 4 +-
.../crunch-dispatch-slurm_test.go | 2 +-
services/keepstore/azure_blob_volume.go | 22 ++-
services/keepstore/azure_blob_volume_test.go | 11 +-
services/keepstore/collision.go | 16 +-
services/keepstore/config.go | 9 ++
services/keepstore/config_test.go | 9 ++
services/keepstore/handler_test.go | 25 +--
services/keepstore/handlers.go | 87 ++++++++---
.../keepstore/handlers_with_generic_volume_test.go | 15 +-
services/keepstore/keepstore_test.go | 49 +++---
services/keepstore/pull_worker.go | 3 +-
services/keepstore/s3_volume.go | 174 ++++++++++++++++-----
services/keepstore/s3_volume_test.go | 9 +-
services/keepstore/trash_worker_test.go | 19 +--
services/keepstore/volume.go | 7 +-
services/keepstore/volume_generic_test.go | 87 ++++++-----
services/keepstore/volume_test.go | 7 +-
services/keepstore/volume_unix.go | 23 ++-
services/keepstore/volume_unix_test.go | 37 ++---
tools/keep-exercise/keep-exercise.go | 19 ++-
53 files changed, 854 insertions(+), 319 deletions(-)
create mode 100644 apps/workbench/app/views/projects/_show_workflows.html.erb
create mode 100644 apps/workbench/test/controllers/disabled_api_test.rb
create mode 100644 apps/workbench/test/unit/disabled_api_test.rb
create mode 100644 services/api/db/migrate/20161111143147_add_scheduling_parameters_to_container.rb
create mode 100644 services/keepstore/config_test.go
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commit c14246b9a21d038fc6fa850f4032659a98397784
Merge: 90c48f8 0201043
Author: Jiayong Li <jiayong at math.mit.edu>
Date: Tue Nov 15 14:59:55 2016 -0500
Merge master to output-tags branch and resolve conflict
diff --cc sdk/cwl/arvados_cwl/__init__.py
index 6778eb0,92be92d..b3d47dd
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@@ -235,14 -248,13 +249,20 @@@ class ArvCwlRunner(object)
final.api_response()["name"],
final.manifest_locator())
+ final_uuid = final.manifest_locator()
+ tags = tagsString.split(',')
+ for tag in tags:
+ self.api.links().create(body={
+ "head_uuid": final_uuid, "link_class": "tag", "name": tag
+ }).execute(num_retries=self.num_retries)
+
- self.final_output_collection = final
+ def finalcollection(fileobj):
+ fileobj["location"] = "keep:%s/%s" % (final.portable_data_hash(), fileobj["location"])
+
+ adjustDirObjs(outputObj, finalcollection)
+ adjustFileObjs(outputObj, finalcollection)
+
+ return (outputObj, final)
def set_crunch_output(self):
if self.work_api == "containers":
@@@ -398,9 -410,7 +418,9 @@@
else:
if self.output_name is None:
self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
- self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.final_output)
+ if self.output_tags is None:
+ self.output_tags = ""
- self.make_output_collection(self.output_name, self.output_tags, self.final_output)
++ self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.output_tags, self.final_output)
self.set_crunch_output()
if self.final_status != "success":
diff --cc sdk/cwl/tests/test_make_output.py
index a1cb605,3228ad7..53f379f
--- a/sdk/cwl/tests/test_make_output.py
+++ b/sdk/cwl/tests/test_make_output.py
@@@ -35,7 -32,7 +35,7 @@@ class TestMakeOutput(unittest.TestCase)
final.open.return_value = openmock
openmock.__enter__.return_value = cwlout
- runner.make_output_collection("Test output", "tag0,tag1,tag2", {
- _, runner.final_output_collection = runner.make_output_collection("Test output", {
++ _, runner.final_output_collection = runner.make_output_collection("Test output", "tag0,tag1,tag2", {
"foo": {
"class": "File",
"location": "keep:99999999999999999999999999999991+99/foo.txt",
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