[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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