[ARVADOS] updated: 1.1.4-619-g080c940d7

Git user git at public.curoverse.com
Tue Jul 17 16:56:13 EDT 2018


Summary of changes:
 .licenseignore                                     |   10 +
 AUTHORS                                            |    1 +
 apps/workbench/.gitignore                          |    1 +
 apps/workbench/Gemfile                             |    6 +-
 apps/workbench/Gemfile.lock                        |  109 +-
 .../app/assets/javascripts/models/session_db.js    |   23 +-
 apps/workbench/app/controllers/users_controller.rb |    9 +-
 .../app/controllers/work_units_controller.rb       |   36 +-
 apps/workbench/app/helpers/application_helper.rb   |   13 +-
 apps/workbench/app/helpers/version_helper.rb       |    6 +
 apps/workbench/app/models/arvados_base.rb          |   21 +-
 apps/workbench/app/models/user.rb                  |   41 +
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 apps/workbench/app/views/layouts/body.html.erb     |    3 +-
 apps/workbench/app/views/tests/mithril.html        |    4 +
 apps/workbench/app/views/users/inactive.html.erb   |    5 +
 .../app/views/users/link_account.html.erb          |  112 +
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 apps/workbench/lib/app_version.rb                  |   15 +
 .../controllers/application_controller_test.rb     |    2 +-
 .../controllers/collections_controller_test.rb     |    2 +-
 .../test/controllers/projects_controller_test.rb   |    2 +-
 .../controllers/repositories_controller_test.rb    |    6 +-
 .../test/controllers/users_controller_test.rb      |    8 +-
 .../workbench/test/integration/collections_test.rb |    2 +-
 .../test/integration/link_account_test.rb          |  172 +
 apps/workbench/test/integration_helper.rb          |    2 +
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 build/build-dev-docker-jobs-image.sh               |    6 +-
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 cmd/arvados-client/cmd.go                          |   25 +-
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 ...ados-on-kubernetes-minikube.html.textile.liquid |   34 +
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 doc/install/cheat_sheet.html.textile.liquid        |    4 +-
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 .../configure-fs-storage.html.textile.liquid       |   56 +
 ...configure-s3-object-storage.html.textile.liquid |  112 +
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 doc/install/install-composer.html.textile.liquid   |   59 +
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 lib/controller/handler.go                          |  164 +
 lib/controller/handler_test.go                     |  130 +
 lib/dispatchcloud/node_size.go                     |   34 +-
 lib/dispatchcloud/node_size_test.go                |   76 +-
 lib/service/cmd.go                                 |  120 +
 sdk/R/NAMESPACE                                    |    3 +-
 sdk/R/R/Arvados.R                                  | 5870 +++++++++++++++++++-
 sdk/R/R/ArvadosFile.R                              |    4 +
 sdk/R/R/Collection.R                               |   67 +-
 sdk/R/R/CollectionTree.R                           |    4 +
 sdk/R/R/HttpParser.R                               |    4 +
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 sdk/R/R/RESTService.R                              |  173 +-
 sdk/R/R/Subcollection.R                            |    6 +-
 sdk/R/R/autoGenAPI.R                               |  575 ++
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 sdk/R/R/zzz.R                                      |   10 +
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 sdk/R/install_deps.R                               |   15 +-
 sdk/R/man/Arvados.Rd                               |  200 +-
 sdk/R/man/api_client_authorizations.create.Rd      |   20 +
 ...api_client_authorizations.create_system_auth.Rd |   20 +
 sdk/R/man/api_client_authorizations.current.Rd     |   14 +
 sdk/R/man/api_client_authorizations.delete.Rd      |   17 +
 sdk/R/man/api_client_authorizations.get.Rd         |   17 +
 sdk/R/man/api_client_authorizations.list.Rd        |   34 +
 sdk/R/man/api_client_authorizations.update.Rd      |   20 +
 sdk/R/man/api_clients.create.Rd                    |   20 +
 sdk/R/man/api_clients.delete.Rd                    |   17 +
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 sdk/R/man/api_clients.update.Rd                    |   20 +
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 sdk/cwl/tests/wf-defaults/wf3.cwl                  |   13 +
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 .../tests/{wf/echo-wf.cwl => wf-defaults/wf6.cwl}  |   15 +-
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 sdk/cwl/tests/wf/check_mem.py                      |    4 +
 sdk/cwl/tests/wf/echo-subwf.cwl                    |    4 +
 sdk/cwl/tests/wf/echo-wf.cwl                       |    4 +
 sdk/cwl/tests/wf/echo_a.cwl                        |    4 +
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 sdk/cwl/tests/wf/expect_packed.cwl                 |  128 +-
 sdk/cwl/tests/wf/runin-reqs-wf.cwl                 |    4 +-
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 sdk/cwl/tests/wf/secret_job.cwl                    |    4 +
 sdk/cwl/tests/wf/secret_wf.cwl                     |    4 +
 sdk/cwl/tests/wf/submit_wf_runner_resources.cwl    |   31 +
 sdk/go/arvados/byte_size.go                        |   91 +
 sdk/go/arvados/byte_size_test.go                   |   70 +
 sdk/go/arvados/client.go                           |   39 +-
 sdk/go/arvados/client_test.go                      |   17 +
 sdk/go/arvados/collection.go                       |   30 +-
 sdk/go/arvados/config.go                           |  114 +-
 sdk/go/arvados/config_test.go                      |   37 +
 sdk/go/arvados/container.go                        |    4 +-
 sdk/go/arvados/fs_backend.go                       |   29 +
 sdk/go/arvados/fs_base.go                          |  595 ++
 .../arvados/{collection_fs.go => fs_collection.go} |  790 +--
 ...collection_fs_test.go => fs_collection_test.go} |   12 +-
 sdk/go/arvados/fs_deferred.go                      |  103 +
 sdk/go/arvados/fs_filehandle.go                    |  112 +
 sdk/go/arvados/fs_getternode.go                    |   66 +
 sdk/go/arvados/fs_lookup.go                        |   73 +
 sdk/go/arvados/fs_project.go                       |  117 +
 sdk/go/arvados/fs_project_test.go                  |  201 +
 sdk/go/arvados/fs_site.go                          |  200 +
 sdk/go/arvados/fs_site_test.go                     |   99 +
 sdk/go/arvados/fs_users.go                         |   48 +
 sdk/go/arvados/group.go                            |   11 +-
 sdk/go/arvados/keep_service.go                     |    7 +
 sdk/go/arvados/keep_service_test.go                |   27 +
 sdk/go/arvadosclient/arvadosclient.go              |    6 +
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 sdk/go/keepclient/keepclient.go                    |   69 +-
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 sdk/python/arvados/__init__.py                     |    2 -
 sdk/python/arvados/api.py                          |    9 +-
 sdk/python/arvados/collection.py                   |   98 +-
 sdk/python/arvados/commands/_util.py               |   19 +
 sdk/python/arvados/commands/keepdocker.py          |  241 +-
 sdk/python/arvados/commands/put.py                 |   43 +-
 sdk/python/arvados/commands/run.py                 |   11 +-
 sdk/python/arvados/keep.py                         |   19 +-
 sdk/python/arvados/safeapi.py                      |   12 +-
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 sdk/python/tests/run_test_server.py                |  106 +-
 sdk/python/tests/test_arv_put.py                   |   17 +
 sdk/python/tests/test_collections.py               |   44 +-
 sdk/python/tests/test_keep_client.py               |   25 +
 sdk/ruby/arvados.gemspec                           |    4 +-
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 .../arvados/v1/containers_controller.rb            |    3 +-
 .../controllers/arvados/v1/schema_controller.rb    |    2 +
 .../app/controllers/arvados/v1/users_controller.rb |   58 +-
 .../app/controllers/user_sessions_controller.rb    |   14 +-
 .../api/app/models/api_client_authorization.rb     |    5 +-
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 services/api/app/models/container_request.rb       |   50 +-
 services/api/app/models/group.rb                   |    3 +
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 .../20170706141334_json_collection_properties.rb   |    4 +
 .../20171027183824_add_index_to_containers.rb      |    4 +
 .../20171208203841_fix_trash_flag_follow.rb        |    4 +
 ...53352_add_gin_index_to_collection_properties.rb |    4 +
 ...180228220311_add_secret_mounts_to_containers.rb |    4 +
 ...80313180114_change_container_priority_bigint.rb |    4 +
 ...501182859_add_redirect_to_user_uuid_to_users.rb |   19 +
 ...20180514135529_add_container_auth_uuid_index.rb |    9 +
 .../migrate/20180607175050_properties_to_jsonb.rb  |   32 +
 .../20180608123145_add_properties_to_groups.rb     |   18 +
 services/api/db/structure.sql                      |   69 +-
 services/api/lib/app_version.rb                    |   15 +
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 services/api/lib/update_priority.rb                |   57 +
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 .../test/fixtures/api_client_authorizations.yml    |    7 +
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 .../arvados/v1/schema_controller_test.rb           |   14 +-
 .../functional/arvados/v1/users_controller_test.rb |  119 +-
 services/api/test/integration/remote_user_test.rb  |   33 +
 .../api/test/integration/user_sessions_test.rb     |   21 +-
 services/api/test/integration/users_test.rb        |   35 +
 services/api/test/unit/arvados_model_test.rb       |    2 +-
 services/api/test/unit/container_request_test.rb   |  127 +-
 services/api/test/unit/update_priority_test.rb     |   30 +
 services/api/test/unit/user_test.rb                |    4 +-
 .../crunch-dispatch-slurm/crunch-dispatch-slurm.go |   51 +-
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 .../crunch-dispatch-slurm_test.go                  |   36 +-
 services/crunch-dispatch-slurm/squeue.go           |    9 +-
 services/crunch-run/copier.go                      |  357 ++
 services/crunch-run/copier_test.go                 |  222 +
 services/crunch-run/crunchrun.go                   |  589 +-
 services/crunch-run/crunchrun_test.go              |  341 +-
 services/crunch-run/git_mount.go                   |    4 +
 services/crunch-run/logging_test.go                |   47 +-
 services/crunch-run/upload.go                      |  342 --
 services/crunch-run/upload_test.go                 |  189 -
 services/fuse/arvados_fuse/fusedir.py              |   25 +-
 services/fuse/setup.py                             |    5 +-
 services/fuse/tests/test_mount.py                  |   17 +-
 services/health/main.go                            |    6 +-
 services/keep-balance/balance.go                   |  679 ++-
 services/keep-balance/balance_run_test.go          |   12 +-
 services/keep-balance/balance_test.go              |  408 +-
 services/keep-balance/block_state.go               |   38 +-
 services/keep-balance/change_set.go                |   20 +-
 services/keep-balance/change_set_test.go           |   11 +-
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 services/keep-web/cadaver_test.go                  |  147 +-
 services/keep-web/doc.go                           |   25 +-
 services/keep-web/handler.go                       |  181 +-
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 services/keep-web/main.go                          |    6 +-
 services/keep-web/server.go                        |    2 +-
 services/keep-web/server_test.go                   |    1 -
 services/keep-web/webdav.go                        |   21 +-
 services/keep-web/webdav_test.go                   |    4 +
 services/keepproxy/keepproxy.go                    |   26 +-
 services/keepproxy/keepproxy_test.go               |   46 +-
 services/keepproxy/proxy_client.go                 |    6 +-
 services/keepstore/azure_blob_volume.go            |   77 +-
 services/keepstore/azure_blob_volume_test.go       |   13 +-
 services/keepstore/config.go                       |    8 +-
 services/keepstore/handlers.go                     |    4 +-
 services/keepstore/keepstore.go                    |   18 +-
 services/keepstore/s3_volume.go                    |   84 +-
 services/keepstore/server.go                       |   78 +
 services/keepstore/server_test.go                  |   47 +
 services/keepstore/usage.go                        |   30 +
 services/keepstore/volume_unix.go                  |   51 +-
 services/login-sync/arvados-login-sync.gemspec     |    4 +-
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 services/login-sync/test/test_add_user.rb          |    7 +-
 .../nodemanager/arvnodeman/computenode/__init__.py |    2 +-
 .../arvnodeman/computenode/dispatch/__init__.py    |    7 +-
 .../arvnodeman/computenode/dispatch/slurm.py       |    2 +-
 .../arvnodeman/computenode/driver/__init__.py      |    2 +-
 .../arvnodeman/computenode/driver/azure.py         |    5 +-
 .../arvnodeman/computenode/driver/ec2.py           |    9 +
 .../arvnodeman/computenode/driver/gce.py           |   22 +-
 services/nodemanager/arvnodeman/config.py          |   46 +-
 services/nodemanager/arvnodeman/daemon.py          |    6 +-
 services/nodemanager/arvnodeman/jobqueue.py        |   36 +-
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 .../nodemanager/arvnodeman/test/fake_driver.py     |   19 +-
 services/nodemanager/doc/ec2.example.cfg           |   12 +
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 services/nodemanager/tests/fake_ec2.cfg.template   |    8 +-
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 .../tests/test_computenode_dispatch_slurm.py       |   20 +-
 .../nodemanager/tests/test_computenode_driver.py   |    2 +-
 .../tests/test_computenode_driver_azure.py         |   23 +-
 .../tests/test_computenode_driver_ec2.py           |   27 +-
 .../tests/test_computenode_driver_gce.py           |   11 +
 services/nodemanager/tests/test_config.py          |   24 +-
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 services/nodemanager/tests/test_failure.py         |    5 +-
 services/nodemanager/tests/test_jobqueue.py        |   12 +-
 services/nodemanager/tests/test_nodelist.py        |    5 +-
 services/nodemanager/tests/testutil.py             |    4 +-
 tools/arvbox/bin/arvbox                            |    2 +-
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 vendor/vendor.json                                 |   60 +
 582 files changed, 23626 insertions(+), 5488 deletions(-)
 create mode 100644 apps/workbench/app/views/users/link_account.html.erb
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 delete mode 120000 build/package-testing/test-packages-ubuntu1204.sh
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commit 080c940d7a8134a6e277a53b7e45eb27e2b2c87f
Merge: eef816fa8 42012c474
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Jul 17 16:55:52 2018 -0400

    Merge branch 'master' into 13804-no-shutdown-wanted-nodes
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --cc services/nodemanager/arvnodeman/daemon.py
index 8ca75a270,6e85b85ab..1edf4dc47
--- a/services/nodemanager/arvnodeman/daemon.py
+++ b/services/nodemanager/arvnodeman/daemon.py
@@@ -393,25 -390,22 +393,25 @@@ class NodeManagerDaemonActor(actor_clas
          nodes_wanted = self._nodes_wanted(cloud_size)
          if nodes_wanted < 1:
              return None
 -        arvados_node = self.arvados_nodes.find_stale_node(self.node_stale_after)
 -        self._logger.info("Want %i more %s nodes.  Booting a node.",
 -                          nodes_wanted, cloud_size.id)
 -        new_setup = self._node_setup.start(
 -            timer_actor=self._timer,
 -            arvados_client=self._new_arvados(),
 -            arvados_node=arvados_node,
 -            cloud_client=self._new_cloud(),
 -            cloud_size=self.server_calculator.find_size(cloud_size.id))
 -        self.booting[new_setup.actor_urn] = new_setup.proxy()
 -        self.sizes_booting[new_setup.actor_urn] = cloud_size
 -
 -        if arvados_node is not None:
 -            self.arvados_nodes[arvados_node['uuid']].assignment_time = (
 -                time.time())
 -        new_setup.tell_proxy().subscribe(self._later.node_setup_finished)
 +
 +        if not self.cancel_node_shutdown(cloud_size):
 +            arvados_node = self.arvados_nodes.find_stale_node(self.node_stale_after)
 +            self._logger.info("Want %i more %s nodes.  Booting a node.",
-                               nodes_wanted, cloud_size.name)
++                              nodes_wanted, cloud_size.id)
 +            new_setup = self._node_setup.start(
 +                timer_actor=self._timer,
 +                arvados_client=self._new_arvados(),
 +                arvados_node=arvados_node,
 +                cloud_client=self._new_cloud(),
 +                cloud_size=self.server_calculator.find_size(cloud_size.id))
 +            self.booting[new_setup.actor_urn] = new_setup.proxy()
 +            self.sizes_booting[new_setup.actor_urn] = cloud_size
 +
 +            if arvados_node is not None:
 +                self.arvados_nodes[arvados_node['uuid']].assignment_time = (
 +                    time.time())
 +            new_setup.tell_proxy().subscribe(self._later.node_setup_finished)
 +
          if nodes_wanted > 1:
              self._later.start_node(cloud_size)
  
diff --cc services/nodemanager/tests/integration_test.py
index 284b361ce,69a29019e..1ba2957ee
--- a/services/nodemanager/tests/integration_test.py
+++ b/services/nodemanager/tests/integration_test.py
@@@ -126,10 -115,8 +115,11 @@@ def node_shutdown(g)
      global compute_nodes
      if g.group(1) in compute_nodes:
          del compute_nodes[g.group(1)]
 -    return 0
 +        return 0
 +    else:
 +        return 1
 +
+ 
  def jobs_req(g):
      global all_jobs
      for k,v in all_jobs.items():
diff --cc services/nodemanager/tests/test_computenode_dispatch.py
index ee30502a1,778c9aeaf..aee3cbdac
--- a/services/nodemanager/tests/test_computenode_dispatch.py
+++ b/services/nodemanager/tests/test_computenode_dispatch.py
@@@ -424,8 -424,17 +424,17 @@@ class ComputeNodeMonitorActorTestCase(t
          self.make_actor()
          self.shutdowns._set_state(True, 600)
          self.assertEquals(self.node_actor.shutdown_eligible().get(self.TIMEOUT),
 -                          (False, "node state is ('unpaired', 'open', 'boot wait', 'idle exceeded')"))
 +                          (False, "node state is ('unpaired', 'open', 'boot wait', 'not idle')"))
  
+     def test_shutdown_when_invalid_cloud_node_size(self):
+         self.make_mocks(1)
+         self.cloud_mock.size.id = 'invalid'
+         self.cloud_mock.extra['arvados_node_size'] = 'stale.type'
+         self.make_actor()
+         self.shutdowns._set_state(True, 600)
+         self.assertEquals((True, "node's size tag 'stale.type' not recognizable"),
+                           self.node_actor.shutdown_eligible().get(self.TIMEOUT))
+ 
      def test_shutdown_without_arvados_node(self):
          self.make_actor(start_time=0)
          self.shutdowns._set_state(True, 600)

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