[ARVADOS] updated: 1.1.3-261-g177a913

Git user git at public.curoverse.com
Mon Mar 19 14:40:35 EDT 2018


Summary of changes:
 .gitignore                                         |   1 +
 apps/workbench/Gemfile                             |  19 +-
 apps/workbench/Gemfile.lock                        | 270 ++++++++---------
 .../app/assets/javascripts/components/search.js    |  15 +-
 .../app/assets/javascripts/components/sessions.js  |  51 ++--
 .../workbench/app/assets/javascripts/filterable.js |  20 ++
 .../app/assets/javascripts/models/session_db.js    | 331 +++++++++++----------
 .../app/assets/javascripts/work_unit_log.js        |   2 +-
 .../app/assets/stylesheets/application.css.scss    |  22 +-
 .../app/controllers/work_units_controller.rb       |  19 +-
 apps/workbench/app/models/container_work_unit.rb   |   2 +-
 .../app/models/pipeline_instance_work_unit.rb      |  18 ++
 apps/workbench/app/models/proxy_work_unit.rb       |   4 +-
 .../_show_object_description_cell.html.erb         |   2 +-
 .../views/container_requests/_state_label.html.erb |   8 +
 apps/workbench/app/views/jobs/_show_log.html.erb   |   4 +-
 apps/workbench/app/views/layouts/body.html.erb     |   9 +-
 .../_show_components_running.html.erb              |   2 +
 .../views/pipeline_instances/_show_log.html.erb    |   4 +-
 apps/workbench/app/views/search/index.html         |   7 -
 apps/workbench/app/views/sessions/index.html       |   7 -
 .../views/work_units/_show_all_processes.html.erb  |  28 +-
 .../app/views/work_units/_show_log.html.erb        |   4 +-
 apps/workbench/config/application.default.yml      |   2 +-
 apps/workbench/config/initializers/mime_types.rb   |   1 +
 .../container_requests_controller_test.rb          |   4 +-
 .../test/controllers/disabled_api_test.rb          |   3 +
 .../controllers/healthcheck_controller_test.rb     |   3 +
 .../test/controllers/work_units_controller_test.rb |   2 +-
 .../test/integration/pipeline_instances_test.rb    |  30 +-
 apps/workbench/test/integration/work_units_test.rb |  46 ++-
 apps/workbench/test/test_helper.rb                 |   6 +-
 apps/workbench/test/unit/work_unit_test.rb         |   1 +
 build/build.list                                   |   6 +-
 build/libcloud-pin.sh                              |   2 +-
 .../package-testing/test-package-python-cwltest.sh |   1 +
 .../test-package-python27-python-cwltest.sh        |   4 +-
 build/package-testing/test-packages-debian9.sh     |  41 +--
 build/run-build-packages.sh                        |  19 +-
 build/run-library.sh                               |   3 +
 build/run-tests.sh                                 |  80 +++--
 doc/Rakefile                                       |  17 +-
 doc/_config.yml                                    |   3 +
 doc/_includes/_mount_types.liquid                  |   2 +-
 doc/_includes/_tutorial_expectations.liquid        |   2 +-
 .../install-compute-node.html.textile.liquid       |   2 +-
 .../install-dispatch.html.textile.liquid           |  45 +--
 doc/install/migrate-docker19.html.textile.liquid   |   2 +-
 .../index.html.textile.liquid}                     |   4 +-
 doc/sdk/index.html.textile.liquid                  |   1 +
 doc/sdk/python/arvados-fuse.html.textile.liquid    |  64 ++++
 doc/user/cwl/cwl-extensions.html.textile.liquid    |  10 +
 .../tutorial-keep-mount.html.textile.liquid        |   2 +-
 {services/ws => lib/dispatchcloud}/gocheck_test.go |   5 +-
 lib/dispatchcloud/node_size.go                     | 117 ++++++++
 lib/dispatchcloud/node_size_test.go                |  93 ++++++
 sdk/R/.Rbuildignore                                |   2 +
 sdk/R/DESCRIPTION                                  |   2 +-
 sdk/R/NAMESPACE                                    |   8 +-
 sdk/R/R/Arvados.R                                  |  75 ++++-
 sdk/R/R/ArvadosFile.R                              |  68 ++++-
 sdk/R/R/Collection.R                               |  58 +++-
 sdk/R/R/CollectionTree.R                           |   5 -
 sdk/R/R/HttpParser.R                               |   2 -
 sdk/R/R/Subcollection.R                            |  61 +++-
 sdk/R/README                                       | 251 ----------------
 sdk/R/README.Rmd                                   | 298 +++++++++++++++++++
 sdk/R/install_deps.R                               |  18 ++
 sdk/R/man/Arvados.Rd                               |  63 +++-
 sdk/R/man/ArvadosFile.Rd                           |  58 +++-
 sdk/R/man/Collection.Rd                            |  52 +++-
 sdk/R/man/CollectionTree.Rd                        |  17 --
 sdk/R/man/HttpParser.Rd                            |  14 -
 sdk/R/man/Subcollection.Rd                         |  49 ++-
 sdk/R/man/print.Arvados.Rd                         |  16 +
 sdk/R/man/print.ArvadosFile.Rd                     |  16 +
 sdk/R/man/print.Collection.Rd                      |  16 +
 sdk/R/man/print.Subcollection.Rd                   |  16 +
 sdk/cwl/arvados_cwl/__init__.py                    |  37 ++-
 sdk/cwl/arvados_cwl/arv-cwl-schema.yml             |  20 ++
 sdk/cwl/arvados_cwl/arvcontainer.py                |  47 ++-
 sdk/cwl/arvados_cwl/arvdocker.py                   |   2 +-
 sdk/cwl/arvados_cwl/arvjob.py                      |   2 +-
 sdk/cwl/arvados_cwl/arvtool.py                     |   2 +-
 sdk/cwl/arvados_cwl/arvworkflow.py                 |  68 +++++
 sdk/cwl/arvados_cwl/crunch_script.py               |   1 +
 sdk/cwl/arvados_cwl/fsaccess.py                    |   4 +-
 sdk/cwl/arvados_cwl/runner.py                      |   8 +-
 sdk/cwl/setup.py                                   |   2 +-
 sdk/cwl/tests/arvados-tests.yml                    |  12 +
 sdk/cwl/tests/secret_test_job.yml                  |   1 +
 sdk/cwl/tests/test_container.py                    | 150 ++++++++--
 sdk/cwl/tests/test_job.py                          |  81 ++++-
 sdk/cwl/tests/test_submit.py                       | 249 ++++++++++++++--
 sdk/cwl/tests/wf/echo-subwf.cwl                    |  19 ++
 sdk/cwl/tests/{secondary/wf.cwl => wf/echo-wf.cwl} |  21 +-
 sdk/cwl/tests/wf/echo_a.cwl                        |  11 +
 sdk/cwl/tests/wf/echo_b.cwl                        |  11 +
 sdk/cwl/tests/wf/secret_job.cwl                    |  20 ++
 sdk/cwl/tests/wf/secret_wf.cwl                     |  21 ++
 sdk/go/arvados/config.go                           |  14 +
 sdk/go/arvados/container.go                        |   9 +-
 sdk/go/arvados/fs_collection_test.go               |   2 +-
 sdk/go/httpserver/logger.go                        |  29 +-
 sdk/go/httpserver/responsewriter.go                |   7 +
 sdk/python/arvados/__init__.py                     |   6 +-
 sdk/python/arvados/arvfile.py                      |   3 +
 sdk/python/arvados/collection.py                   |  10 +-
 sdk/python/arvados/commands/migrate19.py           |   2 +-
 sdk/python/arvados/commands/put.py                 |  24 +-
 sdk/python/arvados/keep.py                         | 180 +++++------
 sdk/python/tests/test_arv_put.py                   |  63 +++-
 sdk/python/tests/test_keep_client.py               |  28 +-
 sdk/ruby/arvados.gemspec                           |   3 +-
 services/api/Gemfile                               |  10 +-
 services/api/Gemfile.lock                          | 205 ++++++-------
 .../api/app/controllers/application_controller.rb  |   7 +-
 .../arvados/v1/container_requests_controller.rb    |   1 +
 .../arvados/v1/containers_controller.rb            |  10 +
 .../app/controllers/arvados/v1/nodes_controller.rb |  33 +-
 .../controllers/arvados/v1/schema_controller.rb    |   2 +-
 services/api/app/models/arvados_model.rb           |  87 +++---
 services/api/app/models/blob.rb                    |   6 +-
 services/api/app/models/collection.rb              |  47 ++-
 services/api/app/models/commit.rb                  |   4 +-
 services/api/app/models/container.rb               |  91 ++++--
 services/api/app/models/container_request.rb       |  50 +++-
 services/api/app/models/job.rb                     |   2 +-
 services/api/app/models/node.rb                    |  44 +--
 services/api/config/initializers/lograge.rb        |  12 +
 services/api/config/routes.rb                      |   1 +
 ...216203422_add_storage_classes_to_collections.rb |  17 ++
 ...180228220311_add_secret_mounts_to_containers.rb |   8 +
 ...80313180114_change_container_priority_bigint.rb |   5 +
 services/api/db/structure.sql                      |  27 +-
 .../request_error.rb}                              |   2 +-
 services/api/test/fixtures/collections.yml         |  42 +++
 services/api/test/fixtures/containers.yml          |  27 ++
 services/api/test/fixtures/pipeline_instances.yml  |   2 +
 .../v1/container_requests_controller_test.rb       |  74 ++++-
 .../arvados/v1/containers_controller_test.rb       |  22 +-
 .../api/test/functional/arvados/v1/filters_test.rb |  38 ++-
 .../functional/arvados/v1/nodes_controller_test.rb |  42 +++
 services/api/test/helpers/container_test_helper.rb |  15 +
 services/api/test/unit/collection_test.rb          |  75 +++++
 services/api/test/unit/container_request_test.rb   | 235 +++++++++++----
 services/api/test/unit/container_test.rb           |  30 +-
 .../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 238 ++++++++-------
 .../crunch-dispatch-slurm_test.go                  | 258 ++++++++--------
 services/crunch-dispatch-slurm/priority.go         |  56 ++++
 services/crunch-dispatch-slurm/priority_test.go    | 143 +++++++++
 services/crunch-dispatch-slurm/slurm.go            |  11 +-
 services/crunch-dispatch-slurm/squeue.go           | 132 ++++++--
 services/crunch-dispatch-slurm/squeue_test.go      | 168 +++++++++++
 services/crunch-dispatch-slurm/usage.go            |   3 +-
 services/crunch-run/crunchrun.go                   | 156 +++++++---
 services/crunch-run/crunchrun_test.go              | 161 +++++++++-
 services/crunch-run/logging_test.go                |   9 +-
 services/crunch-run/upload.go                      |   1 +
 services/crunch-run/upload_test.go                 |  27 +-
 services/fuse/arvados_fuse/__init__.py             |  27 +-
 services/fuse/arvados_fuse/fresh.py                |   4 +
 services/fuse/arvados_fuse/fusefile.py             |   4 +
 services/keepstore/azure_blob_volume.go            | 171 +++++++----
 services/keepstore/azure_blob_volume_test.go       |  22 +-
 services/keepstore/bufferpool.go                   |   2 -
 services/keepstore/bufferpool_test.go              |   3 +-
 services/keepstore/config.go                       | 105 +++++--
 services/keepstore/config_test.go                  |   3 +-
 services/keepstore/handlers.go                     |  50 ++--
 services/keepstore/keepstore.go                    |   7 +-
 services/keepstore/mounts_test.go                  |  75 ++++-
 services/keepstore/pull_worker.go                  |   2 -
 services/keepstore/s3_volume.go                    |   7 +-
 services/keepstore/s3_volume_test.go               |  14 +-
 services/keepstore/trash_worker.go                 |   1 -
 services/keepstore/volume.go                       |  31 +-
 services/keepstore/volume_test.go                  |   4 +
 services/keepstore/volume_unix.go                  |   8 +-
 services/keepstore/volume_unix_test.go             |  13 +
 .../arvnodeman/computenode/dispatch/__init__.py    |  25 +-
 .../arvnodeman/computenode/dispatch/slurm.py       |  56 ++--
 .../arvnodeman/computenode/driver/gce.py           |   4 +-
 services/nodemanager/arvnodeman/daemon.py          |   1 -
 services/nodemanager/arvnodeman/jobqueue.py        |  58 ++--
 services/nodemanager/arvnodeman/nodelist.py        |  33 +-
 services/nodemanager/setup.py                      |   7 +-
 services/nodemanager/tests/integration_test.py     |  22 +-
 .../nodemanager/tests/test_computenode_dispatch.py |  30 +-
 .../tests/test_computenode_dispatch_slurm.py       |  21 +-
 .../tests/test_computenode_driver_gce.py           |   2 +-
 services/nodemanager/tests/test_daemon.py          |   9 +-
 services/nodemanager/tests/test_jobqueue.py        |  20 +-
 services/nodemanager/tests/test_nodelist.py        |  24 +-
 services/nodemanager/tests/testutil.py             |   4 +-
 tools/arvbox/bin/arvbox                            |   9 +-
 tools/arvbox/lib/arvbox/docker/Dockerfile.base     |   2 +-
 tools/arvbox/lib/arvbox/docker/common.sh           |   1 +
 .../lib/arvbox/docker/service/doc/run-service      |   4 +
 .../arvbox/lib/arvbox/docker/service/workbench/run |   4 +-
 .../arvbox/docker/service/workbench/run-service    |   3 +-
 tools/sync-groups/sync-groups.go                   |   2 +-
 vendor/vendor.json                                 | 146 ++++++++-
 203 files changed, 5488 insertions(+), 1994 deletions(-)
 copy apps/workbench/app/views/{pipeline_instances => container_requests}/_show_object_description_cell.html.erb (64%)
 create mode 100644 apps/workbench/app/views/container_requests/_state_label.html.erb
 create mode 120000 build/package-testing/test-package-python-cwltest.sh
 copy tools/arvbox/lib/arvbox/docker/logger => build/package-testing/test-package-python27-python-cwltest.sh (74%)
 mode change 100755 => 120000 build/package-testing/test-packages-debian9.sh
 copy doc/sdk/{python/python.html.textile.liquid => R/index.html.textile.liquid} (86%)
 create mode 100644 doc/sdk/python/arvados-fuse.html.textile.liquid
 copy {services/ws => lib/dispatchcloud}/gocheck_test.go (70%)
 create mode 100644 lib/dispatchcloud/node_size.go
 create mode 100644 lib/dispatchcloud/node_size_test.go
 delete mode 100644 sdk/R/README
 create mode 100644 sdk/R/README.Rmd
 create mode 100644 sdk/R/install_deps.R
 delete mode 100644 sdk/R/man/CollectionTree.Rd
 delete mode 100644 sdk/R/man/HttpParser.Rd
 create mode 100644 sdk/R/man/print.Arvados.Rd
 create mode 100644 sdk/R/man/print.ArvadosFile.Rd
 create mode 100644 sdk/R/man/print.Collection.Rd
 create mode 100644 sdk/R/man/print.Subcollection.Rd
 create mode 100644 sdk/cwl/tests/secret_test_job.yml
 create mode 100644 sdk/cwl/tests/wf/echo-subwf.cwl
 copy sdk/cwl/tests/{secondary/wf.cwl => wf/echo-wf.cwl} (53%)
 create mode 100644 sdk/cwl/tests/wf/echo_a.cwl
 create mode 100644 sdk/cwl/tests/wf/echo_b.cwl
 create mode 100644 sdk/cwl/tests/wf/secret_job.cwl
 create mode 100644 sdk/cwl/tests/wf/secret_wf.cwl
 create mode 100644 services/api/db/migrate/20180216203422_add_storage_classes_to_collections.rb
 create mode 100644 services/api/db/migrate/20180228220311_add_secret_mounts_to_containers.rb
 create mode 100644 services/api/db/migrate/20180313180114_change_container_priority_bigint.rb
 copy services/api/{app/helpers/commit_ancestors_helper.rb => lib/request_error.rb} (74%)
 create mode 100644 services/api/test/helpers/container_test_helper.rb
 create mode 100644 services/crunch-dispatch-slurm/priority.go
 create mode 100644 services/crunch-dispatch-slurm/priority_test.go
 create mode 100644 services/crunch-dispatch-slurm/squeue_test.go

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Those revisions listed above that are new to this repository have
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commit 177a91367f6c547dce717736bae38170d3f0961f
Merge: 2c3b9be f7fe9cc
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date:   Mon Mar 19 14:39:16 2018 -0400

    12308: Merge branch 'master' into 12308-go-fuse
    
    Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>

diff --cc build/run-tests.sh
index fbb935a,b89c8d9..2f4c491
--- a/build/run-tests.sh
+++ b/build/run-tests.sh
@@@ -74,7 -74,7 +74,8 @@@ do
  lib/cli
  lib/cmd
  lib/crunchstat
+ lib/dispatchcloud
 +lib/mount
  services/api
  services/arv-git-httpd
  services/crunchstat
@@@ -884,7 -899,7 +900,8 @@@ gostuff=
      lib/cli
      lib/cmd
      lib/crunchstat
+     lib/dispatchcloud
 +    lib/mount
      sdk/go/arvados
      sdk/go/arvadosclient
      sdk/go/blockdigest
diff --cc vendor/vendor.json
index 1bff878,a4f750b..1189ca8
--- a/vendor/vendor.json
+++ b/vendor/vendor.json
@@@ -42,18 -84,12 +84,18 @@@
  			"revisionTime": "2018-01-08T08:51:32Z"
  		},
  		{
- 			"checksumSHA1": "pAu+do4x7E5SFLfIqJeGwhcOd6E=",
- 			"path": "github.com/curoverse/azure-sdk-for-go/storage",
- 			"revision": "1620af6b32398bfc91827ceae54a8cc1f55df04d",
- 			"revisionTime": "2016-12-14T20:08:43Z"
+ 			"checksumSHA1": "+TKtBzv23ywvmmqRiGEjUba4YmI=",
+ 			"path": "github.com/dgrijalva/jwt-go",
+ 			"revision": "dbeaa9332f19a944acb5736b4456cfcc02140e29",
+ 			"revisionTime": "2017-10-19T21:57:19Z"
  		},
  		{
 +			"checksumSHA1": "gMBls0ytB5wHvZizUQE8Eivv9WQ=",
 +			"path": "github.com/curoverse/cgofuse/fuse",
 +			"revision": "d08d9e36b4ca1364eb7a4eb9db0b7fa76c9250a2",
 +			"revisionTime": "2017-12-17T05:18:50Z"
 +		},
 +		{
  			"checksumSHA1": "Gj+xR1VgFKKmFXYOJMnAczC3Znk=",
  			"path": "github.com/docker/distribution/digestset",
  			"revision": "277ed486c948042cab91ad367c379524f3b25e18",

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