[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
not appeared on any other notification email; so we list those
revisions in full, below.
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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