[ARVADOS] updated: 1.1.4-163-g2957b91

Git user git at public.curoverse.com
Thu Apr 26 13:15:01 EDT 2018


Summary of changes:
 .../app/assets/javascripts/models/session_db.js    |   23 +-
 build/build-dev-docker-jobs-image.sh               |    6 +-
 build/build.list                                   |   72 +-
 build/package-build-dockerfiles/Makefile           |    2 +-
 build/package-build-dockerfiles/centos7/Dockerfile |    2 +-
 build/package-build-dockerfiles/debian8/Dockerfile |    2 +-
 build/package-build-dockerfiles/debian9/Dockerfile |    2 +-
 .../ubuntu1404/Dockerfile                          |    4 +-
 .../ubuntu1604/Dockerfile                          |    2 +-
 .../package-test-dockerfiles/ubuntu1404/Dockerfile |    4 +-
 build/package-testing/test-packages-ubuntu1204.sh  |    1 -
 build/run-build-packages-one-target.sh             |    9 +-
 build/run-build-packages.sh                        |   52 -
 build/run-tests.sh                                 |   12 +-
 doc/Rakefile                                       |   56 +-
 doc/_config.yml                                    |    3 +-
 .../install-nodemanager.html.textile.liquid        |    8 +-
 doc/sdk/R/index.html.textile.liquid                |   15 -
 sdk/R/NAMESPACE                                    |    3 +-
 sdk/R/R/Arvados.R                                  | 5866 +++++++++++++++++++-
 sdk/R/R/Collection.R                               |   63 +-
 sdk/R/R/HttpRequest.R                              |   75 +-
 sdk/R/R/RESTService.R                              |  137 +-
 sdk/R/R/Subcollection.R                            |    2 +-
 sdk/R/R/autoGenAPI.R                               |  571 ++
 sdk/R/R/util.R                                     |   37 +-
 sdk/R/README.Rmd                                   |   46 +-
 sdk/R/createDoc.R                                  |   20 +
 sdk/R/install_deps.R                               |   11 +-
 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 +
 sdk/R/man/api_clients.get.Rd                       |   17 +
 sdk/R/man/api_clients.list.Rd                      |   34 +
 sdk/R/man/api_clients.update.Rd                    |   20 +
 sdk/R/man/authorized_keys.create.Rd                |   20 +
 sdk/R/man/authorized_keys.delete.Rd                |   17 +
 sdk/R/man/authorized_keys.get.Rd                   |   17 +
 sdk/R/man/authorized_keys.list.Rd                  |   34 +
 sdk/R/man/authorized_keys.update.Rd                |   20 +
 sdk/R/man/collections.create.Rd                    |   20 +
 sdk/R/man/collections.delete.Rd                    |   17 +
 sdk/R/man/collections.get.Rd                       |   17 +
 sdk/R/man/collections.list.Rd                      |   36 +
 sdk/R/man/collections.provenance.Rd                |   17 +
 sdk/R/man/collections.trash.Rd                     |   17 +
 sdk/R/man/collections.untrash.Rd                   |   17 +
 sdk/R/man/collections.update.Rd                    |   20 +
 sdk/R/man/collections.used_by.Rd                   |   17 +
 sdk/R/man/container_requests.create.Rd             |   20 +
 sdk/R/man/container_requests.delete.Rd             |   17 +
 sdk/R/man/container_requests.get.Rd                |   17 +
 sdk/R/man/container_requests.list.Rd               |   34 +
 sdk/R/man/container_requests.update.Rd             |   20 +
 sdk/R/man/containers.auth.Rd                       |   17 +
 sdk/R/man/containers.create.Rd                     |   20 +
 sdk/R/man/containers.current.Rd                    |   14 +
 sdk/R/man/containers.delete.Rd                     |   17 +
 sdk/R/man/containers.get.Rd                        |   17 +
 sdk/R/man/containers.list.Rd                       |   34 +
 sdk/R/man/containers.lock.Rd                       |   17 +
 sdk/R/man/containers.secret_mounts.Rd              |   17 +
 sdk/R/man/containers.unlock.Rd                     |   17 +
 sdk/R/man/containers.update.Rd                     |   20 +
 sdk/R/man/groups.contents.Rd                       |   38 +
 sdk/R/man/groups.create.Rd                         |   19 +
 sdk/R/man/groups.delete.Rd                         |   17 +
 sdk/R/man/groups.get.Rd                            |   17 +
 sdk/R/man/groups.list.Rd                           |   36 +
 sdk/R/man/groups.trash.Rd                          |   17 +
 sdk/R/man/groups.untrash.Rd                        |   17 +
 sdk/R/man/groups.update.Rd                         |   19 +
 sdk/R/man/humans.create.Rd                         |   19 +
 sdk/R/man/humans.delete.Rd                         |   17 +
 sdk/R/man/humans.get.Rd                            |   17 +
 sdk/R/man/humans.list.Rd                           |   34 +
 sdk/R/man/humans.update.Rd                         |   19 +
 sdk/R/man/job_tasks.create.Rd                      |   19 +
 sdk/R/man/job_tasks.delete.Rd                      |   17 +
 sdk/R/man/job_tasks.get.Rd                         |   17 +
 sdk/R/man/job_tasks.list.Rd                        |   34 +
 sdk/R/man/job_tasks.update.Rd                      |   19 +
 sdk/R/man/jobs.cancel.Rd                           |   17 +
 sdk/R/man/jobs.create.Rd                           |   29 +
 sdk/R/man/jobs.delete.Rd                           |   17 +
 sdk/R/man/jobs.get.Rd                              |   17 +
 sdk/R/man/jobs.list.Rd                             |   33 +
 sdk/R/man/jobs.lock.Rd                             |   17 +
 sdk/R/man/jobs.queue.Rd                            |   34 +
 sdk/R/man/jobs.queue_size.Rd                       |   14 +
 sdk/R/man/jobs.update.Rd                           |   19 +
 sdk/R/man/keep_disks.create.Rd                     |   20 +
 sdk/R/man/keep_disks.delete.Rd                     |   17 +
 sdk/R/man/keep_disks.get.Rd                        |   17 +
 sdk/R/man/keep_disks.list.Rd                       |   34 +
 sdk/R/man/keep_disks.ping.Rd                       |   31 +
 sdk/R/man/keep_disks.update.Rd                     |   20 +
 sdk/R/man/keep_services.accessible.Rd              |   14 +
 sdk/R/man/keep_services.create.Rd                  |   20 +
 sdk/R/man/keep_services.delete.Rd                  |   17 +
 sdk/R/man/keep_services.get.Rd                     |   17 +
 sdk/R/man/keep_services.list.Rd                    |   34 +
 sdk/R/man/keep_services.update.Rd                  |   20 +
 sdk/R/man/links.create.Rd                          |   19 +
 sdk/R/man/links.delete.Rd                          |   17 +
 sdk/R/man/links.get.Rd                             |   17 +
 sdk/R/man/links.get_permissions.Rd                 |   17 +
 sdk/R/man/links.list.Rd                            |   34 +
 sdk/R/man/links.update.Rd                          |   19 +
 sdk/R/man/listAll.Rd                               |   22 +
 sdk/R/man/logs.create.Rd                           |   19 +
 sdk/R/man/logs.delete.Rd                           |   17 +
 sdk/R/man/logs.get.Rd                              |   17 +
 sdk/R/man/logs.list.Rd                             |   33 +
 sdk/R/man/logs.update.Rd                           |   19 +
 sdk/R/man/nodes.create.Rd                          |   22 +
 sdk/R/man/nodes.delete.Rd                          |   17 +
 sdk/R/man/nodes.get.Rd                             |   17 +
 sdk/R/man/nodes.list.Rd                            |   34 +
 sdk/R/man/nodes.ping.Rd                            |   19 +
 sdk/R/man/nodes.update.Rd                          |   21 +
 sdk/R/man/pipeline_instances.cancel.Rd             |   17 +
 sdk/R/man/pipeline_instances.create.Rd             |   20 +
 sdk/R/man/pipeline_instances.delete.Rd             |   17 +
 sdk/R/man/pipeline_instances.get.Rd                |   17 +
 sdk/R/man/pipeline_instances.list.Rd               |   34 +
 sdk/R/man/pipeline_instances.update.Rd             |   20 +
 sdk/R/man/pipeline_templates.create.Rd             |   20 +
 sdk/R/man/pipeline_templates.delete.Rd             |   17 +
 sdk/R/man/pipeline_templates.get.Rd                |   17 +
 sdk/R/man/pipeline_templates.list.Rd               |   34 +
 sdk/R/man/pipeline_templates.update.Rd             |   20 +
 sdk/R/man/print.Arvados.Rd                         |   16 -
 sdk/R/man/projects.create.Rd                       |   19 +
 sdk/R/man/projects.delete.Rd                       |   17 +
 sdk/R/man/projects.get.Rd                          |   17 +
 sdk/R/man/projects.list.Rd                         |   38 +
 sdk/R/man/projects.update.Rd                       |   19 +
 sdk/R/man/repositories.create.Rd                   |   20 +
 sdk/R/man/repositories.delete.Rd                   |   17 +
 sdk/R/man/repositories.get.Rd                      |   17 +
 sdk/R/man/repositories.get_all_permissions.Rd      |   14 +
 sdk/R/man/repositories.list.Rd                     |   34 +
 sdk/R/man/repositories.update.Rd                   |   20 +
 sdk/R/man/specimens.create.Rd                      |   20 +
 sdk/R/man/specimens.delete.Rd                      |   17 +
 sdk/R/man/specimens.get.Rd                         |   17 +
 sdk/R/man/specimens.list.Rd                        |   34 +
 sdk/R/man/specimens.update.Rd                      |   20 +
 sdk/R/man/traits.create.Rd                         |   19 +
 sdk/R/man/traits.delete.Rd                         |   17 +
 sdk/R/man/traits.get.Rd                            |   17 +
 sdk/R/man/traits.list.Rd                           |   34 +
 sdk/R/man/traits.update.Rd                         |   19 +
 sdk/R/man/user_agreements.create.Rd                |   20 +
 sdk/R/man/user_agreements.delete.Rd                |   17 +
 sdk/R/man/user_agreements.get.Rd                   |   17 +
 sdk/R/man/user_agreements.list.Rd                  |   34 +
 sdk/R/man/user_agreements.new.Rd                   |   14 +
 sdk/R/man/user_agreements.sign.Rd                  |   14 +
 sdk/R/man/user_agreements.signatures.Rd            |   14 +
 sdk/R/man/user_agreements.update.Rd                |   20 +
 sdk/R/man/users.activate.Rd                        |   17 +
 sdk/R/man/users.create.Rd                          |   19 +
 sdk/R/man/users.current.Rd                         |   14 +
 sdk/R/man/users.delete.Rd                          |   17 +
 sdk/R/man/users.get.Rd                             |   17 +
 sdk/R/man/users.list.Rd                            |   34 +
 sdk/R/man/users.setup.Rd                           |   26 +
 sdk/R/man/users.system.Rd                          |   14 +
 sdk/R/man/users.unsetup.Rd                         |   17 +
 sdk/R/man/users.update.Rd                          |   19 +
 sdk/R/man/users.update_uuid.Rd                     |   19 +
 sdk/R/man/virtual_machines.create.Rd               |   20 +
 sdk/R/man/virtual_machines.delete.Rd               |   17 +
 sdk/R/man/virtual_machines.get.Rd                  |   17 +
 sdk/R/man/virtual_machines.get_all_logins.Rd       |   14 +
 sdk/R/man/virtual_machines.list.Rd                 |   34 +
 sdk/R/man/virtual_machines.logins.Rd               |   17 +
 sdk/R/man/virtual_machines.update.Rd               |   20 +
 sdk/R/man/workflows.create.Rd                      |   20 +
 sdk/R/man/workflows.delete.Rd                      |   17 +
 sdk/R/man/workflows.get.Rd                         |   17 +
 sdk/R/man/workflows.list.Rd                        |   34 +
 sdk/R/man/workflows.update.Rd                      |   20 +
 sdk/R/tests/testthat/test-Arvados.R                |  306 -
 sdk/R/tests/testthat/test-ArvadosFile.R            |    2 +-
 sdk/R/tests/testthat/test-HttpRequest.R            |   19 +-
 sdk/R/tests/testthat/test-RESTService.R            |  258 -
 sdk/R/tests/testthat/test-Subcollection.R          |    2 +-
 sdk/R/tests/testthat/test-util.R                   |   24 +
 sdk/cli/arvados-cli.gemspec                        |    4 +-
 sdk/cwl/arvados_cwl/__init__.py                    |  175 +-
 sdk/cwl/arvados_cwl/arvcontainer.py                |   36 +-
 sdk/cwl/arvados_cwl/arvdocker.py                   |    3 +-
 sdk/cwl/arvados_cwl/arvjob.py                      |   54 +-
 sdk/cwl/arvados_cwl/crunch_script.py               |    3 +-
 sdk/cwl/arvados_cwl/runner.py                      |    3 +-
 sdk/cwl/arvados_cwl/task_queue.py                  |   60 +
 sdk/cwl/setup.py                                   |    2 +-
 sdk/cwl/tests/arvados-tests.yml                    |    1 +
 sdk/cwl/tests/test_submit.py                       |   76 +-
 sdk/cwl/tests/test_tq.py                           |   50 +
 sdk/cwl/tests/wf/runin-reqs-wf.cwl                 |    4 +-
 sdk/cwl/tests/wf/runin-reqs-wf2.cwl                |    4 +-
 sdk/cwl/tests/wf/runin-reqs-wf3.cwl                |    4 +-
 sdk/cwl/tests/wf/runin-reqs-wf4.cwl                |    4 +-
 sdk/go/arvados/collection.go                       |    1 +
 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                    |  108 +
 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                     |   98 +
 sdk/go/arvados/fs_users.go                         |   48 +
 sdk/go/arvados/group.go                            |   11 +-
 sdk/go/arvadostest/fixtures.go                     |    4 +
 sdk/go/httpserver/responsewriter.go                |    3 +
 sdk/go/keepclient/discover_test.go                 |    5 +-
 sdk/go/keepclient/keepclient.go                    |   48 +-
 sdk/python/arvados/commands/_util.py               |   19 +
 sdk/python/arvados/commands/keepdocker.py          |  239 +-
 sdk/python/arvados/commands/put.py                 |   18 +-
 sdk/python/arvados/safeapi.py                      |    6 +-
 sdk/ruby/arvados.gemspec                           |    4 +-
 .../app/controllers/arvados/v1/users_controller.rb |    2 +-
 .../functional/arvados/v1/users_controller_test.rb |    2 +-
 .../crunch-dispatch-slurm.service                  |    1 +
 services/crunch-run/crunchrun_test.go              |    4 +
 services/fuse/arvados_fuse/fusedir.py              |   25 +-
 services/fuse/tests/test_mount.py                  |   17 +-
 services/keep-web/cadaver_test.go                  |  143 +-
 services/keep-web/doc.go                           |   25 +-
 services/keep-web/handler.go                       |  163 +-
 services/keep-web/handler_test.go                  |   93 +-
 services/keep-web/server_test.go                   |    1 -
 services/keep-web/webdav.go                        |   21 +-
 services/login-sync/arvados-login-sync.gemspec     |    4 +-
 services/login-sync/bin/arvados-login-sync         |   25 +-
 services/login-sync/test/test_add_user.rb          |    7 +-
 .../tests/test_computenode_dispatch_slurm.py       |   12 +
 tools/arvbox/bin/arvbox                            |    2 +-
 tools/arvbox/lib/arvbox/docker/Dockerfile.base     |    2 +-
 .../lib/arvbox/docker/service/sdk/run-service      |    2 +-
 257 files changed, 12945 insertions(+), 2173 deletions(-)
 delete mode 120000 build/package-testing/test-packages-ubuntu1204.sh
 delete mode 100644 doc/sdk/R/index.html.textile.liquid
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commit 2957b917aaaefc1485e1c5293d413f0931b3030a
Merge: 4d93904 6feade3
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date:   Thu Apr 26 13:14:38 2018 -0400

    12708: Merge branch 'master' into 12708-balance-storage-classes
    
    Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>

diff --cc sdk/go/arvados/collection.go
index 8a8330a,aea0cc0..79be2f3
--- a/sdk/go/arvados/collection.go
+++ b/sdk/go/arvados/collection.go
@@@ -15,22 -15,20 +15,23 @@@ import 
  
  // Collection is an arvados#collection resource.
  type Collection struct {
 -	UUID                   string     `json:"uuid,omitempty"`
 -	OwnerUUID              string     `json:"owner_uuid,omitempty"`
 -	TrashAt                *time.Time `json:"trash_at,omitempty"`
 -	ManifestText           string     `json:"manifest_text,omitempty"`
 -	UnsignedManifestText   string     `json:"unsigned_manifest_text,omitempty"`
 -	Name                   string     `json:"name,omitempty"`
 -	CreatedAt              *time.Time `json:"created_at,omitempty"`
 -	ModifiedAt             *time.Time `json:"modified_at,omitempty"`
 -	PortableDataHash       string     `json:"portable_data_hash,omitempty"`
 -	ReplicationConfirmed   *int       `json:"replication_confirmed,omitempty"`
 -	ReplicationConfirmedAt *time.Time `json:"replication_confirmed_at,omitempty"`
 -	ReplicationDesired     *int       `json:"replication_desired,omitempty"`
 -	DeleteAt               *time.Time `json:"delete_at,omitempty"`
 -	IsTrashed              bool       `json:"is_trashed,omitempty"`
 +	UUID                      string     `json:"uuid,omitempty"`
++	OwnerUUID                 string     `json:"owner_uuid,omitempty"`
 +	TrashAt                   *time.Time `json:"trash_at,omitempty"`
 +	ManifestText              string     `json:"manifest_text,omitempty"`
 +	UnsignedManifestText      string     `json:"unsigned_manifest_text,omitempty"`
 +	Name                      string     `json:"name,omitempty"`
 +	CreatedAt                 *time.Time `json:"created_at,omitempty"`
 +	ModifiedAt                *time.Time `json:"modified_at,omitempty"`
 +	PortableDataHash          string     `json:"portable_data_hash,omitempty"`
 +	ReplicationConfirmed      *int       `json:"replication_confirmed,omitempty"`
 +	ReplicationConfirmedAt    *time.Time `json:"replication_confirmed_at,omitempty"`
 +	ReplicationDesired        *int       `json:"replication_desired,omitempty"`
 +	StorageClassesDesired     []string   `json:"storage_classes_desired,omitempty"`
 +	StorageClassesConfirmed   []string   `json:"storage_classes_confirmed,omitempty"`
 +	StorageClassesConfirmedAt *time.Time `json:"storage_classes_confirmed_at,omitempty"`
 +	DeleteAt                  *time.Time `json:"delete_at,omitempty"`
 +	IsTrashed                 bool       `json:"is_trashed,omitempty"`
  }
  
  func (c Collection) resourceName() string {

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