[ARVADOS] updated: b73985d8a0c9173aec57f6a81fe540b2813a5bff
Git user
git at public.curoverse.com
Fri Oct 21 15:28:06 EDT 2016
Summary of changes:
.../app/controllers/application_controller.rb | 46 +++-
apps/workbench/app/helpers/application_helper.rb | 6 +-
apps/workbench/app/models/arvados_api_client.rb | 4 +
apps/workbench/app/models/container_work_unit.rb | 4 +-
apps/workbench/app/models/proxy_work_unit.rb | 25 --
apps/workbench/app/models/work_unit.rb | 8 -
.../app/views/projects/_show_dashboard.html.erb | 57 ++++-
.../views/work_units/_component_detail.html.erb | 11 +-
.../app/views/work_units/_show_child.html.erb | 2 +-
.../app/views/work_units/_show_component.html.erb | 32 ++-
.../app/views/work_units/_show_log.html.erb | 8 +-
.../app/views/work_units/_show_log_link.html.erb | 14 ++
apps/workbench/config/application.default.yml | 10 +
apps/workbench/config/initializers/lograge.rb | 4 +-
.../controllers/application_controller_test.rb | 24 ++
.../container_requests_controller_test.rb | 17 +-
.../test/controllers/projects_controller_test.rb | 54 ++++
.../test/controllers/work_units_controller_test.rb | 23 ++
apps/workbench/test/diagnostics/pipeline_test.rb | 2 +-
apps/workbench/test/diagnostics_test_helper.rb | 7 +-
apps/workbench/test/helpers/share_object_helper.rb | 8 +-
.../test/integration/application_layout_test.rb | 9 +-
apps/workbench/test/integration/download_test.rb | 4 +-
.../test/integration/pipeline_instances_test.rb | 8 +-
apps/workbench/test/integration/users_test.rb | 3 +-
apps/workbench/test/integration/work_units_test.rb | 6 +-
apps/workbench/test/integration_helper.rb | 18 +-
apps/workbench/test/unit/work_unit_test.rb | 30 +--
.../postinst | 11 +
.../prerm | 8 +
build/package-build-dockerfiles/Makefile | 2 +-
build/package-build-dockerfiles/centos6/Dockerfile | 2 +-
build/package-build-dockerfiles/centos7/Dockerfile | 2 +-
build/package-build-dockerfiles/debian7/Dockerfile | 2 +-
build/package-build-dockerfiles/debian8/Dockerfile | 2 +-
.../ubuntu1204/Dockerfile | 2 +-
.../ubuntu1404/Dockerfile | 2 +-
.../test-package-python-arvados-cwl-runner.sh | 1 +
.../test-package-python-arvados-fuse.sh | 1 +
.../test-package-python-arvados-python-client.sh | 1 +
...t-package-python27-python-arvados-cwl-runner.sh | 6 +
...ackage-python27-python-arvados-python-client.sh | 2 +-
build/run-build-docker-images.sh | 2 +-
build/run-build-packages.sh | 14 +-
build/run-library.sh | 14 +-
crunch_scripts/cwl-runner | 74 +++---
.../_container_runtime_constraints.liquid | 1 +
.../methods/container_requests.html.textile.liquid | 1 +
.../schema/ContainerRequest.html.textile.liquid | 22 +-
.../install-dispatch.html.textile.liquid | 44 +++-
.../crunch2-slurm/install-test.html.textile.liquid | 2 +-
.../install-arv-git-httpd.html.textile.liquid | 52 ++--
sdk/cli/bin/arv-run-pipeline-instance | 31 +--
sdk/cli/bin/crunch-job | 2 +-
sdk/cli/test/test_arv-keep-get.rb | 4 +-
sdk/cwl/arvados_cwl/__init__.py | 183 +++++++++++---
sdk/cwl/arvados_cwl/arv-cwl-schema.yml | 85 +++++++
sdk/cwl/arvados_cwl/arvcontainer.py | 33 ++-
sdk/cwl/arvados_cwl/arvdocker.py | 14 +-
sdk/cwl/arvados_cwl/arvjob.py | 141 +++++++----
sdk/cwl/arvados_cwl/arvworkflow.py | 93 ++++++-
sdk/cwl/arvados_cwl/crunch_script.py | 102 ++++++++
sdk/cwl/arvados_cwl/fsaccess.py | 6 +-
sdk/cwl/arvados_cwl/pathmapper.py | 53 ++--
sdk/cwl/arvados_cwl/perf.py | 2 +-
sdk/cwl/arvados_cwl/runner.py | 141 +++++++----
sdk/cwl/setup.py | 18 +-
sdk/cwl/tests/hw.py | 1 +
sdk/cwl/tests/submit_test_job.json | 17 ++
sdk/cwl/tests/test_container.py | 16 +-
sdk/cwl/tests/test_job.py | 142 +++++++++--
sdk/cwl/tests/test_make_output.py | 62 +++++
sdk/cwl/tests/test_pathmapper.py | 95 +++++++
sdk/cwl/tests/test_submit.py | 146 ++++++++---
sdk/cwl/tests/wf/expect_packed.cwl | 10 +
sdk/cwl/tests/wf/scatter2.cwl | 56 +++++
sdk/cwl/tests/wf/scatter2_subwf.cwl | 33 +++
sdk/cwl/tests/wf/submit_wf.cwl | 4 +
sdk/go/arvados/client.go | 4 +-
sdk/go/arvados/container.go | 7 +-
sdk/go/arvados/duration.go | 16 +-
sdk/go/arvadosclient/arvadosclient.go | 38 ++-
sdk/go/arvadosclient/pool.go | 36 ++-
sdk/go/arvadostest/run_servers.go | 9 +
sdk/go/config/load.go | 24 ++
sdk/go/crunchrunner/crunchrunner.go | 71 +++++-
sdk/go/crunchrunner/crunchrunner_test.go | 28 +++
sdk/go/dispatch/dispatch.go | 2 +-
sdk/go/keepclient/collectionreader_test.go | 4 +-
sdk/go/keepclient/discover_test.go | 6 +-
sdk/go/keepclient/keepclient_test.go | 62 ++---
sdk/go/logger/logger.go | 6 +-
sdk/go/streamer/streamer.go | 30 ++-
sdk/go/streamer/streamer_test.go | 10 +
sdk/go/util/util.go | 4 +-
sdk/pam/setup.py | 7 +
sdk/python/arvados/arvfile.py | 84 ++++++-
sdk/python/arvados/collection.py | 25 +-
sdk/python/tests/run_test_server.py | 3 +-
sdk/python/tests/test_collections.py | 21 +-
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 6 +-
.../api/app/controllers/application_controller.rb | 8 +
.../controllers/arvados/v1/schema_controller.rb | 4 +
.../app/controllers/user_sessions_controller.rb | 3 +
services/api/app/models/arvados_model.rb | 2 +-
services/api/app/models/collection.rb | 2 +-
services/api/app/models/container.rb | 70 +++++-
services/api/app/models/container_request.rb | 50 +++-
services/api/app/models/user.rb | 36 +--
services/api/config/application.default.yml | 18 ++
.../migrate/20160926194129_add_container_count.rb | 9 +
...71346_add_use_existing_to_container_requests.rb | 9 +
services/api/db/structure.sql | 12 +-
services/api/lib/josh_id.rb | 1 +
.../api/lib/tasks/delete_old_container_logs.rake | 14 ++
services/api/lib/tasks/delete_old_job_logs.rake | 11 +-
services/api/test/fixtures/collections.yml | 17 +-
services/api/test/fixtures/container_requests.yml | 97 +++++++-
services/api/test/fixtures/containers.yml | 63 ++++-
services/api/test/fixtures/logs.yml | 114 +++++++++
.../functional/arvados/v1/jobs_controller_test.rb | 13 +
.../arvados/v1/schema_controller_test.rb | 19 ++
.../api/test/integration/user_sessions_test.rb | 21 +-
.../test/tasks/delete_old_container_logs_test.rb | 50 ++++
services/api/test/unit/container_request_test.rb | 129 ++++++++--
services/api/test/unit/container_test.rb | 18 +-
services/api/test/unit/repository_test.rb | 8 +-
.../arvados-git-httpd.service} | 5 +-
services/arv-git-httpd/auth_handler.go | 28 ++-
services/arv-git-httpd/doc.go | 35 ---
services/arv-git-httpd/git_handler.go | 33 ++-
services/arv-git-httpd/git_handler_test.go | 12 +-
services/arv-git-httpd/gitolite_test.go | 22 +-
services/arv-git-httpd/integration_test.go | 27 +-
services/arv-git-httpd/main.go | 78 ++++--
services/arv-git-httpd/server.go | 4 +-
services/arv-git-httpd/usage.go | 77 ++++++
.../crunch-dispatch-local_test.go | 2 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 65 +++--
.../crunch-dispatch-slurm.service | 1 +
.../crunch-dispatch-slurm_test.go | 26 +-
services/crunch-dispatch-slurm/squeue.go | 8 +-
services/crunch-dispatch-slurm/usage.go | 1 +
services/crunch-run/crunchrun.go | 27 +-
services/crunch-run/crunchrun_test.go | 10 +
services/datamanager/collection/collection.go | 2 +-
services/datamanager/collection/collection_test.go | 2 +-
services/datamanager/datamanager.go | 6 +-
services/datamanager/datamanager_test.go | 4 +-
services/datamanager/keep/keep.go | 8 +-
services/datamanager/keep/keep_test.go | 16 +-
services/dockercleaner/MANIFEST.in | 1 +
.../dockercleaner/arvados-docker-cleaner.service | 14 ++
services/dockercleaner/arvados_docker/cleaner.py | 107 ++++++--
services/dockercleaner/setup.py | 17 +-
services/dockercleaner/tests/test_cleaner.py | 85 +++++--
services/fuse/arvados_fuse/__init__.py | 51 ++--
services/fuse/arvados_fuse/command.py | 6 +-
services/fuse/arvados_fuse/fresh.py | 21 +-
services/fuse/arvados_fuse/fusedir.py | 73 +++---
services/fuse/arvados_fuse/fusefile.py | 4 +-
services/fuse/tests/test_cache.py | 4 +-
services/fuse/tests/test_command_args.py | 14 ++
services/fuse/tests/test_inodes.py | 41 ++-
services/fuse/tests/test_mount.py | 47 +++-
services/fuse/tests/test_token_expiry.py | 4 +-
services/keep-balance/integration_test.go | 2 +-
services/keep-balance/keep-balance.service | 14 ++
services/keep-balance/main.go | 18 +-
services/keep-balance/main_test.go | 7 +-
services/keep-balance/usage.go | 24 +-
services/keep-web/anonymous.go | 35 ---
services/keep-web/doc.go | 61 +++--
services/keep-web/handler.go | 51 ++--
services/keep-web/handler_test.go | 55 ++--
.../keep-web.service} | 5 +-
services/keep-web/main.go | 66 ++++-
services/keep-web/server.go | 17 +-
services/keep-web/server_test.go | 22 +-
services/keep-web/usage.go | 71 ++++++
services/keepproxy/keepproxy.go | 161 +++++++-----
.../keepproxy.service} | 5 +-
services/keepproxy/keepproxy_test.go | 4 +-
services/keepproxy/usage.go | 82 ++++++
services/keepstore/azure_blob_volume.go | 161 ++++++------
services/keepstore/azure_blob_volume_test.go | 12 +-
services/keepstore/bufferpool_test.go | 4 +-
services/keepstore/config.go | 179 +++++++++++++
services/keepstore/deprecated.go | 43 ++++
services/keepstore/handler_test.go | 110 ++++----
services/keepstore/handlers.go | 26 +-
services/keepstore/keepstore.go | 276 ++++-----------------
.../keepstore.service} | 5 +-
services/keepstore/keepstore_test.go | 28 +--
services/keepstore/perms.go | 9 +-
services/keepstore/perms_test.go | 28 ++-
services/keepstore/pull_worker_integration_test.go | 2 +-
services/keepstore/pull_worker_test.go | 36 +--
services/keepstore/s3_volume.go | 254 +++++++++++--------
services/keepstore/s3_volume_test.go | 110 ++++----
services/keepstore/trash_worker.go | 12 +-
services/keepstore/trash_worker_test.go | 22 +-
services/keepstore/usage.go | 124 +++++++++
services/keepstore/volume.go | 22 +-
services/keepstore/volume_generic_test.go | 51 ++--
services/keepstore/volume_test.go | 11 +-
services/keepstore/volume_unix.go | 138 +++++++----
services/keepstore/volume_unix_test.go | 37 ++-
services/login-sync/bin/arvados-login-sync | 43 +++-
tools/arvbox/bin/arvbox | 27 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 20 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.demo | 2 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.dev | 11 +-
tools/arvbox/lib/arvbox/docker/common.sh | 7 +-
.../docker/service/arv-git-httpd/run-service | 9 +-
.../lib/arvbox/docker/service/sdk/run-service | 8 +-
.../crunchstat_summary/summarizer.py | 141 +++++------
218 files changed, 5129 insertions(+), 2034 deletions(-)
create mode 100644 apps/workbench/app/views/work_units/_show_log_link.html.erb
rename build/{go-package-scripts => go-python-package-scripts}/postinst (74%)
rename build/{go-package-scripts => go-python-package-scripts}/prerm (61%)
create mode 120000 build/package-testing/test-package-python-arvados-cwl-runner.sh
create mode 120000 build/package-testing/test-package-python-arvados-fuse.sh
create mode 120000 build/package-testing/test-package-python-arvados-python-client.sh
create mode 100755 build/package-testing/test-package-python27-python-arvados-cwl-runner.sh
create mode 100644 sdk/cwl/arvados_cwl/arv-cwl-schema.yml
create mode 100644 sdk/cwl/arvados_cwl/crunch_script.py
create mode 100644 sdk/cwl/tests/hw.py
create mode 100644 sdk/cwl/tests/test_make_output.py
create mode 100644 sdk/cwl/tests/test_pathmapper.py
create mode 100644 sdk/cwl/tests/wf/scatter2.cwl
create mode 100644 sdk/cwl/tests/wf/scatter2_subwf.cwl
create mode 100644 sdk/go/config/load.go
create mode 100644 services/api/db/migrate/20160926194129_add_container_count.rb
create mode 100644 services/api/db/migrate/20161019171346_add_use_existing_to_container_requests.rb
create mode 100644 services/api/lib/tasks/delete_old_container_logs.rake
create mode 100644 services/api/test/tasks/delete_old_container_logs_test.rb
copy services/{crunch-dispatch-slurm/crunch-dispatch-slurm.service => arv-git-httpd/arvados-git-httpd.service} (53%)
delete mode 100644 services/arv-git-httpd/doc.go
create mode 100644 services/arv-git-httpd/usage.go
create mode 100644 services/dockercleaner/arvados-docker-cleaner.service
create mode 100644 services/keep-balance/keep-balance.service
delete mode 100644 services/keep-web/anonymous.go
copy services/{crunch-dispatch-slurm/crunch-dispatch-slurm.service => keep-web/keep-web.service} (55%)
create mode 100644 services/keep-web/usage.go
copy services/{crunch-dispatch-slurm/crunch-dispatch-slurm.service => keepproxy/keepproxy.service} (55%)
create mode 100644 services/keepproxy/usage.go
create mode 100644 services/keepstore/config.go
create mode 100644 services/keepstore/deprecated.go
copy services/{crunch-dispatch-slurm/crunch-dispatch-slurm.service => keepstore/keepstore.service} (53%)
create mode 100644 services/keepstore/usage.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
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commit b73985d8a0c9173aec57f6a81fe540b2813a5bff
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Oct 21 15:27:34 2016 -0400
10008: Move test setup from __init__() to setUp()
diff --git a/services/fuse/tests/test_token_expiry.py b/services/fuse/tests/test_token_expiry.py
index 16611dc..415f9bb 100644
--- a/services/fuse/tests/test_token_expiry.py
+++ b/services/fuse/tests/test_token_expiry.py
@@ -15,8 +15,8 @@ from .integration_test import IntegrationTest
logger = logging.getLogger('arvados.arv-mount')
class TokenExpiryTest(IntegrationTest):
- def __init__(self, *args, **kwargs):
- super(TokenExpiryTest, self).__init__(*args, **kwargs)
+ def setUp(self):
+ super(TokenExpiryTest, self).setUp()
self.test_start_time = time.time()
self.time_now = int(time.time())+1
commit dfe0ec7bfec3fd72cd40d3962e5c8af08d2413d2
Merge: 6349237 2431a07
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Oct 21 15:19:51 2016 -0400
10008: Merge branch 'master' into 10008-flaky-token-test
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