[ARVADOS] updated: 734335da27f27e2177d3b931b1e5e9e8e83a042f
Git user
git at public.curoverse.com
Fri Oct 28 14:35:55 EDT 2016
Summary of changes:
COPYING | 14 ++--
.../app/assets/javascripts/work_unit_component.js | 18 +++++
.../app/controllers/work_units_controller.rb | 54 +++++++++++++
apps/workbench/app/models/container.rb | 2 +-
apps/workbench/app/models/container_request.rb | 2 +-
apps/workbench/app/models/container_work_unit.rb | 6 +-
apps/workbench/app/models/job.rb | 2 +-
apps/workbench/app/models/job_task.rb | 2 +-
apps/workbench/app/models/pipeline_instance.rb | 2 +-
.../app/models/pipeline_instance_work_unit.rb | 4 +-
apps/workbench/app/models/proxy_work_unit.rb | 9 ++-
apps/workbench/app/models/work_unit.rb | 4 +
.../pipeline_instances/_show_components.html.erb | 2 +-
.../views/work_units/_component_detail.html.erb | 28 ++++++-
.../app/views/work_units/_show_child.html.erb | 29 ++-----
.../app/views/work_units/_show_component.html.erb | 47 +----------
.../app/views/work_units/_show_status.html.erb | 2 +-
apps/workbench/config/routes.rb | 4 +-
.../test/controllers/work_units_controller_test.rb | 23 ------
apps/workbench/test/integration/jobs_test.rb | 2 +-
apps/workbench/test/integration/work_units_test.rb | 25 ++++++
.../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-docker-jobs-image.sh | 69 ++++++++++++----
build/run-build-packages.sh | 8 +-
build/run-library.sh | 12 ++-
docker/jobs/Dockerfile | 12 ++-
sdk/cli/bin/crunch-job | 2 +-
sdk/cwl/arvados_cwl/__init__.py | 33 ++++++--
sdk/cwl/arvados_cwl/arvcontainer.py | 21 +++--
sdk/cwl/arvados_cwl/arvdocker.py | 14 ++--
sdk/cwl/arvados_cwl/arvjob.py | 28 +++----
sdk/cwl/arvados_cwl/crunch_script.py | 19 ++---
sdk/cwl/arvados_cwl/runner.py | 8 ++
sdk/cwl/gittaggers.py | 38 ++++++++-
sdk/cwl/setup.py | 15 ++++
sdk/cwl/tests/test_job.py | 36 ++++++---
sdk/cwl/tests/test_submit.py | 17 ++--
sdk/python/arvados/arvfile.py | 7 +-
.../arvados/v1/containers_controller.rb | 17 ++++
services/api/app/models/container.rb | 48 ++++++++---
services/api/config/routes.rb | 1 +
.../test/fixtures/api_client_authorizations.yml | 14 ++++
services/api/test/fixtures/collections.yml | 13 +++
services/api/test/fixtures/containers.yml | 4 +-
.../arvados/v1/containers_controller_test.rb | 19 +++++
services/api/test/unit/container_request_test.rb | 2 +-
services/api/test/unit/container_test.rb | 92 ++++++++++++++++++----
services/crunch-run/crunchrun.go | 15 ++++
services/crunch-run/crunchrun_test.go | 49 ++++++++++++
services/fuse/arvados_fuse/__init__.py | 14 ++++
services/fuse/tests/integration_test.py | 1 -
services/fuse/tests/test_mount.py | 34 --------
services/fuse/tests/test_token_expiry.py | 68 ++++++++++++++++
services/login-sync/bin/arvados-login-sync | 56 +++++++++----
services/login-sync/test/test_add_user.rb | 2 +-
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 +-
.../lib/arvbox/docker/service/sdk/run-service | 8 +-
66 files changed, 825 insertions(+), 332 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/work_unit_component.js
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
mode change 120000 => 100644 sdk/cwl/gittaggers.py
create mode 100644 services/fuse/tests/test_token_expiry.py
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commit 734335da27f27e2177d3b931b1e5e9e8e83a042f
Merge: 5c05b48 ceec074
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Fri Oct 28 15:35:19 2016 -0300
10315: Merge branch 'master' into 10315-new-arv-put-performance
commit 5c05b488a1f2318e73780b67f6f654b4a12c32b3
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Fri Oct 28 15:33:03 2016 -0300
10315: Moved conditional on pending write size checking
diff --git a/sdk/python/arvados/arvfile.py b/sdk/python/arvados/arvfile.py
index 7ee028d..610fd7d 100644
--- a/sdk/python/arvados/arvfile.py
+++ b/sdk/python/arvados/arvfile.py
@@ -576,10 +576,9 @@ class _BlockManager(object):
# Update the pending write size count with its true value, just in case
# some small file was opened, written and closed several times.
- if not force:
- self._pending_write_size = sum([b.size() for b in small_blocks])
- if self._pending_write_size < config.KEEP_BLOCK_SIZE:
- return
+ self._pending_write_size = sum([b.size() for b in small_blocks])
+ if self._pending_write_size < config.KEEP_BLOCK_SIZE and not force:
+ return
new_bb = self._alloc_bufferblock()
while len(small_blocks) > 0 and (new_bb.write_pointer + small_blocks[0].size()) <= config.KEEP_BLOCK_SIZE:
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