[ARVADOS] updated: 925a1526383299a1ade38a18e616564ab8c38da4
Git user
git at public.curoverse.com
Fri Feb 3 16:14:27 EST 2017
Summary of changes:
.../app/controllers/collections_controller.rb | 8 +-
apps/workbench/app/controllers/jobs_controller.rb | 1 +
.../controllers/pipeline_instances_controller.rb | 1 +
apps/workbench/app/models/proxy_work_unit.rb | 23 +-
.../app/views/work_units/_show_child.html.erb | 2 +-
.../app/views/work_units/_show_component.html.erb | 2 +-
apps/workbench/test/integration/projects_test.rb | 8 -
apps/workbench/test/unit/work_unit_test.rb | 12 +-
backports/python-ciso8601/fpm-info.sh | 3 -
backports/python-llfuse/fpm-info.sh | 7 -
backports/python-pycrypto/fpm-info.sh | 3 -
backports/python-pycurl/fpm-info.sh | 44 ---
backports/rpm-fuse-devel/fpm-info.sh | 5 -
backports/rpm-fuse/fpm-info.sh | 5 -
build/build.list | 44 +++
build/libcloud-pin | 2 +-
build/package-build-dockerfiles/Makefile | 6 +-
.../{ubuntu1204 => ubuntu1604}/Dockerfile | 12 +-
.../{ubuntu1204 => ubuntu1604}/Dockerfile | 11 +-
.../ubuntu1604/etc-apt-preferences.d-arvados | 3 +
build/package-testing/deb-common-test-packages.sh | 2 +-
...ages-debian7.sh => test-packages-ubuntu1604.sh} | 0
build/rails-package-scripts/postinst.sh | 6 +-
build/run-build-packages-one-target.sh | 10 +-
build/run-build-packages.sh | 382 ++++++++++++---------
build/run-library.sh | 103 +++++-
build/run-tests.sh | 13 +-
doc/_includes/_install_git.liquid | 8 +-
doc/_includes/_install_postgres_database.liquid | 4 +-
doc/_includes/_install_ruby_and_bundler.liquid | 4 +-
doc/_includes/_navbar_top.liquid | 2 +-
doc/api/methods.html.textile.liquid | 2 +
.../install-compute-node.html.textile.liquid | 9 +-
.../install-dispatch.html.textile.liquid | 12 +
.../install-compute-node.html.textile.liquid | 9 +-
.../install-crunch-dispatch.html.textile.liquid | 2 +-
doc/install/install-docker.html.textile.liquid | 241 -------------
...nstall-manual-prerequisites.html.textile.liquid | 16 +-
doc/install/install-postgresql.html.textile.liquid | 16 -
.../install-shell-server.html.textile.liquid | 20 +-
.../install-workbench-app.html.textile.liquid | 10 +-
doc/sdk/cli/reference.html.textile.liquid | 13 +-
doc/sdk/python/sdk-python.html.textile.liquid | 9 +-
doc/user/index.html.textile.liquid | 2 +-
doc/user/topics/arv-copy.html.textile.liquid | 23 ++
doc/user/topics/arv-docker.html.textile.liquid | 114 +++---
sdk/cli/bin/crunch-job | 10 +
sdk/cwl/arvados_cwl/__init__.py | 103 ++++--
sdk/cwl/arvados_cwl/arvcontainer.py | 47 +--
sdk/cwl/arvados_cwl/arvdocker.py | 2 +
sdk/cwl/arvados_cwl/arvjob.py | 41 ++-
sdk/cwl/arvados_cwl/arvworkflow.py | 57 +--
sdk/cwl/arvados_cwl/crunch_script.py | 15 +-
sdk/cwl/arvados_cwl/done.py | 35 +-
sdk/cwl/arvados_cwl/fsaccess.py | 31 +-
sdk/cwl/arvados_cwl/pathmapper.py | 8 +-
sdk/cwl/arvados_cwl/runner.py | 181 +++++++---
sdk/cwl/setup.py | 6 +-
sdk/cwl/tests/test_job.py | 17 +-
sdk/cwl/tests/test_submit.py | 285 ++++++++++-----
sdk/cwl/tests/wf/expect_arvworkflow.cwl | 22 +-
sdk/cwl/tests/wf/expect_packed.cwl | 4 +-
sdk/cwl/tests/wf/scatter2_subwf.cwl | 116 ++++---
.../wf/{expect_packed.cwl => submit_wf_packed.cwl} | 8 +-
sdk/go/arvados/collection.go | 11 +-
sdk/go/arvados/resource_list.go | 2 +
sdk/go/config/dump.go | 27 ++
sdk/go/dispatch/dispatch.go | 104 +++---
sdk/go/dispatch/throttle.go | 58 ++++
sdk/go/dispatch/throttle_test.go | 38 ++
sdk/go/keepclient/block_cache.go | 104 ++++++
sdk/go/keepclient/collectionreader.go | 321 +++++++----------
sdk/go/keepclient/collectionreader_test.go | 98 +++++-
sdk/go/keepclient/keepclient.go | 9 +
sdk/python/arvados/arvfile.py | 14 +-
sdk/python/arvados/collection.py | 20 +-
sdk/python/arvados/commands/arv_copy.py | 64 +++-
sdk/python/arvados/commands/keepdocker.py | 40 +++
sdk/python/arvados/commands/put.py | 45 ++-
sdk/python/arvados/commands/run.py | 10 +-
sdk/python/setup.py | 3 +-
sdk/python/tests/test_arv_keepdocker.py | 80 +++++
sdk/python/tests/test_events.py | 56 ++-
.../api/app/controllers/application_controller.rb | 43 ++-
.../arvados/v1/collections_controller.rb | 6 +-
.../controllers/arvados/v1/schema_controller.rb | 11 +-
services/api/app/models/collection.rb | 2 +
services/api/app/models/container_request.rb | 56 ++-
services/api/app/models/job.rb | 2 +-
services/api/app/models/node.rb | 28 +-
services/api/app/models/user.rb | 90 ++---
services/api/config/application.default.yml | 11 +
services/api/config/application.rb | 17 +
.../api/config/initializers/noop_deep_munge.rb | 9 +
...090712_add_output_name_to_container_requests.rb | 9 +
...tput_name_to_container_request_search_index.rb} | 6 +-
...170105160301_add_output_name_to_cr_fts_index.rb | 22 ++
...t_finished_at_on_finished_pipeline_instances.rb | 5 +
services/api/db/structure.sql | 17 +-
services/api/lib/create_permission_view.sql | 41 +++
services/api/lib/crunch_dispatch.rb | 24 +-
services/api/test/fixtures/jobs.yml | 2 +
.../arvados/v1/collections_controller_test.rb | 37 +-
.../arvados/v1/groups_controller_test.rb | 5 +-
.../api/test/functional/arvados/v1/query_test.rb | 29 ++
services/api/test/integration/noop_deep_munge.rb | 35 ++
services/api/test/unit/arvados_model_test.rb | 22 ++
services/api/test/unit/container_request_test.rb | 29 ++
services/api/test/unit/crunch_dispatch_test.rb | 3 +-
services/api/test/unit/job_test.rb | 18 +
services/api/test/unit/node_test.rb | 27 ++
services/api/test/unit/user_test.rb | 10 +-
services/arv-git-httpd/main.go | 5 +
.../crunch-dispatch-local/crunch-dispatch-local.go | 20 +-
.../crunch-dispatch-local_test.go | 24 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 165 ++++-----
.../crunch-dispatch-slurm_test.go | 28 +-
services/crunch-dispatch-slurm/squeue.go | 164 ++++-----
services/crunch-run/crunchrun.go | 2 +-
services/crunch-run/crunchrun_test.go | 14 +-
services/keep-balance/balance_run_test.go | 4 +-
services/keep-balance/collection.go | 77 ++++-
services/keep-balance/collection_test.go | 57 +++
services/keep-balance/main.go | 19 +-
services/keep-web/handler.go | 52 +--
services/keep-web/handler_test.go | 43 ---
services/keep-web/main.go | 6 +
services/keep-web/ranges_test.go | 90 +++++
services/keepproxy/keepproxy.go | 11 +-
services/keepstore/azure_blob_volume.go | 14 +-
services/keepstore/keepstore.go | 8 +-
services/keepstore/volume_unix.go | 157 +++++++--
services/keepstore/volume_unix_test.go | 61 ++++
tools/arvbox/lib/arvbox/docker/api-setup.sh | 1 +
.../lib/arvbox/docker/service/sso/run-service | 1 +
135 files changed, 3120 insertions(+), 1845 deletions(-)
delete mode 100644 backports/rpm-fuse-devel/fpm-info.sh
delete mode 100644 backports/rpm-fuse/fpm-info.sh
create mode 100644 build/build.list
copy build/package-build-dockerfiles/{ubuntu1204 => ubuntu1604}/Dockerfile (67%)
copy build/package-test-dockerfiles/{ubuntu1204 => ubuntu1604}/Dockerfile (55%)
create mode 100644 build/package-test-dockerfiles/ubuntu1604/etc-apt-preferences.d-arvados
rename build/package-testing/{test-packages-debian7.sh => test-packages-ubuntu1604.sh} (100%)
delete mode 100644 doc/install/install-docker.html.textile.liquid
copy sdk/cwl/tests/wf/{expect_packed.cwl => submit_wf_packed.cwl} (53%)
create mode 100644 sdk/go/config/dump.go
create mode 100644 sdk/go/dispatch/throttle.go
create mode 100644 sdk/go/dispatch/throttle_test.go
create mode 100644 sdk/go/keepclient/block_cache.go
create mode 100644 services/api/config/initializers/noop_deep_munge.rb
create mode 100644 services/api/db/migrate/20161223090712_add_output_name_to_container_requests.rb
copy services/api/db/migrate/{20161115174218_add_output_and_log_uuids_to_container_request_search_index.rb => 20170102153111_add_output_name_to_container_request_search_index.rb} (87%)
create mode 100644 services/api/db/migrate/20170105160301_add_output_name_to_cr_fts_index.rb
create mode 100644 services/api/db/migrate/20170105160302_set_finished_at_on_finished_pipeline_instances.rb
create mode 100644 services/api/lib/create_permission_view.sql
create mode 100644 services/api/test/integration/noop_deep_munge.rb
create mode 100644 services/keep-balance/collection_test.go
create mode 100644 services/keep-web/ranges_test.go
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commit 925a1526383299a1ade38a18e616564ab8c38da4
Merge: 49d7a1f 74a9dec
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Feb 3 16:13:58 2017 -0500
Merge branch 'master' into 10797-ruby-2.3
Conflicts:
build/package-build-dockerfiles/Makefile
diff --cc build/package-build-dockerfiles/Makefile
index 7359aca,5fae9dc..81d1f13
--- a/build/package-build-dockerfiles/Makefile
+++ b/build/package-build-dockerfiles/Makefile
@@@ -16,7 -16,11 +16,11 @@@ ubuntu1404/generated: common-generated-
test -d ubuntu1404/generated || mkdir ubuntu1404/generated
cp -rlt ubuntu1404/generated common-generated/*
+ ubuntu1604/generated: common-generated-all
+ test -d ubuntu1604/generated || mkdir ubuntu1604/generated
+ cp -rlt ubuntu1604/generated common-generated/*
+
-GOTARBALL=go1.7.1.linux-amd64.tar.gz
+GOTARBALL=go1.7.4.linux-amd64.tar.gz
common-generated-all: common-generated/$(GOTARBALL)
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