[ARVADOS] updated: 7cc39786e4951c102a9d10052096db8b953d9e66
git at public.curoverse.com
git at public.curoverse.com
Thu Oct 15 12:24:00 EDT 2015
Summary of changes:
apps/workbench/Gemfile.lock | 15 +-
apps/workbench/app/helpers/version_helper.rb | 28 +-
.../views/application/_report_issue_popup.html.erb | 15 +-
apps/workbench/config/application.default.yml | 13 +-
apps/workbench/config/application.rb | 1 +
apps/workbench/lib/app_version.rb | 53 ++
backports/python-ciso8601/fpm-info.sh | 8 +
backports/python-llfuse/fpm-info.sh | 4 +-
backports/python-pycrypto/fpm-info.sh | 11 +
backports/python-pycurl/fpm-info.sh | 136 +++-
doc/README.textile | 2 +-
doc/_includes/_alert-incomplete.liquid | 2 +-
doc/_includes/_alert_stub.liquid | 2 +-
doc/_includes/_install_ruby_and_bundler.liquid | 9 +-
doc/_includes/_navbar_top.liquid | 2 +-
doc/index.html.liquid | 8 +-
doc/install/install-api-server.html.textile.liquid | 31 +-
.../install-compute-node.html.textile.liquid | 44 +-
doc/install/install-docker.html.textile.liquid | 2 +-
doc/install/install-sso.html.textile.liquid | 255 ++++----
.../install-workbench-app.html.textile.liquid | 4 +-
doc/sdk/cli/subcommands.html.textile.liquid | 26 +-
doc/sdk/go/index.html.textile.liquid | 4 +-
.../firstpipeline.html.textile.liquid | 2 +-
.../examples/crunch-examples.html.textile.liquid | 16 +-
.../getting_started/community.html.textile.liquid | 4 +-
doc/user/topics/arv-copy.html.textile.liquid | 14 +-
...rial-gatk-variantfiltration.html.textile.liquid | 2 +-
.../tutorials/intro-crunch.html.textile.liquid | 2 +-
.../running-external-program.html.textile.liquid | 6 +-
.../tutorial-keep-mount.html.textile.liquid | 2 +-
docker/compute/Dockerfile | 4 +-
docker/jobs/Dockerfile | 2 +-
sdk/cli/bin/arv | 14 +-
sdk/cli/bin/crunch-job | 19 +-
sdk/cwl/setup.py | 2 +-
sdk/go/keepclient/keepclient.go | 196 ++++--
sdk/go/keepclient/keepclient_test.go | 262 +++++++-
sdk/go/keepclient/perms.go | 99 +++
sdk/go/keepclient/perms_test.go | 98 +++
sdk/go/keepclient/support.go | 56 +-
sdk/go/streamer/streamer_test.go | 1 +
sdk/go/streamer/transfer.go | 4 +-
sdk/pam/setup.py | 2 +-
sdk/python/arvados/arvfile.py | 22 +-
sdk/python/arvados/commands/arv_copy.py | 4 +-
sdk/python/arvados/commands/put.py | 4 +-
sdk/python/arvados/keep.py | 15 +-
sdk/python/fpm-info.sh | 8 -
sdk/python/setup.py | 2 +-
sdk/python/tests/run_test_server.py | 18 +-
sdk/python/tests/test_arv_put.py | 17 +-
sdk/python/tests/test_arvfile.py | 15 +
sdk/python/tests/test_collections.py | 2 +-
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 8 +-
.../controllers/arvados/v1/schema_controller.rb | 2 +-
services/api/app/models/keep_service.rb | 9 +
services/api/config/application.default.yml | 9 +-
services/api/config/initializers/app_version.rb | 1 +
services/api/lib/app_version.rb | 52 ++
services/api/lib/tasks/config_check.rake | 3 +-
services/api/script/crunch-dispatch.rb | 5 +
services/api/script/salvage_collection.rb | 1 +
.../arvados/v1/schema_controller_test.rb | 22 +
services/api/test/unit/app_version_test.rb | 43 ++
services/api/test/unit/keep_service_test.rb | 32 +-
services/arv-git-httpd/gitolite_test.go | 93 +++
services/arv-git-httpd/integration_test.go | 133 ++++
services/arv-git-httpd/server_test.go | 165 +----
services/datamanager/collection/collection.go | 75 ++-
services/datamanager/collection/collection_test.go | 24 +-
services/datamanager/collection/testing.go | 27 +-
services/datamanager/datamanager.go | 30 +-
services/datamanager/datamanager_test.go | 513 +++++++++++++++
services/datamanager/keep/keep.go | 139 ++---
services/datamanager/keep/keep_test.go | 6 +-
services/datamanager/summary/canonical_string.go | 3 +
services/datamanager/summary/file.go | 41 +-
services/datamanager/summary/pull_list.go | 26 +-
services/datamanager/summary/summary.go | 52 +-
services/datamanager/summary/summary_test.go | 2 +-
services/datamanager/summary/trash_list.go | 10 +-
services/datamanager/summary/trash_list_test.go | 2 +-
services/dockercleaner/setup.py | 1 +
services/fuse/setup.py | 2 +-
services/keepproxy/keepproxy.go | 71 +++
services/keepproxy/keepproxy_test.go | 71 ++-
.../keepproxy/pkg-extras/etc/default/keepproxy | 7 +
services/keepproxy/pkg-extras/etc/init.d/keepproxy | 156 +++++
services/keepstore/azure_blob_volume.go | 322 ++++++++++
services/keepstore/azure_blob_volume_test.go | 480 ++++++++++++++
services/keepstore/bufferpool_test.go | 4 +-
services/keepstore/collision.go | 84 +++
services/keepstore/collision_test.go | 53 ++
services/keepstore/handler_test.go | 485 +++++++++------
services/keepstore/handlers.go | 262 ++++----
.../keepstore/handlers_with_generic_volume_test.go | 119 ++++
services/keepstore/keepstore.go | 183 ++----
services/keepstore/keepstore_test.go | 154 ++---
services/keepstore/logging_router.go | 4 +
services/keepstore/mock_mutex_for_test.go | 23 +
services/keepstore/perms.go | 105 +---
services/keepstore/perms_test.go | 127 +---
services/keepstore/pull_worker.go | 56 +-
services/keepstore/pull_worker_integration_test.go | 2 +-
services/keepstore/pull_worker_test.go | 202 +++---
services/keepstore/trash_worker.go | 24 +-
services/keepstore/trash_worker_test.go | 94 +--
services/keepstore/volume.go | 210 ++++++-
services/keepstore/volume_generic_test.go | 688 +++++++++++++++++++++
services/keepstore/volume_test.go | 56 +-
services/keepstore/volume_unix.go | 232 +++++--
services/keepstore/volume_unix_test.go | 491 +++++++--------
services/keepstore/work_queue.go | 2 +
services/login-sync/bin/arvados-login-sync | 1 +
.../nodemanager/arvnodeman/computenode/__init__.py | 13 +
.../arvnodeman/computenode/dispatch/__init__.py | 32 +-
.../arvnodeman/computenode/dispatch/slurm.py | 21 +-
.../arvnodeman/computenode/driver/__init__.py | 79 ++-
.../arvnodeman/computenode/driver/azure.py | 97 +++
.../arvnodeman/computenode/driver/ec2.py | 5 -
services/nodemanager/arvnodeman/daemon.py | 20 +-
.../doc/{ec2.example.cfg => azure.example.cfg} | 103 +--
services/nodemanager/setup.py | 5 +-
.../nodemanager/tests/test_computenode_dispatch.py | 51 +-
.../tests/test_computenode_dispatch_slurm.py | 15 +-
.../tests/test_computenode_driver_azure.py | 89 +++
services/nodemanager/tests/test_daemon.py | 71 ++-
129 files changed, 6400 insertions(+), 2091 deletions(-)
create mode 100644 apps/workbench/lib/app_version.rb
create mode 100644 backports/python-ciso8601/fpm-info.sh
create mode 100644 backports/python-pycrypto/fpm-info.sh
create mode 100644 sdk/go/keepclient/perms.go
create mode 100644 sdk/go/keepclient/perms_test.go
delete mode 100644 sdk/python/fpm-info.sh
create mode 100644 services/api/config/initializers/app_version.rb
create mode 100644 services/api/lib/app_version.rb
create mode 100644 services/api/test/unit/app_version_test.rb
create mode 100644 services/arv-git-httpd/gitolite_test.go
create mode 100644 services/arv-git-httpd/integration_test.go
create mode 100644 services/datamanager/datamanager_test.go
create mode 100644 services/keepproxy/pkg-extras/etc/default/keepproxy
create mode 100755 services/keepproxy/pkg-extras/etc/init.d/keepproxy
create mode 100644 services/keepstore/azure_blob_volume.go
create mode 100644 services/keepstore/azure_blob_volume_test.go
create mode 100644 services/keepstore/collision.go
create mode 100644 services/keepstore/collision_test.go
create mode 100644 services/keepstore/handlers_with_generic_volume_test.go
create mode 100644 services/keepstore/mock_mutex_for_test.go
create mode 100644 services/keepstore/volume_generic_test.go
create mode 100644 services/nodemanager/arvnodeman/computenode/driver/azure.py
copy services/nodemanager/doc/{ec2.example.cfg => azure.example.cfg} (55%)
create mode 100644 services/nodemanager/tests/test_computenode_driver_azure.py
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commit 7cc39786e4951c102a9d10052096db8b953d9e66
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Oct 15 12:22:57 2015 -0400
7173: Update bundle.
Recent firefox requires recent selenium-webdriver.
diff --git a/apps/workbench/Gemfile.lock b/apps/workbench/Gemfile.lock
index 20b8d61..8b2118c 100644
--- a/apps/workbench/Gemfile.lock
+++ b/apps/workbench/Gemfile.lock
@@ -74,7 +74,7 @@ GEM
rack (>= 1.0.0)
rack-test (>= 0.5.4)
xpath (~> 2.0)
- childprocess (0.5.5)
+ childprocess (0.5.6)
ffi (~> 1.0, >= 1.0.11)
cliver (0.3.2)
coffee-rails (4.1.0)
@@ -98,7 +98,7 @@ GEM
fast_stack (0.1.0)
rake
rake-compiler
- ffi (1.9.6)
+ ffi (1.9.10)
flamegraph (0.1.0)
fast_stack
google-api-client (0.6.4)
@@ -139,7 +139,7 @@ GEM
metaclass (~> 0.0.1)
morrisjs-rails (0.5.1)
railties (> 3.1, < 5)
- multi_json (1.11.1)
+ multi_json (1.11.2)
multipart-post (1.2.0)
net-scp (1.2.1)
net-ssh (>= 2.6.5)
@@ -192,7 +192,7 @@ GEM
ref (1.0.5)
ruby-debug-passenger (0.2.0)
ruby-prof (0.15.2)
- rubyzip (1.1.6)
+ rubyzip (1.1.7)
rvm-capistrano (1.5.5)
capistrano (~> 2.15.4)
sass (3.4.9)
@@ -202,7 +202,7 @@ GEM
sprockets (>= 2.8, < 4.0)
sprockets-rails (>= 2.0, < 4.0)
tilt (~> 1.1)
- selenium-webdriver (2.44.0)
+ selenium-webdriver (2.48.1)
childprocess (~> 0.5)
multi_json (~> 1.0)
rubyzip (~> 1.0)
@@ -239,7 +239,7 @@ GEM
execjs (>= 0.3.0)
json (>= 1.8.0)
uuidtools (2.1.5)
- websocket (1.2.1)
+ websocket (1.2.2)
websocket-driver (0.5.1)
websocket-extensions (>= 0.1.0)
websocket-extensions (0.1.1)
@@ -294,3 +294,6 @@ DEPENDENCIES
therubyracer
uglifier (>= 1.0.3)
wiselinks
+
+BUNDLED WITH
+ 1.10.6
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