[ARVADOS] updated: d14dd75b263d8f999603b66d23f74667d36a2412
git at public.curoverse.com
git at public.curoverse.com
Tue May 12 13:50:46 EDT 2015
Summary of changes:
apps/workbench/Gemfile | 5 +-
apps/workbench/Gemfile.lock | 9 +-
apps/workbench/app/assets/images/mouse-move.gif | Bin 26082 -> 26082 bytes
.../app/assets/javascripts/infinite_scroll.js | 36 +-
.../app/assets/javascripts/selection.js.erb | 8 +
apps/workbench/app/assets/javascripts/tab_panes.js | 2 +-
.../app/assets/stylesheets/application.css.scss | 8 +
.../app/controllers/collections_controller.rb | 4 +-
apps/workbench/app/controllers/jobs_controller.rb | 2 -
.../controllers/pipeline_instances_controller.rb | 4 +-
.../app/controllers/projects_controller.rb | 2 +-
.../app/controllers/repositories_controller.rb | 9 -
apps/workbench/app/helpers/application_helper.rb | 20 +-
apps/workbench/app/helpers/jobs_helper.rb | 22 -
apps/workbench/app/models/pipeline_instance.rb | 52 ++
apps/workbench/app/models/repository.rb | 11 +-
.../app/views/application/_choose.html.erb | 4 +
.../app/views/application/_content.html.erb | 12 +-
.../app/views/application/_show_sharing.html.erb | 1 +
.../app/views/collections/_show_files.html.erb | 16 +-
.../app/views/collections/hash_matches.html.erb | 8 +-
.../app/views/layouts/application.html.erb | 6 +-
apps/workbench/app/views/layouts/body.html.erb | 11 +-
.../pipeline_instances/_running_component.html.erb | 3 +-
.../views/pipeline_instances/_show_log.html.erb | 56 +-
.../projects/_index_jobs_and_pipelines.html.erb | 2 +-
.../views/projects/_show_contents_rows.html.erb | 2 +-
.../app/views/projects/_show_description.html.erb | 2 +-
.../app/views/projects/_show_tab_contents.html.erb | 6 +-
apps/workbench/config/application.default.yml | 6 -
apps/workbench/config/database.yml | 40 +-
.../test/controllers/projects_controller_test.rb | 27 +
.../controllers/repositories_controller_test.rb | 4 -
apps/workbench/test/helpers/share_object_helper.rb | 1 +
.../test/integration/anonymous_access_test.rb | 33 +-
.../test/integration/application_layout_test.rb | 4 +-
.../workbench/test/integration/collections_test.rb | 31 +-
apps/workbench/test/integration/errors_test.rb | 4 +-
.../test/integration/integration_test_utils.rb | 12 +
.../test/integration/pipeline_instances_test.rb | 41 ++
apps/workbench/test/integration/projects_test.rb | 108 +++
.../test/integration/repositories_browse_test.rb | 2 -
.../test/integration/user_manage_account_test.rb | 6 +-
.../test/integration/user_profile_test.rb | 4 +-
apps/workbench/test/unit/pipeline_instance_test.rb | 66 +-
crunch_scripts/crunchutil/vwd.py | 81 ++-
crunch_scripts/run-command | 30 +-
.../create-standard-objects.html.textile.liquid | 2 +-
doc/install/install-keepstore.html.textile.liquid | 35 +-
doc/install/install-sso.html.textile.liquid | 176 +++--
.../install-workbench-app.html.textile.liquid | 2 +-
doc/user/topics/run-command.html.textile.liquid | 8 +-
docker/sso/Dockerfile | 1 +
docker/sso/application.yml.in | 26 +
sdk/go/arvadosclient/arvadosclient.go | 64 +-
sdk/go/arvadosclient/arvadosclient_test.go | 14 +-
sdk/python/arvados/arvfile.py | 19 +-
sdk/python/arvados/collection.py | 2 +-
sdk/python/arvados/commands/arv_copy.py | 10 +-
sdk/python/arvados/errors.py | 9 +-
sdk/python/arvados/keep.py | 317 ++++++---
sdk/python/arvados/retry.py | 19 +-
sdk/python/arvados/stream.py | 4 +-
sdk/python/setup.py | 33 +-
sdk/python/tests/arvados_testutil.py | 106 ++-
sdk/python/tests/keepstub.py | 104 +++
sdk/python/tests/run_test_server.py | 2 +-
sdk/python/tests/test_arvfile.py | 19 +-
sdk/python/tests/test_collections.py | 23 +-
sdk/python/tests/test_errors.py | 4 +-
sdk/python/tests/test_keep_client.py | 221 ++++--
sdk/python/tests/test_retry.py | 5 +-
sdk/python/tests/test_stream.py | 16 +-
sdk/ruby/lib/arvados/keep.rb | 16 +-
services/api/Rakefile | 21 +
.../api/app/controllers/application_controller.rb | 37 +-
.../arvados/v1/collections_controller.rb | 4 +
.../app/controllers/arvados/v1/jobs_controller.rb | 27 +-
.../controllers/arvados/v1/schema_controller.rb | 1 +
services/api/app/models/arvados_model.rb | 7 +
services/api/app/models/collection.rb | 4 +-
services/api/app/models/job.rb | 6 +-
services/api/app/models/node.rb | 7 +-
services/api/config/application.default.yml | 45 +-
services/api/lib/tasks/delete_old_job_logs.rake | 17 +
services/api/lib/tasks/test_tasks.rake | 6 +
services/api/test/fixtures/groups.yml | 26 +
services/api/test/fixtures/jobs.yml | 53 +-
services/api/test/fixtures/links.yml | 30 +
services/api/test/fixtures/logs.yml | 38 ++
services/api/test/fixtures/pipeline_instances.yml | 42 +-
services/api/test/fixtures/pipeline_templates.yml | 40 ++
services/api/test/fixtures/repositories.yml | 7 +
.../arvados/v1/collections_controller_test.rb | 39 ++
.../arvados/v1/job_reuse_controller_test.rb | 108 ++-
.../api/test/tasks/delete_old_job_logs_test.rb | 50 ++
services/api/test/test.git.tar | Bin 194560 -> 256000 bytes
services/api/test/unit/collection_test.rb | 7 +
services/api/test/unit/commit_test.rb | 60 ++
services/api/test/unit/job_test.rb | 30 +
services/arv-git-httpd/auth_handler.go | 2 +-
services/arv-git-httpd/basic_auth_test.go | 12 +-
services/arv-git-httpd/server_test.go | 18 +-
services/crunchstat/.gitignore | 1 +
services/crunchstat/crunchstat.go | 26 +-
services/{nodemanager => dockercleaner}/.gitignore | 0
.../arvados_docker}/__init__.py | 0
services/dockercleaner/arvados_docker/cleaner.py | 260 +++++++
.../{nodemanager => dockercleaner}/gittaggers.py | 0
services/dockercleaner/setup.py | 33 +
services/dockercleaner/tests/__init__.py | 4 +
services/dockercleaner/tests/test_cleaner.py | 356 ++++++++++
services/fuse/arvados_fuse/__init__.py | 755 +++------------------
services/fuse/arvados_fuse/fresh.py | 72 ++
.../fuse/arvados_fuse/{__init__.py => fusedir.py} | 545 +++------------
services/fuse/arvados_fuse/fusefile.py | 71 ++
services/fuse/bin/arv-mount | 15 +-
services/fuse/setup.py | 2 +-
services/fuse/tests/test_inodes.py | 146 ++++
services/fuse/tests/test_mount.py | 3 +-
services/keepproxy/.gitignore | 1 +
services/keepproxy/keepproxy.go | 5 +
services/keepproxy/keepproxy_test.go | 16 +
services/keepstore/.gitignore | 1 +
services/keepstore/bufferpool.go | 44 ++
services/keepstore/bufferpool_test.go | 85 +++
services/keepstore/handler_test.go | 26 +-
services/keepstore/handlers.go | 127 ++--
services/keepstore/keepstore.go | 119 ++--
services/keepstore/keepstore_test.go | 10 +-
services/keepstore/logging_router.go | 8 +-
services/keepstore/perms_test.go | 10 +-
services/keepstore/pull_worker_integration_test.go | 19 +-
services/keepstore/pull_worker_test.go | 17 +-
services/keepstore/trash_worker.go | 34 +-
services/keepstore/trash_worker_test.go | 51 +-
services/keepstore/volume.go | 8 +-
services/keepstore/volume_test.go | 34 +-
services/keepstore/volume_unix.go | 219 +++---
services/keepstore/volume_unix_test.go | 15 +-
.../arvnodeman/computenode/dispatch/__init__.py | 62 +-
.../arvnodeman/computenode/dispatch/slurm.py | 2 +-
services/nodemanager/arvnodeman/daemon.py | 9 +-
services/nodemanager/tests/__init__.py | 2 +-
.../nodemanager/tests/test_computenode_dispatch.py | 29 +-
.../tests/test_computenode_dispatch_slurm.py | 5 +
services/nodemanager/tests/test_daemon.py | 37 +
147 files changed, 3993 insertions(+), 2115 deletions(-)
delete mode 100644 apps/workbench/app/helpers/jobs_helper.rb
create mode 100644 apps/workbench/test/integration/integration_test_utils.rb
create mode 100644 docker/sso/application.yml.in
create mode 100644 sdk/python/tests/keepstub.py
create mode 100644 services/api/lib/tasks/delete_old_job_logs.rake
create mode 100644 services/api/lib/tasks/test_tasks.rake
create mode 100644 services/api/test/tasks/delete_old_job_logs_test.rb
create mode 100644 services/crunchstat/.gitignore
copy services/{nodemanager => dockercleaner}/.gitignore (100%)
copy services/{fuse/tests => dockercleaner/arvados_docker}/__init__.py (100%)
create mode 100755 services/dockercleaner/arvados_docker/cleaner.py
copy services/{nodemanager => dockercleaner}/gittaggers.py (100%)
create mode 100644 services/dockercleaner/setup.py
create mode 100644 services/dockercleaner/tests/__init__.py
create mode 100644 services/dockercleaner/tests/test_cleaner.py
create mode 100644 services/fuse/arvados_fuse/fresh.py
copy services/fuse/arvados_fuse/{__init__.py => fusedir.py} (57%)
create mode 100644 services/fuse/arvados_fuse/fusefile.py
create mode 100644 services/fuse/tests/test_inodes.py
create mode 100644 services/keepproxy/.gitignore
create mode 100644 services/keepstore/.gitignore
create mode 100644 services/keepstore/bufferpool.go
create mode 100644 services/keepstore/bufferpool_test.go
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commit d14dd75b263d8f999603b66d23f74667d36a2412
Merge: 17fb6bc 2b43d35
Author: Radhika Chippada <radhika at curoverse.com>
Date: Tue May 12 13:50:31 2015 -0400
Merge branch 'master' into 5720-ajax-loading-error
commit 17fb6bca5786bad5cff83a187e70adbca9c1d14a
Author: Radhika Chippada <radhika at curoverse.com>
Date: Tue May 12 13:46:56 2015 -0400
5720: when jqxhr readyState == 0 or status == 0, instead of skipping show "Cancelled" message.
diff --git a/apps/workbench/app/assets/javascripts/infinite_scroll.js b/apps/workbench/app/assets/javascripts/infinite_scroll.js
index b380505..17ce8a4 100644
--- a/apps/workbench/app/assets/javascripts/infinite_scroll.js
+++ b/apps/workbench/app/assets/javascripts/infinite_scroll.js
@@ -74,7 +74,7 @@ function maybe_load_more_content(event) {
return;
}
if (jqxhr.readyState == 0 || jqxhr.status == 0) {
- message = "Cancelled";
+ message = "Cancelled.";
} else if (jqxhr.responseJSON && jqxhr.responseJSON.errors) {
message = jqxhr.responseJSON.errors.join("; ");
} else {
diff --git a/apps/workbench/app/assets/javascripts/tab_panes.js b/apps/workbench/app/assets/javascripts/tab_panes.js
index 6f7bfe0..eb57479 100644
--- a/apps/workbench/app/assets/javascripts/tab_panes.js
+++ b/apps/workbench/app/assets/javascripts/tab_panes.js
@@ -134,7 +134,7 @@ $(document).on('arv:pane:reload', '[data-pane-content-url]', function(e) {
var errhtml;
var contentType = jqxhr.getResponseHeader('Content-Type');
if (jqxhr.readyState == 0 || jqxhr.status == 0) {
- message = "Cancelled";
+ errhtml = "Cancelled.";
} else if (contentType && contentType.match(/\btext\/html\b/)) {
var $response = $(jqxhr.responseText);
var $wrapper = $('div#page-wrapper', $response);
commit 7e78bad94194f9ce7a39888cbac30eaf4fbf4af7
Author: Radhika Chippada <radhika at curoverse.com>
Date: Tue May 12 13:39:05 2015 -0400
5720: when jqxhr readyState == 0 or status == 0, instead of skipping show "Cancelled" message.
diff --git a/apps/workbench/app/assets/javascripts/infinite_scroll.js b/apps/workbench/app/assets/javascripts/infinite_scroll.js
index 282d9ed..b380505 100644
--- a/apps/workbench/app/assets/javascripts/infinite_scroll.js
+++ b/apps/workbench/app/assets/javascripts/infinite_scroll.js
@@ -74,7 +74,7 @@ function maybe_load_more_content(event) {
return;
}
if (jqxhr.readyState == 0 || jqxhr.status == 0) {
- return; // User may have navigated away; skip.
+ message = "Cancelled";
} else if (jqxhr.responseJSON && jqxhr.responseJSON.errors) {
message = jqxhr.responseJSON.errors.join("; ");
} else {
diff --git a/apps/workbench/app/assets/javascripts/tab_panes.js b/apps/workbench/app/assets/javascripts/tab_panes.js
index a92582c..6f7bfe0 100644
--- a/apps/workbench/app/assets/javascripts/tab_panes.js
+++ b/apps/workbench/app/assets/javascripts/tab_panes.js
@@ -134,7 +134,7 @@ $(document).on('arv:pane:reload', '[data-pane-content-url]', function(e) {
var errhtml;
var contentType = jqxhr.getResponseHeader('Content-Type');
if (jqxhr.readyState == 0 || jqxhr.status == 0) {
- return; // User may have navigated away; skip.
+ message = "Cancelled";
} else if (contentType && contentType.match(/\btext\/html\b/)) {
var $response = $(jqxhr.responseText);
var $wrapper = $('div#page-wrapper', $response);
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