[ARVADOS] updated: eff3277fa6800bbc4ac81654f8883bbfd3a85d30

git at public.curoverse.com git at public.curoverse.com
Wed May 7 19:54:46 EDT 2014


Summary of changes:
 .gitignore                                         |    2 +
 apps/workbench/.gitignore                          |    3 +
 apps/workbench/Gemfile                             |    5 +
 apps/workbench/Gemfile.lock                        |    8 +
 .../app/assets/javascripts/application.js          |    1 -
 apps/workbench/app/assets/javascripts/editable.js  |   55 ++-
 apps/workbench/app/assets/javascripts/folders.js   |   12 +
 ..._authorizations.js.coffee => folders.js.coffee} |    0
 apps/workbench/app/assets/javascripts/selection.js |   18 +-
 .../app/assets/stylesheets/application.css.scss    |   72 ++--
 .../app/assets/stylesheets/cards.css.scss          |   85 +++
 .../{jobs.css.scss => folders.css.scss}            |    2 +-
 .../app/assets/stylesheets/sb-admin.css.scss       |  164 ++++++
 .../workbench/app/assets/stylesheets/selection.css |   22 +-
 .../app/controllers/actions_controller.rb          |   42 ++-
 .../app/controllers/application_controller.rb      |   47 ++-
 .../app/controllers/collections_controller.rb      |    1 -
 .../app/controllers/folders_controller.rb          |   99 ++++
 .../workbench/app/controllers/groups_controller.rb |    7 +-
 apps/workbench/app/helpers/application_helper.rb   |   21 +-
 apps/workbench/app/helpers/folders_helper.rb       |    2 +
 .../app/helpers/pipeline_instances_helper.rb       |    1 -
 apps/workbench/app/models/arvados_base.rb          |   48 ++-
 apps/workbench/app/models/arvados_resource_list.rb |    6 +
 apps/workbench/app/models/collection.rb            |    5 +
 apps/workbench/app/models/group.rb                 |   10 +
 apps/workbench/app/models/log.rb                   |    5 +
 .../app/views/application/_content.html.erb        |    2 +-
 .../application/_delete_object_button.html.erb     |    2 +-
 .../views/application/_show_object_button.html.erb |    3 +
 .../app/views/application/_show_recent.html.erb    |   21 +-
 .../workbench/app/views/application/index.html.erb |    6 +-
 .../app/views/folders/_show_my_folders.html.erb    |    2 +
 .../views/folders/_show_shared_with_me.html.erb    |    2 +
 .../workbench/app/views/folders/remove_item.js.erb |    5 +
 apps/workbench/app/views/folders/show.html.erb     |  193 +++++++
 .../app/views/layouts/application.html.erb         |  321 ++++++-----
 apps/workbench/app/views/logs/show.html.erb        |    1 -
 apps/workbench/config/routes.rb                    |    3 +
 .../folders_controller_test.rb}                    |    2 +-
 apps/workbench/test/integration/folders_test.rb    |   48 ++
 apps/workbench/test/integration/smoke_test.rb      |    2 +-
 apps/workbench/test/integration/users_test.rb      |   51 +-
 .../test/integration/virtual_machines_test.rb      |    4 +-
 apps/workbench/test/integration_helper.rb          |   26 +
 apps/workbench/test/test_helper.rb                 |   41 +-
 .../test/unit/helpers/folders_helper_test.rb       |    4 +
 doc/_config.yml                                    |    5 +-
 doc/api/index.html.textile.liquid                  |    2 -
 doc/api/methods.html.textile.liquid                |   39 ++-
 doc/api/methods/logs.html.textile.liquid           |   22 +-
 doc/api/schema/Collection.html.textile.liquid      |    2 +-
 doc/api/schema/Job.html.textile.liquid             |    1 +
 doc/install/index.html.md.liquid                   |   18 -
 doc/install/index.html.textile.liquid              |   18 +
 doc/install/install-api-server.html.textile.liquid |    5 +-
 .../install-crunch-dispatch.html.textile.liquid    |   44 +-
 doc/install/install-sso.html.textile.liquid        |    3 +-
 .../install-workbench-app.html.textile.liquid      |   30 +-
 doc/sdk/index.html.textile.liquid                  |    3 +-
 doc/sdk/java/index.html.textile.liquid             |  140 +++++
 doc/sdk/perl/index.html.textile.liquid             |    2 +-
 doc/sdk/python/sdk-python.html.textile.liquid      |   10 +-
 doc/sdk/ruby/index.html.textile.liquid             |    2 +-
 docker/build_tools/Makefile                        |   10 +
 docker/jobs/Dockerfile                             |   20 +
 sdk/cli/bin/arv-run-pipeline-instance              |   11 +-
 sdk/cli/bin/crunch-job                             |   49 ++-
 sdk/java/.classpath                                |   21 +
 sdk/java/.project                                  |   14 +
 sdk/java/.settings/org.eclipse.jdt.core.prefs      |    5 +
 sdk/java/ArvadosSDKJavaExample.java                |   80 +++
 sdk/java/ArvadosSDKJavaExampleWithPrompt.java      |  123 ++++
 sdk/java/README                                    |    4 +
 sdk/java/pom.xml                                   |  106 ++++
 .../main/java/org/arvados/sdk/java/Arvados.java    |  366 ++++++++++++
 .../java/org/arvados/sdk/java/MethodDetails.java   |   22 +
 sdk/java/src/main/resources/log4j.properties       |   11 +
 .../java/org/arvados/sdk/java/ArvadosTest.java     |  387 +++++++++++++
 sdk/java/src/test/resources/first_pipeline.json    |   16 +
 sdk/python/.gitignore                              |    1 -
 sdk/python/arvados/events.py                       |   33 ++
 sdk/python/arvados/fuse.py                         |  317 -----------
 sdk/python/arvados/fuse/__init__.py                |  585 ++++++++++++++++++++
 sdk/python/bin/arv-mount                           |   51 ++-
 sdk/python/build.sh                                |   16 -
 sdk/python/requirements.txt                        |    3 +
 sdk/python/run_test_server.py                      |   86 +++
 sdk/python/{setup.py.src => setup.py}              |    9 +-
 sdk/python/setup.py.src                            |    8 +-
 sdk/python/setup_fuse.py                           |   21 +
 sdk/python/setup_header.py                         |   11 +
 sdk/python/test_mount.py                           |  246 +++++++--
 sdk/python/test_websockets.py                      |   32 ++
 sdk/ruby/.gitignore                                |    1 +
 sdk/ruby/Gemfile.lock                              |   58 --
 services/api/.gitignore                            |    2 +
 services/api/Gemfile                               |    6 +-
 services/api/Gemfile.lock                          |   10 +-
 services/api/Rakefile                              |    6 +
 .../api/app/controllers/application_controller.rb  |   67 ---
 .../controllers/arvados/v1/groups_controller.rb    |   68 +++
 .../controllers/arvados/v1/schema_controller.rb    |   15 +-
 .../app/controllers/user_sessions_controller.rb    |    3 +-
 services/api/app/models/arvados_model.rb           |   20 +
 services/api/app/models/group.rb                   |    1 +
 services/api/app/models/pipeline_instance.rb       |    4 +
 services/api/app/models/user.rb                    |    4 +
 services/api/lib/record_filters.rb                 |   13 +-
 services/api/script/import_commits.rb              |    9 -
 services/api/test/fixtures/specimens.yml           |   18 +
 .../arvados/v1/groups_controller_test.rb           |   37 ++
 .../functional/arvados/v1/jobs_controller_test.rb  |   34 ++
 .../api/test/integration/user_sessions_test.rb     |   28 +
 services/api/test/test_helper.rb                   |   21 +
 115 files changed, 3965 insertions(+), 952 deletions(-)
 create mode 100644 apps/workbench/app/assets/javascripts/folders.js
 copy apps/workbench/app/assets/javascripts/{api_client_authorizations.js.coffee => folders.js.coffee} (100%)
 create mode 100644 apps/workbench/app/assets/stylesheets/cards.css.scss
 copy apps/workbench/app/assets/stylesheets/{jobs.css.scss => folders.css.scss} (64%)
 create mode 100644 apps/workbench/app/assets/stylesheets/sb-admin.css.scss
 create mode 100644 apps/workbench/app/controllers/folders_controller.rb
 create mode 100644 apps/workbench/app/helpers/folders_helper.rb
 create mode 100644 apps/workbench/app/views/application/_show_object_button.html.erb
 create mode 100644 apps/workbench/app/views/folders/_show_my_folders.html.erb
 create mode 100644 apps/workbench/app/views/folders/_show_shared_with_me.html.erb
 create mode 100644 apps/workbench/app/views/folders/remove_item.js.erb
 create mode 100644 apps/workbench/app/views/folders/show.html.erb
 delete mode 100644 apps/workbench/app/views/logs/show.html.erb
 copy apps/workbench/test/{unit/job_test.rb => functional/folders_controller_test.rb} (57%)
 create mode 100644 apps/workbench/test/integration/folders_test.rb
 create mode 100644 apps/workbench/test/unit/helpers/folders_helper_test.rb
 delete mode 100644 doc/install/index.html.md.liquid
 create mode 100644 doc/install/index.html.textile.liquid
 create mode 100644 doc/sdk/java/index.html.textile.liquid
 create mode 100644 docker/jobs/Dockerfile
 create mode 100644 sdk/java/.classpath
 create mode 100644 sdk/java/.project
 create mode 100644 sdk/java/.settings/org.eclipse.jdt.core.prefs
 create mode 100644 sdk/java/ArvadosSDKJavaExample.java
 create mode 100644 sdk/java/ArvadosSDKJavaExampleWithPrompt.java
 create mode 100644 sdk/java/README
 create mode 100644 sdk/java/pom.xml
 create mode 100644 sdk/java/src/main/java/org/arvados/sdk/java/Arvados.java
 create mode 100644 sdk/java/src/main/java/org/arvados/sdk/java/MethodDetails.java
 create mode 100644 sdk/java/src/main/resources/log4j.properties
 create mode 100644 sdk/java/src/test/java/org/arvados/sdk/java/ArvadosTest.java
 create mode 100644 sdk/java/src/test/resources/first_pipeline.json
 create mode 100644 sdk/python/arvados/events.py
 delete mode 100644 sdk/python/arvados/fuse.py
 create mode 100644 sdk/python/arvados/fuse/__init__.py
 delete mode 100755 sdk/python/build.sh
 create mode 100644 sdk/python/run_test_server.py
 copy sdk/python/{setup.py.src => setup.py} (82%)
 create mode 100644 sdk/python/setup_fuse.py
 create mode 100644 sdk/python/setup_header.py
 create mode 100644 sdk/python/test_websockets.py
 delete mode 100644 sdk/ruby/Gemfile.lock
 delete mode 100755 services/api/script/import_commits.rb
 create mode 100644 services/api/test/integration/user_sessions_test.rb

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commit eff3277fa6800bbc4ac81654f8883bbfd3a85d30
Author: radhika <radhika at curoverse.com>
Date:   Wed May 7 19:54:23 2014 -0400

    2352: set active to nil when Ready

diff --git a/sdk/cli/bin/arv-run-pipeline-instance b/sdk/cli/bin/arv-run-pipeline-instance
index f0ada5d..5f925ef 100755
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -416,7 +416,8 @@ class WhRunPipelineInstance
     if $options[:submit]
       @instance ||= PipelineInstance.
         create(:components => @components,
-              :pipeline_template_uuid => @template[:uuid])
+              :pipeline_template_uuid => @template[:uuid],
+              :state => 'New')
     else
       @instance ||= PipelineInstance.
         create(:components => @components,
diff --git a/services/api/app/models/pipeline_instance.rb b/services/api/app/models/pipeline_instance.rb
index 258ee27..32c284b 100644
--- a/services/api/app/models/pipeline_instance.rb
+++ b/services/api/app/models/pipeline_instance.rb
@@ -199,6 +199,10 @@ class PipelineInstance < ArvadosModel
         self.state = Ready
       end
     end
+
+    if self.state == Ready || self.state == New
+      self.active = nil
+    end 
   end
 
 end

commit 002f863605469cee7e112f4c16a78e3b6278672c
Author: radhika <radhika at curoverse.com>
Date:   Wed May 7 19:34:24 2014 -0400

    2352: when --submit is used, set the state to Ready, not RunningOnClient.
    And do not set Active to true.

diff --git a/sdk/cli/bin/arv-run-pipeline-instance b/sdk/cli/bin/arv-run-pipeline-instance
index 60d5c38..f0ada5d 100755
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -413,10 +413,16 @@ class WhRunPipelineInstance
   end
 
   def setup_instance
-    @instance ||= PipelineInstance.
-      create(:components => @components,
+    if $options[:submit]
+      @instance ||= PipelineInstance.
+        create(:components => @components,
+              :pipeline_template_uuid => @template[:uuid])
+    else
+      @instance ||= PipelineInstance.
+        create(:components => @components,
              :pipeline_template_uuid => @template[:uuid],
              :state => 'RunningOnClient')
+    end
     self
   end
 

commit 6c2a704b7a2d721087976b2b8ec4f22cdaf44178
Merge: 01436e8 cdf7b16
Author: radhika <radhika at curoverse.com>
Date:   Wed May 7 15:04:40 2014 -0400

    Merge branch 'master' into 2352-use-state


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