[ARVADOS] updated: 05f378abc55181607383c7035671d306e9c4b96e

git at public.curoverse.com git at public.curoverse.com
Tue Feb 11 17:13:45 EST 2014


Summary of changes:
 .gitignore                                         |    3 +-
 apps/workbench/Gemfile                             |    6 +-
 apps/workbench/Gemfile.lock                        |   19 +-
 .../app/assets/javascripts/application.js          |   13 +-
 apps/workbench/app/assets/javascripts/editable.js  |   10 +
 .../workbench/app/assets/javascripts/provenance.js |   53 ----
 apps/workbench/app/assets/javascripts/sizing.js    |   30 +++
 .../app/assets/stylesheets/application.css         |   91 -------
 .../app/assets/stylesheets/application.css.scss    |  127 +++++++++
 .../app/assets/stylesheets/badges.css.scss         |   28 ++
 .../stylesheets/bootstrap_and_overrides.css.less   |   30 ---
 apps/workbench/app/assets/stylesheets/loading.css  |    2 +-
 .../api_client_authorizations_controller.rb        |    5 +
 .../app/controllers/application_controller.rb      |   87 ++++++-
 .../app/controllers/authorized_keys_controller.rb  |    2 +-
 .../app/controllers/collections_controller.rb      |    6 +-
 .../workbench/app/controllers/groups_controller.rb |    3 +-
 apps/workbench/app/controllers/jobs_controller.rb  |   12 +
 .../controllers/pipeline_instances_controller.rb   |   10 +
 .../app/controllers/sessions_controller.rb         |    3 +-
 apps/workbench/app/controllers/users_controller.rb |    4 +-
 apps/workbench/app/helpers/application_helper.rb   |    6 +-
 .../app/helpers/pipeline_instances_helper.rb       |   31 ++-
 apps/workbench/app/helpers/provenance_helper.rb    |    4 +-
 .../{_help.html.erb => _show_help.html.erb}        |    0
 .../views/application/_arvados_attr_value.html.erb |    2 +-
 .../app/views/application/_arvados_object.html.erb |   88 -------
 .../application/_breadcrumb_page_name.html.erb     |    2 +-
 .../app/views/application/_breadcrumbs.html.erb    |   18 --
 .../app/views/application/_content.html.erb        |   31 +++
 .../app/views/application/_content_layout.html.erb |    3 +
 .../application/_delete_object_button.html.erb     |    5 +
 .../.gitkeep => views/application/_index.html.erb} |    0
 .../app/views/application/_recent.html.erb         |   61 -----
 .../app/views/application/_show_api.html.erb       |   42 +++
 .../views/application/_show_attributes.html.erb    |   14 +-
 .../app/views/application/_show_json.html.erb      |    3 +
 .../app/views/application/_show_metadata.html.erb  |   58 ++++
 .../app/views/application/_show_recent.html.erb    |   57 ++++
 .../app/views/application/_svg_div.html.erb        |   13 +-
 .../workbench/app/views/application/index.html.erb |   25 +--
 apps/workbench/app/views/application/show.html.erb |   48 ++--
 .../{_help.html.erb => _show_help.html.erb}        |    0
 .../app/views/authorized_keys/index.html.erb       |    1 -
 .../app/views/collections/_index_tbody.html.erb    |   24 ++-
 .../app/views/collections/_recent.html.erb         |   43 ---
 .../app/views/collections/_show_files.html.erb     |   23 +-
 .../collections/_show_provenance_graph.html.erb    |    6 -
 .../app/views/collections/_show_recent.html.erb    |   48 ++++
 .../app/views/collections/_show_used_by.html.erb   |    6 -
 .../app/views/groups/_show_recent.html.erb         |   38 +++
 apps/workbench/app/views/groups/index.html.erb     |   42 ---
 apps/workbench/app/views/jobs/_recent.html.erb     |  141 ----------
 .../app/views/jobs/_show_provenance.html.erb       |    4 +
 .../workbench/app/views/jobs/_show_recent.html.erb |  136 ++++++++++
 apps/workbench/app/views/jobs/show.html.erb        |    6 -
 .../app/views/layouts/application.html.erb         |  250 ++++++++++++++----
 apps/workbench/app/views/links/_recent.html.erb    |    2 +-
 .../_collections_notification.html.erb             |    7 +
 .../notifications/_jobs_notification.html.erb      |    8 +
 .../notifications/_pipelines_notification.html.erb |    7 +
 .../notifications/_ssh_key_notification.html.erb   |   20 ++
 .../app/views/pipeline_instances/_recent.html.erb  |   91 -------
 .../pipeline_instances/_show_components.html.erb   |   74 ++++++
 .../views/pipeline_instances/_show_graph.html.erb  |   19 ++
 .../{show.js.erb => _show_graph.js.erb}            |    0
 .../views/pipeline_instances/_show_recent.html.erb |   98 +++++++
 .../pipeline_instances/_show_text_compare.html.erb |   78 ++++++
 .../app/views/pipeline_instances/compare.html.erb  |   88 +-------
 .../app/views/pipeline_instances/show.html.erb     |   89 -------
 .../pipeline_templates/_show_attributes.html.erb   |   39 +++
 .../{_recent.html.erb => _show_recent.html.erb}    |    0
 .../app/views/pipeline_templates/show.html.erb     |   42 ---
 .../{_help.html.erb => _show_help.html.erb}        |    0
 apps/workbench/app/views/users/_home.html.erb      |   31 +---
 .../app/views/users/_notifications.html.erb        |  107 --------
 apps/workbench/app/views/users/_tables.html.erb    |   93 +++++--
 .../{_help.html.erb => _show_help.html.erb}        |    0
 doc/Gemfile                                        |    4 +-
 doc/Gemfile.lock                                   |   63 ++---
 doc/README_FOR_APP                                 |    2 -
 doc/Rakefile                                       |   25 ++
 doc/_config.yml                                    |   96 +++++++-
 doc/_includes/{0-filter.py => _0_filter_py.liquid} |    0
 ...rt-incomplete.html => _alert-incomplete.liquid} |    0
 .../{alert-stub.html => _alert_stub.liquid}        |    0
 doc/_includes/_navbar_left.liquid                  |   20 ++
 .../{navbar_top.html => _navbar_top.liquid}        |    0
 .../{notebox-begin.html => _notebox_begin.liquid}  |    0
 .../{notebox-end.html => _notebox_end.liquid}      |    0
 ...h_script.py => _parallel_hash_script_py.liquid} |    0
 .../{run-md5sum.py => _run_md5sum_py.liquid}       |    0
 ...h_script.py => _tutorial_hash_script_py.liquid} |    0
 doc/_includes/navbar_left.html                     |   27 --
 doc/_layouts/default.html                          |  120 ---------
 doc/_layouts/default.html.liquid                   |  120 +++++++++
 doc/admin/cheat_sheet.html.textile.liquid          |   72 +++++
 doc/admin/cheat_sheet.textile                      |   73 ------
 doc/admin/index.html.md.liquid                     |   14 +
 doc/admin/index.md                                 |   15 -
 doc/api/authentication.html.textile.liquid         |   40 +++
 doc/api/authentication.textile                     |   40 ---
 doc/api/crunch-scripts.html.textile.liquid         |   46 ++++
 doc/api/crunch-scripts.textile                     |   46 ----
 doc/api/index.html.textile.liquid                  |   52 ++++
 doc/api/index.textile                              |   52 ----
 doc/api/methods.html.textile.liquid                |   80 ++++++
 doc/api/methods.textile                            |   80 ------
 .../api_client_authorizations.html.textile.liquid  |  109 ++++++++
 doc/api/methods/api_client_authorizations.textile  |  109 --------
 doc/api/methods/api_clients.html.textile.liquid    |   98 +++++++
 doc/api/methods/api_clients.textile                |   98 -------
 .../methods/authorized_keys.html.textile.liquid    |   98 +++++++
 doc/api/methods/authorized_keys.textile            |   98 -------
 doc/api/methods/collections.html.textile.liquid    |   98 +++++++
 doc/api/methods/collections.textile                |   98 -------
 doc/api/methods/groups.html.textile.liquid         |   98 +++++++
 doc/api/methods/groups.textile                     |   98 -------
 doc/api/methods/humans.html.textile.liquid         |   98 +++++++
 doc/api/methods/humans.textile                     |   98 -------
 doc/api/methods/job_tasks.html.textile.liquid      |   98 +++++++
 doc/api/methods/job_tasks.textile                  |   98 -------
 doc/api/methods/jobs.html.textile.liquid           |  130 ++++++++++
 doc/api/methods/jobs.textile                       |  130 ----------
 doc/api/methods/keep_disks.html.textile.liquid     |  114 ++++++++
 doc/api/methods/keep_disks.textile                 |  114 --------
 doc/api/methods/links.html.textile.liquid          |  109 ++++++++
 doc/api/methods/links.textile                      |  109 --------
 doc/api/methods/logs.html.textile.liquid           |   98 +++++++
 doc/api/methods/logs.textile                       |   98 -------
 doc/api/methods/nodes.html.textile.liquid          |  109 ++++++++
 doc/api/methods/nodes.textile                      |  109 --------
 .../methods/pipeline_instances.html.textile.liquid |   98 +++++++
 doc/api/methods/pipeline_instances.textile         |   98 -------
 .../methods/pipeline_templates.html.textile.liquid |   98 +++++++
 doc/api/methods/pipeline_templates.textile         |   98 -------
 doc/api/methods/repositories.html.textile.liquid   |  107 ++++++++
 doc/api/methods/repositories.textile               |  107 --------
 doc/api/methods/specimens.html.textile.liquid      |   98 +++++++
 doc/api/methods/specimens.textile                  |   98 -------
 doc/api/methods/traits.html.textile.liquid         |   98 +++++++
 doc/api/methods/traits.textile                     |   98 -------
 doc/api/methods/users.html.textile.liquid          |  126 +++++++++
 doc/api/methods/users.textile                      |  126 ---------
 .../methods/virtual_machines.html.textile.liquid   |  117 +++++++++
 doc/api/methods/virtual_machines.textile           |  117 ---------
 doc/api/permission-model.html.textile.liquid       |  107 ++++++++
 doc/api/permission-model.textile                   |  107 --------
 doc/api/resources.html.textile.liquid              |   49 ++++
 doc/api/resources.textile                          |   49 ----
 doc/api/schema/ApiClient.html.textile.liquid       |   38 +++
 doc/api/schema/ApiClient.textile                   |   38 ---
 .../ApiClientAuthorization.html.textile.liquid     |   44 ++++
 doc/api/schema/ApiClientAuthorization.textile      |   44 ----
 doc/api/schema/AuthorizedKey.html.textile.liquid   |   40 +++
 doc/api/schema/AuthorizedKey.textile               |   40 ---
 doc/api/schema/Collection.html.textile.liquid      |   45 ++++
 doc/api/schema/Collection.textile                  |   45 ----
 doc/api/schema/Commit.html.textile.liquid          |   38 +++
 doc/api/schema/Commit.textile                      |   38 ---
 doc/api/schema/CommitAncestor.html.textile.liquid  |   39 +++
 doc/api/schema/CommitAncestor.textile              |   39 ---
 doc/api/schema/Group.html.textile.liquid           |   37 +++
 doc/api/schema/Group.textile                       |   37 ---
 doc/api/schema/Human.html.textile.liquid           |   36 +++
 doc/api/schema/Human.textile                       |   36 ---
 doc/api/schema/Job.html.textile.liquid             |   83 ++++++
 doc/api/schema/Job.textile                         |   83 ------
 doc/api/schema/JobTask.html.textile.liquid         |   51 ++++
 doc/api/schema/JobTask.textile                     |   51 ----
 doc/api/schema/KeepDisk.html.textile.liquid        |   48 ++++
 doc/api/schema/KeepDisk.textile                    |   48 ----
 doc/api/schema/Link.html.textile.liquid            |   87 +++++++
 doc/api/schema/Link.textile                        |   87 -------
 doc/api/schema/Log.html.textile.liquid             |   39 +++
 doc/api/schema/Log.textile                         |   39 ---
 doc/api/schema/Node.html.textile.liquid            |   42 +++
 doc/api/schema/Node.textile                        |   42 ---
 .../schema/PipelineInstance.html.textile.liquid    |   41 +++
 doc/api/schema/PipelineInstance.textile            |   41 ---
 .../schema/PipelineTemplate.html.textile.liquid    |   37 +++
 doc/api/schema/PipelineTemplate.textile            |   37 ---
 doc/api/schema/Repository.html.textile.liquid      |   38 +++
 doc/api/schema/Repository.textile                  |   38 ---
 doc/api/schema/Specimen.html.textile.liquid        |   37 +++
 doc/api/schema/Specimen.textile                    |   37 ---
 doc/api/schema/Trait.html.textile.liquid           |   37 +++
 doc/api/schema/Trait.textile                       |   37 ---
 doc/api/schema/User.html.textile.liquid            |   43 +++
 doc/api/schema/User.textile                        |   43 ---
 doc/api/schema/VirtualMachine.html.textile.liquid  |   36 +++
 doc/api/schema/VirtualMachine.textile              |   36 ---
 doc/gen_api_method_docs.py                         |    1 -
 doc/index.html                                     |   46 ----
 doc/index.html.liquid                              |   47 ++++
 doc/install/client.html.textile.liquid             |   36 +++
 doc/install/client.textile                         |   36 ---
 .../create-standard-objects.html.textile.liquid    |   60 +++++
 doc/install/create-standard-objects.textile        |   60 -----
 doc/install/index.html.md.liquid                   |   17 ++
 doc/install/index.md                               |   18 --
 doc/install/install-api-server.html.md             |  114 ++++++++
 doc/install/install-api-server.md                  |  114 --------
 .../install-crunch-dispatch.html.textile.liquid    |  102 ++++++++
 doc/install/install-crunch-dispatch.textile        |  102 --------
 doc/install/install-workbench-app.html.md          |   63 +++++
 doc/install/install-workbench-app.md               |   63 -----
 doc/mkpydoc.sh                                     |    5 -
 doc/sdk/index.html.textile.liquid                  |   12 +
 doc/sdk/index.textile                              |   12 -
 .../crunch-utility-libraries.html.textile.liquid   |  225 ++++++++++++++++
 doc/sdk/python/crunch-utility-libraries.textile    |  225 ----------------
 doc/sdk/python/python.html.textile.liquid          |   10 +
 doc/sdk/python/python.textile                      |   10 -
 doc/sdk/python/sdk-python.html.textile.liquid      |  120 +++++++++
 doc/sdk/python/sdk-python.textile                  |  120 ---------
 .../examples/crunch-examples.html.textile.liquid   |   98 +++++++
 doc/user/examples/crunch-examples.textile          |   98 -------
 .../check-environment.html.textile.liquid          |   54 ++++
 doc/user/getting_started/check-environment.textile |   54 ----
 .../getting_started/community.html.textile.liquid  |   25 ++
 doc/user/getting_started/community.textile         |   25 --
 .../getting_started/ssh-access.html.textile.liquid |  217 ++++++++++++++++
 doc/user/getting_started/ssh-access.textile        |  217 ----------------
 .../getting_started/workbench.html.textile.liquid  |   18 ++
 doc/user/getting_started/workbench.textile         |   18 --
 doc/user/index.html.textile.liquid                 |   51 ++++
 doc/user/index.textile                             |   51 ----
 doc/user/reference/api-tokens.html.textile.liquid  |   47 ++++
 doc/user/reference/api-tokens.textile              |   47 ----
 doc/user/reference/sdk-cli.html.textile.liquid     |   81 ++++++
 doc/user/reference/sdk-cli.textile                 |   81 ------
 .../running-external-program.html.textile.liquid   |   67 +++++
 .../tutorials/running-external-program.textile     |   67 -----
 .../tutorial-firstscript.html.textile.liquid       |  124 +++++++++
 doc/user/tutorials/tutorial-firstscript.textile    |  124 ---------
 ...rial-gatk-variantfiltration.html.textile.liquid |  216 ++++++++++++++++
 .../tutorial-gatk-variantfiltration.textile        |  216 ----------------
 .../tutorial-job-debug.html.textile.liquid         |  156 +++++++++++
 doc/user/tutorials/tutorial-job-debug.textile      |  156 -----------
 .../tutorials/tutorial-job1.html.textile.liquid    |  233 +++++++++++++++++
 doc/user/tutorials/tutorial-job1.textile           |  233 -----------------
 .../tutorials/tutorial-keep.html.textile.liquid    |  136 ++++++++++
 doc/user/tutorials/tutorial-keep.textile           |  136 ----------
 .../tutorial-new-pipeline.html.textile.liquid      |  158 +++++++++++
 doc/user/tutorials/tutorial-new-pipeline.textile   |  158 -----------
 .../tutorial-parallel.html.textile.liquid          |   81 ++++++
 doc/user/tutorials/tutorial-parallel.textile       |   81 ------
 .../tutorial-trait-search.html.textile.liquid      |  273 ++++++++++++++++++++
 doc/user/tutorials/tutorial-trait-search.textile   |  273 --------------------
 doc/zenweb-liquid.rb                               |   41 +++
 doc/zenweb-textile.rb                              |   17 ++
 docker/Makefile                                    |    2 +-
 docker/api/production.rb.in                        |    4 +
 docker/workbench/production.rb.in                  |    9 +-
 sdk/cli/Gemfile                                    |    2 +-
 sdk/cli/Gemfile.lock                               |   24 +-
 sdk/cli/arvados-cli.gemspec                        |    2 +-
 sdk/cli/bin/arv                                    |    2 +-
 sdk/python/arvados/collection.py                   |    9 +-
 sdk/python/arvados/keep.py                         |   40 ++-
 sdk/python/bin/arv-get                             |   11 +-
 services/api/app/models/job.rb                     |   11 +
 263 files changed, 8144 insertions(+), 7703 deletions(-)
 create mode 100644 apps/workbench/app/assets/javascripts/editable.js
 delete mode 100644 apps/workbench/app/assets/javascripts/provenance.js
 create mode 100644 apps/workbench/app/assets/javascripts/sizing.js
 delete mode 100644 apps/workbench/app/assets/stylesheets/application.css
 create mode 100644 apps/workbench/app/assets/stylesheets/application.css.scss
 create mode 100644 apps/workbench/app/assets/stylesheets/badges.css.scss
 delete mode 100644 apps/workbench/app/assets/stylesheets/bootstrap_and_overrides.css.less
 rename apps/workbench/app/views/api_client_authorizations/{_help.html.erb => _show_help.html.erb} (100%)
 create mode 100644 apps/workbench/app/views/application/_content.html.erb
 create mode 100644 apps/workbench/app/views/application/_content_layout.html.erb
 create mode 100644 apps/workbench/app/views/application/_delete_object_button.html.erb
 copy apps/workbench/app/{mailers/.gitkeep => views/application/_index.html.erb} (100%)
 delete mode 100644 apps/workbench/app/views/application/_recent.html.erb
 create mode 100644 apps/workbench/app/views/application/_show_api.html.erb
 create mode 100644 apps/workbench/app/views/application/_show_json.html.erb
 create mode 100644 apps/workbench/app/views/application/_show_metadata.html.erb
 create mode 100644 apps/workbench/app/views/application/_show_recent.html.erb
 rename apps/workbench/app/views/authorized_keys/{_help.html.erb => _show_help.html.erb} (100%)
 delete mode 100644 apps/workbench/app/views/authorized_keys/index.html.erb
 delete mode 100644 apps/workbench/app/views/collections/_recent.html.erb
 create mode 100644 apps/workbench/app/views/collections/_show_recent.html.erb
 create mode 100644 apps/workbench/app/views/groups/_show_recent.html.erb
 delete mode 100644 apps/workbench/app/views/groups/index.html.erb
 delete mode 100644 apps/workbench/app/views/jobs/_recent.html.erb
 create mode 100644 apps/workbench/app/views/jobs/_show_provenance.html.erb
 create mode 100644 apps/workbench/app/views/jobs/_show_recent.html.erb
 delete mode 100644 apps/workbench/app/views/jobs/show.html.erb
 create mode 100644 apps/workbench/app/views/notifications/_collections_notification.html.erb
 create mode 100644 apps/workbench/app/views/notifications/_jobs_notification.html.erb
 create mode 100644 apps/workbench/app/views/notifications/_pipelines_notification.html.erb
 create mode 100644 apps/workbench/app/views/notifications/_ssh_key_notification.html.erb
 delete mode 100644 apps/workbench/app/views/pipeline_instances/_recent.html.erb
 create mode 100644 apps/workbench/app/views/pipeline_instances/_show_components.html.erb
 create mode 100644 apps/workbench/app/views/pipeline_instances/_show_graph.html.erb
 rename apps/workbench/app/views/pipeline_instances/{show.js.erb => _show_graph.js.erb} (100%)
 create mode 100644 apps/workbench/app/views/pipeline_instances/_show_recent.html.erb
 create mode 100644 apps/workbench/app/views/pipeline_instances/_show_text_compare.html.erb
 delete mode 100644 apps/workbench/app/views/pipeline_instances/show.html.erb
 create mode 100644 apps/workbench/app/views/pipeline_templates/_show_attributes.html.erb
 rename apps/workbench/app/views/pipeline_templates/{_recent.html.erb => _show_recent.html.erb} (100%)
 delete mode 100644 apps/workbench/app/views/pipeline_templates/show.html.erb
 rename apps/workbench/app/views/repositories/{_help.html.erb => _show_help.html.erb} (100%)
 delete mode 100644 apps/workbench/app/views/users/_notifications.html.erb
 rename apps/workbench/app/views/virtual_machines/{_help.html.erb => _show_help.html.erb} (100%)
 delete mode 100644 doc/README_FOR_APP
 create mode 100644 doc/Rakefile
 rename doc/_includes/{0-filter.py => _0_filter_py.liquid} (100%)
 rename doc/_includes/{alert-incomplete.html => _alert-incomplete.liquid} (100%)
 rename doc/_includes/{alert-stub.html => _alert_stub.liquid} (100%)
 create mode 100644 doc/_includes/_navbar_left.liquid
 rename doc/_includes/{navbar_top.html => _navbar_top.liquid} (100%)
 rename doc/_includes/{notebox-begin.html => _notebox_begin.liquid} (100%)
 rename doc/_includes/{notebox-end.html => _notebox_end.liquid} (100%)
 rename doc/_includes/{parallel_hash_script.py => _parallel_hash_script_py.liquid} (100%)
 rename doc/_includes/{run-md5sum.py => _run_md5sum_py.liquid} (100%)
 rename doc/_includes/{tutorial_hash_script.py => _tutorial_hash_script_py.liquid} (100%)
 delete mode 100644 doc/_includes/navbar_left.html
 delete mode 100644 doc/_layouts/default.html
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 delete mode 100644 doc/api/methods/collections.textile
 create mode 100644 doc/api/methods/groups.html.textile.liquid
 delete mode 100644 doc/api/methods/groups.textile
 create mode 100644 doc/api/methods/humans.html.textile.liquid
 delete mode 100644 doc/api/methods/humans.textile
 create mode 100644 doc/api/methods/job_tasks.html.textile.liquid
 delete mode 100644 doc/api/methods/job_tasks.textile
 create mode 100644 doc/api/methods/jobs.html.textile.liquid
 delete mode 100644 doc/api/methods/jobs.textile
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commit 05f378abc55181607383c7035671d306e9c4b96e
Merge: 3b39427 715869b
Author: Tim Pierce <twp at curoverse.com>
Date:   Tue Feb 11 15:05:14 2014 -0500

    Merge branch 'master' into 2013-search-all-the-things

diff --cc services/api/app/models/job.rb
index 71b006d,f32f001..a483418
--- a/services/api/app/models/job.rb
+++ b/services/api/app/models/job.rb
@@@ -35,12 -35,9 +35,13 @@@ class Job < ArvadosMode
      t.add :tasks_summary
      t.add :dependencies
      t.add :log_stream_href
+     t.add :log_buffer
    end
  
 +  def self.searchable?
 +    true
 +  end
 +
    def assert_finished
      update_attributes(finished_at: finished_at || Time.now,
                        success: success.nil? ? false : success,

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