[ARVADOS] updated: 956093639196f92f3ad4b9e0795bcc7e30520e0d
git at public.curoverse.com
git at public.curoverse.com
Mon Feb 10 16:51:30 EST 2014
Summary of changes:
.gitignore | 3 +-
apps/admin/list-inactive-users.rb | 24 ++
apps/admin/setup-new-user.rb | 2 +-
apps/workbench/Gemfile | 6 +-
apps/workbench/Gemfile.lock | 19 +-
.../app/assets/javascripts/application.js | 20 +-
apps/workbench/app/assets/javascripts/editable.js | 10 +
.../app/assets/javascripts/keep_disks.js.coffee | 0
apps/workbench/app/assets/javascripts/sizing.js | 30 ++
.../app/assets/stylesheets/application.css | 77 ----
.../app/assets/stylesheets/application.css.scss | 127 ++++++
.../app/assets/stylesheets/badges.css.scss | 28 ++
.../stylesheets/bootstrap_and_overrides.css.less | 30 --
.../app/assets/stylesheets/keep_disks.css.scss | 0
apps/workbench/app/assets/stylesheets/loading.css | 374 +++++++++++++++++
.../api_client_authorizations_controller.rb | 5 +
.../app/controllers/application_controller.rb | 114 +++++-
.../app/controllers/authorized_keys_controller.rb | 4 +
.../app/controllers/collections_controller.rb | 13 +-
.../workbench/app/controllers/groups_controller.rb | 3 +-
apps/workbench/app/controllers/jobs_controller.rb | 42 ++-
.../app/controllers/keep_disks_controller.rb | 2 +
.../controllers/pipeline_instances_controller.rb | 153 +++++++
.../app/controllers/repositories_controller.rb | 3 +
.../app/controllers/sessions_controller.rb | 3 +-
apps/workbench/app/controllers/users_controller.rb | 10 +-
.../app/controllers/virtual_machines_controller.rb | 3 +
apps/workbench/app/helpers/application_helper.rb | 12 +-
.../workbench}/app/helpers/keep_disks_helper.rb | 0
.../app/helpers/pipeline_instances_helper.rb | 98 ++++--
apps/workbench/app/helpers/provenance_helper.rb | 339 ++++++++++++++++
apps/workbench/app/models/arvados_api_client.rb | 7 +
apps/workbench/app/models/arvados_base.rb | 49 ++-
apps/workbench/app/models/collection.rb | 12 +
apps/workbench/app/models/keep_disk.rb | 5 +
apps/workbench/app/models/node.rb | 6 +-
apps/workbench/app/models/pipeline_instance.rb | 4 +
apps/workbench/app/models/user.rb | 6 +-
apps/workbench/app/models/virtual_machine.rb | 2 +-
.../api_client_authorizations/_show_help.html.erb | 14 +
.../views/api_client_authorizations/index.html.erb | 16 -
.../views/application/_arvados_attr_value.html.erb | 5 +-
.../app/views/application/_arvados_object.html.erb | 88 ----
.../application/_arvados_object_attr.html.erb | 5 +-
.../application/_breadcrumb_page_name.html.erb | 1 +
.../application/_breadcrumbs.html.erb} | 0
.../app/views/application/_content.html.erb | 31 ++
.../app/views/application/_content_layout.html.erb | 3 +
.../application/_delete_object_button.html.erb | 5 +
.../app/views/application/_index.html.erb | 73 ----
.../app/views/application/_loading.html.erb | 190 +++++++++
.../app/views/application/_show_api.html.erb | 42 ++
.../views/application/_show_attributes.html.erb | 13 +
.../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 | 38 ++
.../workbench/app/views/application/destroy.js.erb | 3 +
.../workbench/app/views/application/index.html.erb | 16 +-
apps/workbench/app/views/application/show.html.erb | 36 +-
.../app/views/authorized_keys/_show_help.html.erb | 10 +
.../app/views/authorized_keys/index.html.erb | 10 -
.../app/views/collections/_index_tbody.html.erb | 24 +-
apps/workbench/app/views/collections/_nav.html.erb | 8 -
.../app/views/collections/_show_files.html.erb | 39 ++
.../app/views/collections/_show_jobs.html.erb | 64 +++
.../views/collections/_show_provenance.html.erb | 84 ++++
.../collections/_show_provenance_graph.html.erb | 4 +
.../app/views/collections/_show_recent.html.erb | 48 +++
.../views/collections/_show_source_data.html.erb | 44 ++
.../app/views/collections/_show_used_by.html.erb | 5 +
.../workbench/app/views/collections/index.html.erb | 45 ---
apps/workbench/app/views/collections/show.html.erb | 251 ------------
.../app/views/groups/_show_recent.html.erb | 38 ++
apps/workbench/app/views/groups/index.html.erb | 42 --
.../app/views/jobs/_show_provenance.html.erb | 4 +
.../workbench/app/views/jobs/_show_recent.html.erb | 136 +++++++
apps/workbench/app/views/jobs/index.html.erb | 137 -------
apps/workbench/app/views/jobs/show.html.erb | 1 -
.../app/views/layouts/application.html.erb | 269 ++++++++++----
.../app/views/links/_breadcrumb_page_name.html.erb | 8 +
apps/workbench/app/views/links/_recent.html.erb | 57 +++
apps/workbench/app/views/links/index.html.erb | 57 ---
.../_collections_notification.html.erb | 7 +
.../notifications/_jobs_notification.html.erb | 8 +
.../notifications/_pipelines_notification.html.erb | 7 +
.../notifications/_ssh_key_notification.html.erb | 20 +
.../pipeline_instances/_show_components.html.erb | 74 ++++
.../views/pipeline_instances/_show_graph.html.erb | 19 +
.../views/pipeline_instances/_show_graph.js.erb | 3 +
.../views/pipeline_instances/_show_recent.html.erb | 98 +++++
.../pipeline_instances/_show_text_compare.html.erb | 78 ++++
.../app/views/pipeline_instances/compare.html.erb | 1 +
.../app/views/pipeline_instances/index.html.erb | 61 ---
.../app/views/pipeline_instances/show.html.erb | 33 --
.../pipeline_templates/_show_attributes.html.erb | 39 ++
.../{index.html.erb => _show_recent.html.erb} | 0
.../app/views/pipeline_templates/show.html.erb | 42 --
.../app/views/repositories/_show_help.html.erb | 27 ++
.../app/views/repositories/index.html.erb | 29 --
.../app/views/user_agreements/index.html.erb | 2 +
apps/workbench/app/views/users/_home.html.erb | 30 +--
.../app/views/users/_notifications.html.erb | 20 +-
apps/workbench/app/views/users/_tables.html.erb | 99 ++++--
apps/workbench/app/views/users/home.js.erb | 4 +
apps/workbench/app/views/users/index.html.erb | 62 ---
apps/workbench/app/views/users/welcome.html.erb | 2 +
.../app/views/virtual_machines/_show_help.html.erb | 26 ++
.../app/views/virtual_machines/index.html.erb | 30 --
apps/workbench/config/routes.rb | 5 +-
.../test/functional/keep_disks_controller_test.rb | 4 +
.../test/unit/helpers/keep_disks_helper_test.rb | 0
apps/workbench/test/unit/keep_disk_test.rb | 4 +
doc/Gemfile | 1 +
doc/Gemfile.lock | 2 +
doc/Rakefile | 13 +-
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
doc/_includes/_run-md5sum_py.liquid | 35 ++
...h_script.py => _tutorial_hash_script_py.liquid} | 0
doc/_includes/navbar_left.html | 27 --
doc/_includes/run-md5sum.py | 35 --
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 | 43 ++-
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/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 | 65 ---
.../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 | 27 ++-
doc/zenweb-textile.rb | 8 +-
docker/build.sh | 42 ++
docker/run.sh | 18 +-
sdk/cli/Gemfile | 8 +-
sdk/cli/Gemfile.lock | 22 +-
sdk/cli/arvados-cli.gemspec | 14 +-
sdk/cli/bin/arv | 44 ++-
sdk/cli/test/test_arv-collection-create.rb | 38 ++
sdk/cli/test/test_arv-tag.rb | 10 +-
sdk/perl/lib/Arvados.pm | 32 ++-
sdk/python/.gitignore | 1 +
sdk/python/arvados/__init__.py | 419 +-------------------
sdk/python/arvados/api.py | 91 +++++
sdk/python/arvados/collection.py | 6 +-
sdk/python/arvados/config.py | 34 ++
sdk/python/arvados/errors.py | 14 +
sdk/python/arvados/keep.py | 18 +-
sdk/python/arvados/stream.py | 7 +-
sdk/python/arvados/util.py | 306 ++++++++++++++
sdk/python/bin/arv-mount | 158 ++++++++
sdk/python/requirements.txt | 1 +
sdk/python/setup.py | 4 +
sdk/python/test_util.py | 22 +
sdk/ruby/Gemfile | 4 +
sdk/ruby/Gemfile.lock | 58 +++
sdk/{cli => ruby}/Rakefile | 0
sdk/ruby/arvados.gemspec | 3 +-
sdk/ruby/lib/arvados.rb | 86 ++++-
sdk/ruby/test/test_big_request.rb | 38 ++
.../api/app/controllers/application_controller.rb | 63 ++--
.../arvados/v1/collections_controller.rb | 170 ++++++++
.../app/controllers/arvados/v1/jobs_controller.rb | 1 +
.../arvados/v1/keep_disks_controller.rb | 35 +-
.../app/controllers/arvados/v1/nodes_controller.rb | 1 +
.../arvados/v1/repositories_controller.rb | 2 +
.../controllers/arvados/v1/schema_controller.rb | 57 ++--
.../arvados/v1/user_agreements_controller.rb | 3 +-
.../app/controllers/arvados/v1/users_controller.rb | 7 +-
.../arvados/v1/virtual_machines_controller.rb | 1 +
services/api/app/controllers/static_controller.rb | 2 +
.../app/controllers/user_sessions_controller.rb | 1 +
services/api/app/models/arvados_model.rb | 42 ++
services/api/app/models/collection.rb | 4 +-
services/api/app/models/job.rb | 16 +-
services/api/app/models/node.rb | 20 +-
services/api/app/models/user.rb | 20 +-
services/api/config/environments/test.rb.example | 3 +-
services/api/config/routes.rb | 2 +
.../20140117231056_normalize_collection_uuid.rb | 91 +++++
.../20140124222114_fix_link_kind_underscores.rb | 17 +
...malize_collection_uuids_in_script_parameters.rb | 45 +++
services/api/db/schema.rb | 2 +-
services/api/lib/kind_and_etag.rb | 2 +-
.../test/fixtures/api_client_authorizations.yml | 6 +
services/api/test/fixtures/collections.yml | 30 ++
services/api/test/fixtures/groups.yml | 18 +
services/api/test/fixtures/jobs.yml | 70 ++++
services/api/test/fixtures/links.yml | 145 +++++++
services/api/test/fixtures/users.yml | 10 +
services/api/test/fixtures/virtual_machines.yml | 4 +
.../arvados/v1/collections_controller_test.rb | 88 ++++
.../arvados/v1/groups_controller_test.rb | 8 +-
.../functional/arvados/v1/jobs_controller_test.rb | 17 +
.../arvados/v1/keep_disks_controller_test.rb | 30 +-
.../functional/arvados/v1/links_controller_test.rb | 21 +
.../arvados/v1/repositories_controller_test.rb | 11 +
.../functional/arvados/v1/users_controller_test.rb | 2 +-
.../api/test/integration/collections_api_test.rb | 21 +-
services/keep/INSTALL | 20 -
services/keep/keep.rb | 241 -----------
355 files changed, 11746 insertions(+), 8681 deletions(-)
create mode 100755 apps/admin/list-inactive-users.rb
create mode 100644 apps/workbench/app/assets/javascripts/editable.js
copy {services/api => apps/workbench}/app/assets/javascripts/keep_disks.js.coffee (100%)
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
copy {services/api => apps/workbench}/app/assets/stylesheets/keep_disks.css.scss (100%)
create mode 100644 apps/workbench/app/assets/stylesheets/loading.css
create mode 100644 apps/workbench/app/controllers/keep_disks_controller.rb
copy {services/api => apps/workbench}/app/helpers/keep_disks_helper.rb (100%)
create mode 100644 apps/workbench/app/helpers/provenance_helper.rb
create mode 100644 apps/workbench/app/models/keep_disk.rb
create mode 100644 apps/workbench/app/views/api_client_authorizations/_show_help.html.erb
delete mode 100644 apps/workbench/app/views/api_client_authorizations/index.html.erb
create mode 100644 apps/workbench/app/views/application/_breadcrumb_page_name.html.erb
copy apps/workbench/app/{mailers/.gitkeep => views/application/_breadcrumbs.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
create mode 100644 apps/workbench/app/views/application/_loading.html.erb
create mode 100644 apps/workbench/app/views/application/_show_api.html.erb
create mode 100644 apps/workbench/app/views/application/_show_attributes.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
create mode 100644 apps/workbench/app/views/application/_svg_div.html.erb
create mode 100644 apps/workbench/app/views/application/destroy.js.erb
create mode 100644 apps/workbench/app/views/authorized_keys/_show_help.html.erb
delete mode 100644 apps/workbench/app/views/authorized_keys/index.html.erb
delete mode 100644 apps/workbench/app/views/collections/_nav.html.erb
create mode 100644 apps/workbench/app/views/collections/_show_files.html.erb
create mode 100644 apps/workbench/app/views/collections/_show_jobs.html.erb
create mode 100644 apps/workbench/app/views/collections/_show_provenance.html.erb
create mode 100644 apps/workbench/app/views/collections/_show_provenance_graph.html.erb
create mode 100644 apps/workbench/app/views/collections/_show_recent.html.erb
create mode 100644 apps/workbench/app/views/collections/_show_source_data.html.erb
create mode 100644 apps/workbench/app/views/collections/_show_used_by.html.erb
delete mode 100644 apps/workbench/app/views/collections/index.html.erb
delete mode 100644 apps/workbench/app/views/collections/show.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
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/index.html.erb
delete mode 100644 apps/workbench/app/views/jobs/show.html.erb
create mode 100644 apps/workbench/app/views/links/_breadcrumb_page_name.html.erb
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Those revisions listed above that are new to this repository have
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commit 956093639196f92f3ad4b9e0795bcc7e30520e0d
Merge: b54a5ea 419a2af
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Feb 10 16:42:30 2014 -0500
Merge remote-tracking branch 'origin/master' into 1786-replace-jekyll-with-zenweb
commit b54a5ea817d3d2087eaa07dcf98ec8a82af56d06
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Feb 10 16:39:03 2014 -0500
Jekyll is dead, long live Zenweb!
diff --git a/.gitignore b/.gitignore
index 471e7cc..4d6cc39 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,5 @@
docker/*/generated/*
docker/config.yml
doc/_site/*
-doc/.site/*
\ No newline at end of file
+doc/.site/*
+doc/sdk/python/arvados
\ No newline at end of file
diff --git a/doc/Gemfile b/doc/Gemfile
index ad695f0..497682b 100644
--- a/doc/Gemfile
+++ b/doc/Gemfile
@@ -2,3 +2,4 @@ source 'https://rubygems.org'
gem 'zenweb'
gem 'liquid'
+gem 'RedCloth'
diff --git a/doc/Gemfile.lock b/doc/Gemfile.lock
index 5de90b1..048f27a 100644
--- a/doc/Gemfile.lock
+++ b/doc/Gemfile.lock
@@ -1,6 +1,7 @@
GEM
remote: https://rubygems.org/
specs:
+ RedCloth (4.2.9)
coderay (1.1.0)
kramdown (1.3.1)
less (1.2.21)
@@ -26,5 +27,6 @@ PLATFORMS
ruby
DEPENDENCIES
+ RedCloth
liquid
zenweb
diff --git a/doc/Rakefile b/doc/Rakefile
index 65d2855..2ebd272 100644
--- a/doc/Rakefile
+++ b/doc/Rakefile
@@ -1,7 +1,18 @@
#!/usr/bin/env rake
require "rubygems"
-require "zenweb/tasks"
+Rake.application.rake_require "zenweb/tasks"
load "zenweb-textile.rb"
load "zenweb-liquid.rb"
+file ".site/sdk/python/arvados/index.html" do |t|
+ sh "epydoc --html -o sdk/python/arvados arvados"
+ Dir["sdk/python/arvados/*"].each do |f|
+ puts f
+ $website.pages[f] = Zenweb::Page.new($website, f)
+ end
+end
+
+task :extra_wirings do
+ $website.pages["sdk/python/python.html.textile.liquid"].depends_on(".site/sdk/python/arvados/index.html")
+end
diff --git a/doc/_config.yml b/doc/_config.yml
index cd13810..c9dab0f 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -1,16 +1,92 @@
exclude: ["Rakefile", "tmp"]
baseurl: /doc
arvados_api_host: qr1hi.arvadosapi.com
-layout: default
+
navbar:
userguide:
- - Getting Started
- - Tutorials
- - Examples
- - Reference
- api:
- - Concepts
- - API Methods
- - Schema
+ - Getting Started:
+ - user/getting_started/workbench.html.textile.liquid
+ - user/getting_started/ssh-access.html.textile.liquid
+ - user/getting_started/check-environment.html.textile.liquid
+ - user/getting_started/community.html.textile.liquid
+ - Tutorials:
+ - user/tutorials/tutorial-keep.html.textile.liquid
+ - user/tutorials/tutorial-job1.html.textile.liquid
+ - user/tutorials/tutorial-firstscript.html.textile.liquid
+ - user/tutorials/tutorial-job-debug.html.textile.liquid
+ - user/tutorials/tutorial-new-pipeline.html.textile.liquid
+ - user/tutorials/tutorial-parallel.html.textile.liquid
+ - user/tutorials/tutorial-trait-search.html.textile.liquid
+ - user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
+ - user/tutorials/running-external-program.html.textile.liquid
+ - Examples:
+ - user/examples/crunch-examples.html.textile.liquid
+ - Reference:
+ - user/reference/api-tokens.html.textile.liquid
+ - user/reference/sdk-cli.html.textile.liquid
sdk:
- - Python
+ - Python:
+ - sdk/python/sdk-python.html.textile.liquid
+ - sdk/python/python.html.textile.liquid
+ - sdk/python/crunch-utility-libraries.html.textile.liquid
+ api:
+ - Concepts:
+ - api/authentication.html.textile.liquid
+ - api/methods.html.textile.liquid
+ - api/resources.html.textile.liquid
+ - api/crunch-scripts.html.textile.liquid
+ - api/permission-model.html.textile.liquid
+ - API Methods:
+ - api/methods/api_client_authorizations.html.textile.liquid
+ - api/methods/api_clients.html.textile.liquid
+ - api/methods/authorized_keys.html.textile.liquid
+ - api/methods/collections.html.textile.liquid
+ - api/methods/groups.html.textile.liquid
+ - api/methods/humans.html.textile.liquid
+ - api/methods/jobs.html.textile.liquid
+ - api/methods/job_tasks.html.textile.liquid
+ - api/methods/keep_disks.html.textile.liquid
+ - api/methods/links.html.textile.liquid
+ - api/methods/logs.html.textile.liquid
+ - api/methods/nodes.html.textile.liquid
+ - api/methods/pipeline_instances.html.textile.liquid
+ - api/methods/pipeline_templates.html.textile.liquid
+ - api/methods/repositories.html.textile.liquid
+ - api/methods/specimens.html.textile.liquid
+ - api/methods/traits.html.textile.liquid
+ - api/methods/users.html.textile.liquid
+ - api/methods/virtual_machines.html.textile.liquid
+ - Schema:
+ - api/schema/ApiClientAuthorization.html.textile.liquid
+ - api/schema/ApiClient.html.textile.liquid
+ - api/schema/AuthorizedKey.html.textile.liquid
+ - api/schema/Collection.html.textile.liquid
+ - api/schema/CommitAncestor.html.textile.liquid
+ - api/schema/Commit.html.textile.liquid
+ - api/schema/Group.html.textile.liquid
+ - api/schema/Human.html.textile.liquid
+ - api/schema/Job.html.textile.liquid
+ - api/schema/JobTask.html.textile.liquid
+ - api/schema/KeepDisk.html.textile.liquid
+ - api/schema/Link.html.textile.liquid
+ - api/schema/Log.html.textile.liquid
+ - api/schema/Node.html.textile.liquid
+ - api/schema/PipelineInstance.html.textile.liquid
+ - api/schema/PipelineTemplate.html.textile.liquid
+ - api/schema/Repository.html.textile.liquid
+ - api/schema/Specimen.html.textile.liquid
+ - api/schema/Trait.html.textile.liquid
+ - api/schema/User.html.textile.liquid
+ - api/schema/VirtualMachine.html.textile.liquid
+ admin:
+ - Admin:
+ - admin/index.html.md.liquid
+ - admin/cheat_sheet.html.textile.liquid
+ installguide:
+ - Install:
+ - install/install-api-server.html.md.liquid
+ - install/index.html.md.liquid
+ - install/install-workbench-app.html.md.liquid
+ - install/client.html.textile.liquid
+ - install/create-standard-objects.html.textile.liquid
+ - install/install-crunch-dispatch.html.textile.liquid
diff --git a/doc/_includes/0-filter.py b/doc/_includes/_0-filter_py.liquid
similarity index 100%
rename from doc/_includes/0-filter.py
rename to doc/_includes/_0-filter_py.liquid
diff --git a/doc/_includes/alert-incomplete.html b/doc/_includes/_alert-incomplete.liquid
similarity index 100%
rename from doc/_includes/alert-incomplete.html
rename to doc/_includes/_alert-incomplete.liquid
diff --git a/doc/_includes/alert-stub.html b/doc/_includes/_alert_stub.liquid
similarity index 100%
rename from doc/_includes/alert-stub.html
rename to doc/_includes/_alert_stub.liquid
diff --git a/doc/_includes/_navbar_left.liquid b/doc/_includes/_navbar_left.liquid
new file mode 100644
index 0000000..92d2082
--- /dev/null
+++ b/doc/_includes/_navbar_left.liquid
@@ -0,0 +1,20 @@
+<div class="span3">
+ <div class="affix-top">
+ <div class="well sidebar-nav">
+ <ol class="nav nav-list">
+ {% for section in site.navbar[page.navsection] %}
+ {% for entry in section %}
+ <li><span class="nav-header">{{ entry[0] }}</span>
+ <ol class="nav nav-list">
+ {% for item in entry[1] %}
+ {% assign p = site.pages[item] %}
+ <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}>
+ <a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
+ {% endfor %}
+ </ol>
+ {% endfor %}
+ {% endfor %}
+ </ol>
+ </div>
+ </div>
+</div>
diff --git a/doc/_includes/navbar_top.html b/doc/_includes/_navbar_top.liquid
similarity index 100%
rename from doc/_includes/navbar_top.html
rename to doc/_includes/_navbar_top.liquid
diff --git a/doc/_includes/notebox-begin.html b/doc/_includes/_notebox-begin.liquid
similarity index 100%
rename from doc/_includes/notebox-begin.html
rename to doc/_includes/_notebox-begin.liquid
diff --git a/doc/_includes/notebox-end.html b/doc/_includes/_notebox-end.liquid
similarity index 100%
rename from doc/_includes/notebox-end.html
rename to doc/_includes/_notebox-end.liquid
diff --git a/doc/_includes/parallel_hash_script.py b/doc/_includes/_parallel_hash_script_py.liquid
similarity index 100%
rename from doc/_includes/parallel_hash_script.py
rename to doc/_includes/_parallel_hash_script_py.liquid
diff --git a/doc/_includes/run-md5sum.py b/doc/_includes/_run-md5sum_py.liquid
similarity index 100%
rename from doc/_includes/run-md5sum.py
rename to doc/_includes/_run-md5sum_py.liquid
diff --git a/doc/_includes/tutorial_hash_script.py b/doc/_includes/_tutorial_hash_script_py.liquid
similarity index 100%
rename from doc/_includes/tutorial_hash_script.py
rename to doc/_includes/_tutorial_hash_script_py.liquid
diff --git a/doc/_includes/navbar_left.html b/doc/_includes/navbar_left.html
deleted file mode 100644
index ff5726f..0000000
--- a/doc/_includes/navbar_left.html
+++ /dev/null
@@ -1,27 +0,0 @@
- <div class="span3">
- <div class="affix-top">
- <div class="well sidebar-nav">
- {% if page.navsection == 'userguide' or page.navsection == 'api' or page.navsection == 'sdk' %}
- <ol class="nav nav-list">
- {% for menu_item in site.navbar[page.navsection] %}
- <li><span class="nav-header">{{ menu_item }}</span>
- <ol class="nav nav-list">
- {% for navorder in (0..99) %}
- {% for p in site.pages %}
- {% if p.navsection == page.navsection and p.navmenu == menu_item and p.navorder == navorder %}
- <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
- {% endif %}{% endfor %}{% endfor %}
- </ol>
- </li>
- {% endfor %}
- </ol>
- {% else %}
- <ol class="nav nav-list">
- {% for navorder in (0..99) %}{% for p in site.pages %}{% if p.navsection == page.navsection and p.navorder == navorder %}
- <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}><a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
- {% endif %}{% endfor %}{% endfor %}
- </ol>
- {% endif %}
- </div>
- </div>
- </div>
diff --git a/doc/_layouts/default.html b/doc/_layouts/default.html.liquid
similarity index 97%
rename from doc/_layouts/default.html
rename to doc/_layouts/default.html.liquid
index 4e2f08a..ba3ce3a 100644
--- a/doc/_layouts/default.html
+++ b/doc/_layouts/default.html.liquid
@@ -76,7 +76,7 @@
<![endif]-->
</head>
<body class="nopad">
- {% include navbar_top.html %}
+ {% include 'navbar_top' %}
{% if page.navsection == 'top' or page.no_nav_left %}
{{ content }}
@@ -86,7 +86,7 @@
<div class="container-fluid">
<div class="row-fluid">
- {% include navbar_left.html %}
+ {% include 'navbar_left' %}
<div class="span9"><div style="padding-left: 2em;">
{{ content }}
</div></div>
diff --git a/doc/admin/cheat_sheet.textile b/doc/admin/cheat_sheet.html.textile.liquid
similarity index 97%
rename from doc/admin/cheat_sheet.textile
rename to doc/admin/cheat_sheet.html.textile.liquid
index d817827..f811755 100644
--- a/doc/admin/cheat_sheet.textile
+++ b/doc/admin/cheat_sheet.html.textile.liquid
@@ -1,8 +1,7 @@
---
layout: default
-navsection: adminguide
+navsection: admin
title: Cheat Sheet
-navorder: 1
...
h1. Cheat Sheet
diff --git a/doc/admin/index.md b/doc/admin/index.html.md.liquid
similarity index 79%
rename from doc/admin/index.md
rename to doc/admin/index.html.md.liquid
index 53e4e42..f0ed3ad 100644
--- a/doc/admin/index.md
+++ b/doc/admin/index.html.md.liquid
@@ -1,11 +1,10 @@
---
layout: default
-navsection: adminguide
+navsection: admin
title: Overview
-navorder: 0
...
-{% include alert-stub.html %}
+{% include 'alert_stub' %}
# Administration Overview
diff --git a/doc/api/authentication.textile b/doc/api/authentication.html.textile.liquid
similarity index 99%
rename from doc/api/authentication.textile
rename to doc/api/authentication.html.textile.liquid
index 20dfcf7..1b5e240 100644
--- a/doc/api/authentication.textile
+++ b/doc/api/authentication.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Concepts
title: Authentication
-navorder: 2
+
...
h1. Authentication
diff --git a/doc/api/crunch-scripts.textile b/doc/api/crunch-scripts.html.textile.liquid
similarity index 99%
rename from doc/api/crunch-scripts.textile
rename to doc/api/crunch-scripts.html.textile.liquid
index dcf004e..98634cd 100644
--- a/doc/api/crunch-scripts.textile
+++ b/doc/api/crunch-scripts.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Concepts
title: Crunch scripts
-navorder: 5
+
...
h2. Crunch scripts
diff --git a/doc/api/index.textile b/doc/api/index.html.textile.liquid
similarity index 99%
rename from doc/api/index.textile
rename to doc/api/index.html.textile.liquid
index 64fe57b..097216d 100644
--- a/doc/api/index.textile
+++ b/doc/api/index.html.textile.liquid
@@ -2,7 +2,7 @@
layout: default
navsection: api
title: API Reference
-navorder: 0
+
...
h1. API Reference
diff --git a/doc/api/methods.textile b/doc/api/methods.html.textile.liquid
similarity index 99%
rename from doc/api/methods.textile
rename to doc/api/methods.html.textile.liquid
index c7ddbc3..2bfb9c4 100644
--- a/doc/api/methods.textile
+++ b/doc/api/methods.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Concepts
title: REST methods
-navorder: 3
+
...
h1. REST Methods
diff --git a/doc/api/methods/api_client_authorizations.textile b/doc/api/methods/api_client_authorizations.html.textile.liquid
similarity index 99%
rename from doc/api/methods/api_client_authorizations.textile
rename to doc/api/methods/api_client_authorizations.html.textile.liquid
index c9f6d82..74fd21e 100644
--- a/doc/api/methods/api_client_authorizations.textile
+++ b/doc/api/methods/api_client_authorizations.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "api_client_authorizations"
-navorder: 1
+
...
h1. api_client_authorizations
diff --git a/doc/api/methods/api_clients.textile b/doc/api/methods/api_clients.html.textile.liquid
similarity index 99%
rename from doc/api/methods/api_clients.textile
rename to doc/api/methods/api_clients.html.textile.liquid
index 2b014ad..37eaa0a 100644
--- a/doc/api/methods/api_clients.textile
+++ b/doc/api/methods/api_clients.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "api_clients"
-navorder: 2
+
...
h1. api_clients
diff --git a/doc/api/methods/authorized_keys.textile b/doc/api/methods/authorized_keys.html.textile.liquid
similarity index 99%
rename from doc/api/methods/authorized_keys.textile
rename to doc/api/methods/authorized_keys.html.textile.liquid
index e1c5892..0c5b7ee 100644
--- a/doc/api/methods/authorized_keys.textile
+++ b/doc/api/methods/authorized_keys.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "authorized_keys"
-navorder: 3
+
...
h1. authorized_keys
diff --git a/doc/api/methods/collections.textile b/doc/api/methods/collections.html.textile.liquid
similarity index 99%
rename from doc/api/methods/collections.textile
rename to doc/api/methods/collections.html.textile.liquid
index 100f86e..9c631c2 100644
--- a/doc/api/methods/collections.textile
+++ b/doc/api/methods/collections.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "collections"
-navorder: 4
+
...
h1. collections
diff --git a/doc/api/methods/groups.textile b/doc/api/methods/groups.html.textile.liquid
similarity index 99%
rename from doc/api/methods/groups.textile
rename to doc/api/methods/groups.html.textile.liquid
index 8db062d..f897eab 100644
--- a/doc/api/methods/groups.textile
+++ b/doc/api/methods/groups.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "groups"
-navorder: 5
+
...
h1. groups
diff --git a/doc/api/methods/humans.textile b/doc/api/methods/humans.html.textile.liquid
similarity index 99%
rename from doc/api/methods/humans.textile
rename to doc/api/methods/humans.html.textile.liquid
index d395b14..a0e715b 100644
--- a/doc/api/methods/humans.textile
+++ b/doc/api/methods/humans.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "humans"
-navorder: 6
+
...
h1. humans
diff --git a/doc/api/methods/job_tasks.textile b/doc/api/methods/job_tasks.html.textile.liquid
similarity index 99%
rename from doc/api/methods/job_tasks.textile
rename to doc/api/methods/job_tasks.html.textile.liquid
index 220cf26..daf4aa2 100644
--- a/doc/api/methods/job_tasks.textile
+++ b/doc/api/methods/job_tasks.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "job_tasks"
-navorder: 7
+
...
h1. job_tasks
diff --git a/doc/api/methods/jobs.textile b/doc/api/methods/jobs.html.textile.liquid
similarity index 99%
rename from doc/api/methods/jobs.textile
rename to doc/api/methods/jobs.html.textile.liquid
index 8109387..f3e51fc 100644
--- a/doc/api/methods/jobs.textile
+++ b/doc/api/methods/jobs.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "jobs"
-navorder: 8
+
...
h1. jobs
diff --git a/doc/api/methods/keep_disks.textile b/doc/api/methods/keep_disks.html.textile.liquid
similarity index 99%
rename from doc/api/methods/keep_disks.textile
rename to doc/api/methods/keep_disks.html.textile.liquid
index 94eb420..720130f 100644
--- a/doc/api/methods/keep_disks.textile
+++ b/doc/api/methods/keep_disks.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "keep_disks"
-navorder: 9
+
...
h1. keep_disks
diff --git a/doc/api/methods/links.textile b/doc/api/methods/links.html.textile.liquid
similarity index 99%
rename from doc/api/methods/links.textile
rename to doc/api/methods/links.html.textile.liquid
index f046783..0885f42 100644
--- a/doc/api/methods/links.textile
+++ b/doc/api/methods/links.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "links"
-navorder: 10
+
...
h1. links
diff --git a/doc/api/methods/logs.textile b/doc/api/methods/logs.html.textile.liquid
similarity index 99%
rename from doc/api/methods/logs.textile
rename to doc/api/methods/logs.html.textile.liquid
index 600cc3a..b7934e5 100644
--- a/doc/api/methods/logs.textile
+++ b/doc/api/methods/logs.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "logs"
-navorder: 11
+
...
h1. logs
diff --git a/doc/api/methods/nodes.textile b/doc/api/methods/nodes.html.textile.liquid
similarity index 99%
rename from doc/api/methods/nodes.textile
rename to doc/api/methods/nodes.html.textile.liquid
index 9521d3f..081734d 100644
--- a/doc/api/methods/nodes.textile
+++ b/doc/api/methods/nodes.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "nodes"
-navorder: 12
+
...
h1. nodes
diff --git a/doc/api/methods/pipeline_instances.textile b/doc/api/methods/pipeline_instances.html.textile.liquid
similarity index 99%
rename from doc/api/methods/pipeline_instances.textile
rename to doc/api/methods/pipeline_instances.html.textile.liquid
index f50fe85..5e9cb30 100644
--- a/doc/api/methods/pipeline_instances.textile
+++ b/doc/api/methods/pipeline_instances.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "pipeline_instances"
-navorder: 13
+
...
h1. pipeline_instances
diff --git a/doc/api/methods/pipeline_templates.textile b/doc/api/methods/pipeline_templates.html.textile.liquid
similarity index 99%
rename from doc/api/methods/pipeline_templates.textile
rename to doc/api/methods/pipeline_templates.html.textile.liquid
index fafd240..d353c7c 100644
--- a/doc/api/methods/pipeline_templates.textile
+++ b/doc/api/methods/pipeline_templates.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "pipeline_templates"
-navorder: 14
+
...
h1. pipeline_templates
diff --git a/doc/api/methods/repositories.textile b/doc/api/methods/repositories.html.textile.liquid
similarity index 99%
rename from doc/api/methods/repositories.textile
rename to doc/api/methods/repositories.html.textile.liquid
index 3d4aedc..90dc0f5 100644
--- a/doc/api/methods/repositories.textile
+++ b/doc/api/methods/repositories.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "repositories"
-navorder: 15
+
...
h1. repositories
diff --git a/doc/api/methods/specimens.textile b/doc/api/methods/specimens.html.textile.liquid
similarity index 99%
rename from doc/api/methods/specimens.textile
rename to doc/api/methods/specimens.html.textile.liquid
index 4fa095e..f56542d 100644
--- a/doc/api/methods/specimens.textile
+++ b/doc/api/methods/specimens.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "specimens"
-navorder: 16
+
...
h1. specimens
diff --git a/doc/api/methods/traits.textile b/doc/api/methods/traits.html.textile.liquid
similarity index 99%
rename from doc/api/methods/traits.textile
rename to doc/api/methods/traits.html.textile.liquid
index 28d5678..b2548b9 100644
--- a/doc/api/methods/traits.textile
+++ b/doc/api/methods/traits.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "traits"
-navorder: 17
+
...
h1. traits
diff --git a/doc/api/methods/users.textile b/doc/api/methods/users.html.textile.liquid
similarity index 99%
rename from doc/api/methods/users.textile
rename to doc/api/methods/users.html.textile.liquid
index 2ae5eee..9fbbda5 100644
--- a/doc/api/methods/users.textile
+++ b/doc/api/methods/users.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "users"
-navorder: 18
+
...
h1. users
diff --git a/doc/api/methods/virtual_machines.textile b/doc/api/methods/virtual_machines.html.textile.liquid
similarity index 99%
rename from doc/api/methods/virtual_machines.textile
rename to doc/api/methods/virtual_machines.html.textile.liquid
index a96fcb4..e815232 100644
--- a/doc/api/methods/virtual_machines.textile
+++ b/doc/api/methods/virtual_machines.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: API Methods
title: "virtual_machines"
-navorder: 19
+
...
h1. virtual_machines
diff --git a/doc/api/permission-model.textile b/doc/api/permission-model.html.textile.liquid
similarity index 99%
rename from doc/api/permission-model.textile
rename to doc/api/permission-model.html.textile.liquid
index cc4c0d8..73c99c1 100644
--- a/doc/api/permission-model.textile
+++ b/doc/api/permission-model.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Concepts
title: "Permission model"
-navorder: 6
+
...
h1. Permission model
diff --git a/doc/api/resources.textile b/doc/api/resources.html.textile.liquid
similarity index 99%
rename from doc/api/resources.textile
rename to doc/api/resources.html.textile.liquid
index 8a54a14..05517fc 100644
--- a/doc/api/resources.textile
+++ b/doc/api/resources.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Concepts
title: Resources
-navorder: 4
+
...
h1. Resources
diff --git a/doc/api/schema/ApiClient.textile b/doc/api/schema/ApiClient.html.textile.liquid
similarity index 98%
rename from doc/api/schema/ApiClient.textile
rename to doc/api/schema/ApiClient.html.textile.liquid
index 86f9345..90f1eeb 100644
--- a/doc/api/schema/ApiClient.textile
+++ b/doc/api/schema/ApiClient.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: ApiClient
-navorder: 2
+
...
h1. ApiClient
diff --git a/doc/api/schema/ApiClientAuthorization.textile b/doc/api/schema/ApiClientAuthorization.html.textile.liquid
similarity index 98%
rename from doc/api/schema/ApiClientAuthorization.textile
rename to doc/api/schema/ApiClientAuthorization.html.textile.liquid
index d9ee87d..1dec2bb 100644
--- a/doc/api/schema/ApiClientAuthorization.textile
+++ b/doc/api/schema/ApiClientAuthorization.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: ApiClientAuthorization
-navorder: 1
+
...
h1. ApiClientAuthorization
diff --git a/doc/api/schema/AuthorizedKey.textile b/doc/api/schema/AuthorizedKey.html.textile.liquid
similarity index 98%
rename from doc/api/schema/AuthorizedKey.textile
rename to doc/api/schema/AuthorizedKey.html.textile.liquid
index c60ce71..7d8bc20 100644
--- a/doc/api/schema/AuthorizedKey.textile
+++ b/doc/api/schema/AuthorizedKey.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: AuthorizedKey
-navorder: 3
+
...
h1. AuthorizedKey
diff --git a/doc/api/schema/Collection.textile b/doc/api/schema/Collection.html.textile.liquid
similarity index 99%
rename from doc/api/schema/Collection.textile
rename to doc/api/schema/Collection.html.textile.liquid
index fb39ff9..4704d63 100644
--- a/doc/api/schema/Collection.textile
+++ b/doc/api/schema/Collection.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Collection
-navorder: 4
+
...
h1. Collection
diff --git a/doc/api/schema/Commit.textile b/doc/api/schema/Commit.html.textile.liquid
similarity index 98%
rename from doc/api/schema/Commit.textile
rename to doc/api/schema/Commit.html.textile.liquid
index 71791eb..403d8d5 100644
--- a/doc/api/schema/Commit.textile
+++ b/doc/api/schema/Commit.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Commit
-navorder: 6
+
...
h1. Commit
diff --git a/doc/api/schema/CommitAncestor.textile b/doc/api/schema/CommitAncestor.html.textile.liquid
similarity index 98%
rename from doc/api/schema/CommitAncestor.textile
rename to doc/api/schema/CommitAncestor.html.textile.liquid
index e4788f8..ab4dd5b 100644
--- a/doc/api/schema/CommitAncestor.textile
+++ b/doc/api/schema/CommitAncestor.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: CommitAncestor
-navorder: 5
+
...
h1. CommitAncestor
diff --git a/doc/api/schema/Group.textile b/doc/api/schema/Group.html.textile.liquid
similarity index 98%
rename from doc/api/schema/Group.textile
rename to doc/api/schema/Group.html.textile.liquid
index 4315d75..71a006c 100644
--- a/doc/api/schema/Group.textile
+++ b/doc/api/schema/Group.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Group
-navorder: 7
+
...
h1. Group
diff --git a/doc/api/schema/Human.textile b/doc/api/schema/Human.html.textile.liquid
similarity index 98%
rename from doc/api/schema/Human.textile
rename to doc/api/schema/Human.html.textile.liquid
index 31766c9..837fc42 100644
--- a/doc/api/schema/Human.textile
+++ b/doc/api/schema/Human.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Human
-navorder: 8
+
...
h1. Human
diff --git a/doc/api/schema/Job.textile b/doc/api/schema/Job.html.textile.liquid
similarity index 99%
rename from doc/api/schema/Job.textile
rename to doc/api/schema/Job.html.textile.liquid
index 631c549..3fe631f 100644
--- a/doc/api/schema/Job.textile
+++ b/doc/api/schema/Job.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Job
-navorder: 9
+
...
h1. Job
diff --git a/doc/api/schema/JobTask.textile b/doc/api/schema/JobTask.html.textile.liquid
similarity index 99%
rename from doc/api/schema/JobTask.textile
rename to doc/api/schema/JobTask.html.textile.liquid
index fbbc8ef..f6818f4 100644
--- a/doc/api/schema/JobTask.textile
+++ b/doc/api/schema/JobTask.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: JobTask
-navorder: 10
+
...
h1. JobTask
diff --git a/doc/api/schema/KeepDisk.textile b/doc/api/schema/KeepDisk.html.textile.liquid
similarity index 98%
rename from doc/api/schema/KeepDisk.textile
rename to doc/api/schema/KeepDisk.html.textile.liquid
index d9f36ab..edac4d5 100644
--- a/doc/api/schema/KeepDisk.textile
+++ b/doc/api/schema/KeepDisk.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: KeepDisk
-navorder: 11
+
...
h1. KeepDisk
diff --git a/doc/api/schema/Link.textile b/doc/api/schema/Link.html.textile.liquid
similarity index 99%
rename from doc/api/schema/Link.textile
rename to doc/api/schema/Link.html.textile.liquid
index 952d6f0..abad383 100644
--- a/doc/api/schema/Link.textile
+++ b/doc/api/schema/Link.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Link
-navorder: 12
+
...
h1. Link
diff --git a/doc/api/schema/Log.textile b/doc/api/schema/Log.html.textile.liquid
similarity index 98%
rename from doc/api/schema/Log.textile
rename to doc/api/schema/Log.html.textile.liquid
index 7c94d34..533ca5c 100644
--- a/doc/api/schema/Log.textile
+++ b/doc/api/schema/Log.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Log
-navorder: 14
+
...
h1. Log
diff --git a/doc/api/schema/Node.textile b/doc/api/schema/Node.html.textile.liquid
similarity index 98%
rename from doc/api/schema/Node.textile
rename to doc/api/schema/Node.html.textile.liquid
index ccdd3e5..827ce18 100644
--- a/doc/api/schema/Node.textile
+++ b/doc/api/schema/Node.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Node
-navorder: 15
+
...
h1. Node
diff --git a/doc/api/schema/PipelineInstance.textile b/doc/api/schema/PipelineInstance.html.textile.liquid
similarity index 98%
rename from doc/api/schema/PipelineInstance.textile
rename to doc/api/schema/PipelineInstance.html.textile.liquid
index 4eeb989..7fd62f0 100644
--- a/doc/api/schema/PipelineInstance.textile
+++ b/doc/api/schema/PipelineInstance.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: PipelineInstance
-navorder: 16
+
...
h1. PipelineInstance
diff --git a/doc/api/schema/PipelineTemplate.textile b/doc/api/schema/PipelineTemplate.html.textile.liquid
similarity index 98%
rename from doc/api/schema/PipelineTemplate.textile
rename to doc/api/schema/PipelineTemplate.html.textile.liquid
index c54ba58..75b9981 100644
--- a/doc/api/schema/PipelineTemplate.textile
+++ b/doc/api/schema/PipelineTemplate.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: PipelineTemplate
-navorder: 17
+
...
h1. PipelineTemplate
diff --git a/doc/api/schema/Repository.textile b/doc/api/schema/Repository.html.textile.liquid
similarity index 98%
rename from doc/api/schema/Repository.textile
rename to doc/api/schema/Repository.html.textile.liquid
index 4989c69..e21b743 100644
--- a/doc/api/schema/Repository.textile
+++ b/doc/api/schema/Repository.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Repository
-navorder: 18
+
...
h1. Repository
diff --git a/doc/api/schema/Specimen.textile b/doc/api/schema/Specimen.html.textile.liquid
similarity index 98%
rename from doc/api/schema/Specimen.textile
rename to doc/api/schema/Specimen.html.textile.liquid
index 04afddc..7c0eff9 100644
--- a/doc/api/schema/Specimen.textile
+++ b/doc/api/schema/Specimen.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Specimen
-navorder: 19
+
...
h1. Specimen
diff --git a/doc/api/schema/Trait.textile b/doc/api/schema/Trait.html.textile.liquid
similarity index 98%
rename from doc/api/schema/Trait.textile
rename to doc/api/schema/Trait.html.textile.liquid
index d6829d3..8f077ef 100644
--- a/doc/api/schema/Trait.textile
+++ b/doc/api/schema/Trait.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: Trait
-navorder: 20
+
...
h1. Trait
diff --git a/doc/api/schema/User.textile b/doc/api/schema/User.html.textile.liquid
similarity index 98%
rename from doc/api/schema/User.textile
rename to doc/api/schema/User.html.textile.liquid
index d141ec0..cd7e64b 100644
--- a/doc/api/schema/User.textile
+++ b/doc/api/schema/User.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: User
-navorder: 21
+
...
h1. User
diff --git a/doc/api/schema/VirtualMachine.textile b/doc/api/schema/VirtualMachine.html.textile.liquid
similarity index 98%
rename from doc/api/schema/VirtualMachine.textile
rename to doc/api/schema/VirtualMachine.html.textile.liquid
index 0b5ccb8..ba5b3a7 100644
--- a/doc/api/schema/VirtualMachine.textile
+++ b/doc/api/schema/VirtualMachine.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: api
navmenu: Schema
title: VirtualMachine
-navorder: 22
+
...
h1. VirtualMachine
diff --git a/doc/gen_api_method_docs.py b/doc/gen_api_method_docs.py
index ac8fe03..afbe9e7 100755
--- a/doc/gen_api_method_docs.py
+++ b/doc/gen_api_method_docs.py
@@ -61,7 +61,6 @@ for resource in sorted(api[u'resources']):
outf = open(out_fname, 'w')
outf.write(
"""---
-layout: default
navsection: api
navmenu: API Methods
title: "{resource}"
diff --git a/doc/index.html b/doc/index.html.liquid
similarity index 99%
rename from doc/index.html
rename to doc/index.html.liquid
index 9d5fb79..0fdc757 100644
--- a/doc/index.html
+++ b/doc/index.html.liquid
@@ -1,5 +1,6 @@
---
layout: default
+no_nav_left: true
navsection: top
title: Arvados | Documentation
...
diff --git a/doc/install/client.textile b/doc/install/client.html.textile.liquid
similarity index 87%
rename from doc/install/client.textile
rename to doc/install/client.html.textile.liquid
index 7827a13..cc21938 100644
--- a/doc/install/client.textile
+++ b/doc/install/client.html.textile.liquid
@@ -2,16 +2,16 @@
layout: default
navsection: installguide
title: Install client libraries
-navorder: 5
+
...
h1. Install client libraries
h3. Python
-{% include notebox-begin.html %}
+{% include 'notebox-begin' %}
The Python package includes the Python API client library module and the CLI utilities @arv-get@ and @arv-put at .
-{% include notebox-end.html %}
+{% include 'notebox-end' %}
Get the arvados source tree.
@@ -29,8 +29,8 @@ Alternatively, build the package (without sudo) using @python setup.py bdist_egg
h3. Ruby
-{% include notebox-begin.html %}
+{% include 'notebox-begin' %}
The arvados package includes the Ruby client library module. The arvados-cli package includes the CLI utilities @arv@, @arv-run-pipeline-instance@, and @crunch-job at .
-{% include notebox-end.html %}
+{% include 'notebox-end' %}
notextile. <pre><code>$ <span class="userinput">sudo gem install arvados arvados-cli</span></code></pre>
diff --git a/doc/install/create-standard-objects.textile b/doc/install/create-standard-objects.html.textile.liquid
similarity index 99%
rename from doc/install/create-standard-objects.textile
rename to doc/install/create-standard-objects.html.textile.liquid
index 857679f..e8018b2 100644
--- a/doc/install/create-standard-objects.textile
+++ b/doc/install/create-standard-objects.html.textile.liquid
@@ -2,7 +2,7 @@
layout: default
navsection: installguide
title: Create standard objects
-navorder: 4
+
...
h1. Create standard objects
diff --git a/doc/install/index.md b/doc/install/index.html.md.liquid
similarity index 91%
rename from doc/install/index.md
rename to doc/install/index.html.md.liquid
index 39b3d97..f11cac9 100644
--- a/doc/install/index.md
+++ b/doc/install/index.html.md.liquid
@@ -2,10 +2,9 @@
layout: default
navsection: installguide
title: Overview
-navorder: 0
...
-{% include alert-stub.html %}
+{% include 'alert_stub' %}
# Installation Overview
diff --git a/doc/install/install-api-server.md b/doc/install/install-api-server.html.md
similarity index 99%
rename from doc/install/install-api-server.md
rename to doc/install/install-api-server.html.md
index c959e1b..37bafcf 100644
--- a/doc/install/install-api-server.md
+++ b/doc/install/install-api-server.html.md
@@ -5,7 +5,7 @@ title: Install the API server
navorder: 1
...
-{% include alert-stub.html %}
+{% include 'alert-stub' %}
# API server setup
diff --git a/doc/install/install-crunch-dispatch.textile b/doc/install/install-crunch-dispatch.html.textile.liquid
similarity index 99%
rename from doc/install/install-crunch-dispatch.textile
rename to doc/install/install-crunch-dispatch.html.textile.liquid
index d6525aa..893a8aa 100644
--- a/doc/install/install-crunch-dispatch.textile
+++ b/doc/install/install-crunch-dispatch.html.textile.liquid
@@ -2,7 +2,7 @@
layout: default
navsection: installguide
title: Install the Crunch dispatcher
-navorder: 3
+
...
h1. Crunch setup
diff --git a/doc/install/install-workbench-app.md b/doc/install/install-workbench-app.html.md
similarity index 98%
rename from doc/install/install-workbench-app.md
rename to doc/install/install-workbench-app.html.md
index c598785..e9c2168 100644
--- a/doc/install/install-workbench-app.md
+++ b/doc/install/install-workbench-app.html.md
@@ -5,7 +5,7 @@ title: Install the Arvados workbench application
navorder: 2
...
-{% include alert-stub.html %}
+{% include 'alert-stub' %}
# Workbench setup
diff --git a/doc/sdk/index.textile b/doc/sdk/index.html.textile.liquid
similarity index 95%
rename from doc/sdk/index.textile
rename to doc/sdk/index.html.textile.liquid
index ee001d9..e15eb1b 100644
--- a/doc/sdk/index.textile
+++ b/doc/sdk/index.html.textile.liquid
@@ -2,7 +2,7 @@
layout: default
navsection: sdk
title: "SDK Reference"
-navorder: 0
+
...
h1. Arvados SDK Reference
diff --git a/doc/sdk/python/crunch-utility-libraries.textile b/doc/sdk/python/crunch-utility-libraries.html.textile.liquid
similarity index 99%
rename from doc/sdk/python/crunch-utility-libraries.textile
rename to doc/sdk/python/crunch-utility-libraries.html.textile.liquid
index c0b54fa..a897e94 100644
--- a/doc/sdk/python/crunch-utility-libraries.textile
+++ b/doc/sdk/python/crunch-utility-libraries.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: sdk
navmenu: Python
title: "Crunch utility libraries"
-navorder: 20
+
...
h1. Crunch utility libraries
diff --git a/doc/sdk/python/python.textile b/doc/sdk/python/python.html.textile.liquid
similarity index 93%
rename from doc/sdk/python/python.textile
rename to doc/sdk/python/python.html.textile.liquid
index 4483cd9..26fbc88 100644
--- a/doc/sdk/python/python.textile
+++ b/doc/sdk/python/python.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: sdk
navmenu: Python
title: "PyDoc Reference"
-navorder: 30
+
no_nav_left: true
...
diff --git a/doc/sdk/python/sdk-python.textile b/doc/sdk/python/sdk-python.html.textile.liquid
similarity index 99%
rename from doc/sdk/python/sdk-python.textile
rename to doc/sdk/python/sdk-python.html.textile.liquid
index 2e9660e..22a2167 100644
--- a/doc/sdk/python/sdk-python.textile
+++ b/doc/sdk/python/sdk-python.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: sdk
navmenu: Python
title: "Python SDK"
-navorder: 10
+
...
h1. Python SDK
diff --git a/doc/user/examples/crunch-examples.textile b/doc/user/examples/crunch-examples.html.textile.liquid
similarity index 99%
rename from doc/user/examples/crunch-examples.textile
rename to doc/user/examples/crunch-examples.html.textile.liquid
index b1ada1f..65fd316 100644
--- a/doc/user/examples/crunch-examples.textile
+++ b/doc/user/examples/crunch-examples.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Examples
title: "Crunch examples"
-navorder: 30
+
...
h1. Crunch examples
diff --git a/doc/user/getting_started/check-environment.textile b/doc/user/getting_started/check-environment.html.textile.liquid
similarity index 99%
rename from doc/user/getting_started/check-environment.textile
rename to doc/user/getting_started/check-environment.html.textile.liquid
index 1516c7f..ac3d90c 100644
--- a/doc/user/getting_started/check-environment.textile
+++ b/doc/user/getting_started/check-environment.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Getting Started
title: "Checking your environment"
-navorder: 10
+
...
h1. Checking your environment
diff --git a/doc/user/getting_started/community.textile b/doc/user/getting_started/community.html.textile.liquid
similarity index 99%
rename from doc/user/getting_started/community.textile
rename to doc/user/getting_started/community.html.textile.liquid
index 7c63038..c910ac1 100644
--- a/doc/user/getting_started/community.textile
+++ b/doc/user/getting_started/community.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Getting Started
title: Arvados Community and Getting Help
-navorder: 11
+
...
h1. Arvados Community and Getting Help
diff --git a/doc/user/getting_started/ssh-access.textile b/doc/user/getting_started/ssh-access.html.textile.liquid
similarity index 99%
rename from doc/user/getting_started/ssh-access.textile
rename to doc/user/getting_started/ssh-access.html.textile.liquid
index 7d11040..74ecde2 100644
--- a/doc/user/getting_started/ssh-access.textile
+++ b/doc/user/getting_started/ssh-access.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Getting Started
title: Accessing an Arvados VM over ssh
-navorder: 2
+
...
h1. Accessing an Arvados Virtual Machine over ssh
diff --git a/doc/user/getting_started/workbench.textile b/doc/user/getting_started/workbench.html.textile.liquid
similarity index 98%
rename from doc/user/getting_started/workbench.textile
rename to doc/user/getting_started/workbench.html.textile.liquid
index 2b72cd3..71041b3 100644
--- a/doc/user/getting_started/workbench.textile
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Getting Started
title: Accessing Arvados Workbench
-navorder: 1
+
...
h1. Accessing Arvados Workbench
diff --git a/doc/user/index.textile b/doc/user/index.html.textile.liquid
similarity index 99%
rename from doc/user/index.textile
rename to doc/user/index.html.textile.liquid
index cc723f6..17c435e 100644
--- a/doc/user/index.textile
+++ b/doc/user/index.html.textile.liquid
@@ -2,7 +2,7 @@
layout: default
navsection: userguide
title: Welcome to Arvados!
-navorder: 0
+
...
h1. Welcome to Arvados!
diff --git a/doc/user/reference/api-tokens.textile b/doc/user/reference/api-tokens.html.textile.liquid
similarity index 99%
rename from doc/user/reference/api-tokens.textile
rename to doc/user/reference/api-tokens.html.textile.liquid
index b3938f2..48fea0a 100644
--- a/doc/user/reference/api-tokens.textile
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Reference
title: "Getting an API token"
-navorder: 01
+
...
h1. Reference: Getting an API token
diff --git a/doc/user/reference/sdk-cli.textile b/doc/user/reference/sdk-cli.html.textile.liquid
similarity index 99%
rename from doc/user/reference/sdk-cli.textile
rename to doc/user/reference/sdk-cli.html.textile.liquid
index 5a7753c..55e9c3c 100644
--- a/doc/user/reference/sdk-cli.textile
+++ b/doc/user/reference/sdk-cli.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Reference
title: "Command line interface"
-navorder: 22
+
...
h1. Reference: Command Line Interface
diff --git a/doc/user/tutorials/running-external-program.textile b/doc/user/tutorials/running-external-program.html.textile.liquid
similarity index 96%
rename from doc/user/tutorials/running-external-program.textile
rename to doc/user/tutorials/running-external-program.html.textile.liquid
index 34cb71a..5a4320c 100644
--- a/doc/user/tutorials/running-external-program.textile
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Tutorials
title: "Running external programs"
-navorder: 18
+
...
h1. Running external programs
@@ -23,7 +23,7 @@ Start by entering the @crunch_scripts@ directory of your git repository:
Next, using your favorite text editor, create a new file called @run-md5sum.py@ in the @crunch_scripts@ directory. Add the following code to use the @md5sum@ program to compute the hash of each file in a collection:
-<pre><code class="userinput">{% include run-md5sum.py %}</code></pre>
+<pre><code class="userinput">{% include 'run-md5sum_py' %}</code></pre>
Make the file executable:
diff --git a/doc/user/tutorials/tutorial-firstscript.textile b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
similarity index 96%
rename from doc/user/tutorials/tutorial-firstscript.textile
rename to doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 5cb8c26..d0108ea 100644
--- a/doc/user/tutorials/tutorial-firstscript.textile
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Tutorials
title: "Writing a Crunch script"
-navorder: 13
+
...
h1. Writing a Crunch script
@@ -36,13 +36,13 @@ Cloning into 'you'...</code></pre>
This will create an git checkout in the directory called @you at .
-{% include notebox-begin.html %}
+{% include 'notebox-begin' %}
For more information about using @git@, try
notextile. <pre><code>$ <span class="userinput">man gittutorial</span></code></pre>
or <b>"click here to search Google for git tutorials":http://google.com/#q=git+tutorial</b>
-{% include notebox-end.html %}
+{% include 'notebox-end' %}
h2. Creating a Crunch script
@@ -60,7 +60,7 @@ notextile. <pre>$ <code class="userinput">nano hash.py</code></pre>
Add the following code to compute the md5 hash of each file in a collection:
-<pre><code class="userinput">{% include tutorial_hash_script.py %}</code></pre>
+<pre><code class="userinput">{% include 'tutorial_hash_script_py' %}</code></pre>
Make the file executable:
diff --git a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile b/doc/user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
similarity index 99%
rename from doc/user/tutorials/tutorial-gatk-variantfiltration.textile
rename to doc/user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
index 1748565..04894fd 100644
--- a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
+++ b/doc/user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Tutorials
title: "Using GATK with Arvados"
-navorder: 16
+
...
h1. Using GATK with Arvados
diff --git a/doc/user/tutorials/tutorial-job-debug.textile b/doc/user/tutorials/tutorial-job-debug.html.textile.liquid
similarity index 99%
rename from doc/user/tutorials/tutorial-job-debug.textile
rename to doc/user/tutorials/tutorial-job-debug.html.textile.liquid
index 570713b..063eb12 100644
--- a/doc/user/tutorials/tutorial-job-debug.textile
+++ b/doc/user/tutorials/tutorial-job-debug.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Tutorials
title: "Debugging a Crunch script"
-navorder: 14
+
...
h1. Debugging a Crunch script
diff --git a/doc/user/tutorials/tutorial-job1.textile b/doc/user/tutorials/tutorial-job1.html.textile.liquid
similarity index 99%
rename from doc/user/tutorials/tutorial-job1.textile
rename to doc/user/tutorials/tutorial-job1.html.textile.liquid
index be159db..b88ba60 100644
--- a/doc/user/tutorials/tutorial-job1.textile
+++ b/doc/user/tutorials/tutorial-job1.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Tutorials
title: "Running a Crunch job"
-navorder: 12
+
...
h1. Running a crunch job
diff --git a/doc/user/tutorials/tutorial-keep.textile b/doc/user/tutorials/tutorial-keep.html.textile.liquid
similarity index 99%
rename from doc/user/tutorials/tutorial-keep.textile
rename to doc/user/tutorials/tutorial-keep.html.textile.liquid
index eb0f969..01ef78a 100644
--- a/doc/user/tutorials/tutorial-keep.textile
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Tutorials
title: "Storing and Retrieving data using Arvados Keep"
-navorder: 11
+
...
h1. Storing and Retrieving data using Arvados Keep
diff --git a/doc/user/tutorials/tutorial-new-pipeline.textile b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
similarity index 98%
rename from doc/user/tutorials/tutorial-new-pipeline.textile
rename to doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
index ee92090..8312237 100644
--- a/doc/user/tutorials/tutorial-new-pipeline.textile
+++ b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Tutorials
title: "Constructing a Crunch pipeline"
-navorder: 15
+
...
h1. Constructing a Crunch pipeline
@@ -16,7 +16,7 @@ h2. Create a new script
Our second script will filter the output of @parallel_hash.py@ and only include hashes that start with 0. Create a new script in @crunch_scripts/@ called @0-filter.py@:
-<pre><code class="userinput">{% include 0-filter.py %}</code></pre>
+<pre><code class="userinput">{% include '0-filter_py' %}</code></pre>
Now add it to git:
diff --git a/doc/user/tutorials/tutorial-parallel.textile b/doc/user/tutorials/tutorial-parallel.html.textile.liquid
similarity index 97%
rename from doc/user/tutorials/tutorial-parallel.textile
rename to doc/user/tutorials/tutorial-parallel.html.textile.liquid
index 1cad88c..d8254a6 100644
--- a/doc/user/tutorials/tutorial-parallel.textile
+++ b/doc/user/tutorials/tutorial-parallel.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Tutorials
title: "Parallel Crunch tasks"
-navorder: 15
+
...
h1. Parallel Crunch tasks
@@ -19,7 +19,7 @@ Start by entering the @crunch_scripts@ directory of your git repository:
Next, using your favorite text editor, create a new file called @parallel-hash.py@ in the @crunch_scripts@ directory. Add the following code to compute the md5 hash of each file in a collection:
-<pre><code class="userinput">{% include parallel_hash_script.py %}</code></pre>
+<pre><code class="userinput">{% include 'parallel_hash_script_py' %}</code></pre>
Make the file executable:
diff --git a/doc/user/tutorials/tutorial-trait-search.textile b/doc/user/tutorials/tutorial-trait-search.html.textile.liquid
similarity index 99%
rename from doc/user/tutorials/tutorial-trait-search.textile
rename to doc/user/tutorials/tutorial-trait-search.html.textile.liquid
index 1fcbbc3..b602411 100644
--- a/doc/user/tutorials/tutorial-trait-search.textile
+++ b/doc/user/tutorials/tutorial-trait-search.html.textile.liquid
@@ -3,7 +3,7 @@ layout: default
navsection: userguide
navmenu: Tutorials
title: "Querying the Metadata Database"
-navorder: 16
+
...
h1. Querying the Metadata Database
diff --git a/doc/zenweb-liquid.rb b/doc/zenweb-liquid.rb
index f301aa4..545a0d8 100644
--- a/doc/zenweb-liquid.rb
+++ b/doc/zenweb-liquid.rb
@@ -5,18 +5,37 @@ module ZenwebLiquid
end
module Zenweb
+
class Page
+
+ def render_liquid page, content
+ liquid self.body, content, page, binding
+ end
##
# Render a page's liquid and return the intermediate result
- def render_liquid page, content, binding = TOPLEVEL_BINDING
+ def liquid template, content, page, binding = TOPLEVEL_BINDING
require 'liquid'
+ Liquid::Template.file_system = Liquid::LocalFileSystem.new(File.join(File.dirname(Rake.application().rakefile), "_includes"))
+ unless defined? @liquid_template
+ @liquid_template = Liquid::Template.parse(template)
+ end
- unless defined? @liquid_template then
- @liquid_template = Liquid::Template.parse(content).render()
+ vars = {}
+ vars["content"] = content
+
+ vars["site"] = site.config.h.clone
+ pages = {}
+ site.pages.each do |f, p|
+ pages[f] = p.config.h.clone
+ pages[f]["url"] = p.url
end
+ vars["site"]["pages"] = pages
+
+ vars["page"] = page.config.h.clone
+ vars["page"]["url"] = page.url
- @liquid_template.render(binding)
+ @liquid_template.render(vars)
end
end
end
diff --git a/doc/zenweb-textile.rb b/doc/zenweb-textile.rb
index bdd7162..0a4bb6f 100644
--- a/doc/zenweb-textile.rb
+++ b/doc/zenweb-textile.rb
@@ -10,14 +10,8 @@ module Zenweb
##
# Render a page's textile and return the resulting html
def render_textile page, content
- textile body
- end
-
- ##
- # Render textile in +content+
- def textile content
require 'RedCloth'
- @textile = RedCloth.new(content).to_html
+ RedCloth.new(content ? content : self.body).to_html
end
end
end
commit da51b9328abab2df757ed13eadc7c3557315094b
Merge: 7b66e00 e9e3b56
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Feb 7 16:38:15 2014 -0500
Merge branch 'master' into 1786-replace-jekyll-with-zenweb
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