[ARVADOS] updated: 5dbf5c8ea2d9eb2bc8e10a03ca625f12ed71f12c
git at public.curoverse.com
git at public.curoverse.com
Wed Feb 11 15:59:36 EST 2015
Summary of changes:
.gitignore | 7 +-
apps/workbench/.gitignore | 1 +
apps/workbench/Gemfile | 6 +-
apps/workbench/Gemfile.lock | 4 +-
.../workbench/app/assets/javascripts/filterable.js | 6 +-
.../app/controllers/application_controller.rb | 6 +-
.../app/controllers/collections_controller.rb | 20 +-
apps/workbench/app/controllers/jobs_controller.rb | 9 +-
.../controllers/pipeline_instances_controller.rb | 5 +
.../controllers/pipeline_templates_controller.rb | 5 +
.../app/controllers/projects_controller.rb | 29 +-
.../workbench/app/controllers/search_controller.rb | 3 +-
apps/workbench/app/helpers/application_helper.rb | 6 +-
apps/workbench/app/models/arvados_api_client.rb | 11 +-
apps/workbench/app/models/arvados_base.rb | 2 +-
apps/workbench/app/models/authorized_key.rb | 4 +
apps/workbench/app/models/collection.rb | 4 -
apps/workbench/app/models/job.rb | 4 -
apps/workbench/app/views/application/404.html.erb | 22 +-
.../views/application/_browser_unsupported.html | 24 ++
.../application/_create_new_object_button.html.erb | 7 +
.../app/views/application/_show_sharing.html.erb | 9 +
.../views/application/_title_and_buttons.html.erb | 6 +-
.../workbench/app/views/application/index.html.erb | 19 +-
.../collections/_create_new_object_button.html.erb | 1 +
.../app/views/collections/_index_tbody.html.erb | 2 +-
.../app/views/collections/_show_files.html.erb | 171 +++++----
.../views/jobs/_create_new_object_button.html.erb | 1 +
.../jobs/_rerun_job_with_options_popup.html.erb | 6 +-
.../app/views/jobs/_show_job_buttons.html.erb | 2 +-
apps/workbench/app/views/layouts/body.html.erb | 3 +
.../pipeline_instances/_running_component.html.erb | 2 +-
.../views/pipeline_instances/_show_inputs.html.erb | 15 +-
.../pipeline_instances/_show_tab_buttons.html.erb | 2 +
.../app/views/pipeline_instances/show.html.erb | 4 +-
.../app/views/pipeline_templates/show.html.erb | 38 +-
.../app/views/projects/_show_dashboard.html.erb | 10 +-
.../app/views/projects/_show_tab_contents.html.erb | 108 +++---
apps/workbench/app/views/projects/show.html.erb | 2 +-
.../app/views/users/_add_ssh_key_popup.html.erb | 2 +-
.../views/users/_create_new_object_button.html.erb | 6 +
.../app/views/users/_setup_popup.html.erb | 2 +-
apps/workbench/app/views/users/welcome.html.erb | 4 +-
apps/workbench/config/application.default.yml | 5 +
apps/workbench/public/browser_unsupported.js | 14 +
.../controllers/application_controller_test.rb | 37 ++
.../controllers/collections_controller_test.rb | 42 ++-
.../test/controllers/projects_controller_test.rb | 14 +
.../test/integration/anonymous_access_test.rb | 161 +++++++++
.../test/integration/browser_unsupported_test.rb | 17 +
apps/workbench/test/integration/errors_test.rb | 1 -
.../integration/filterable_infinite_scroll_test.rb | 14 +-
.../test/integration/pipeline_instances_test.rb | 70 ++--
apps/workbench/test/integration/projects_test.rb | 28 ++
.../test/integration/user_manage_account_test.rb | 25 +-
apps/workbench/test/integration/websockets_test.rb | 3 +-
apps/workbench/test/integration_helper.rb | 17 +-
apps/workbench/test/performance_test_helper.rb | 2 +-
apps/workbench/test/support/remove_file_api.js | 1 +
apps/workbench/test/test_helper.rb | 126 +++----
crunch_scripts/crunchutil/subst.py | 7 +-
doc/_config.yml | 1 +
doc/_includes/_arv_run_redirection.liquid | 19 +
doc/api/methods/collections.html.textile.liquid | 2 +-
doc/api/methods/groups.html.textile.liquid | 9 +-
doc/images/keyfeatures/chooseinputs.png | Bin 76641 -> 67586 bytes
doc/images/keyfeatures/collectionpage.png | Bin 84533 -> 68735 bytes
doc/images/keyfeatures/dashboard2.png | Bin 44396 -> 39651 bytes
doc/images/keyfeatures/graph.png | Bin 49127 -> 37727 bytes
doc/images/keyfeatures/log.png | Bin 135214 -> 94845 bytes
doc/images/keyfeatures/provenance.png | Bin 67060 -> 53567 bytes
doc/images/keyfeatures/rerun.png | Bin 73314 -> 56872 bytes
doc/images/keyfeatures/running2.png | Bin 56959 -> 40453 bytes
doc/images/keyfeatures/shared.png | Bin 62395 -> 46090 bytes
doc/images/keyfeatures/webupload.png | Bin 88061 -> 70592 bytes
doc/images/quickstart/1.png | Bin 47239 -> 36164 bytes
doc/images/quickstart/2.png | Bin 74431 -> 58616 bytes
doc/images/quickstart/3.png | Bin 80668 -> 68576 bytes
doc/images/quickstart/4.png | Bin 66686 -> 45334 bytes
doc/images/quickstart/5.png | Bin 83038 -> 66066 bytes
doc/images/quickstart/6.png | Bin 98604 -> 83813 bytes
doc/images/quickstart/7.png | Bin 77820 -> 60031 bytes
doc/sdk/cli/index.html.textile.liquid | 44 ++-
doc/sdk/cli/reference.html.textile.liquid | 13 +-
doc/sdk/cli/subcommands.html.textile.liquid | 7 +-
doc/user/topics/arv-run.html.textile.liquid | 20 +-
.../crunch-tools-overview.html.textile.liquid | 63 ++++
doc/user/topics/run-command.html.textile.liquid | 10 +
sdk/cli/bin/crunch-job | 16 +-
sdk/go/arvadosclient/arvadosclient.go | 4 +-
sdk/go/arvadosclient/arvadosclient_test.go | 49 +--
sdk/go/arvadostest/run_servers.go | 123 +++++++
sdk/go/keepclient/keepclient_test.go | 48 +--
sdk/go/keepclient/support.go | 9 -
sdk/python/arvados/api.py | 16 +-
sdk/python/arvados/collection.py | 27 +-
sdk/python/arvados/commands/arv_copy.py | 3 +-
sdk/python/arvados/commands/put.py | 40 ++-
sdk/python/arvados/commands/ws.py | 4 +-
sdk/python/arvados/errors.py | 2 +
sdk/python/arvados/events.py | 85 +++--
sdk/python/arvados/keep.py | 19 +-
sdk/python/gittaggers.py | 20 ++
sdk/python/setup.py | 31 +-
sdk/python/tests/arvados_testutil.py | 35 ++
sdk/python/tests/run_test_server.py | 395 ++++++++++++++-------
sdk/python/tests/test_api.py | 15 +-
sdk/python/tests/test_arv_put.py | 29 +-
sdk/python/tests/test_collections.py | 65 ++--
sdk/python/tests/test_keep_client.py | 68 ++--
sdk/python/tests/test_pipeline_template.py | 19 +-
sdk/python/tests/test_websockets.py | 64 ++--
sdk/ruby/lib/arvados/keep.rb | 5 +-
sdk/ruby/test/test_keep_manifest.rb | 66 ++++
services/api/.gitignore | 1 +
services/api/Gemfile | 6 +-
services/api/Gemfile.lock | 20 +-
.../api/app/controllers/application_controller.rb | 19 +-
.../arvados/v1/collections_controller.rb | 7 +-
.../controllers/arvados/v1/groups_controller.rb | 76 ++--
.../app/controllers/arvados/v1/links_controller.rb | 2 +-
.../app/controllers/arvados/v1/users_controller.rb | 11 +-
services/api/app/models/arvados_model.rb | 26 ++
services/api/app/models/collection.rb | 27 +-
services/api/app/models/database_seeds.rb | 1 +
services/api/app/models/user.rb | 2 +-
services/api/config/application.default.yml | 1 -
.../db/migrate/20150123142953_full_text_search.rb | 18 +
...203180223_set_group_class_on_anonymous_group.rb | 14 +
...206210804_all_users_can_read_anonymous_group.rb | 12 +
services/api/db/structure.sql | 43 ++-
services/api/lib/current_api_client.rb | 159 +++++----
services/api/lib/record_filters.rb | 20 +-
services/api/test/fixtures/collections.yml | 29 +-
services/api/test/fixtures/groups.yml | 5 +-
services/api/test/fixtures/jobs.yml | 24 ++
services/api/test/fixtures/links.yml | 28 ++
services/api/test/fixtures/pipeline_instances.yml | 16 +
services/api/test/fixtures/pipeline_templates.yml | 39 ++
.../arvados/v1/collections_controller_test.rb | 26 +-
.../api/test/functional/arvados/v1/filters_test.rb | 41 +++
.../arvados/v1/groups_controller_test.rb | 17 +-
.../api/test/integration/collections_api_test.rb | 79 ++++-
services/api/test/integration/groups_test.rb | 35 ++
services/api/test/unit/arvados_model_test.rb | 22 ++
services/api/test/unit/collection_test.rb | 47 +++
services/api/test/unit/link_test.rb | 5 +
services/api/test/websocket_runner.rb | 10 +-
services/fuse/arvados_fuse/__init__.py | 4 +-
services/fuse/gittaggers.py | 1 +
services/fuse/setup.py | 33 +-
services/fuse/tests/test_mount.py | 46 ++-
services/keepproxy/keepproxy_test.go | 99 ++----
services/{fuse => nodemanager}/MANIFEST.in | 0
services/nodemanager/gittaggers.py | 1 +
services/nodemanager/setup.py | 34 +-
156 files changed, 2550 insertions(+), 1185 deletions(-)
create mode 100644 apps/workbench/app/views/application/_browser_unsupported.html
create mode 100644 apps/workbench/app/views/application/_create_new_object_button.html.erb
create mode 100644 apps/workbench/app/views/collections/_create_new_object_button.html.erb
create mode 100644 apps/workbench/app/views/jobs/_create_new_object_button.html.erb
create mode 100644 apps/workbench/app/views/users/_create_new_object_button.html.erb
create mode 100644 apps/workbench/public/browser_unsupported.js
create mode 100644 apps/workbench/test/integration/anonymous_access_test.rb
create mode 100644 apps/workbench/test/integration/browser_unsupported_test.rb
create mode 100644 apps/workbench/test/support/remove_file_api.js
create mode 100644 doc/_includes/_arv_run_redirection.liquid
create mode 100644 doc/user/topics/crunch-tools-overview.html.textile.liquid
create mode 100644 sdk/go/arvadostest/run_servers.go
create mode 100644 sdk/python/gittaggers.py
create mode 100644 services/api/db/migrate/20150123142953_full_text_search.rb
create mode 100644 services/api/db/migrate/20150203180223_set_group_class_on_anonymous_group.rb
create mode 100644 services/api/db/migrate/20150206210804_all_users_can_read_anonymous_group.rb
create mode 120000 services/fuse/gittaggers.py
copy services/{fuse => nodemanager}/MANIFEST.in (100%)
create mode 120000 services/nodemanager/gittaggers.py
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commit 5dbf5c8ea2d9eb2bc8e10a03ca625f12ed71f12c
Merge: c9ff743 b80db28
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Feb 11 16:01:24 2015 -0500
Merge branch 'master' into 4904-arv-web
Conflicts:
sdk/python/arvados/events.py
diff --cc sdk/python/arvados/events.py
index a26c70a,2686926..09f2a87
--- a/sdk/python/arvados/events.py
+++ b/sdk/python/arvados/events.py
@@@ -58,6 -65,6 +65,7 @@@ class PollClient(threading.Thread)
self.filters = [[]]
self.on_event = on_event
self.poll_time = poll_time
++ self.daemon = True
self.stop = threading.Event()
def run(self):
@@@ -105,30 -112,36 +113,41 @@@
del self.filters[self.filters.index(filters)]
+ def _subscribe_websocket(api, filters, on_event):
+ endpoint = api._rootDesc.get('websocketUrl', None)
+ if not endpoint:
+ raise errors.FeatureNotEnabledError(
+ "Server does not advertise a websocket endpoint")
+ uri_with_token = "{}?api_token={}".format(endpoint, api.api_token)
+ client = EventClient(uri_with_token, filters, on_event)
+ ok = False
+ try:
+ client.connect()
+ ok = True
+ return client
+ finally:
+ if not ok:
+ client.close_connection()
+
def subscribe(api, filters, on_event, poll_fallback=15):
-- '''
- api: Must be a newly created from arvados.api(cache=False), not shared with the caller, as it may be used by a background thread.
- api: a client object retrieved from arvados.api(). The caller should not use this client object for anything else after calling subscribe().
-- filters: Initial subscription filters.
- on_event: The callback when a message is received
- on_event: The callback when a message is received.
-- poll_fallback: If websockets are not available, fall back to polling every N seconds. If poll_fallback=False, this will return None if websockets are not available.
-- '''
- ws = None
- if 'websocketUrl' in api._rootDesc:
- try:
- url = "{}?api_token={}".format(api._rootDesc['websocketUrl'], api.api_token)
- ws = EventClient(url, filters, on_event)
- ws.connect()
- return ws
- except Exception as e:
- _logger.warn("Got exception %s trying to connect to websockets at %s" % (e, api._rootDesc['websocketUrl']))
- if ws:
- ws.close_connection()
- if poll_fallback:
- _logger.warn("Websockets not available, falling back to log table polling")
- p = PollClient(api, filters, on_event, poll_fallback)
- p.daemon = True
- p.start()
- return p
- else:
- _logger.error("Websockets not available")
- return None
++ """
++ :api:
++ a client object retrieved from arvados.api(). The caller should not use this client object for anything else after calling subscribe().
++ :filters:
++ Initial subscription filters.
++ :on_event:
++ The callback when a message is received.
++ :poll_fallback:
++ If websockets are not available, fall back to polling every N seconds. If poll_fallback=False, this will return None if websockets are not available.
++ """
++
+ if not poll_fallback:
+ return _subscribe_websocket(api, filters, on_event)
+
+ try:
+ return _subscribe_websocket(api, filters, on_event)
+ except Exception as e:
+ _logger.warn("Falling back to polling after websocket error: %s" % e)
+ p = PollClient(api, filters, on_event, poll_fallback)
+ p.start()
+ return p
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