arvados.git
10 years agoMerge branch 'master' into 1979-workbench-ui
Tom Clegg [Tue, 4 Feb 2014 09:14:03 +0000 (01:14 -0800)]
Merge branch 'master' into 1979-workbench-ui

10 years agoHide loading indicator after refreshing dashboard tables.
Tom Clegg [Tue, 4 Feb 2014 09:13:19 +0000 (01:13 -0800)]
Hide loading indicator after refreshing dashboard tables.

refs #1976

10 years agoMerge top nav menus into brand dropdown, move breadcrumbs into top
Tom Clegg [Tue, 4 Feb 2014 09:11:22 +0000 (01:11 -0800)]
Merge top nav menus into brand dropdown, move breadcrumbs into top
nav, and lighten up the top nav.

refs #1979

10 years agoMerge branch '1977-provenance-report'
Tom Clegg [Tue, 4 Feb 2014 07:52:28 +0000 (23:52 -0800)]
Merge branch '1977-provenance-report'

10 years agoMove can_read permission logic into ArvadosModel.readable_by scope,
Tom Clegg [Tue, 4 Feb 2014 07:50:54 +0000 (23:50 -0800)]
Move can_read permission logic into ArvadosModel.readable_by scope,
and use that in collections.provenance instead of plain where().

refs #1977
refs #2037

10 years agoAdd tests for permissions enforcement in collections.provenance.
Tom Clegg [Tue, 4 Feb 2014 01:49:20 +0000 (17:49 -0800)]
Add tests for permissions enforcement in collections.provenance.

refs #2037
refs #1977

10 years agoEnsure permissions can be propagated via group owner_uuid attribute.
Tom Clegg [Tue, 4 Feb 2014 00:24:06 +0000 (16:24 -0800)]
Ensure permissions can be propagated via group owner_uuid attribute.

Closes #1945
Closes #2022

10 years agoHide this/other/both legend if only one pipeline_instance is shown.
Tom Clegg [Mon, 3 Feb 2014 22:52:10 +0000 (14:52 -0800)]
Hide this/other/both legend if only one pipeline_instance is shown.

10 years agoMerge branch '1976-pipeline-progress'
Tom Clegg [Mon, 3 Feb 2014 22:56:30 +0000 (14:56 -0800)]
Merge branch '1976-pipeline-progress'

Conflicts:
apps/workbench/app/views/pipeline_instances/show.html.erb

10 years agoMerge branch 'master' into 1977-provenance-report
Tom Clegg [Mon, 3 Feb 2014 22:44:19 +0000 (14:44 -0800)]
Merge branch 'master' into 1977-provenance-report

Conflicts:
apps/workbench/app/controllers/pipeline_instances_controller.rb
apps/workbench/app/views/jobs/show.html.erb

10 years agoFix build.sh bugs.
Tim Pierce [Mon, 3 Feb 2014 20:32:59 +0000 (15:32 -0500)]
Fix build.sh bugs.

10 years agoFix breadcrumbs crash if link has no tail_kind or head_kind.
Tom Clegg [Mon, 3 Feb 2014 19:04:06 +0000 (11:04 -0800)]
Fix breadcrumbs crash if link has no tail_kind or head_kind.

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Mon, 3 Feb 2014 19:04:56 +0000 (14:04 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoTweaked text a little to make tail/subject head/object correspondence a little clearer.
Peter Amstutz [Mon, 3 Feb 2014 19:04:26 +0000 (14:04 -0500)]
Tweaked text a little to make tail/subject head/object correspondence a little clearer.

10 years agoEnsure util.mkdir_dash_p() fails if its target is a non-directory, and
Tom Clegg [Mon, 3 Feb 2014 16:21:05 +0000 (08:21 -0800)]
Ensure util.mkdir_dash_p() fails if its target is a non-directory, and
succeeds if the target directory exists after an mkdir() race with
another process.

10 years agoShow "loading" indicator in nav bar while waiting for AJAX requests.
Tom Clegg [Mon, 3 Feb 2014 16:01:19 +0000 (08:01 -0800)]
Show "loading" indicator in nav bar while waiting for AJAX requests.

refs #1976
closes #2040

10 years agoRefresh dashboard with AJAX every 60 seconds.
Tom Clegg [Mon, 3 Feb 2014 08:45:11 +0000 (00:45 -0800)]
Refresh dashboard with AJAX every 60 seconds.

refs #1976
closes #2004

10 years agoUse AJAX/remote requests when deleting objects. Add delete button to
Tom Clegg [Mon, 3 Feb 2014 08:21:52 +0000 (00:21 -0800)]
Use AJAX/remote requests when deleting objects. Add delete button to
pipeline_instances index.

refs #1976

10 years agoImprove progress view on pipeline_instances.show page and add AJAX
Tom Clegg [Mon, 3 Feb 2014 08:07:24 +0000 (00:07 -0800)]
Improve progress view on pipeline_instances.show page and add AJAX
auto-refresh.

refs #1976
refs #2004

10 years agoAdd arv-mount.
Tom Clegg [Mon, 3 Feb 2014 01:49:24 +0000 (17:49 -0800)]
Add arv-mount.

10 years agoAdd StreamFileReader.seek() method.
Tom Clegg [Mon, 3 Feb 2014 01:27:26 +0000 (17:27 -0800)]
Add StreamFileReader.seek() method.

10 years agoFix scoping for error classes.
Tom Clegg [Mon, 3 Feb 2014 01:26:59 +0000 (17:26 -0800)]
Fix scoping for error classes.

10 years agoFix crash when component has missing attributes (e.g., no job was run).
Tom Clegg [Sun, 2 Feb 2014 00:06:33 +0000 (16:06 -0800)]
Fix crash when component has missing attributes (e.g., no job was run).

refs #1978

10 years agoAdd basic select-and-compare interface to pipeline_instances#index.
Tom Clegg [Sun, 2 Feb 2014 00:05:55 +0000 (16:05 -0800)]
Add basic select-and-compare interface to pipeline_instances#index.

refs #1978

10 years agoMerge branch 'master' into 1978-compare-pipelines
Tom Clegg [Sat, 1 Feb 2014 23:34:44 +0000 (15:34 -0800)]
Merge branch 'master' into 1978-compare-pipelines

Conflicts:
apps/workbench/app/controllers/pipeline_instances_controller.rb
apps/workbench/app/views/pipeline_instances/compare.html.erb

10 years agoRemove extra breadcrumbs bar.
Tom Clegg [Sat, 1 Feb 2014 23:17:10 +0000 (15:17 -0800)]
Remove extra breadcrumbs bar.

10 years agoAllow controller to override page name for breadcrumbs.
Tom Clegg [Sat, 1 Feb 2014 23:16:52 +0000 (15:16 -0800)]
Allow controller to override page name for breadcrumbs.

10 years agoAdd breadcrumbs bar to #index and #show pages.
Tom Clegg [Fri, 31 Jan 2014 21:59:33 +0000 (13:59 -0800)]
Add breadcrumbs bar to #index and #show pages.

10 years agoUse generic index page for /users
Tom Clegg [Fri, 31 Jan 2014 21:32:39 +0000 (13:32 -0800)]
Use generic index page for /users

10 years agoShow condensed data about pipeline instances side by side on "compare"
Tom Clegg [Wed, 29 Jan 2014 02:15:43 +0000 (18:15 -0800)]
Show condensed data about pipeline instances side by side on "compare"
page.

refs #1978

10 years agoAdd pipeline_instances/compare page
Tom Clegg [Tue, 28 Jan 2014 15:57:47 +0000 (07:57 -0800)]
Add pipeline_instances/compare page

10 years agoFix "show all pipeline templates" link target on dashboard page.
Tom Clegg [Fri, 31 Jan 2014 20:50:35 +0000 (12:50 -0800)]
Fix "show all pipeline templates" link target on dashboard page.

10 years agoFixed bug in vertical scrolling by setting padding to size of graph or max size inste...
Peter Amstutz [Sat, 1 Feb 2014 20:19:57 +0000 (15:19 -0500)]
Fixed bug in vertical scrolling by setting padding to size of graph or max size instead of dynamic size based on screen position.

10 years agoFix some arv unit tests.
Tim Pierce [Fri, 31 Jan 2014 22:59:04 +0000 (17:59 -0500)]
Fix some arv unit tests.

10 years agoTweak to account for width of scrolbar
Peter Amstutz [Fri, 31 Jan 2014 21:59:31 +0000 (16:59 -0500)]
Tweak to account for width of scrolbar

10 years agoWorking on javascript magic to resize svg div so scrolling works nicely. Seems to...
Peter Amstutz [Fri, 31 Jan 2014 21:43:36 +0000 (16:43 -0500)]
Working on javascript magic to resize svg div so scrolling works nicely.  Seems to work pretty well except when the svg div is the last thing on the page.

10 years agoRefactored code for managing divs containing svg (manages scrollbars, zoom buttons).
Peter Amstutz [Fri, 31 Jan 2014 17:48:57 +0000 (12:48 -0500)]
Refactored code for managing divs containing svg (manages scrollbars, zoom buttons).

10 years agoColor-coded graphical pipeline comparison, alternate approach to Tom's
Peter Amstutz [Thu, 30 Jan 2014 22:34:36 +0000 (17:34 -0500)]
Color-coded graphical pipeline comparison, alternate approach to Tom's

10 years agoFurther improvements to provenance graphs, added ability to select a few jobs and...
Peter Amstutz [Thu, 30 Jan 2014 21:18:43 +0000 (16:18 -0500)]
Further improvements to provenance graphs, added ability to select a few jobs and shows the graph for those jobs.

10 years agoMerge branch '2036-fix-python-sdk' of git.clinicalfuture.com:arvados into 2036-fix...
Tim Pierce [Thu, 30 Jan 2014 20:42:13 +0000 (15:42 -0500)]
Merge branch '2036-fix-python-sdk' of git.clinicalfuture.com:arvados into 2036-fix-python-sdk

Conflicts:
sdk/python/arvados/__init__.py
sdk/python/arvados/api.py
sdk/python/arvados/collection.py
sdk/python/arvados/keep.py

10 years agoResolving scoping problems. Python unit tests now pass. (fixes #2036)
Tim Pierce [Thu, 30 Jan 2014 20:37:39 +0000 (15:37 -0500)]
Resolving scoping problems. Python unit tests now pass. (fixes #2036)

10 years agoRearranging modules to eliminate recursive imports.
Tim Pierce [Wed, 29 Jan 2014 23:07:22 +0000 (18:07 -0500)]
Rearranging modules to eliminate recursive imports.

10 years agoRearranging modules to eliminate recursive imports.
Tim Pierce [Wed, 29 Jan 2014 23:07:22 +0000 (18:07 -0500)]
Rearranging modules to eliminate recursive imports.

10 years agoNow renders collections using up to the first three files in the collection
Peter Amstutz [Wed, 29 Jan 2014 21:58:03 +0000 (16:58 -0500)]
Now renders collections using up to the first three files in the collection

10 years agoVery nice provenance diagram for pipelines.
Peter Amstutz [Wed, 29 Jan 2014 21:36:53 +0000 (16:36 -0500)]
Very nice provenance diagram for pipelines.

10 years agoAdd functional test for "skip script_version validation when not
Tom Clegg [Wed, 29 Jan 2014 20:08:54 +0000 (12:08 -0800)]
Add functional test for "skip script_version validation when not
changing that attribute".

10 years agoMerge remote-tracking branch 'origin/master' into 1977-provenance-report
Peter Amstutz [Wed, 29 Jan 2014 19:58:53 +0000 (14:58 -0500)]
Merge remote-tracking branch 'origin/master' into 1977-provenance-report

10 years agoStarted refactoring
Peter Amstutz [Wed, 29 Jan 2014 19:58:11 +0000 (14:58 -0500)]
Started refactoring

10 years agoSkip "specified commit exists" validation when updating an existing
Tom Clegg [Wed, 29 Jan 2014 19:52:59 +0000 (11:52 -0800)]
Skip "specified commit exists" validation when updating an existing
job without modifying script_version.

10 years agoMerge branch 'master' into 1977-provenance-report
Peter Amstutz [Wed, 29 Jan 2014 19:41:55 +0000 (14:41 -0500)]
Merge branch 'master' into 1977-provenance-report

10 years agoFix jobs.cancelled_by_*_changed? calls to jobs.cancelled_by_*_uuid_changed?
Tom Clegg [Wed, 29 Jan 2014 19:37:32 +0000 (11:37 -0800)]
Fix jobs.cancelled_by_*_changed? calls to jobs.cancelled_by_*_uuid_changed?

Missed in 64f3cccd176b214b2e9a571c54973c4e546c606a

10 years agoMerge commit '2728f59' into 1977-provenance-report
Peter Amstutz [Wed, 29 Jan 2014 19:15:25 +0000 (14:15 -0500)]
Merge commit '2728f59' into 1977-provenance-report

10 years agoWorking on visualization of pipelines
Peter Amstutz [Wed, 29 Jan 2014 19:14:36 +0000 (14:14 -0500)]
Working on visualization of pipelines

10 years agoRemove +K@foo parts from collection uuids in jobs' script_parameters
Tom Clegg [Wed, 29 Jan 2014 19:04:12 +0000 (11:04 -0800)]
Remove +K@foo parts from collection uuids in jobs' script_parameters
and other job fields cached in PipelineInstances.

refs #1881

10 years agoFix regular expressions in database migration.
Tom Clegg [Wed, 29 Jan 2014 18:41:19 +0000 (10:41 -0800)]
Fix regular expressions in database migration.

refs #1881

10 years agoFixed bugs in creating graph from API provenance report.
Peter Amstutz [Wed, 29 Jan 2014 16:38:27 +0000 (11:38 -0500)]
Fixed bugs in creating graph from API provenance report.

10 years agoShow condensed data about pipeline instances side by side on "compare"
Tom Clegg [Wed, 29 Jan 2014 02:15:43 +0000 (18:15 -0800)]
Show condensed data about pipeline instances side by side on "compare"
page.

refs #1978

10 years agoPython SDK uses ~/.config/arvados/settings.conf like other SDKs.
Tim Pierce [Tue, 28 Jan 2014 22:31:39 +0000 (17:31 -0500)]
Python SDK uses ~/.config/arvados/settings.conf like other SDKs.

Also: Update ~/.config/arvados/settings.conf when docker images are restarted.

10 years agoWorkbench is able to put together a graph from the provenance document served by...
Peter Amstutz [Tue, 28 Jan 2014 21:24:01 +0000 (16:24 -0500)]
Workbench is able to put together a graph from the provenance document served by the API server.  Needs more testing.

10 years agoUpdating dependencies.
Tim Pierce [Tue, 28 Jan 2014 21:11:38 +0000 (16:11 -0500)]
Updating dependencies.

10 years agoUpdating dependencies to satisfy RubyGems.
Tim Pierce [Tue, 28 Jan 2014 21:05:01 +0000 (16:05 -0500)]
Updating dependencies to satisfy RubyGems.

10 years agoAPI server /collections/uuid/provenance endpoint works.
Peter Amstutz [Tue, 28 Jan 2014 19:06:40 +0000 (14:06 -0500)]
API server /collections/uuid/provenance endpoint works.

10 years agoMerge commit 'e17169e05c2e69d5bb46792bc33ef3c92f9c5237' into 1977-provenance-report
Peter Amstutz [Tue, 28 Jan 2014 16:10:47 +0000 (11:10 -0500)]
Merge commit 'e17169e05c2e69d5bb46792bc33ef3c92f9c5237' into 1977-provenance-report

10 years agoClean up /arvados/v1/../../discovery/v1/ hack before sending request
Tom Clegg [Tue, 28 Jan 2014 16:04:48 +0000 (08:04 -0800)]
Clean up /arvados/v1/../../discovery/v1/ hack before sending request
to server.

10 years agoAdd pipeline_instances/compare page
Tom Clegg [Tue, 28 Jan 2014 15:57:47 +0000 (07:57 -0800)]
Add pipeline_instances/compare page

10 years agoMerge branch 'master' into 1977-provenance-report
Peter Amstutz [Tue, 28 Jan 2014 15:47:07 +0000 (10:47 -0500)]
Merge branch 'master' into 1977-provenance-report

10 years agoWork in progress
Peter Amstutz [Tue, 28 Jan 2014 15:45:54 +0000 (10:45 -0500)]
Work in progress

10 years agoProvenance graph now uses full width of window
Peter Amstutz [Tue, 28 Jan 2014 14:09:35 +0000 (09:09 -0500)]
Provenance graph now uses full width of window

10 years agoInitial work adding provenance query to API server
Peter Amstutz [Mon, 27 Jan 2014 22:07:42 +0000 (17:07 -0500)]
Initial work adding provenance query to API server

10 years agoLeft navbar uses bootstrap "nav-header" class for section headers.
Peter Amstutz [Mon, 27 Jan 2014 21:44:44 +0000 (16:44 -0500)]
Left navbar uses bootstrap "nav-header" class for section headers.

10 years agoHooked into bootstrap/jquery to resize svg box when tab is shown.
Peter Amstutz [Mon, 27 Jan 2014 21:43:36 +0000 (16:43 -0500)]
Hooked into bootstrap/jquery to resize svg box when tab is shown.

10 years agoAdjusts scrollbar to maintain center of image when zooming
Peter Amstutz [Mon, 27 Jan 2014 21:19:05 +0000 (16:19 -0500)]
Adjusts scrollbar to maintain center of image when zooming

10 years agoMerge branch '1946-request-body-vs-parameters'
Tom Clegg [Mon, 27 Jan 2014 21:17:55 +0000 (13:17 -0800)]
Merge branch '1946-request-body-vs-parameters'

closes #1946

10 years agoRemove request body object from parameters lists in *.create and
Tom Clegg [Mon, 27 Jan 2014 20:43:50 +0000 (12:43 -0800)]
Remove request body object from parameters lists in *.create and
*.update -- mark it required in the request body instead.

refs #1946

10 years agoAdd version string to arv (assume "gem install" makes the version
Tom Clegg [Mon, 27 Jan 2014 20:31:59 +0000 (12:31 -0800)]
Add version string to arv (assume "gem install" makes the version
apparent in the executable path).

10 years agoDo not add body object to discovery parameters.
Tom Clegg [Mon, 27 Jan 2014 20:11:08 +0000 (12:11 -0800)]
Do not add body object to discovery parameters.

10 years agoFix up dependencies, pin google-api-client at 0.6.x
Tom Clegg [Mon, 27 Jan 2014 20:10:34 +0000 (12:10 -0800)]
Fix up dependencies, pin google-api-client at 0.6.x

10 years agoAdd Gemfile.lock
Tom Clegg [Mon, 27 Jan 2014 19:25:19 +0000 (11:25 -0800)]
Add Gemfile.lock

10 years agoSend parameters in the request body instead of query parameters if
Tom Clegg [Mon, 27 Jan 2014 19:23:07 +0000 (11:23 -0800)]
Send parameters in the request body instead of query parameters if
discovery document specifies request.properties.(key).$ref.

refs #1946

10 years agoUse javascript to set the size of the svg box so that the horizontal scrollbar stays...
Peter Amstutz [Mon, 27 Jan 2014 21:02:06 +0000 (16:02 -0500)]
Use javascript to set the size of the svg box so that the horizontal scrollbar stays on screen.
Use javascript to enlarge/shrink the svg image ("zoom in" and "zoom out" buttons).

10 years agoAdd tests, fix dependencies so "bundle exec rake test" runs.
Tom Clegg [Mon, 27 Jan 2014 19:17:27 +0000 (11:17 -0800)]
Add tests, fix dependencies so "bundle exec rake test" runs.

10 years agoFix crash when no config file exists, and fix config access from Model
Tom Clegg [Mon, 27 Jan 2014 17:39:47 +0000 (09:39 -0800)]
Fix crash when no config file exists, and fix config access from Model
class.

refs #1943

10 years agoRemove Keep prototype (moved to branch 1747-keep-prototype-ruby).
Tom Clegg [Mon, 27 Jan 2014 15:58:00 +0000 (07:58 -0800)]
Remove Keep prototype (moved to branch 1747-keep-prototype-ruby).

refs #1747

10 years agoPerformance fix to only visit a node once.
Peter Amstutz [Sun, 26 Jan 2014 03:04:01 +0000 (22:04 -0500)]
Performance fix to only visit a node once.
Fix to not add blank/nil nodes.
Only adds nodes for script inputs that are collections.

10 years agoDo not offer to let non-admin users create new keepDisks and nodes.
Tom Clegg [Sat, 25 Jan 2014 06:43:36 +0000 (22:43 -0800)]
Do not offer to let non-admin users create new keepDisks and nodes.

10 years agoChange underscores to camelcase in "kind" strings as documented.
Tom Clegg [Sat, 25 Jan 2014 06:41:29 +0000 (22:41 -0800)]
Change underscores to camelcase in "kind" strings as documented.

10 years agoAdd virtualMachine test fixture.
Tom Clegg [Sat, 25 Jan 2014 06:40:37 +0000 (22:40 -0800)]
Add virtualMachine test fixture.

10 years agoReplace Admin menu with System menu (users can see those things too).
Tom Clegg [Sat, 25 Jan 2014 06:38:54 +0000 (22:38 -0800)]
Replace Admin menu with System menu (users can see those things too).

10 years agoAlways use symbol keys for object attribute names and string keys
Tom Clegg [Sat, 25 Jan 2014 06:24:37 +0000 (22:24 -0800)]
Always use symbol keys for object attribute names and string keys
inside serialized hashes, rather than HashWithIndifferentAccess.

This ensures serialized attributes go into the database as plain
hashes with string keys, even when Rails was responsible for
unserializing the data coming from the client.

refs #1944
refs #1987

10 years agoEnsure we always respond with json (except the redirect at the root
Tom Clegg [Sat, 25 Jan 2014 05:42:04 +0000 (21:42 -0800)]
Ensure we always respond with json (except the redirect at the root
URI).

closes #1739

10 years agoDo not run ec2 commands in test mode.
Tom Clegg [Sat, 25 Jan 2014 05:31:29 +0000 (21:31 -0800)]
Do not run ec2 commands in test mode.

10 years agoUpdate tests to match recent permission changes; dry up "404 if no
Tom Clegg [Sat, 25 Jan 2014 05:08:58 +0000 (21:08 -0800)]
Update tests to match recent permission changes; dry up "404 if no
object found" logic; fix status codes in some error responses.

10 years agoFollows both jobs and links to show provenance for a collection
Peter Amstutz [Sat, 25 Jan 2014 04:04:47 +0000 (23:04 -0500)]
Follows both jobs and links to show provenance for a collection
Collapses similar jobs into a single node by script name and version
Node hrefs work except for git hashes.

10 years agoUse discovery document to build infix->kind map instead of using a
Tom Clegg [Fri, 24 Jan 2014 22:59:51 +0000 (14:59 -0800)]
Use discovery document to build infix->kind map instead of using a
hard-coded list.

10 years agoProvide UUID prefix used for each schema in discovery document.
Tom Clegg [Fri, 24 Jan 2014 22:59:07 +0000 (14:59 -0800)]
Provide UUID prefix used for each schema in discovery document.

10 years agoFix crash on error pages by removing before_filters that assume there
Tom Clegg [Fri, 24 Jan 2014 22:57:21 +0000 (14:57 -0800)]
Fix crash on error pages by removing before_filters that assume there
is a current_user.

10 years agoChange underscores to camelcase in "kind" strings as documented.
Tom Clegg [Fri, 24 Jan 2014 22:54:38 +0000 (14:54 -0800)]
Change underscores to camelcase in "kind" strings as documented.

10 years agoCheckpoint, draws a somewhat useful graph, needs a lot of work though.
Peter Amstutz [Fri, 24 Jan 2014 22:10:24 +0000 (17:10 -0500)]
Checkpoint, draws a somewhat useful graph, needs a lot of work though.

10 years agoAdd /keep_disks page to Admin menu.
Tom Clegg [Fri, 24 Jan 2014 18:17:21 +0000 (10:17 -0800)]
Add /keep_disks page to Admin menu.

10 years agoFix keep_disks.ping to accept a correct ping_secret in lieu of a
Tom Clegg [Fri, 24 Jan 2014 16:45:36 +0000 (08:45 -0800)]
Fix keep_disks.ping to accept a correct ping_secret in lieu of a
sufficiently authorized token.