arvados.git
10 years agoRefuse to run rake tasks without "bundle exec".
Tom Clegg [Wed, 7 May 2014 03:15:40 +0000 (23:15 -0400)]
Refuse to run rake tasks without "bundle exec".

Otherwise you can accidentally load (or dump) schemas without having
the pg_power gem loaded, which will leave you with incorrect indexes
in your database (or schema.rb).

10 years ago2525: Add ArvadosSDKJavaExampleWithPrompt.java to serve as an easier tool to make...
radhika [Wed, 7 May 2014 02:59:11 +0000 (22:59 -0400)]
2525: Add ArvadosSDKJavaExampleWithPrompt.java to serve as an easier tool to make quick calls to API server.

10 years agoAvoided printing graph if no data. Added date histogram was generated.
Misha Zatsman [Wed, 7 May 2014 02:48:40 +0000 (02:48 +0000)]
Avoided printing graph if no data. Added date histogram was generated.

10 years agoAdded cache age histogram!
Misha Zatsman [Wed, 7 May 2014 02:33:06 +0000 (02:33 +0000)]
Added cache age histogram!

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Wed, 7 May 2014 01:47:04 +0000 (21:47 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years agoFix crash creating new user during initial login. Add test.
Tom Clegg [Wed, 7 May 2014 01:46:04 +0000 (21:46 -0400)]
Fix crash creating new user during initial login. Add test.

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Wed, 7 May 2014 01:34:04 +0000 (21:34 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years ago2525: Address review feedback.
radhika [Wed, 7 May 2014 01:33:26 +0000 (21:33 -0400)]
2525: Address review feedback.

10 years agoFix up workbench and apiserver install docs.
Tom Clegg [Tue, 6 May 2014 23:40:27 +0000 (19:40 -0400)]
Fix up workbench and apiserver install docs.

10 years agoFix prompt paths.
Tom Clegg [Tue, 6 May 2014 23:40:19 +0000 (19:40 -0400)]
Fix prompt paths.

10 years agoAdded printing of histogram json.
Misha Zatsman [Tue, 6 May 2014 23:30:26 +0000 (23:30 +0000)]
Added printing of histogram json.

10 years agoClean up install docs
Tom Clegg [Tue, 6 May 2014 22:42:41 +0000 (18:42 -0400)]
Clean up install docs

10 years agoAdd wait_for_ajax after using x-editable in tests.
Tom Clegg [Tue, 6 May 2014 22:27:01 +0000 (18:27 -0400)]
Add wait_for_ajax after using x-editable in tests.

10 years agoReset enforce_permissions between tests. (refs #2328)
Tim Pierce [Tue, 6 May 2014 21:46:41 +0000 (17:46 -0400)]
Reset enforce_permissions between tests. (refs #2328)

10 years agoAdded permission flags and unit tests.
Tim Pierce [Tue, 6 May 2014 21:40:28 +0000 (17:40 -0400)]
Added permission flags and unit tests.

New flags:
  --enforce-permissions enables permission checking for GET requests.
  --permission-ttl sets the expiration time on signed locators returned
    by PUT.
  --data-manager-token defines a privileged token for the Data Manager
    to issue DELETE and "GET /index" requests.

PUT now responds with a signed locator if a permission key has been
set.

Unit test TestGetHandler tests the GetBlockHandler both when permission
checking is off, and tests signed, unsigned and expired requests when
permission checking is enabled.

Refs #2328

10 years agoFix Perl and Python SDK instructions on crunch install page
Tom Clegg [Tue, 6 May 2014 21:38:38 +0000 (17:38 -0400)]
Fix Perl and Python SDK instructions on crunch install page

10 years agoMerge branch 'master' into 2744-update-dev-docs
Tom Clegg [Tue, 6 May 2014 21:32:35 +0000 (17:32 -0400)]
Merge branch 'master' into 2744-update-dev-docs

10 years agoFix dead links
Tom Clegg [Tue, 6 May 2014 21:28:12 +0000 (17:28 -0400)]
Fix dead links

10 years agoAdded div for histogram and style for it.
Misha Zatsman [Tue, 6 May 2014 21:13:07 +0000 (21:13 +0000)]
Added div for histogram and style for it.

10 years agoMerge branch '2733-coverage-report'
Tom Clegg [Tue, 6 May 2014 20:54:12 +0000 (16:54 -0400)]
Merge branch '2733-coverage-report'

closes #2733

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Tue, 6 May 2014 20:30:39 +0000 (16:30 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years agoSynchronize repository and crunch setup instructions with current behavior.
Tom Clegg [Tue, 6 May 2014 20:17:58 +0000 (16:17 -0400)]
Synchronize repository and crunch setup instructions with current behavior.

10 years agoFix copy/paste error in gem build instructions.
Tom Clegg [Tue, 6 May 2014 19:53:10 +0000 (15:53 -0400)]
Fix copy/paste error in gem build instructions.

10 years agoRemove Gemfile.lock from repo
Tom Clegg [Tue, 6 May 2014 19:52:10 +0000 (15:52 -0400)]
Remove Gemfile.lock from repo

see http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/

10 years agoRemove stray debug puts.
Tom Clegg [Tue, 6 May 2014 17:10:05 +0000 (13:10 -0400)]
Remove stray debug puts.

10 years agoMerge branch '1970-folder-view'
Tom Clegg [Tue, 6 May 2014 17:01:44 +0000 (13:01 -0400)]
Merge branch '1970-folder-view'

closes #1970

10 years agoMerge branch 'master' into 1970-folder-view
Tom Clegg [Tue, 6 May 2014 17:01:34 +0000 (13:01 -0400)]
Merge branch 'master' into 1970-folder-view

10 years agoAdd find?() method so "assert find?(...), msg" can be used in test cases.
Tom Clegg [Tue, 6 May 2014 16:58:14 +0000 (12:58 -0400)]
Add find?() method so "assert find?(...), msg" can be used in test cases.

10 years agoReplace unfailable assert() with a comment explaining what it means
Tom Clegg [Tue, 6 May 2014 16:37:29 +0000 (12:37 -0400)]
Replace unfailable assert() with a comment explaining what it means
for find() to raise an exception.

10 years ago2525: correct indentation for pom.xml
radhika [Tue, 6 May 2014 16:28:17 +0000 (12:28 -0400)]
2525: correct indentation for pom.xml

10 years ago2525: use -Dmaven.test.skip=true when packaging the SDK.
radhika [Tue, 6 May 2014 16:08:40 +0000 (12:08 -0400)]
2525: use -Dmaven.test.skip=true when packaging the SDK.

10 years agoAdded test for group mount. Passes.
Peter Amstutz [Tue, 6 May 2014 15:43:31 +0000 (11:43 -0400)]
Added test for group mount.  Passes.

10 years agoImproved fresh/stale handling with base class, added property fuse inode cache
Peter Amstutz [Tue, 6 May 2014 15:25:34 +0000 (11:25 -0400)]
Improved fresh/stale handling with base class, added property fuse inode cache
invalidation.  Added common merge function for handling directory updates.
arv-mount now daemonizes by default.

10 years agoCheck GET permissions in the HTTP handler.
Tim Pierce [Tue, 6 May 2014 15:16:19 +0000 (11:16 -0400)]
Check GET permissions in the HTTP handler.

Move the check for the permission signature to the HTTP handler, so the
back end can still call GetBlock without having to move permissions all
the way down the stack. Refs #2328

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Tue, 6 May 2014 14:54:54 +0000 (10:54 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years ago2352: initial tests for arv-run-pipeline-instance
radhika [Tue, 6 May 2014 14:47:06 +0000 (10:47 -0400)]
2352: initial tests for arv-run-pipeline-instance

10 years agoMerge branch 'master' into 2352-use-state
radhika [Tue, 6 May 2014 13:57:07 +0000 (09:57 -0400)]
Merge branch 'master' into 2352-use-state

10 years agoAdding support for groups and viewing arvados objects as files (serialized
Peter Amstutz [Tue, 6 May 2014 02:42:55 +0000 (22:42 -0400)]
Adding support for groups and viewing arvados objects as files (serialized
json).  Work in progress.

10 years agoMerge branch 'master' into origin-2035-arv-mount-tags-folders
Peter Amstutz [Tue, 6 May 2014 01:25:20 +0000 (21:25 -0400)]
Merge branch 'master' into origin-2035-arv-mount-tags-folders

10 years agoFix so that a present but empty select parameter in queries no longer yields
Peter Amstutz [Tue, 6 May 2014 01:24:45 +0000 (21:24 -0400)]
Fix so that a present but empty select parameter in queries no longer yields
an error.

10 years agoAdded PyYAML to requirements.txt
Peter Amstutz [Tue, 6 May 2014 01:15:47 +0000 (21:15 -0400)]
Added PyYAML to requirements.txt

10 years agoMerge branch 'master' into origin-2035-arv-mount-tags-folders
Peter Amstutz [Tue, 6 May 2014 00:41:45 +0000 (20:41 -0400)]
Merge branch 'master' into origin-2035-arv-mount-tags-folders

10 years agoRemove duplicate ERROR_ACTIONS constant from merge.
Tom Clegg [Tue, 6 May 2014 00:31:45 +0000 (20:31 -0400)]
Remove duplicate ERROR_ACTIONS constant from merge.

10 years agoEnsure edited description really gets saved.
Tom Clegg [Tue, 6 May 2014 00:31:18 +0000 (20:31 -0400)]
Ensure edited description really gets saved.

10 years agoUse send(symbol) instead of send(string).
Tom Clegg [Tue, 6 May 2014 00:22:38 +0000 (20:22 -0400)]
Use send(symbol) instead of send(string).

10 years agoChange icon for virtual machines nav.
Tom Clegg [Tue, 6 May 2014 00:21:08 +0000 (20:21 -0400)]
Change icon for virtual machines nav.

10 years agoRemove confusing return value.
Tom Clegg [Tue, 6 May 2014 00:20:46 +0000 (20:20 -0400)]
Remove confusing return value.

10 years agoMerge branch '2640-folder-api' into 1970-folder-view
Tom Clegg [Mon, 5 May 2014 22:33:04 +0000 (18:33 -0400)]
Merge branch '2640-folder-api' into 1970-folder-view

Conflicts:
apps/workbench/app/controllers/application_controller.rb
services/api/app/controllers/application_controller.rb

10 years agoAdd --permissions-key flag.
Tim Pierce [Mon, 5 May 2014 21:31:47 +0000 (17:31 -0400)]
Add --permissions-key flag.

The --permissions-key flag initializes the PermissionSecret to the
string of bytes in its argument. (refs #2328)

10 years agoMove contents action to GroupsController.
Tom Clegg [Mon, 5 May 2014 21:30:11 +0000 (17:30 -0400)]
Move contents action to GroupsController.

10 years agoFix broken test case.
Tom Clegg [Mon, 5 May 2014 21:24:10 +0000 (17:24 -0400)]
Fix broken test case.

10 years ago2352: when using arv-run-pipeline-instance, set state to RunningOnClient.
radhika [Mon, 5 May 2014 21:12:27 +0000 (17:12 -0400)]
2352: when using arv-run-pipeline-instance, set state to RunningOnClient.

10 years agoMerge branch 'master' of git.curoverse.com:arvados
Ward Vandewege [Mon, 5 May 2014 21:09:43 +0000 (17:09 -0400)]
Merge branch 'master' of git.curoverse.com:arvados

10 years agoDocumentation tweaks:
Ward Vandewege [Mon, 5 May 2014 21:06:01 +0000 (17:06 -0400)]
Documentation tweaks:
* Python SDK requires Python 2.7, make that clear up front
* Remove duplicated SDK installation instructions

10 years agoMerge branch '2640-folder-api'
Tom Clegg [Mon, 5 May 2014 21:02:37 +0000 (17:02 -0400)]
Merge branch '2640-folder-api'

10 years agoMerge branch 'master' into 2640-folder-api
Tom Clegg [Mon, 5 May 2014 21:01:50 +0000 (17:01 -0400)]
Merge branch 'master' into 2640-folder-api

Conflicts:
apps/workbench/app/models/arvados_api_client.rb

10 years agoRaise PermissionDeniedError even more consistently
Tom Clegg [Mon, 5 May 2014 20:55:19 +0000 (16:55 -0400)]
Raise PermissionDeniedError even more consistently

10 years agoMerge branch 'master' into 2035-arv-mount-tags-folders
Peter Amstutz [Mon, 5 May 2014 20:52:28 +0000 (16:52 -0400)]
Merge branch 'master' into 2035-arv-mount-tags-folders

10 years agoRefactored freshness/updating to be more generic for different virtual
Peter Amstutz [Mon, 5 May 2014 20:49:08 +0000 (16:49 -0400)]
Refactored freshness/updating to be more generic for different virtual
directory types.  Added polling based on timeout as an alternative to
websockets.  Refactored tests a bit.

10 years agoMerge branch '2640-folder-api' into 1970-folder-view
Tom Clegg [Mon, 5 May 2014 20:14:34 +0000 (16:14 -0400)]
Merge branch '2640-folder-api' into 1970-folder-view

10 years agoRaise PermissionDeniedError more consistently
Tom Clegg [Mon, 5 May 2014 20:05:22 +0000 (16:05 -0400)]
Raise PermissionDeniedError more consistently

10 years agoComment mysterious testing code.
Tom Clegg [Mon, 5 May 2014 20:02:29 +0000 (16:02 -0400)]
Comment mysterious testing code.

10 years agoAdd test for links_for + multiple link_classes.
Tom Clegg [Mon, 5 May 2014 19:59:44 +0000 (15:59 -0400)]
Add test for links_for + multiple link_classes.

10 years agoAdded websockets support to Python SDK, with integration test. Also built out
Peter Amstutz [Mon, 5 May 2014 19:27:31 +0000 (15:27 -0400)]
Added websockets support to Python SDK, with integration test.  Also built out
runner script for running test server from python.

10 years agoMerge branch '1904-workbench-reader-tokens'
Brett Smith [Mon, 5 May 2014 19:20:45 +0000 (15:20 -0400)]
Merge branch '1904-workbench-reader-tokens'

Refs #1904.  Closes #2663, #2736.

10 years agoworkbench: Reader tokens show collection files.
Brett Smith [Mon, 5 May 2014 16:55:29 +0000 (12:55 -0400)]
workbench: Reader tokens show collection files.

Fundamentally, this commit aims to support reader tokens when showing
a file from a Collection.  Because this requires changing the token
handling generally, I also took this opportunity to improve error
reporting by checking the request's validity against the API server
before we pipe out to arv-get to render the file.

As a consequence, Workbench now returns a 404 if you request a file
using a token that does not have permission to read the collection.
Maybe this is not the best result, but previously it returned a 422,
so I think this counts as an improvement.

10 years agoworkbench: Add initial reader tokens support.
Brett Smith [Mon, 5 May 2014 14:54:53 +0000 (10:54 -0400)]
workbench: Add initial reader tokens support.

The API server recently gained support for reader tokens, which
optionally supplement the user's permissions for read-only
operations.  This commit extends Workbench to pass on reader tokens
for general index and show operations.

10 years agoworkbench: Add Collections controller tests.
Brett Smith [Wed, 30 Apr 2014 14:38:08 +0000 (10:38 -0400)]
workbench: Add Collections controller tests.

Working to establish a baseline of behavior before I go mucking with
this.

10 years agoworkbench: Remove trailing whitespace.
Brett Smith [Thu, 1 May 2014 14:42:33 +0000 (10:42 -0400)]
workbench: Remove trailing whitespace.

10 years agoMerge branch 'master' into 2352-use-state
radhika [Mon, 5 May 2014 18:19:58 +0000 (14:19 -0400)]
Merge branch 'master' into 2352-use-state

10 years agoMerge branch '2328-keep-permission-hints'
Tim Pierce [Mon, 5 May 2014 18:03:10 +0000 (14:03 -0400)]
Merge branch '2328-keep-permission-hints'

10 years agoResolve code review (closes #2328)
Tim Pierce [Mon, 5 May 2014 17:52:06 +0000 (13:52 -0400)]
Resolve code review (closes #2328)

Fix doc comments and argument names for the expiry timestamp arguments
for SignLocator and makePermSignature.

10 years ago2525: Now that we have the doc page updated with Java SDK details, updated the README...
radhika [Mon, 5 May 2014 17:40:26 +0000 (13:40 -0400)]
2525: Now that we have the doc page updated with Java SDK details, updated the README file to
point to the doc page instead of maintaining two copies of the same content.

10 years agoAdd simplecov-rcov.
Tom Clegg [Mon, 5 May 2014 17:30:37 +0000 (13:30 -0400)]
Add simplecov-rcov.

10 years ago2525: Add java SDK to documentation site.
radhika [Mon, 5 May 2014 17:24:20 +0000 (13:24 -0400)]
2525: Add java SDK to documentation site.

10 years agoFinished implementing FuseTagsTest, fixed bugs in arv-mount, test passes.
Peter Amstutz [Mon, 5 May 2014 14:28:46 +0000 (10:28 -0400)]
Finished implementing FuseTagsTest, fixed bugs in arv-mount, test passes.

10 years agoFix ajax->refresh race condition in test case.
Tom Clegg [Mon, 5 May 2014 10:58:54 +0000 (06:58 -0400)]
Fix ajax->refresh race condition in test case.

10 years agoFix tests, make model.editable? work for new records.
Tom Clegg [Mon, 5 May 2014 10:32:27 +0000 (06:32 -0400)]
Fix tests, make model.editable? work for new records.

10 years agoBehave nicer if supplied owner_uuid is not a valid uuid at all.
Tom Clegg [Mon, 5 May 2014 10:08:30 +0000 (06:08 -0400)]
Behave nicer if supplied owner_uuid is not a valid uuid at all.

10 years agoEdit objects after creating them with x-editable.
Tom Clegg [Mon, 5 May 2014 10:06:16 +0000 (06:06 -0400)]
Edit objects after creating them with x-editable.

10 years agoImplement simple client-side folder contents search.
Tom Clegg [Mon, 5 May 2014 08:01:48 +0000 (04:01 -0400)]
Implement simple client-side folder contents search.

10 years agoImplement "remove from folder"
Tom Clegg [Mon, 5 May 2014 07:47:50 +0000 (03:47 -0400)]
Implement "remove from folder"

10 years agoName new folders "New folder", fix crash if folder name is nil
Tom Clegg [Mon, 5 May 2014 07:25:53 +0000 (03:25 -0400)]
Name new folders "New folder", fix crash if folder name is nil

10 years agoUpdate name in breadcrumb after editing elsewhere on page.
Tom Clegg [Mon, 5 May 2014 07:21:09 +0000 (03:21 -0400)]
Update name in breadcrumb after editing elsewhere on page.

10 years agoMerge branch '2640-folder-api' into 1970-folder-view
Tom Clegg [Mon, 5 May 2014 06:51:30 +0000 (02:51 -0400)]
Merge branch '2640-folder-api' into 1970-folder-view

10 years agoOmit locally configurable files and testing code from coverage report
Tom Clegg [Mon, 5 May 2014 02:23:51 +0000 (22:23 -0400)]
Omit locally configurable files and testing code from coverage report

10 years agoSkip simplecov if gem fails to load or NO_COVERAGE_TEST env is set.
Tom Clegg [Mon, 5 May 2014 02:02:08 +0000 (22:02 -0400)]
Skip simplecov if gem fails to load or NO_COVERAGE_TEST env is set.

10 years ago2525: Remove unused imports
radhika [Sun, 4 May 2014 21:56:11 +0000 (17:56 -0400)]
2525: Remove unused imports

10 years ago2525: Better handling of unsupported api name and version
radhika [Sun, 4 May 2014 21:53:23 +0000 (17:53 -0400)]
2525: Better handling of unsupported api name and version

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Sun, 4 May 2014 21:35:00 +0000 (17:35 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years ago2525: return map instead of json string for the call method.
radhika [Sun, 4 May 2014 21:34:10 +0000 (17:34 -0400)]
2525: return map instead of json string for the call method.

10 years ago2525: small refactoring
radhika [Sun, 4 May 2014 20:47:25 +0000 (16:47 -0400)]
2525: small refactoring

10 years ago2525: add map parameter type handling to request processing
radhika [Sun, 4 May 2014 19:53:17 +0000 (15:53 -0400)]
2525: add map parameter type handling to request processing

10 years ago2525: add float handling to request parameters
radhika [Sun, 4 May 2014 18:53:32 +0000 (14:53 -0400)]
2525: add float handling to request parameters

10 years agoDo not try to record object_owner_uuid during earlier migrations.
Tom Clegg [Sun, 4 May 2014 18:49:11 +0000 (14:49 -0400)]
Do not try to record object_owner_uuid during earlier migrations.

10 years ago2525: Add support for array request parameter type
radhika [Sun, 4 May 2014 18:13:31 +0000 (14:13 -0400)]
2525: Add support for array request parameter type

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Sun, 4 May 2014 02:18:52 +0000 (22:18 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years ago2525: readme and test updates
radhika [Sun, 4 May 2014 02:17:30 +0000 (22:17 -0400)]
2525: readme and test updates

10 years agoMerge branch 'master' into 2640-folder-api
Tom Clegg [Sun, 4 May 2014 01:25:19 +0000 (21:25 -0400)]
Merge branch 'master' into 2640-folder-api

10 years agoFix crashing "grant access to my own object" permission check.
Tom Clegg [Sun, 4 May 2014 01:22:17 +0000 (21:22 -0400)]
Fix crashing "grant access to my own object" permission check.