arvados.git
10 years agoMerged branch 1741-internal-git-repo into 2333-crunch-dispatch-token-management
Peter Amstutz [Thu, 27 Mar 2014 13:27:13 +0000 (09:27 -0400)]
Merged branch 1741-internal-git-repo into 2333-crunch-dispatch-token-management

10 years agoFixed dangling 'end'
Peter Amstutz [Thu, 27 Mar 2014 12:54:53 +0000 (08:54 -0400)]
Fixed dangling 'end'

10 years agoMerge branch 'master' into 2333-crunch-dispatch-token-management
Peter Amstutz [Thu, 27 Mar 2014 12:41:10 +0000 (08:41 -0400)]
Merge branch 'master' into 2333-crunch-dispatch-token-management

10 years agoStylistic changes based on comments from Tom/Brett
Peter Amstutz [Thu, 27 Mar 2014 12:41:01 +0000 (08:41 -0400)]
Stylistic changes based on comments from Tom/Brett

10 years agoMerge branch '2051-nondeterministic-jobs'
Peter Amstutz [Thu, 27 Mar 2014 12:37:33 +0000 (08:37 -0400)]
Merge branch '2051-nondeterministic-jobs'

10 years agoMerge branch '2291-new-keepd-read-blocks' (fixes #2291)
Tim Pierce [Wed, 26 Mar 2014 21:34:50 +0000 (17:34 -0400)]
Merge branch '2291-new-keepd-read-blocks' (fixes #2291)

10 years agoIncorporating code review comments (refs #2291, refs #2438)
Tim Pierce [Wed, 26 Mar 2014 21:06:59 +0000 (17:06 -0400)]
Incorporating code review comments (refs #2291, refs #2438)

10 years agoImprove readability of unit tests. (refs #2291)
Tim Pierce [Wed, 26 Mar 2014 20:58:49 +0000 (16:58 -0400)]
Improve readability of unit tests. (refs #2291)

Pass *testing.T object into setup/store functions to reduce
error-checking overhead.

10 years agoAdd list of in-progress/planned SDKs.
Tom Clegg [Tue, 25 Mar 2014 22:50:31 +0000 (18:50 -0400)]
Add list of in-progress/planned SDKs.

10 years agoAdd Ruby SDK page.
Tom Clegg [Tue, 25 Mar 2014 22:36:17 +0000 (18:36 -0400)]
Add Ruby SDK page.

10 years agoFix broken links and duplicate titles.
Tom Clegg [Tue, 25 Mar 2014 21:38:02 +0000 (17:38 -0400)]
Fix broken links and duplicate titles.

10 years agoAdd command line SDK page.
Tom Clegg [Mon, 10 Mar 2014 23:00:38 +0000 (19:00 -0400)]
Add command line SDK page.

10 years agoAdd Perl SDK page.
Tom Clegg [Mon, 10 Mar 2014 22:33:17 +0000 (18:33 -0400)]
Add Perl SDK page.

10 years agoFixes "sec_error_reused_issuer_and_serial" SSL error in Firefox.
Peter Amstutz [Wed, 26 Mar 2014 18:58:57 +0000 (14:58 -0400)]
Fixes "sec_error_reused_issuer_and_serial" SSL error in Firefox.

10 years agoAdded fix to workbench dashboard so that workbench integration tests pass.
Peter Amstutz [Wed, 26 Mar 2014 18:19:10 +0000 (14:19 -0400)]
Added fix to workbench dashboard so that workbench integration tests pass.
Added slightly helpful failure message to test assertion.
Fixed non-normalized collection uuids in fixtures.

10 years agoMerge branch 'master' into 2051-nondeterministic-jobs
Peter Amstutz [Wed, 26 Mar 2014 17:16:37 +0000 (13:16 -0400)]
Merge branch 'master' into 2051-nondeterministic-jobs

Conflicts:
doc/README
doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid

10 years agoAdded more tests and more aggressive input checking.
Peter Amstutz [Wed, 26 Mar 2014 12:57:00 +0000 (08:57 -0400)]
Added more tests and more aggressive input checking.

10 years agoMerge branch '2412-do-not-reuse-task-work-dirs'
Tom Clegg [Tue, 25 Mar 2014 23:14:09 +0000 (19:14 -0400)]
Merge branch '2412-do-not-reuse-task-work-dirs'

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Tue, 25 Mar 2014 21:01:59 +0000 (17:01 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoFixes #2047: Catch connection errors in 'arv' and report the error nicely
Peter Amstutz [Tue, 25 Mar 2014 21:01:45 +0000 (17:01 -0400)]
Fixes #2047: Catch connection errors in 'arv' and report the error nicely
instead of dumping a backtrace.

10 years agoIncorporating comments from code review (refs #2438, refs #2291)
Tim Pierce [Tue, 25 Mar 2014 20:57:37 +0000 (16:57 -0400)]
Incorporating comments from code review (refs #2438, refs #2291)

10 years agoReworked input validation on find_commit_range (for real this time!) and added tests.
Peter Amstutz [Tue, 25 Mar 2014 20:51:57 +0000 (16:51 -0400)]
Reworked input validation on find_commit_range (for real this time!) and added tests.
Fixed descriptive text in tutorial-job1.
Removed dead code.

10 years agoMerge branch '2288-smoke-test'
Brett Smith [Tue, 25 Mar 2014 20:11:48 +0000 (16:11 -0400)]
Merge branch '2288-smoke-test'

10 years agoRemoved trailing whitespace.
Peter Amstutz [Tue, 25 Mar 2014 19:24:55 +0000 (15:24 -0400)]
Removed trailing whitespace.

10 years agoFixed tests
Peter Amstutz [Tue, 25 Mar 2014 19:24:15 +0000 (15:24 -0400)]
Fixed tests
Improved version string validation in find_commit_range
Removed spurious debugging flags
Removed dead code from commit.rb
Removed trailing whitespace
Fixed capitalization of Arvados in documentation

10 years agoworkbench: Timeout integration test Rails launch.
Brett Smith [Tue, 25 Mar 2014 19:10:24 +0000 (15:10 -0400)]
workbench: Timeout integration test Rails launch.

10 years agoMerge branch 'master' into 2187-enhance-user-setup
radhika chippada [Tue, 25 Mar 2014 18:50:38 +0000 (14:50 -0400)]
Merge branch 'master' into 2187-enhance-user-setup

10 years agoMinor test updates
radhika chippada [Tue, 25 Mar 2014 18:50:02 +0000 (14:50 -0400)]
Minor test updates

10 years agoMerge branch 'master' into 2051-nondeterministic-jobs
Peter Amstutz [Tue, 25 Mar 2014 18:40:01 +0000 (14:40 -0400)]
Merge branch 'master' into 2051-nondeterministic-jobs

10 years agoworkbench: Improve integration test Rails launch.
Brett Smith [Tue, 25 Mar 2014 18:36:48 +0000 (14:36 -0400)]
workbench: Improve integration test Rails launch.

The previous version was susceptible to a race condition where it
would read the file after Rails created it, but before it actually
wrote a pid to it.  This would cause the rake test task to kill itself
later by running Process.kill('TERM', 0).

10 years agoThe controller invokes the create links method from the model when working on an...
radhika chippada [Tue, 25 Mar 2014 18:09:44 +0000 (14:09 -0400)]
The controller invokes the create links method from the model when working on an existing user.

10 years agoworkbench: Document deployment Bundle testing.
Brett Smith [Tue, 25 Mar 2014 18:01:23 +0000 (14:01 -0400)]
workbench: Document deployment Bundle testing.

10 years agoUpdate controller action name in functional test. refs #1750
Tom Clegg [Tue, 25 Mar 2014 17:59:20 +0000 (13:59 -0400)]
Update controller action name in functional test. refs #1750

10 years agoMerge branch '1750-remove-old-schema-doc'
Tom Clegg [Tue, 25 Mar 2014 17:43:24 +0000 (13:43 -0400)]
Merge branch '1750-remove-old-schema-doc'

closes #1750

10 years agosetup method in user model assumes that the user object passed in is valid and hence...
radhika chippada [Tue, 25 Mar 2014 17:23:28 +0000 (13:23 -0400)]
setup method in user model assumes that the user object passed in is valid and hence no longer tries to find it.

10 years agoUnit test TestGetBlockCorrupt. (refs #2291)
Tim Pierce [Tue, 25 Mar 2014 16:53:40 +0000 (12:53 -0400)]
Unit test TestGetBlockCorrupt. (refs #2291)

10 years agoGround work to remove found object logic from user model's setup method
radhika chippada [Tue, 25 Mar 2014 16:32:35 +0000 (12:32 -0400)]
Ground work to remove found object logic from user model's setup method

10 years agoUpdate all functional tests to work with the new response format of List
radhika chippada [Tue, 25 Mar 2014 14:55:54 +0000 (10:55 -0400)]
Update all functional tests to work with the new response format of List

10 years agoAdded unit tests TestGetBlockOneKeepOK and TestGetBlockFail (refs #2291)
Tim Pierce [Tue, 25 Mar 2014 14:32:15 +0000 (10:32 -0400)]
Added unit tests TestGetBlockOneKeepOK and TestGetBlockFail (refs #2291)

10 years agoUpdate user model to return a List instead of HashList
radhika chippada [Tue, 25 Mar 2014 03:20:05 +0000 (23:20 -0400)]
Update user model to return a List instead of HashList

10 years agosome minor refactoring
radhika chippada [Mon, 24 Mar 2014 23:27:35 +0000 (19:27 -0400)]
some minor refactoring

10 years agoWhen uuid is passed, openid_prefix can be optional
radhika chippada [Mon, 24 Mar 2014 22:53:58 +0000 (18:53 -0400)]
When uuid is passed, openid_prefix can be optional

10 years agoMerge branch 'master' into 2187-enhance-user-setup
radhika chippada [Mon, 24 Mar 2014 22:10:32 +0000 (18:10 -0400)]
Merge branch 'master' into 2187-enhance-user-setup

10 years agoMore unit testing
radhika chippada [Mon, 24 Mar 2014 22:09:24 +0000 (18:09 -0400)]
More unit testing

10 years agoAdd unit test for user model
radhika chippada [Mon, 24 Mar 2014 22:05:08 +0000 (18:05 -0400)]
Add unit test for user model

10 years agoAdding unit tests for GetBlock. (refs #2291)
Tim Pierce [Mon, 24 Mar 2014 21:15:43 +0000 (17:15 -0400)]
Adding unit tests for GetBlock. (refs #2291)

10 years agoAllow disabling of output for rake config:check via a QUIET environment
Ward Vandewege [Mon, 24 Mar 2014 20:16:10 +0000 (16:16 -0400)]
Allow disabling of output for rake config:check via a QUIET environment
variable.

10 years agoDo not print secrets in the config:check rake task.
Ward Vandewege [Mon, 24 Mar 2014 19:55:29 +0000 (15:55 -0400)]
Do not print secrets in the config:check rake task.

10 years agoMerge branch 'master' into 2187-enhance-user-setup
radhika chippada [Mon, 24 Mar 2014 18:19:48 +0000 (14:19 -0400)]
Merge branch 'master' into 2187-enhance-user-setup

10 years agoInclude first link of a given type even on reruns of the setup method.
radhika chippada [Mon, 24 Mar 2014 18:17:39 +0000 (14:17 -0400)]
Include first link of a given type even on reruns of the setup method.

10 years agoMerge branch '2209-test-limit-offset'
Tom Clegg [Mon, 24 Mar 2014 14:24:47 +0000 (10:24 -0400)]
Merge branch '2209-test-limit-offset'

closes #2209

10 years agoMerge branch '2290-user-activity'
Tom Clegg [Mon, 24 Mar 2014 14:22:20 +0000 (10:22 -0400)]
Merge branch '2290-user-activity'

closes #2290

10 years agoMerge branch 'master' into 2187-enhance-user-setup
radhika chippada [Mon, 24 Mar 2014 13:02:04 +0000 (09:02 -0400)]
Merge branch 'master' into 2187-enhance-user-setup

10 years agoRaise error if both uuid and user.email are omitted in input parameters
radhika chippada [Mon, 24 Mar 2014 12:58:50 +0000 (08:58 -0400)]
Raise error if both uuid and user.email are omitted in input parameters

10 years agoAvoid reusing per-task work directories.
Tom Clegg [Mon, 24 Mar 2014 06:17:42 +0000 (02:17 -0400)]
Avoid reusing per-task work directories.

10 years agoAdd tests for limit and offset parameters. refs #2075 refs #2209
Tom Clegg [Mon, 24 Mar 2014 02:38:05 +0000 (22:38 -0400)]
Add tests for limit and offset parameters. refs #2075 refs #2209

10 years agoAccept ...&filters=&... in query string as "none" instead of "unparseable JSON".
Tom Clegg [Mon, 24 Mar 2014 02:33:40 +0000 (22:33 -0400)]
Accept ...&filters=&... in query string as "none" instead of "unparseable JSON".

10 years agoRaise ArgumentError when required openid_prefix is not passed.
radhika chippada [Mon, 24 Mar 2014 01:17:26 +0000 (21:17 -0400)]
Raise ArgumentError when required openid_prefix is not passed.

10 years agoRaise exceptions on errors such as 'All users' group does not exist and a vm for...
radhika chippada [Sun, 23 Mar 2014 21:20:37 +0000 (17:20 -0400)]
Raise exceptions on errors such as 'All users' group does not exist and a vm for the vm_uuid param does not exist. Add additional functional tests and update previous tests accordingly.

10 years agoFix tabs in the test class
radhika chippada [Sun, 23 Mar 2014 20:51:59 +0000 (16:51 -0400)]
Fix tabs in the test class

10 years agoMake sure oid_login_perm exists when setup is executed for an existing user
radhika chippada [Sun, 23 Mar 2014 20:37:56 +0000 (16:37 -0400)]
Make sure oid_login_perm exists when setup is executed for an existing user

10 years agoInclude all the newly created link objects in the response from the setup method...
radhika chippada [Sun, 23 Mar 2014 19:50:13 +0000 (15:50 -0400)]
Include all the newly created link objects in the response from the setup method. Update all functional tests to verify links found in teh response.

10 years agoRepo name and VM are optional to the setup method
radhika chippada [Sun, 23 Mar 2014 03:44:04 +0000 (23:44 -0400)]
Repo name and VM are optional to the setup method

10 years agoRender 404 if no user is found for the uuid provided
radhika chippada [Sun, 23 Mar 2014 02:59:32 +0000 (22:59 -0400)]
Render 404 if no user is found for the uuid provided

10 years agoExpect openid_prefix from the clients instead of managing it on the api server.
radhika chippada [Sun, 23 Mar 2014 00:21:12 +0000 (20:21 -0400)]
Expect openid_prefix from the clients instead of managing it on the api server.

10 years agoAPI server: strip all arvados-specific settings from the .example
Ward Vandewege [Sat, 22 Mar 2014 14:59:17 +0000 (10:59 -0400)]
API server: strip all arvados-specific settings from the .example
environment files. These are now all configured via
application(.defaults).yml

10 years agoFix link, this fixes bug 2403
Ward Vandewege [Sat, 22 Mar 2014 14:32:24 +0000 (10:32 -0400)]
Fix link, this fixes bug 2403

10 years agoFix textile formatting.
Tom Clegg [Sat, 22 Mar 2014 02:14:46 +0000 (22:14 -0400)]
Fix textile formatting.

10 years agoFix up README, convert to textile.
Tom Clegg [Sat, 22 Mar 2014 00:38:23 +0000 (20:38 -0400)]
Fix up README, convert to textile.

10 years agoInitial checkin: simple Keep server handling block reads only. (refs #2291)
Tim Pierce [Fri, 21 Mar 2014 21:54:25 +0000 (17:54 -0400)]
Initial checkin: simple Keep server handling block reads only. (refs #2291)

10 years agoworkbench: Add basic smoke test.
Brett Smith [Fri, 21 Mar 2014 21:24:07 +0000 (17:24 -0400)]
workbench: Add basic smoke test.

This visits all the link on a user's front page and makes sure they
all return 200.

It's easy to extend this to crawl the entire site, checking for
success.  I've included the code for that.  We need to squash some
bugs and check the timing before we start doing that, though.

This overlaps api_client_authorizations_test, so I deleted that.

10 years agoworkbench: Add ids to other navbar dropdowns.
Brett Smith [Fri, 21 Mar 2014 20:22:55 +0000 (16:22 -0400)]
workbench: Add ids to other navbar dropdowns.

This makes them easier to click in integration tests.

10 years agoFixed paging so that it won't fail if the necessary methods are missing on the result...
Peter Amstutz [Fri, 21 Mar 2014 20:51:39 +0000 (16:51 -0400)]
Fixed paging so that it won't fail if the necessary methods are missing on the results object.

10 years agoAdd negative functional tests where a non-admin user invokes create or setup actions
radhika chippada [Fri, 21 Mar 2014 20:36:47 +0000 (16:36 -0400)]
Add negative functional tests where a non-admin user invokes create or setup actions

10 years agoTypo.
Ward Vandewege [Fri, 21 Mar 2014 20:16:35 +0000 (16:16 -0400)]
Typo.

10 years agoOne more print statement
radhika chippada [Fri, 21 Mar 2014 20:10:29 +0000 (16:10 -0400)]
One more print statement

10 years agoRemove print statement
radhika chippada [Fri, 21 Mar 2014 20:07:43 +0000 (16:07 -0400)]
Remove print statement

10 years agoPass openid_prefix to setup method only when -o option is used
radhika chippada [Fri, 21 Mar 2014 20:05:37 +0000 (16:05 -0400)]
Pass openid_prefix to setup method only when -o option is used

10 years agoMerge branch 'master' of git.curoverse.com:arvados
Ward Vandewege [Fri, 21 Mar 2014 20:03:38 +0000 (16:03 -0400)]
Merge branch 'master' of git.curoverse.com:arvados

10 years agoStrip all arvados-specific settings from the .example environment files.
Ward Vandewege [Fri, 21 Mar 2014 20:02:29 +0000 (16:02 -0400)]
Strip all arvados-specific settings from the .example environment files.
These are now all configured via application(.defaults).yml

10 years agoFixed pipeline templates page that was broken by paging merge.
Peter Amstutz [Fri, 21 Mar 2014 20:02:03 +0000 (16:02 -0400)]
Fixed pipeline templates page that was broken by paging merge.

10 years agosome more refactoring and attention to coding standards
radhika chippada [Fri, 21 Mar 2014 19:46:57 +0000 (15:46 -0400)]
some more refactoring and attention to coding standards

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Fri, 21 Mar 2014 19:30:56 +0000 (15:30 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoFixed syntax error typo. We need tests for crunch-dispatcher.rb!
Peter Amstutz [Fri, 21 Mar 2014 19:30:42 +0000 (15:30 -0400)]
Fixed syntax error typo.  We need tests for crunch-dispatcher.rb!

10 years agoAll functional tests passing with refactored code.
radhika chippada [Fri, 21 Mar 2014 19:13:57 +0000 (15:13 -0400)]
All functional tests passing with refactored code.

10 years agoworkbench: Add developer docs.
Brett Smith [Fri, 21 Mar 2014 19:00:15 +0000 (15:00 -0400)]
workbench: Add developer docs.

This adds a new README with information that's useful for people who
want to develop Workbench.  Right now it's just information about how
to run and write tests.  We can add to this as we go.

Some of this information was pulled from the installation guide.  I
also deleted Rails' stock README while I was at it.

10 years agoMerge branch '1750-use-supported-discovery-doc'
Tom Clegg [Fri, 21 Mar 2014 18:44:58 +0000 (14:44 -0400)]
Merge branch '1750-use-supported-discovery-doc'

refs #1750

10 years agoExpiring pipeline tokens works.
Peter Amstutz [Fri, 21 Mar 2014 18:11:36 +0000 (14:11 -0400)]
Expiring pipeline tokens works.

10 years agoWorking on re-using token per pipeline and expiring token when the pipeline is done.
Peter Amstutz [Fri, 21 Mar 2014 17:53:28 +0000 (13:53 -0400)]
Working on re-using token per pipeline and expiring token when the pipeline is done.

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Fri, 21 Mar 2014 17:02:28 +0000 (13:02 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Fri, 21 Mar 2014 16:57:04 +0000 (12:57 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

10 years agoMerge branch '2316-no-clear-tmp-flag'
Tom Clegg [Fri, 21 Mar 2014 16:56:08 +0000 (12:56 -0400)]
Merge branch '2316-no-clear-tmp-flag'

closes #2316
refs #2372

10 years agoMerge branch 'master' into 2316-no-clear-tmp-flag
Tom Clegg [Fri, 21 Mar 2014 16:55:29 +0000 (12:55 -0400)]
Merge branch 'master' into 2316-no-clear-tmp-flag

10 years agoRemove old schema#show method used by Workbench before
Tom Clegg [Fri, 21 Mar 2014 16:53:43 +0000 (12:53 -0400)]
Remove old schema#show method used by Workbench before
14ea55f217bbd7061fafc1fe69f4f453ad7c3e59.

10 years agoUse the supported discovery document instead of the old schema#show shim.
Tom Clegg [Fri, 21 Mar 2014 16:52:04 +0000 (12:52 -0400)]
Use the supported discovery document instead of the old schema#show shim.

10 years agoworkbench: Bundle integration env bugfix.
Brett Smith [Fri, 21 Mar 2014 15:47:06 +0000 (11:47 -0400)]
workbench: Bundle integration env bugfix.

The previous version did not unpack arguments correctly.

10 years agoWhen running with WEBrick, auto-generate a new self-signed SSL
Ward Vandewege [Fri, 21 Mar 2014 15:36:25 +0000 (11:36 -0400)]
When running with WEBrick, auto-generate a new self-signed SSL
certificate for each run, rather than hardcoding a path to a certificate
and key file.

10 years agoworkbench: Expound Bundle+integration interaction.
Brett Smith [Fri, 21 Mar 2014 15:34:05 +0000 (11:34 -0400)]
workbench: Expound Bundle+integration interaction.

Unsurprisingly, I don't write my best code and comments when I'm
frantically trying to fix the build.

10 years agoworkbench: Make SERVER_PID_PATH a constant.
Brett Smith [Fri, 21 Mar 2014 15:16:14 +0000 (11:16 -0400)]
workbench: Make SERVER_PID_PATH a constant.

10 years agoworkbench: Tweak integration test environment.
Brett Smith [Fri, 21 Mar 2014 15:12:53 +0000 (11:12 -0400)]
workbench: Tweak integration test environment.

RUBYLIB and RUBYOPT seem to be necessary on the build server.