Phil Hodgson [Sun, 24 Aug 2014 17:07:34 +0000 (13:07 -0400)]
3354: Rename render_content_from_database helper to render_markup, as a more directly descriptive method name.
Phil Hodgson [Wed, 20 Aug 2014 13:04:54 +0000 (09:04 -0400)]
Merge branch 'master' into 3354-render-textile
Conflicts (resolved):
apps/workbench/app/controllers/application_controller.rb
Tom Clegg [Mon, 18 Aug 2014 22:58:06 +0000 (18:58 -0400)]
Merge branch '3114-copy-to-project' closes #3114
Tom Clegg [Mon, 18 Aug 2014 22:19:29 +0000 (18:19 -0400)]
3114: Follow return_to param, if given, when redirecting users#show to projects#show.
Don't redirect non-html requests.
Tom Clegg [Mon, 18 Aug 2014 22:18:55 +0000 (18:18 -0400)]
3114: Update test case: searching for own uuid now shows home project.
Tom Clegg [Mon, 18 Aug 2014 22:02:47 +0000 (18:02 -0400)]
3114: Merge branch 'master' into 3114-copy-to-project
Brett Smith [Mon, 18 Aug 2014 18:38:57 +0000 (14:38 -0400)]
3593: Add explanatory comment about Workbench's user cache.
Refs #3593.
Tom Clegg [Mon, 18 Aug 2014 20:51:13 +0000 (16:51 -0400)]
3114: Fix href in json response for generic #create action too. See
7485476.
Tom Clegg [Mon, 18 Aug 2014 18:26:59 +0000 (14:26 -0400)]
Merge branch '2800-pgs' refs #2800
Tom Clegg [Mon, 18 Aug 2014 18:25:47 +0000 (14:25 -0400)]
2800: Sort import statements.
Tom Clegg [Mon, 18 Aug 2014 18:17:49 +0000 (14:17 -0400)]
Merge branch '3604-theme-and-new-user-process' closes #3604
Tom Clegg [Mon, 18 Aug 2014 18:02:42 +0000 (14:02 -0400)]
2800: Restore deleted comment which is still relevant.
Tom Clegg [Mon, 18 Aug 2014 18:01:54 +0000 (14:01 -0400)]
2800: Remove unnecessary sha1. Just use the tuple as an array key.
Tom Clegg [Mon, 18 Aug 2014 17:37:21 +0000 (13:37 -0400)]
3604: Remove useless slice.
Tom Clegg [Mon, 18 Aug 2014 17:35:59 +0000 (13:35 -0400)]
3604: Remove useless loop.
Tom Clegg [Mon, 18 Aug 2014 17:23:03 +0000 (13:23 -0400)]
Do not try to predict uuid of new collection. refs #3261 refs #3504
Tom Clegg [Mon, 18 Aug 2014 17:15:13 +0000 (13:15 -0400)]
Do not throw away permission hints when writing data. refs #3261
Tom Clegg [Mon, 18 Aug 2014 16:52:53 +0000 (12:52 -0400)]
3604: Update comment to reflect lack of built-in default.
Tom Clegg [Mon, 18 Aug 2014 16:51:27 +0000 (12:51 -0400)]
3604: Remove unused style.
Tom Clegg [Mon, 18 Aug 2014 15:39:49 +0000 (11:39 -0400)]
Display progress by default when writing to regular files and stderr isatty. No issue #
Peter Amstutz [Mon, 18 Aug 2014 13:39:22 +0000 (09:39 -0400)]
Merge branch '3441-python-keep-log-level' refs #3441
Tom Clegg [Sun, 17 Aug 2014 21:14:35 +0000 (17:14 -0400)]
3604: Fix user deactivation test.
Tom Clegg [Sun, 17 Aug 2014 20:40:46 +0000 (16:40 -0400)]
3604: Fix tests, and restore ability to view user agreement before completing profile.
Tom Clegg [Sun, 17 Aug 2014 19:26:53 +0000 (15:26 -0400)]
3604: Fix up profile and redirect handling.
Tom Clegg [Sun, 17 Aug 2014 18:34:26 +0000 (14:34 -0400)]
3604: Fix user_agreements behavior, update tests to expect redirects.
Tom Clegg [Sun, 17 Aug 2014 18:10:20 +0000 (14:10 -0400)]
3604: Add test for redirect to welcome page
Tom Clegg [Sun, 17 Aug 2014 18:10:08 +0000 (14:10 -0400)]
3604: Verify permission cache behavior in unsetup test
Tom Clegg [Sun, 17 Aug 2014 18:05:11 +0000 (14:05 -0400)]
3604: Remove test for persistent/cache switch on wrong page.
Tom Clegg [Sun, 17 Aug 2014 18:02:19 +0000 (14:02 -0400)]
3604: Do not check for notifications if user is not even activated.
Tom Clegg [Sun, 17 Aug 2014 17:59:13 +0000 (13:59 -0400)]
3604: Fix stale permission cache by using destroy instead of delete.
Tom Clegg [Sun, 17 Aug 2014 17:50:05 +0000 (13:50 -0400)]
3604: Fix theme support for welcome page
Peter Amstutz [Sun, 17 Aug 2014 01:22:56 +0000 (21:22 -0400)]
3441: Change logging level of nonfatal Keep errors to "debug".
Tom Clegg [Sat, 16 Aug 2014 22:55:20 +0000 (18:55 -0400)]
2800: Clean up exceptions, variable names, handling of discoveryServiceUrl vs host args.
Tom Clegg [Sat, 16 Aug 2014 22:23:25 +0000 (18:23 -0400)]
2800: Merge branch 'master' into 2800-pgs
Tom Clegg [Sat, 16 Aug 2014 06:06:20 +0000 (02:06 -0400)]
Merge branch '2800-python-global-state' into 2800-pgs
Conflicts:
sdk/python/arvados/api.py
Ward Vandewege [Fri, 15 Aug 2014 20:56:34 +0000 (16:56 -0400)]
docker: be a bit smarter in the make clean target, so that we also
accomodate diretories underneath the generated directory.
refs #3551
Brett Smith [Fri, 15 Aug 2014 20:45:21 +0000 (16:45 -0400)]
Merge branch '3593-workbench-exception-rendering'
Closes #3593, #3595.
Brett Smith [Thu, 14 Aug 2014 17:59:18 +0000 (13:59 -0400)]
3593: Another round of hardening Workbench's render_exception.
render_exception was counting on session[:user] to help render the
error page. We recently excised that, which is turning exceptions
into 500s. This commit restores the session user object, but uses it
only for error rendering, in keeping with the spirit of the previous
revert. This commit also defends against more possible failure cases
in render_exception, and adds a basic test for it.
Tom Clegg [Fri, 15 Aug 2014 14:06:32 +0000 (10:06 -0400)]
gitignore sdk/cli/vendor. refs #3551
Tom Clegg [Fri, 15 Aug 2014 14:05:01 +0000 (10:05 -0400)]
Restore trailing newline in manifest format sanity check.
Amends
3cc80b447efcaf416ea4d6857d6d40583e462ff8
No issue #
Tom Clegg [Thu, 14 Aug 2014 19:30:28 +0000 (15:30 -0400)]
Merge branch '3551-go-layout' closes #3551
Tom Clegg [Thu, 14 Aug 2014 19:23:43 +0000 (15:23 -0400)]
3551: Merge branch 'master' into 3551-go-layout
Peter Amstutz [Thu, 14 Aug 2014 18:20:07 +0000 (14:20 -0400)]
Merge branch '3505-virtual-work-dir' refs #3505
Peter Amstutz [Thu, 14 Aug 2014 17:23:49 +0000 (13:23 -0400)]
Merge branch 'master' into 3505-virtual-work-dir
Peter Amstutz [Thu, 14 Aug 2014 17:17:06 +0000 (13:17 -0400)]
3505: tinker with logging
Peter Amstutz [Thu, 14 Aug 2014 15:41:45 +0000 (11:41 -0400)]
3505: Fix typo in run-command
Peter Amstutz [Thu, 14 Aug 2014 15:35:06 +0000 (11:35 -0400)]
3505: Move helper scripts into crunchutil module. In run-command, added
task.stdin redirection, and renamed save.stdout to task.stdout for consistency.
Stylistic change "x == None" and "x != None" to "x is None" and "x is not
None".
Tom Clegg [Thu, 14 Aug 2014 14:05:41 +0000 (10:05 -0400)]
3551: Revert "3551: When testing keep clients, write keepstore/keepproxy logs to"
This reverts commit
63871346153fea194b169eec38f6efae3061ebf6.
The default Popen behavior is to use stderr, and that's fine. This was
a mistaken attempt to reveal missing logs, the real solution for which
is
5fcff4c13ae17527ee1efd6fa01d08133212085b.
Tom Clegg [Thu, 14 Aug 2014 13:49:34 +0000 (09:49 -0400)]
3551: Remove superfluous chmod(). Umask is 022 here.
Phil Hodgson [Thu, 14 Aug 2014 12:12:28 +0000 (08:12 -0400)]
3354: try again with edit (pencil) icon to the _right_ of the editable textile-rendered text
(Neither to the right nor underneath look perfect in all circumstances, but to the right is the better compromise.)
Phil Hodgson [Thu, 14 Aug 2014 11:51:35 +0000 (07:51 -0400)]
3114: bug fix: when rendering JSON response to a generic #show action, correctly set an 'href' attribute in the response to be the #show url for the object
Tom Clegg [Wed, 13 Aug 2014 22:15:46 +0000 (18:15 -0400)]
Increase Capybara timeout to accommodate slow test server. No issue #
Tom Clegg [Wed, 13 Aug 2014 21:09:08 +0000 (17:09 -0400)]
Report unexpected slurm states as "down". No issue #
Tom Clegg [Wed, 13 Aug 2014 20:47:50 +0000 (16:47 -0400)]
3551: Use FileUtils.rm_r so deleting stale generated/{dir} works.
Brett Smith [Wed, 13 Aug 2014 20:39:40 +0000 (16:39 -0400)]
Merge branch '3421-wide-project-tables-wip'
Closes #3421, #3584.
Brett Smith [Wed, 13 Aug 2014 16:07:06 +0000 (12:07 -0400)]
3421: Make Workbench project contents tables variable width.
This change will ensure that users can see the "edit name" buttons, by
letting a table row grow as needed to accommodate long names. It puts
each row's buttons in dedicated cells to try to stay true to the
original layout as much as possible.
Brett Smith [Wed, 13 Aug 2014 20:36:42 +0000 (16:36 -0400)]
Merge branch '3405-pipeline-error-logging-wip'
Closes #3405, #3582.
Brett Smith [Tue, 12 Aug 2014 18:48:32 +0000 (14:48 -0400)]
3405: Mark pipeline instances failed when they're aborted.
Brett Smith [Tue, 12 Aug 2014 18:41:55 +0000 (14:41 -0400)]
3405: Log errors about launching pipeline instances.
There's a couple of components to this:
* Do some basic checks on the organization of the pipeline instance
before we start running it, and abort if any of them fail.
* If the pipeline runner aborts for any reason, send that as pipeline
instance stderr to the API server, so other tools like Workbench can
render it for users' benefit.
Tom Clegg [Wed, 13 Aug 2014 20:23:43 +0000 (16:23 -0400)]
3551: Remove chmod 755, no longer necessary now that config.rb does that.
Tom Clegg [Wed, 13 Aug 2014 19:36:30 +0000 (15:36 -0400)]
3551: Set mode of generated files more aggressively (overrule umask).
Tom Clegg [Wed, 13 Aug 2014 19:22:00 +0000 (15:22 -0400)]
3551: Handle missing GOPATH and multiple-entry GOPATH sensibly.
Tom Clegg [Wed, 13 Aug 2014 19:13:43 +0000 (15:13 -0400)]
3551: Merge branch 'master' into 3551-go-layout
Tom Clegg [Wed, 13 Aug 2014 19:10:13 +0000 (15:10 -0400)]
3551: When invoking run_test_server.py during tests, pass stderr
through to caller instead of discarding.
Tom Clegg [Wed, 13 Aug 2014 19:02:51 +0000 (15:02 -0400)]
3551: Behave correctly when Read() yields some data along with the EOF condition.
"a Reader returning a non-zero number of bytes at the end of the input
stream may return either err == EOF or err == nil."
-- http://golang.org/pkg/io/#Reader
Peter Amstutz [Wed, 13 Aug 2014 18:44:27 +0000 (14:44 -0400)]
3505: Fixed typo comparison of list against 0 instead of len(list).
Tom Clegg [Wed, 13 Aug 2014 18:34:29 +0000 (14:34 -0400)]
3551: When invoking run_test_server.py during tests, pass stderr
through to caller instead of discarding.
Tom Clegg [Wed, 13 Aug 2014 18:32:40 +0000 (14:32 -0400)]
3551: When testing keep clients, write keepstore/keepproxy logs to
tmp/run_test_server.log instead of discarding.
Peter Amstutz [Wed, 13 Aug 2014 18:25:44 +0000 (14:25 -0400)]
3505: Adjust order of initialization to reflect potential side effects (e.g. file
creation) on using functions such as $(glob) in the command.
Peter Amstutz [Wed, 13 Aug 2014 18:06:40 +0000 (14:06 -0400)]
Fix degenerate case exponential runtime in regular expression use by
CollectionReader to validate locators and manifests. no issue #
Brett Smith [Wed, 13 Aug 2014 16:15:24 +0000 (12:15 -0400)]
Merge branch '3457-pysdk-logging-wip'
Closes #3457, #3577.
Brett Smith [Wed, 13 Aug 2014 14:32:45 +0000 (10:32 -0400)]
3457: Make arv-get display interface messages directly.
The logger isn't appropriate for this.
Brett Smith [Tue, 12 Aug 2014 21:43:28 +0000 (17:43 -0400)]
3457: Revamp Python SDK and tool logging.
The primary goal of this commit is to introduce a dedicated logging
object to the arvados module, which we configure to our
specifications, and use it consistently throughout the SDK and tools.
This lets us handle our logging configuration consistently in one
place, and avoid interfering with logging in SDK users. I made some
minor style changes to logging calls while I was at it.
Phil Hodgson [Wed, 13 Aug 2014 15:12:36 +0000 (11:12 -0400)]
3114: When current user, show root/home project rather than user attributes when landing on show user page.
(This is meant to be a compromise due to the fact that a home project's uuid has "user" as its arvados type, rather than "group".)
Phil Hodgson [Wed, 13 Aug 2014 15:09:55 +0000 (11:09 -0400)]
3114: bug fix: 'Copy' button is now disabled until a project has been selected for copying to
Peter Amstutz [Wed, 13 Aug 2014 15:04:52 +0000 (11:04 -0400)]
Added virtual working directory "task.vwd" option to run-command. Added
"task.cwd" to set the starting directory. Refactored upload retry logic from
run-command into robust_put.py and modified decompress-all to use it. no issue #
Tom Clegg [Wed, 13 Aug 2014 15:02:25 +0000 (11:02 -0400)]
3551: Fix more package paths.
Tom Clegg [Wed, 13 Aug 2014 13:32:45 +0000 (09:32 -0400)]
Update Gemfile to use crunch-job from latest arvados-cli gem. refs #3570
Phil Hodgson [Wed, 13 Aug 2014 12:44:55 +0000 (08:44 -0400)]
3354: Also render specified attributes as textile when content is read-only
Phil Hodgson [Wed, 13 Aug 2014 12:44:24 +0000 (08:44 -0400)]
3354: Put edit (pencil) icon _below_ textile rather than to the right of it.
Tom Clegg [Tue, 12 Aug 2014 20:43:45 +0000 (16:43 -0400)]
3354: Redirect link#show to "show named object".
This way, if you put a text link like "foo":{uuid-of-name-link} in a
textile description field, it leads to the named object rather than
the generic "show attributes" page for the link object.
radhika [Tue, 12 Aug 2014 20:28:50 +0000 (16:28 -0400)]
closes #3296
Merge branch '3296-user-profile'
radhika [Tue, 12 Aug 2014 20:25:34 +0000 (16:25 -0400)]
3296: fix test issue
radhika [Tue, 12 Aug 2014 19:49:21 +0000 (15:49 -0400)]
3296: fix tests
radhika [Tue, 12 Aug 2014 19:10:46 +0000 (15:10 -0400)]
Merge branch 'master' into 3296-user-profile
Tom Clegg [Tue, 12 Aug 2014 18:57:10 +0000 (14:57 -0400)]
Fix repositories.get_all_permissions to report manage, write, and read. refs #3525
Tom Clegg [Tue, 12 Aug 2014 18:19:48 +0000 (14:19 -0400)]
Merge branch '3531-sort-jobs-with-pipelines' closes #3531
Tom Clegg [Tue, 12 Aug 2014 18:15:51 +0000 (14:15 -0400)]
Fix "undefined method `uuid' for nil:NilClass". closes #3576
Peter Amstutz [Tue, 12 Aug 2014 17:16:04 +0000 (13:16 -0400)]
Fix regular expression in decompress-all.py refs #3373
Peter Amstutz [Tue, 12 Aug 2014 17:07:12 +0000 (13:07 -0400)]
Fix syntax error in decompress-all.py refs #3373
Tom Clegg [Tue, 12 Aug 2014 16:19:06 +0000 (12:19 -0400)]
3531: Pass through tab_pane to reused partials, so element IDs are really unique
across tabs.
Tom Clegg [Tue, 12 Aug 2014 16:15:45 +0000 (12:15 -0400)]
3531: Fix ordering of combined results, add test. Anchor "desc" regexp.
Peter Amstutz [Tue, 12 Aug 2014 15:42:55 +0000 (11:42 -0400)]
Merge branch '3373-improve-gatk3-snv-pipeline' closes #3373
Peter Amstutz [Tue, 12 Aug 2014 15:42:09 +0000 (11:42 -0400)]
3373: Test filename extension before attempting to call dtrx. Non-zero dtrx exit code is now treated as failure.
radhika [Tue, 12 Aug 2014 14:20:55 +0000 (10:20 -0400)]
Merge branch 'master' into 3296-user-profile
Tom Clegg [Tue, 12 Aug 2014 14:11:32 +0000 (10:11 -0400)]
Merge branch '3178-discoverable-parameters' closes #3178
Tom Clegg [Tue, 12 Aug 2014 14:09:41 +0000 (10:09 -0400)]
3572: Set state to RunningOnServer if --submit given. closes #3572
Tom Clegg [Tue, 12 Aug 2014 13:12:27 +0000 (09:12 -0400)]
Merge branch '3570-crunch-race' closes #3570
Brett Smith [Tue, 12 Aug 2014 12:59:23 +0000 (08:59 -0400)]
Merge branch '3412-full-collections-index'
Closes #3412, #3534.
radhika [Tue, 12 Aug 2014 12:59:05 +0000 (08:59 -0400)]
Merge branch 'master' into 3296-user-profile