Brett Smith [Thu, 2 Apr 2015 21:37:53 +0000 (17:37 -0400)]
4253: Gitolite migration makes a name symlink for arvados repository.
This is necessary for other supporting infrastructure around this
repository in Gitolite installs; e.g., the cron job that keeps them in
sync with upstream. Refs #4253.
Peter Amstutz [Thu, 2 Apr 2015 14:24:56 +0000 (10:24 -0400)]
4752: Websockets works. Fix compute node containers to restart correctly. Fix
git server hostname. Arvdock waits for API/workbench to be ready before telling
the user to go to workbench.
Brett Smith [Wed, 1 Apr 2015 19:50:08 +0000 (15:50 -0400)]
5627: Python file-like objects use SEET_SET as the default whence.
This is a brown paper bag commit. All that time I spent grumbling
that we had the wrong default was completely incorrect. We had it
right earlier, and I blew it. See
<https://docs.python.org/2/library/stdtypes.html#file.seek>.
Brett Smith [Mon, 30 Mar 2015 18:28:40 +0000 (14:28 -0400)]
4253: Let Workbench Manage Account partials render their whole pane.
I'm about to add another "Add" button to the Repositories pane, so I'd
rather do it this way than try to maintain a generic loop inside
_manage_account.html.erb.
Brett Smith [Mon, 30 Mar 2015 15:06:51 +0000 (11:06 -0400)]
4253: Sync up Docker with our production Gitolite setup.
This updates our API server Docker image to store repositories by
UUID, with name aliases available. .gitolite.rc enables the aliasing,
and update-gitolite.rb generates the necessary configuration. This
makes it possible to test the recent repository changes in Docker.
Brett Smith [Tue, 31 Mar 2015 13:23:56 +0000 (09:23 -0400)]
4253: Users can manage their own repositories.
This commit allows users to create their own repositories, as long as
the repository name starts with their own username.
To support this change, we've modified our Gitolite setup to store
repositories primarily by UUID, with a name alias for easier
checkout. fetch_url and push_url become generated attributes
accordingly. This makes it easier to rename the repository later and
allow checkouts to continue to work.
Peter Amstutz [Tue, 31 Mar 2015 21:13:06 +0000 (17:13 -0400)]
5612: Wrap munge with startup script that cleans up /var/run/munge of stale
sockets and pidfiles. Can now run jobs after stopping and restarting
containers.
Brett Smith [Thu, 26 Mar 2015 16:29:38 +0000 (12:29 -0400)]
5502: Adjust id and name of Node Manager cloud object mocks.
Some GCE objects like disk types have predictable names, so it's
helpful to be able to mock objects with the same name. Use the
name_id argument is the literal name, and generate an id from it.
Brett Smith [Wed, 18 Mar 2015 20:00:01 +0000 (16:00 -0400)]
4253: Use new username to set up repository and VM logins.
The usernames added in 4253 have stricter limits than past usernames
generated to set up a repository and VM login. Use the new generated
username to avoid a weird disconnect between that and these related
objects. Do a little cleanup in the tests, including removing some
test parameters that now seem redundant under the new rules.
Brett Smith [Tue, 17 Mar 2015 22:10:14 +0000 (18:10 -0400)]
4253: Add a username attribute to users.
* Add the column, and propagate it based on available VM logins or
e-mail address, if possible.
* Add format validation and tests.
* Set new usernames based on e-mail address, with tests.
Radhika Chippada [Wed, 25 Mar 2015 14:16:27 +0000 (10:16 -0400)]
5556: Added select() to @logs in CollectionsController#show to avoid trasporting the unneeded log properties.
Also, added Accept-Encoding request header in workbench request to api server.
Radhika Chippada [Tue, 24 Mar 2015 13:49:38 +0000 (09:49 -0400)]
5534: When a pipeline has long running jobs with hundreds of thousands of log lines, the log line display is timing out
fetching all those lines. Limiting the number of log lines retrieved helped resolve this issue. Using limit size of 2000.
I was able to see log when I limited to 10000 log lines as well, but it took much longer wait time and I felt a quicker
response might provide a better user experience and hence using 2000 log lines as the limit. Thus the most recent 2000
log lines are fetched, followed by newer log lines from event log if the job is still running.
Peter Amstutz [Mon, 23 Mar 2015 21:12:55 +0000 (17:12 -0400)]
5539: Arvados-in-Docker improvements
* arvdock start now restarts existing containers instead of deleting them. Use arvdock reset to delete the containers.
* Uses docker data container for keep.
* Prints a note about adding the nameserver to /etc/resolv.conf
Radhika Chippada [Mon, 23 Mar 2015 16:11:42 +0000 (12:11 -0400)]
3762: create NewWorkQueue instances of pullq and trashq in handers_test and remove this logic from handlers.
it is expected that keepstore or the tests will create these objects and handlers should not have to.
Radhika Chippada [Mon, 23 Mar 2015 16:01:05 +0000 (12:01 -0400)]
3762: undo the api server discovery document update. trash worker can instead use permission_ttl in place of defaultTrashLifetime because these two will be the same.
Brett Smith [Fri, 20 Mar 2015 21:16:43 +0000 (17:16 -0400)]
5319: Bound search in collection PDH fix migration.
Only search collections that exist when the migration begins. This
helps avoid an infinite loop where we yield a bad collection, it gets
fixed a new replacement is created, and then we find and yield the
replacement… Refs #5319.
Radhika Chippada [Fri, 20 Mar 2015 18:30:35 +0000 (14:30 -0400)]
5375: improved mime_types initializer. enhance collections_helper to use mime_type sub_type instead of relying on suffix.
update config param name, value, and comment. add .seq, which is another supported extension of fasta to test.
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