Peter Amstutz [Mon, 9 Dec 2013 14:58:46 +0000 (09:58 -0500)]
Merge remote-tracking branch 'origin/master' into 1637-improve-arv-tutorial
Peter Amstutz [Sun, 8 Dec 2013 02:30:57 +0000 (21:30 -0500)]
A little bit of documentation work from home
Peter Amstutz [Fri, 6 Dec 2013 22:03:15 +0000 (17:03 -0500)]
Documentation work in progress, making evening check-in.
Peter Amstutz [Thu, 5 Dec 2013 22:01:39 +0000 (17:01 -0500)]
Rewriting documentation work in progress.
Tom Clegg [Thu, 5 Dec 2013 21:27:51 +0000 (13:27 -0800)]
Remove spurious "if".
Tom Clegg [Thu, 5 Dec 2013 21:08:28 +0000 (13:08 -0800)]
Use some helpful HTTP status codes, not just generic 422.
* 403 for PermissionDeniedError
* 401 for UnauthorizedError
Tom Clegg [Thu, 5 Dec 2013 21:12:50 +0000 (13:12 -0800)]
Check permission before deleting objects
Peter Amstutz [Thu, 5 Dec 2013 14:41:28 +0000 (09:41 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados into 1637-improve-arv-tutorial
peter [Wed, 4 Dec 2013 21:32:39 +0000 (16:32 -0500)]
Notes on new user documentation
Ward Vandewege [Wed, 4 Dec 2013 02:34:05 +0000 (21:34 -0500)]
Allow overriding of default ports for API, doc, SSO, and workbench
servers when started with run.sh
Tom Clegg [Tue, 3 Dec 2013 23:19:22 +0000 (15:19 -0800)]
Fix failing test by parsing timestamp correctly.
Tom Clegg [Tue, 3 Dec 2013 23:17:30 +0000 (15:17 -0800)]
Fix PermissionDeniedError when a non-admin user is the first to log in
from a given ApiClient.
Tom Clegg [Fri, 29 Nov 2013 19:20:33 +0000 (11:20 -0800)]
Add arvados.getjobparam() convenience function.
Tom Clegg [Fri, 29 Nov 2013 16:36:04 +0000 (08:36 -0800)]
Accept empty string as root stream name "." in
arvados.CollectionWriter, to mirror os.path.split()
Tom Clegg [Fri, 29 Nov 2013 16:35:04 +0000 (08:35 -0800)]
Accept data from a generator in arvados.CollectionWriter.write()
Tom Clegg [Wed, 27 Nov 2013 18:41:02 +0000 (10:41 -0800)]
Sort filenames when writing multi-level streams in
arvados.CollectionWriter.
Tom Clegg [Tue, 26 Nov 2013 22:53:27 +0000 (14:53 -0800)]
Add arvados.util.clear_tmpdir() function.
Tom Clegg [Tue, 26 Nov 2013 22:08:27 +0000 (14:08 -0800)]
Pass through stderr in real time by default in util.run_command()
Tom Clegg [Tue, 26 Nov 2013 20:34:43 +0000 (12:34 -0800)]
Allow caller to override close_fds in util.run_command()
Tom Clegg [Tue, 26 Nov 2013 16:00:35 +0000 (08:00 -0800)]
Use collection hash instead of entire manifest as symlink target
in arvados.collection_extract(), even when the manifest was passed as
a function argument.
Ward Vandewege [Tue, 3 Dec 2013 21:47:26 +0000 (16:47 -0500)]
Only require keep volume when a keep container is being started.
Tom Clegg [Mon, 2 Dec 2013 18:52:52 +0000 (10:52 -0800)]
Make the sample "Add authorized key" button non-clickable.
If it behaves like a real button in the browser, users are inclined to
think it *is* a real button, rather than just an image of what to look
for.
Fixes #1664
Tom Clegg [Mon, 2 Dec 2013 18:49:28 +0000 (10:49 -0800)]
Add delete button to generic Workbench index page.
Fixes #1665
Tom Clegg [Mon, 2 Dec 2013 15:55:55 +0000 (07:55 -0800)]
Remove Rails default scaffold CSS.
Tom Clegg [Thu, 28 Nov 2013 21:09:27 +0000 (13:09 -0800)]
Show how crunch job tasks get their runtime parameters. refs #1513
Tom Clegg [Thu, 28 Nov 2013 21:06:10 +0000 (13:06 -0800)]
Clear TASK_WORK before starting a task.
Tom Clegg [Wed, 27 Nov 2013 21:40:51 +0000 (13:40 -0800)]
Use new-style Python classes (subclass object), so super() can work
Tim Pierce [Tue, 26 Nov 2013 22:04:50 +0000 (17:04 -0500)]
Add --api, --sso, --workbench, --doc, --keep options to run.sh.
Default is to run all servers.
Ward Vandewege [Tue, 26 Nov 2013 19:43:30 +0000 (14:43 -0500)]
Refactored and updated run.sh:
* support ENABLE_SSH environment variable
* start 2 keep containers (backed by the same filesystem for now)
Ward Vandewege [Tue, 26 Nov 2013 19:03:49 +0000 (14:03 -0500)]
build.sh has been superseded by Makefile.
Ward Vandewege [Tue, 26 Nov 2013 19:03:21 +0000 (14:03 -0500)]
Rename docserver to doc for consistency.
Ward Vandewege [Tue, 26 Nov 2013 18:57:48 +0000 (13:57 -0500)]
Add an SSH server in each docker container.
It will not be started by default, but can be enabled by setting an
environment (ENABLE_SSH) when starting a container, and is useful for
debugging.
Tom Clegg [Mon, 25 Nov 2013 16:18:51 +0000 (08:18 -0800)]
Do not require filesystem_uuid in first keep_disks/ping request.
Record it if provided, but do not try to do any sanity-checking with
it.
Tom Clegg [Mon, 25 Nov 2013 16:16:45 +0000 (08:16 -0800)]
Update crunch_refresh_trigger config setting name in tests.
Tom Clegg [Mon, 25 Nov 2013 08:05:45 +0000 (00:05 -0800)]
Add job.cancel API.
Same as job.update(job={"cancelled_at":"2112-12-21 21:12"}) but more
convenient.
Closes #1654
Tom Clegg [Mon, 25 Nov 2013 07:53:55 +0000 (23:53 -0800)]
Fix config setting name.
Tom Clegg [Mon, 25 Nov 2013 07:47:15 +0000 (23:47 -0800)]
Update comments in config/environment/ files.
Tom Clegg [Mon, 25 Nov 2013 07:36:56 +0000 (23:36 -0800)]
Check refresh trigger in crunch-job instead of crunch-dispatch.
Crunch-job now checks the timestamp on the trigger file, rather than
waiting for crunch-dispatch notice that the trigger file appeared and
send HUP to its child processes. This way we don't depend on srun
doing what we want with signals.
See
f99ffd6844ae9b88cfd17c8fe6e9fcc85a55d79c
Tom Clegg [Mon, 25 Nov 2013 07:31:16 +0000 (23:31 -0800)]
Avoid starting new jobs when TERM signal has been received.
Tim Pierce [Sat, 23 Nov 2013 21:48:30 +0000 (16:48 -0500)]
Ruby 2.0.0-p247 -> p353 (now installed as stable).
Tom Clegg [Sat, 23 Nov 2013 00:09:28 +0000 (16:09 -0800)]
Avoid infinite poll loop triggered by (:running and !(:finished or :cancelled))
Tom Clegg [Fri, 22 Nov 2013 23:51:39 +0000 (15:51 -0800)]
Fix scalar gmtime() usage.
Tom Clegg [Fri, 22 Nov 2013 23:47:45 +0000 (15:47 -0800)]
Fix missing "my" scope.
Tom Clegg [Fri, 22 Nov 2013 23:34:31 +0000 (15:34 -0800)]
Allow users to cancel a running crunch job by updating cancelled_at
(to something other than nil).
Also:
* Add test fixtures for jobs
* Take care to update the Job object piecemeal during crunch-job
(avoid overwriting cancelled_at)
Tom Clegg [Fri, 22 Nov 2013 22:10:03 +0000 (14:10 -0800)]
Fix base class of ApiClient model so as_api_response works
Tom Clegg [Fri, 22 Nov 2013 16:28:37 +0000 (08:28 -0800)]
Fix up keep_disks/ping and add tests. refs #1581
Ward Vandewege [Fri, 22 Nov 2013 01:05:27 +0000 (20:05 -0500)]
Only apply the auto_admin_user configuration rule when no admin users
exist yet, but exclude the default root system user from that count.
Just in case.
Ward Vandewege [Thu, 21 Nov 2013 01:22:48 +0000 (20:22 -0500)]
Only apply the auto_admin_user configuration rule when no admin users
exist yet. Just in case.
Tom Clegg [Wed, 20 Nov 2013 23:14:18 +0000 (15:14 -0800)]
add script/create_superuser_token.rb
Ward Vandewege [Wed, 20 Nov 2013 22:22:36 +0000 (17:22 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Ward Vandewege [Wed, 20 Nov 2013 22:19:24 +0000 (17:19 -0500)]
* Docker API container: add support for the auto_admin_user feature (API server).
This closes #1655
* Default WORKBENCH_INSECURE_HTTPS in config.yml.example to true,
because we use self-signed certificates in the development environment.
Tim Pierce [Wed, 20 Nov 2013 22:14:30 +0000 (17:14 -0500)]
Converted README to real markdown.
Tim Pierce [Wed, 20 Nov 2013 21:59:10 +0000 (16:59 -0500)]
Fix dependencies.
Tim Pierce [Wed, 20 Nov 2013 18:32:31 +0000 (13:32 -0500)]
Improve Makefile rules.
Start Keep container from run.sh.
Ward Vandewege [Wed, 20 Nov 2013 22:15:49 +0000 (17:15 -0500)]
Add a config setting: auto_admin_user
This setting is optional, and can be configured to the The e-mail
address of the user you would like to become marked as an admin user on
their first login. This is useful during installation.
In the default configuration, authentication happens through the Arvados
SSO server, which uses openid against Google's servers. In that case
this e-mail address should be an address associated with a Google
account.
Tim Pierce [Wed, 20 Nov 2013 22:14:30 +0000 (17:14 -0500)]
Converted README to real markdown.
Tim Pierce [Wed, 20 Nov 2013 21:59:10 +0000 (16:59 -0500)]
Fix dependencies.
Tim Pierce [Wed, 20 Nov 2013 18:32:31 +0000 (13:32 -0500)]
Improve Makefile rules.
Start Keep container from run.sh.
Ward Vandewege [Wed, 20 Nov 2013 15:15:07 +0000 (10:15 -0500)]
Make workbench work with the API server.
Ward Vandewege [Wed, 20 Nov 2013 15:08:34 +0000 (10:08 -0500)]
Make sure the API rails app tmp directory is writable by www-data
Ward Vandewege [Wed, 20 Nov 2013 04:31:13 +0000 (23:31 -0500)]
* Mention SSO server to documentation in README
* Fix up SSO and API server configuration to allow API and SSO server to communicate
Tom Clegg [Tue, 19 Nov 2013 23:07:21 +0000 (15:07 -0800)]
Add threaded Keep.put()
Tim Pierce [Wed, 20 Nov 2013 00:01:07 +0000 (19:01 -0500)]
Fixed Makefile dependencies, added docker_build script to work around
https://github.com/dotcloud/docker/issues/1875.
Ward Vandewege [Tue, 19 Nov 2013 22:08:22 +0000 (17:08 -0500)]
Optimize docserver/Dockerfile
Ward Vandewege [Tue, 19 Nov 2013 21:09:14 +0000 (16:09 -0500)]
* Make arvados/passenger container
* Build time optimization of the various containers
Tom Clegg [Tue, 19 Nov 2013 21:03:34 +0000 (13:03 -0800)]
Fix encoding issue so Python clients can store binary data in Keep
http://stackoverflow.com/questions/
8705962/python-http-put-with-unencoded-binary-data
Tim Pierce [Tue, 19 Nov 2013 20:46:32 +0000 (15:46 -0500)]
Warehouse docker image no longer requires local checked-out source.
Tom Clegg [Tue, 19 Nov 2013 20:19:53 +0000 (12:19 -0800)]
Refuse to stream responses unless request Accept header has text/plain
or */*. Closes #1604
Tom Clegg [Tue, 19 Nov 2013 20:18:12 +0000 (12:18 -0800)]
Send "Accept: application/json" header with API requests. refs #1604
Tim Pierce [Tue, 19 Nov 2013 20:15:31 +0000 (15:15 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Tim Pierce [Tue, 19 Nov 2013 20:15:04 +0000 (15:15 -0500)]
Updated Makefile for more accurate dependency management.
Tom Clegg [Tue, 19 Nov 2013 18:00:49 +0000 (10:00 -0800)]
Move api/job-tasks to api/crunch-scripts and add some explanation
Tom Clegg [Tue, 19 Nov 2013 17:21:32 +0000 (09:21 -0800)]
Fix navorder of API resource pages
Tim Pierce [Tue, 19 Nov 2013 17:44:34 +0000 (12:44 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Conflicts:
docker/base/Dockerfile
Tim Pierce [Tue, 19 Nov 2013 17:35:58 +0000 (12:35 -0500)]
Added Makefile to track dependencies for Docker images.
Ward Vandewege [Tue, 19 Nov 2013 17:22:17 +0000 (12:22 -0500)]
Update the dockserver Dockerfile to take advantage of the doc/Gemfile,
as well as the fact that locale generation and the DEBIAN_FRONTEND
environment variable are now set in the base container.
Ward Vandewege [Tue, 19 Nov 2013 17:21:43 +0000 (12:21 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Ward Vandewege [Tue, 19 Nov 2013 17:21:14 +0000 (12:21 -0500)]
Move UTF-8 locale generation and the DEBIAN_FRONTEND environment setting
into the base image.
Tom Clegg [Tue, 19 Nov 2013 17:09:51 +0000 (09:09 -0800)]
Fix job script attribute (not script_name), and update script_version
notes to match current code
Tom Clegg [Tue, 19 Nov 2013 16:54:50 +0000 (08:54 -0800)]
Do not re-attempt failed job tasks, unless there is some reason to
believe the failure is temporary (i.e., exit value 111 or slurm
failure). closes #1619
Tom Clegg [Tue, 19 Nov 2013 16:45:36 +0000 (08:45 -0800)]
Update development-mode crunch-job notes
Tom Clegg [Tue, 19 Nov 2013 16:43:21 +0000 (08:43 -0800)]
add doc/Gemfile
Tom Clegg [Tue, 19 Nov 2013 16:42:29 +0000 (08:42 -0800)]
Document user#event_stream. closes #1605
Ward Vandewege [Tue, 19 Nov 2013 16:25:07 +0000 (11:25 -0500)]
* OMNIAUTH_APP_SECRET is no longer used
* We include an omniauth-to-openid gateway container now ('sso')
Tom Clegg [Tue, 19 Nov 2013 09:04:58 +0000 (01:04 -0800)]
Add threading locks in Keep client
Tom Clegg [Tue, 19 Nov 2013 09:02:46 +0000 (01:02 -0800)]
remove unused class DataReader
Tom Clegg [Tue, 19 Nov 2013 08:38:38 +0000 (00:38 -0800)]
Ensure script_version matches before satisfying pipeline component with a job.
Tom Clegg [Tue, 19 Nov 2013 08:37:03 +0000 (00:37 -0800)]
Add /users/:uuid/event_stream action to subscribe to per-user channel
Tom Clegg [Tue, 19 Nov 2013 08:16:22 +0000 (00:16 -0800)]
Send job log messages to owner_uuid redis channel
Tom Clegg [Tue, 19 Nov 2013 00:40:40 +0000 (16:40 -0800)]
Read pipeline template from local file if --template arg is not a uuid
Ward Vandewege [Tue, 19 Nov 2013 03:30:19 +0000 (22:30 -0500)]
un-comment ADD line for api.tar
Ward Vandewege [Tue, 19 Nov 2013 03:24:03 +0000 (22:24 -0500)]
Let API server use SSO container.
This doesn't work quite yet - need to sort out inter-container
communication. But it's very close now.
Ward Vandewege [Tue, 19 Nov 2013 03:23:44 +0000 (22:23 -0500)]
Fixes for SSO rails app.
Ward Vandewege [Tue, 19 Nov 2013 02:51:38 +0000 (21:51 -0500)]
Generated files shouldn't have been committed.
Ward Vandewege [Mon, 18 Nov 2013 22:25:29 +0000 (17:25 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Conflicts:
docker/build.sh
docker/config.yml.example
Tim Pierce [Mon, 18 Nov 2013 21:50:38 +0000 (16:50 -0500)]
Merge branch '1579-keep-server-in-docker' of git.clinicalfuture.com:arvados into 1579-keep-server-in-docker
Tim Pierce [Mon, 18 Nov 2013 20:06:21 +0000 (15:06 -0500)]
Install warehouse-apps into arvados/warehouse directly from github source.
Tim Pierce [Fri, 15 Nov 2013 23:52:56 +0000 (18:52 -0500)]
Add prerequisites for Keep server described in
https://github.com/clinicalfuture/warehouse-apps/blob/master/libwarehouse-perl/server/INSTALL
Tim Pierce [Thu, 14 Nov 2013 22:54:55 +0000 (17:54 -0500)]
Add supervisor to start keepd when container is launched.
Update README with deploy instructions for Keep.
Tim Pierce [Thu, 14 Nov 2013 20:49:18 +0000 (15:49 -0500)]
Build an arvados/warehouse container with locally checked out warehouse-apps
code.
The warehouse-apps repo at git://github.com/clinicalfuture/warehouse-apps.git
must be checked out at the same level as the arvados repo.