arvados.git
9 years ago6279: open the webshell client in a blank window.
radhika [Fri, 10 Jul 2015 22:44:59 +0000 (18:44 -0400)]
6279: open the webshell client in a blank window.

9 years agoMerge branch '6569-smarter-jobs-image'
Ward Vandewege [Fri, 10 Jul 2015 20:18:59 +0000 (16:18 -0400)]
Merge branch '6569-smarter-jobs-image'

closes #6569

9 years agoMerge branch 'master' into 6569-smarter-jobs-image
Ward Vandewege [Fri, 10 Jul 2015 20:18:44 +0000 (16:18 -0400)]
Merge branch 'master' into 6569-smarter-jobs-image

9 years agoMerge branch '6279-web-shell-client' closes #6279
Tom Clegg [Fri, 10 Jul 2015 18:39:22 +0000 (14:39 -0400)]
Merge branch '6279-web-shell-client' closes #6279

9 years ago6279: Hide "reconnect" button because it doesn't auto-login.
Tom Clegg [Fri, 10 Jul 2015 17:35:10 +0000 (13:35 -0400)]
6279: Hide "reconnect" button because it doesn't auto-login.

9 years ago6279: Provide feedback that authentication token has been sent.
Tom Clegg [Fri, 10 Jul 2015 16:55:44 +0000 (12:55 -0400)]
6279: Provide feedback that authentication token has been sent.

9 years ago6279: Do not retry a request that "timed out" in less than 2 seconds.
Tom Clegg [Fri, 10 Jul 2015 16:45:54 +0000 (12:45 -0400)]
6279: Do not retry a request that "timed out" in less than 2 seconds.

In this case it's probably not a timeout -- more likely a CORS problem
that the browser is not allowed to report to the Javascript program.
In such cases, retrying ad infinitum will not help.

9 years ago6279: Do not set content-length headers in XHR.
Tom Clegg [Fri, 10 Jul 2015 15:18:46 +0000 (11:18 -0400)]
6279: Do not set content-length headers in XHR.

According to error messages in Chrome console:

Refused to set unsafe header "Content-Length"
  ShellInABox.sendRequest @ shell_in_a_box.js:178
  ShellInABox.onReadyStateChange @ shell_in_a_box.js:206
  (anonymous function) @ shell_in_a_box.js:183

9 years ago6279: Move keyboard assets to /public/webshell/
Tom Clegg [Fri, 10 Jul 2015 15:16:43 +0000 (11:16 -0400)]
6279: Move keyboard assets to /public/webshell/

9 years agoMake sure to add python-virtualenv to the Docker arvados/jobs image.
Ward Vandewege [Fri, 10 Jul 2015 14:58:43 +0000 (10:58 -0400)]
Make sure to add python-virtualenv to the Docker arvados/jobs image.

refs #6569

9 years agoMerge branch '6222-memory-status' refs #6222
Tom Clegg [Fri, 10 Jul 2015 13:32:16 +0000 (09:32 -0400)]
Merge branch '6222-memory-status' refs #6222

9 years agoMerge branch 'master' into 6569-smarter-jobs-image
Ward Vandewege [Fri, 10 Jul 2015 03:19:04 +0000 (23:19 -0400)]
Merge branch 'master' into 6569-smarter-jobs-image

9 years agoMerge branch '6218-python-sdk-perf' closes #6218
Tom Clegg [Fri, 10 Jul 2015 03:02:59 +0000 (23:02 -0400)]
Merge branch '6218-python-sdk-perf' closes #6218

9 years ago6218: Generate profiling data for a few arvados.collection.Collection scenarios.
Tom Clegg [Tue, 7 Jul 2015 15:28:05 +0000 (11:28 -0400)]
6218: Generate profiling data for a few arvados.collection.Collection scenarios.

9 years agoMake sure that mkimage-debootstrap.sh uses -f when tagging docker
Ward Vandewege [Fri, 10 Jul 2015 03:00:20 +0000 (23:00 -0400)]
Make sure that mkimage-debootstrap.sh uses -f when tagging docker
images.

refs #6528

9 years agoMake sure that mkimage-debootstrap.sh does not try to do an interactive
Ward Vandewege [Fri, 10 Jul 2015 02:20:44 +0000 (22:20 -0400)]
Make sure that mkimage-debootstrap.sh does not try to do an interactive
docker run when there's no tty.

refs #6528

9 years agoMake the arvados/jobs image leaner.
Ward Vandewege [Fri, 10 Jul 2015 02:09:18 +0000 (22:09 -0400)]
Make the arvados/jobs image leaner.

refs #6569

9 years ago6279: Move webshell action into VirtualMachinesController, tweak formatting & config.
Tom Clegg [Thu, 9 Jul 2015 20:38:16 +0000 (16:38 -0400)]
6279: Move webshell action into VirtualMachinesController, tweak formatting & config.

* Document config var

* Accept formatting references like %{hostname} and %{uuid} in config
  var instead of always appending "/#{hostname}"

* Fix favicon, js, and stylesheet paths (use asset_path helper); move
  js and css into public/webshell/

* Use j() quoting helper in js.erb

9 years ago6279: added shell_in_a_box url as comment
radhika [Thu, 9 Jul 2015 14:14:45 +0000 (10:14 -0400)]
6279: added shell_in_a_box url as comment

9 years ago6279: Noticed that enabled.gif is also needed. I see this one when I use the right...
radhika [Thu, 9 Jul 2015 13:43:43 +0000 (09:43 -0400)]
6279: Noticed that enabled.gif is also needed. I see this one when I use the right mouse click in shell_in_a_box terminal,
and use the reset option. Added this gif.

9 years ago6279: add some comments
radhika [Thu, 9 Jul 2015 01:37:11 +0000 (21:37 -0400)]
6279: add some comments

9 years agoi6279: The '-' and '_' are not working in Firefox. Upon googling, found this URL...
radhika [Thu, 9 Jul 2015 01:07:22 +0000 (21:07 -0400)]
i6279: The '-' and '_' are not working in Firefox. Upon googling, found this URL that suggested a workaround:
https://code.google.com/p/shellinabox/issues/detail?id=202

9 years agoMerge branch 'master' into 6279-web-shell-client
radhika [Thu, 9 Jul 2015 00:26:23 +0000 (20:26 -0400)]
Merge branch 'master' into 6279-web-shell-client

9 years ago6279: if hostname ends with .shell, strip it.
radhika [Thu, 9 Jul 2015 00:25:51 +0000 (20:25 -0400)]
6279: if hostname ends with .shell, strip it.

9 years ago6358: Declare FUSE driver's dependency on llfuse >= 0.40.
Brett Smith [Wed, 8 Jul 2015 21:19:53 +0000 (17:19 -0400)]
6358: Declare FUSE driver's dependency on llfuse >= 0.40.

The workaround added in 08284382 requires this version.  Below that,
llfuse's Queue at least lives in a different place.  We may be able to
support older versions with more nuance, but for now, just codify the
current reality.

Closes #6358.  Refs #3198.

9 years agoqiuck fix to arvados-pam vulnerability
Nico Cesar [Wed, 8 Jul 2015 20:44:18 +0000 (16:44 -0400)]
qiuck fix to arvados-pam vulnerability

no issue #

9 years agoMerge branch '6377-dev-startup' refs #6377
Tom Clegg [Wed, 8 Jul 2015 18:56:30 +0000 (14:56 -0400)]
Merge branch '6377-dev-startup' refs #6377

9 years agoMerge branch 'master' into 6279-web-shell-client
radhika [Wed, 8 Jul 2015 18:46:22 +0000 (14:46 -0400)]
Merge branch 'master' into 6279-web-shell-client

9 years agoMerge branch '6384-libpam-arvados'
Nico Cesar [Wed, 8 Jul 2015 18:09:07 +0000 (14:09 -0400)]
Merge branch '6384-libpam-arvados'

closes #6384

9 years agoWhitespace fixes
Ward Vandewege [Wed, 8 Jul 2015 17:58:41 +0000 (13:58 -0400)]
Whitespace fixes

refs #6384

9 years agoMerge branch 'master' into 6384-libpam-arvados
Ward Vandewege [Wed, 8 Jul 2015 17:57:17 +0000 (13:57 -0400)]
Merge branch 'master' into 6384-libpam-arvados

9 years ago6384: reverting names
Nico Cesar [Wed, 8 Jul 2015 17:53:31 +0000 (13:53 -0400)]
6384: reverting names

9 years agoRename file
Ward Vandewege [Wed, 8 Jul 2015 16:47:07 +0000 (12:47 -0400)]
Rename file

refs #2256

9 years agoFix path for arvados_pam.py
Ward Vandewege [Wed, 8 Jul 2015 16:19:18 +0000 (12:19 -0400)]
Fix path for arvados_pam.py

refs #2256

9 years agoFix typo.
Ward Vandewege [Wed, 8 Jul 2015 16:09:17 +0000 (12:09 -0400)]
Fix typo.

refs #2256

9 years agoadded /etc/default/arvados_pam as a parameter
Nico Cesar [Wed, 8 Jul 2015 15:30:49 +0000 (11:30 -0400)]
added /etc/default/arvados_pam as a parameter

refs #6512

9 years agoFix typo. No issue #
Tom Clegg [Wed, 8 Jul 2015 14:13:04 +0000 (10:13 -0400)]
Fix typo. No issue #

9 years ago6377: Update docs to use application.yml instead of omniauth.rb for SSO config.
Tom Clegg [Wed, 8 Jul 2015 05:56:21 +0000 (01:56 -0400)]
6377: Update docs to use application.yml instead of omniauth.rb for SSO config.

9 years ago6377: Fix crash if no asset pipeline.
Tom Clegg [Wed, 8 Jul 2015 05:12:58 +0000 (01:12 -0400)]
6377: Fix crash if no asset pipeline.

9 years ago6377: Update ruby to 2.1.6. Remove bundler version pin (not needed since ca1d997).
Tom Clegg [Tue, 7 Jul 2015 20:45:16 +0000 (16:45 -0400)]
6377: Update ruby to 2.1.6. Remove bundler version pin (not needed since ca1d997).

9 years ago6377: Avoid "incompatible encoding" errors by using blank template0 instead of site...
Tom Clegg [Wed, 1 Jul 2015 02:47:50 +0000 (22:47 -0400)]
6377: Avoid "incompatible encoding" errors by using blank template0 instead of site-specific template1.

9 years ago6377: Fix reversed condition in "site application.yml is optional" fix.
Tom Clegg [Tue, 30 Jun 2015 15:20:38 +0000 (11:20 -0400)]
6377: Fix reversed condition in "site application.yml is optional" fix.

9 years ago6377: Use fork of themes_for_rails with fixed gemspec.
Tom Clegg [Tue, 30 Jun 2015 15:19:04 +0000 (11:19 -0400)]
6377: Use fork of themes_for_rails with fixed gemspec.

Allows installing with current bundler versions, which treat the invalid
gemspec as an error.

9 years ago6377: Support loading omniauth config from application.yml.
Tom Clegg [Tue, 30 Jun 2015 15:07:24 +0000 (11:07 -0400)]
6377: Support loading omniauth config from application.yml.

9 years agoMerge branch 'master' into 6279-web-shell-client
radhika [Wed, 8 Jul 2015 02:30:25 +0000 (22:30 -0400)]
Merge branch 'master' into 6279-web-shell-client

9 years ago6279: add login link in VM panel of manage_account page that takes user to shell_in_a...
radhika [Wed, 8 Jul 2015 02:28:51 +0000 (22:28 -0400)]
6279: add login link in VM panel of manage_account page that takes user to shell_in_a_box.

9 years agoMerge branch '5989-api-all-repos-permissions-wip'
Brett Smith [Tue, 7 Jul 2015 21:02:06 +0000 (17:02 -0400)]
Merge branch '5989-api-all-repos-permissions-wip'

Closes #5989, #6479.

9 years ago5989: API repo perms method always returns all repos.
Brett Smith [Sun, 5 Jul 2015 11:39:09 +0000 (07:39 -0400)]
5989: API repo perms method always returns all repos.

Previously the method would not return repositories that were not
accessible to any authorized key.  This change helps deployment tools
like update-gitolite do repository setup correctly with a single API
call.

9 years ago6377: Missing application.yml is not an error.
Tom Clegg [Fri, 26 Jun 2015 15:19:54 +0000 (11:19 -0400)]
6377: Missing application.yml is not an error.

9 years ago6222: Add memory stats to status.json.
Tom Clegg [Tue, 7 Jul 2015 20:31:55 +0000 (16:31 -0400)]
6222: Add memory stats to status.json.

Reduce malloc activity in status.json.

Remove abandoned GetVolumeStatus, and move its tests over to
volume_unix_test.go.

9 years agoAdd arvados_pam.py and shellinabox pam configuration file.
Ward Vandewege [Mon, 6 Jul 2015 12:28:36 +0000 (08:28 -0400)]
Add arvados_pam.py and shellinabox pam configuration file.

Refs #2256

9 years ago5989: bug_1 added puppet repository patch
Nico Cesar [Thu, 2 Jul 2015 14:35:03 +0000 (10:35 -0400)]
5989: bug_1 added puppet repository patch

this is duplicated code from:

puppet/modules/arvados-git-server/templates/usr-local-arvados-update-gitolite.rb.erb

I just copy the code that was there

9 years ago5989: create directory structure for temp files
Nico Cesar [Wed, 1 Jul 2015 20:23:33 +0000 (16:23 -0400)]
5989: create directory structure for temp files

refs #5989 bug_1

9 years agoMerge branch '5677-plpgsql-warning' closes #5677
Tom Clegg [Tue, 7 Jul 2015 15:42:12 +0000 (11:42 -0400)]
Merge branch '5677-plpgsql-warning' closes #5677

9 years ago5677: Edit structure.sql after db:structure:dump: avoid warnings when loading, and...
Tom Clegg [Fri, 26 Jun 2015 06:54:31 +0000 (02:54 -0400)]
5677: Edit structure.sql after db:structure:dump: avoid warnings when loading, and editwars when committing.

9 years agocloses #6466
Manoj [Tue, 7 Jul 2015 13:08:21 +0000 (09:08 -0400)]
closes #6466
Merge branch '6466-disable-public-projects'

9 years agoMerge branch 'master' into 6466-disable-public-projects
Manoj [Tue, 7 Jul 2015 13:07:33 +0000 (09:07 -0400)]
Merge branch 'master' into 6466-disable-public-projects

9 years agoMerge branch '6438-multiplatform-install-guide-wip'
Brett Smith [Mon, 6 Jul 2015 21:37:21 +0000 (17:37 -0400)]
Merge branch '6438-multiplatform-install-guide-wip'

Closes #6438, #6455.  Refs #6388.

9 years ago6455: Include more steps in Crunch install docs.
Brett Smith [Mon, 6 Jul 2015 21:29:03 +0000 (17:29 -0400)]
6455: Include more steps in Crunch install docs.

* Document the necessary API server configuration change for
  crunch-dispatch.
* Document Docker installation.
* Note compute node crunch users need to be in the fuse group.

9 years ago6438: Modernize Rails server installation guides.
Brett Smith [Mon, 6 Jul 2015 21:27:08 +0000 (17:27 -0400)]
6438: Modernize Rails server installation guides.

Document the package-based installation procedure, and associated
Nginx configuration.

9 years ago6388: Add CentOS 6.6 instructions to install docs.
Brett Smith [Mon, 6 Jul 2015 21:26:10 +0000 (17:26 -0400)]
6388: Add CentOS 6.6 instructions to install docs.

9 years ago6466 - Update body html for enable public page and added tests to project controller...
Manoj [Mon, 6 Jul 2015 18:00:24 +0000 (14:00 -0400)]
6466 - Update body html for enable public page and added tests to project controller test.

9 years agocloses #6013
radhika [Mon, 6 Jul 2015 16:08:29 +0000 (12:08 -0400)]
closes #6013
Merge branch '6013-cleanup-setup-impl'

9 years ago6013: revert back the deactivate user button leading text in workbench user admin...
radhika [Fri, 3 Jul 2015 21:03:32 +0000 (17:03 -0400)]
6013: revert back the deactivate user button leading text in workbench user admin page.

9 years ago6013: update user notification email upon setup.
radhika [Fri, 3 Jul 2015 20:56:53 +0000 (16:56 -0400)]
6013: update user notification email upon setup.

9 years ago6013: remove "repository" from user setup popup in workbench
radhika [Fri, 3 Jul 2015 19:44:26 +0000 (15:44 -0400)]
6013: remove "repository" from user setup popup in workbench

9 years ago6466:Added config parameter to disable public projects page and added a test to proje...
Manoj [Fri, 3 Jul 2015 16:06:22 +0000 (12:06 -0400)]
6466:Added config parameter to disable public projects page and added a test to projects controller.

9 years agoMerge branch '5989-bug_1' merge with puppet repo "copy and paste" to sync up duplicat...
Nico Cesar [Thu, 2 Jul 2015 14:37:38 +0000 (10:37 -0400)]
Merge branch '5989-bug_1' merge with puppet repo "copy and paste" to sync up duplicated code.

refs #5989

9 years ago5989: bug_1 added puppet repository patch
Nico Cesar [Thu, 2 Jul 2015 14:35:03 +0000 (10:35 -0400)]
5989: bug_1 added puppet repository patch

this is duplicated code from:

puppet/modules/arvados-git-server/templates/usr-local-arvados-update-gitolite.rb.erb

I just copy the code that was there

9 years agoMerge branch '6264-run-command-task-env' refs #6264
Peter Amstutz [Thu, 2 Jul 2015 14:25:20 +0000 (10:25 -0400)]
Merge branch '6264-run-command-task-env' refs #6264

9 years ago6264: Add task.env to documentation.
Peter Amstutz [Thu, 2 Jul 2015 13:47:52 +0000 (09:47 -0400)]
6264: Add task.env to documentation.

9 years ago6264: Support setting environment variables.
Peter Amstutz [Wed, 1 Jul 2015 21:43:28 +0000 (17:43 -0400)]
6264: Support setting environment variables.

9 years ago5989: create directory structure for temp files
Nico Cesar [Wed, 1 Jul 2015 20:23:33 +0000 (16:23 -0400)]
5989: create directory structure for temp files

refs #5989 bug_1

9 years agoInvoke crunch-job with `/usr/bin/env perl`.
Brett Smith [Wed, 1 Jul 2015 12:25:15 +0000 (08:25 -0400)]
Invoke crunch-job with `/usr/bin/env perl`.

No issue #.

9 years agoDockerfile had an error. fixed
Nico Cesar [Mon, 29 Jun 2015 15:00:01 +0000 (11:00 -0400)]
Dockerfile had an error. fixed

no issue #

9 years agowe need to manually install python-pyasn1=0.1.7 python-pyasn1-modules=0.0.5 because...
Nico Cesar [Mon, 29 Jun 2015 14:53:18 +0000 (10:53 -0400)]
we need to manually install python-pyasn1=0.1.7 python-pyasn1-modules=0.0.5 because apt-get wont resolve correctly.
apt-get install are less quiet now too.

no issue #

9 years ago6440: Display AJAX errors as text, not HTML. closes #6440
Tom Clegg [Fri, 26 Jun 2015 22:28:57 +0000 (18:28 -0400)]
6440: Display AJAX errors as text, not HTML. closes #6440

9 years agoFix bad CollectionReader reference in arv-put.
Brett Smith [Fri, 26 Jun 2015 19:52:46 +0000 (15:52 -0400)]
Fix bad CollectionReader reference in arv-put.

No issue #.

9 years agoMerge branch '6432-pysdk-more-ca-certs-wip'
Brett Smith [Fri, 26 Jun 2015 15:42:10 +0000 (11:42 -0400)]
Merge branch '6432-pysdk-more-ca-certs-wip'

Closes #6432, #6434.

9 years ago6432: Python SDK can find and use CA certs on Red Hat.
Brett Smith [Thu, 25 Jun 2015 23:36:52 +0000 (19:36 -0400)]
6432: Python SDK can find and use CA certs on Red Hat.

9 years agocloses #6234
radhika [Fri, 26 Jun 2015 14:36:08 +0000 (10:36 -0400)]
closes #6234
Merge branch '6234-user-edit-self'

9 years agoMerge branch 'master' into 6234-user-edit-self
radhika [Fri, 26 Jun 2015 14:34:33 +0000 (10:34 -0400)]
Merge branch 'master' into 6234-user-edit-self

9 years agoUpdate arvados_fuse version dependency on arvados-python-client. refs #3198
Peter Amstutz [Thu, 25 Jun 2015 17:55:07 +0000 (13:55 -0400)]
Update arvados_fuse version dependency on arvados-python-client.  refs #3198

9 years agoMerge branch '3198-writable-fuse' closes #3198
Peter Amstutz [Thu, 25 Jun 2015 17:52:18 +0000 (13:52 -0400)]
Merge branch '3198-writable-fuse' closes #3198

9 years ago3198: Rename --enable-write to --read-write. Tweak docs.
Peter Amstutz [Thu, 25 Jun 2015 14:30:28 +0000 (10:30 -0400)]
3198: Rename --enable-write to --read-write.  Tweak docs.

9 years agorefs #6218
radhika [Wed, 24 Jun 2015 14:24:14 +0000 (10:24 -0400)]
refs #6218
Merge branch '6218-add-performance-profiling-to-python-sdk'

9 years ago6218: update the exception handling.
radhika [Wed, 24 Jun 2015 14:22:46 +0000 (10:22 -0400)]
6218: update the exception handling.

9 years ago6218: correct exception handling.
radhika [Wed, 24 Jun 2015 13:58:39 +0000 (09:58 -0400)]
6218: correct exception handling.

9 years ago6320: Update Workbench test for active user VM setup.
Brett Smith [Tue, 23 Jun 2015 14:21:46 +0000 (10:21 -0400)]
6320: Update Workbench test for active user VM setup.

Now that the test fixtures give the active user access to testvm2,
this test needs to be updated to account for it, just like the API
server tests were.  Refs #6320.

9 years agoRemove unused modules from PySDK setup.py.
Brett Smith [Tue, 23 Jun 2015 14:13:46 +0000 (10:13 -0400)]
Remove unused modules from PySDK setup.py.

No issue #.

9 years ago6218: update the symlink and comment
radhika [Tue, 23 Jun 2015 13:25:08 +0000 (09:25 -0400)]
6218: update the symlink and comment

9 years agoMerge branch '4410-slurm-fails-are-tempfails-wip'
Brett Smith [Mon, 22 Jun 2015 20:55:07 +0000 (16:55 -0400)]
Merge branch '4410-slurm-fails-are-tempfails-wip'

Closes #4410, #6283.

9 years ago6218: Refactor profiler as a decorator
Tom Clegg [Mon, 22 Jun 2015 20:55:06 +0000 (16:55 -0400)]
6218: Refactor profiler as a decorator

9 years ago4410: Crunch retries jobs when all SLURM nodes fail.
Brett Smith [Mon, 15 Jun 2015 17:54:36 +0000 (13:54 -0400)]
4410: Crunch retries jobs when all SLURM nodes fail.

See the ticket for detailed background discussion and implementation
rationale, especially notes 13 and 14.

This required a couple of ancillary changes:

* crunch-job now makes a distinction between "task failed because a
  node failed," and "task failed for other temporary reason."  It uses
  this additional information to decide when it should retry tasks
  itself, and when it needs to give up and kick the problem up to
  crunch-dispatch.

* crunch-job now handles creating log collections itself from
  manifests generated by arv-put.  This enables it to append to logs
  generated during previous attempts to run the job.

9 years ago4410: crunch-dispatch logs crunch-job exit later.
Brett Smith [Mon, 15 Jun 2015 21:04:25 +0000 (17:04 -0400)]
4410: crunch-dispatch logs crunch-job exit later.

This makes it easier to log the exit code, and makes the logs look
nicer because the exit log doesn't interrupt crunch-job's stderr.

9 years ago6218: fix typo in sample test
radhika [Mon, 22 Jun 2015 15:31:40 +0000 (11:31 -0400)]
6218: fix typo in sample test

9 years ago6218: add performance profiling and a sample test in python sdk.
radhika [Fri, 19 Jun 2015 21:01:32 +0000 (17:01 -0400)]
6218: add performance profiling and a sample test in python sdk.

9 years ago3198: Fix test
Peter Amstutz [Thu, 18 Jun 2015 20:55:22 +0000 (16:55 -0400)]
3198: Fix test

9 years ago3198: concurrency test and associated fixes
Peter Amstutz [Thu, 18 Jun 2015 20:32:21 +0000 (16:32 -0400)]
3198: concurrency test and associated fixes

9 years agoWIP
Peter Amstutz [Wed, 17 Jun 2015 21:06:57 +0000 (17:06 -0400)]
WIP