Activity

From 03/08/2015 to 04/06/2015

04/06/2015

11:49 pm Revision 3c2372f0 (arvados): Merge branch 'master' into 5365-not-link-unreadables
Conflicts:
apps/workbench/test/integration/anonymous_access_test.rb
Radhika Chippada
11:43 pm Revision 3cc68fc8 (arvados): 5365: job link in pipeline instance page
Radhika Chippada
09:05 pm Bug #5565 (Resolved): [Workbench] Show (anonymous-appropriate) breadcrumbs when rendering layout ...
Applied in changeset arvados|commit:a2fc3a2158c3c154c3d7fc2b55eea928898cafb5. Radhika Chippada
08:58 pm Bug #5565: [Workbench] Show (anonymous-appropriate) breadcrumbs when rendering layout in anonymou...
commit:675a22d7 is good to merge. Thanks. Brett Smith
08:44 pm Bug #5565: [Workbench] Show (anonymous-appropriate) breadcrumbs when rendering layout in anonymou...
Reviewing commit:2ad69e1. The description specifies that the breadcrumbs should include "Link to parent *project(s)*... Brett Smith
07:17 pm Bug #5565 (In Progress): [Workbench] Show (anonymous-appropriate) breadcrumbs when rendering layo...
Radhika Chippada
08:59 pm Bug #5675 (Resolved): [Workbench] Show project Subprojects tab when in anonymous view.
Now that we are including breadcrumbs in anonymous view, it is possible to see the parent project(s) in anonymous vie... Radhika Chippada
08:58 pm Task #5674 (Resolved): Review branch: 5565-breadcrumbs-in-anonyymous-view
Radhika Chippada
08:14 pm Task #5674 (In Progress): Review branch: 5565-breadcrumbs-in-anonyymous-view
Brett Smith
07:32 pm Task #5674 (Resolved): Review branch: 5565-breadcrumbs-in-anonyymous-view
Radhika Chippada
08:58 pm Revision a2fc3a21 (arvados): closes #5565
Merge branch '5565-breadcrumbs-in-anonyymous-view' Radhika Chippada
08:54 pm Revision 675a22d7 (arvados): 5565: show parent project hierarchy in breadcrumbs in anonymous view...
Radhika Chippada
08:48 pm Revision e1880407 (arvados): Merge branch 'master' into 5565-breadcrumbs-in-anonyymous-view
Radhika Chippada
08:20 pm Feature #5492 (Resolved): [Workbench] Add "home project" link to the "my account" dropdown
Applied in changeset arvados|commit:7a282129315671eaf79bf2a752bf1cd0c45f2588. Radhika Chippada
08:13 pm Feature #5492: [Workbench] Add "home project" link to the "my account" dropdown
commit:55be42bc is good to merge. Thank you. Brett Smith
04:46 pm Feature #5492 (In Progress): [Workbench] Add "home project" link to the "my account" dropdown
Radhika Chippada
08:17 pm Task #5672 (Resolved): Review branch: 5492-home-project-in-my-account
Radhika Chippada
07:49 pm Task #5672 (In Progress): Review branch: 5492-home-project-in-my-account
Brett Smith
05:23 pm Task #5672 (Resolved): Review branch: 5492-home-project-in-my-account
Radhika Chippada
08:16 pm Revision 7a282129 (arvados): closes #5492
Merge branch '5492-home-project-in-my-account' Radhika Chippada
08:15 pm Revision e1c42360 (arvados): Merge branch 'master' into 5492-home-project-in-my-account
Radhika Chippada
07:59 pm Revision be4dfebd (arvados): 4685: First integration test case passes!
Peter Amstutz
07:36 pm Bug #5365: [Workbench] Do not link to objects that are not readable by current user
Reviewing commit:8ad6b6e
* When a logged in user views a pipeline instance page, job UUIDs are not rendered.
* So...
Brett Smith
03:26 pm Bug #5365: [Workbench] Do not link to objects that are not readable by current user
Notes about implementation:
- No longer dead link job and output when they are not readable by current user (or no...
Radhika Chippada
07:31 pm Revision 06d9984f (arvados): Merge branch 'master' into 5565-breadcrumbs-in-anonyymous-view
Radhika Chippada
07:29 pm Revision 2ad69e1a (arvados): 5565: show trimmed down version of breadcrumbs in anonymous view.
Radhika Chippada
07:24 pm Revision 39fc7bc4 (arvados): 4685: Working on cwl_job test harness.
Peter Amstutz
07:24 pm Revision 0ef21f75 (arvados): 4685: Refactor docker image uploading into upload_image().
Peter Amstutz
07:23 pm Revision 9122bc6b (arvados): 4685: run_test_server support for arv-git-httpd.
Peter Amstutz
06:56 pm Task #5671 (In Progress): Review branch: 5365-not-link-unreadables
Brett Smith
03:11 pm Task #5671 (Resolved): Review branch: 5365-not-link-unreadables
Radhika Chippada
06:48 pm Bug #5653: [SDKs] arv-copy of Pipeline Template did not copy all branches required to remote Repo...
5653-arv-copy-multiple-branches-wip is up for review. I tested it by copying the same pipeline template in this bug ... Brett Smith
04:14 pm Bug #5653 (In Progress): [SDKs] arv-copy of Pipeline Template did not copy all branches required ...
Brett Smith
06:45 pm Task #5673 (Resolved): Review 5653-arv-copy-multiple-branches-wip
Brett Smith
06:40 pm Revision 9b0ace39 (arvados): 5653: arv-copy copies multiple commits from the same repository+pipe...
arv-copy previously used the repository name alone to determine which
job scripts it had already copied to the destin...
Brett Smith
05:49 pm Revision 9108a20c (arvados): Tighten up DNS check in arvdock.
I got arvdock stuck in an infinite loop because I had the right
nameserver line in /etc/resolv.conf, except it was co...
Brett Smith
05:47 pm Revision f37409d9 (arvados): 4685: Docker-in-Docker seems to be working for cwl-runner.
Peter Amstutz
05:34 pm A good helping of Docker with a sprinkling of Common Workflow Language
Our most recent sprint contained the usual mix of bug fixes and new features. Here's a quick overview of what happene... Ward Vandewege
04:43 pm Revision 55be42bc (arvados): 5492: add "Home project" link to my account menu.
Radhika Chippada
03:58 pm Revision 8ad6b6ec (arvados): Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada
03:58 pm Revision e6b8eaf0 (arvados): 5365: white space
Radhika Chippada
03:38 pm Revision 7bd9cd28 (arvados): Add missing global declaration in arv-copy.
No issue #. Brett Smith
03:05 pm Story #5585 (In Progress): [Documentation] (recurring) Write blog post in first three days of sprint
Ward Vandewege
03:04 pm Revision 4cb76110 (arvados): 5365: couple more integration tests to access Log tab from within th...
Radhika Chippada
02:58 pm Feature #5416: [API] Clone git repositories without using an SSH private key
The jenkins tests fail consistently (see run 1448-1452) with this error:... Ward Vandewege
02:20 pm Bug #5521: [Workbench] Slow download speed from browser
The second one (download stops) could plausibly be the 1 GiB limit bug. The first one has been observed but not inve... Peter Amstutz
02:15 pm Revision 2e56b93e (arvados): 5365: additional test assertions for pipeline log tab display
Radhika Chippada
02:10 pm Bug #5352: [Crunch] Dispatcher not handling node allocation failures
By running this patch in Docker, I successfully reproduced the race condition and saw the changes complete the job. ... Brett Smith
01:45 pm Revision ccb48a84 (arvados-dev): run-tests.sh can now run the arv-git-httpd tests too.
No issue # Ward Vandewege
01:45 pm Revision ccb48a84 (arvados): run-tests.sh can now run the arv-git-httpd tests too.
No issue # Ward Vandewege
01:25 pm Revision 70e171aa (arvados): Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada

04/05/2015

10:01 pm Task #5651: Fix reported scaling factor for failed jobs (see notes)
@app/views/pipeline_instances/_running_component.html.erb@ sums the runtime of each component task. If the task does... Brett Smith
09:44 pm Bug #5662: [FUSE] cd/ls sometimes takes too long on su92l
For future readers, the manifest in question is not noticeably evil or anything. The most remarkable thing about it ... Brett Smith
09:40 pm Bug #5662: [FUSE] cd/ls sometimes takes too long on su92l
Abram,
After our deployment last week, I'm able to run the same command from a fresh mount in ~5 seconds. Can you...
Brett Smith
09:39 pm Revision 635229a6 (arvados): Fix debug log formatting in PySDK.
When multiple arguments are passed to a logger method, the first
argument is expected to be a printf-style format str...
Brett Smith
09:24 pm Bug #5663: [Documentation] Use "...puts rand()..." instead of "rake secret" in apiserver/workbenc...
It's worth checking whether the API server has the same problem, and addressing it there if so. Brett Smith
09:11 pm Bug #5352: [Crunch] Dispatcher not handling node allocation failures
5352-crunch-dispatch-salloc-tempfail-wip is up for review. Please see the commit message for explanation. Brett Smith
08:55 pm Bug #5352 (In Progress): [Crunch] Dispatcher not handling node allocation failures
Brett Smith
09:10 pm Task #5670 (Resolved): Review 5352-crunch-dispatch-salloc-tempfail-wip
Brett Smith
09:10 pm Revision a9c5882f (arvados): 5352: crunch-dispatch treats node allocation failure as temporary.
Imagine a scenario where multiple crunch-dispatch processes are
sitting idle, then suddenly a new job appears in the ...
Brett Smith
08:35 pm Bug #5518 (Resolved): [SDKs] arvados not defined in arvados.util
Applied in changeset arvados|commit:e88eac059d0c9088edf4d3f60734c4804d7ca500. Brett Smith
08:34 pm Revision e88eac05 (arvados): 5518: PySDK arvados.util must import arvados.
Closes #5518. Brett Smith
08:16 pm Task #5641 (Resolved): Review 5416-repo-dir-is-uuid
Brett Smith

04/03/2015

10:21 pm Bug #5481: [Workbench] Pipeline instance page does not automatically refresh when pipeline does n...
I honestly don't think I could reproduce this. I have tried before and it only happens sometimes. I'm not too familia... Bryan Cosca
09:28 pm Bug #5481: [Workbench] Pipeline instance page does not automatically refresh when pipeline does n...
Bryan,
Is there some trick to reproducing this bug? I just tried a basic pipeline run, and it worked out all righ...
Brett Smith
10:18 pm Bug #5499: [SDKs] arv-copy fails to create collection after copying many blocks
I believe I tried this command twice. The first time I waited after the line before I Ctrl+c from about ~2 hours whil... Bryan Cosca
09:12 pm Bug #5499: [SDKs] arv-copy fails to create collection after copying many blocks
Bryan,
Can you describe the issue in more detail? From the transcript you pasted, it looks like you hit Ctrl-C an...
Brett Smith
09:32 pm Feature #5368 (Closed): [Workbench] job scripts accessible in some way
This is being done in #5416. Closing as duplicate. Brett Smith
09:29 pm Revision ee91e487 (arvados): 5365: add integration test to verify Log tab and other unreadable pr...
Radhika Chippada
09:14 pm Feature #5495: [Workbench] Change "recent pipelines" to curated selection of "public pipelines"
The quickfix above has been implemented. I'll leave this open for the larger dashboard change. Brett Smith
08:59 pm Bug #5521: [Workbench] Slow download speed from browser
I think this might be related to the 1GiB limit bug that was resolved last sprint, but need to investigate. Brett Smith
08:56 pm Bug #4458: [Workbench] Replace e-mail address in menu bar with user icon and make sure bread crum...
behavior better now, switches to mobile, but mobile menu doesn't link to projects/dashboard in any way?
!4458-lack-o...
Nancy Ouyang
08:54 pm Feature #5511: [Workbench] Workbench should support viewing VCF files
I'm making this ticket more specifically about VCF files. If more general preview support is needed, #5375 already c... Brett Smith
08:53 pm Feature #5375 (New): [workbench] Enable in-browser preview for text files in collections
Reopening to address the above. See also #5511, where a user requested the ability to preview VCF files. Brett Smith
08:34 pm Feature #2660: [Tests] [Draft] Make entire test suite run faster by eliminating excess start/stop
#3021 implemented much of the end of the description, but didn't accomplish some of the higher-minded implementation ... Brett Smith
08:32 pm Revision 555c19ac (arvados): 4685: Putting new job runner all together
Peter Amstutz
08:26 pm Feature #5514 (Closed): Workbench enhancements
I have created individual tickets for all these requests to aid prioritization, estimation, and planning. I'm closin... Brett Smith
08:24 pm Bug #5669 (New): [Workbench] Make Dashboard contents filterable
- Allow different views from the dashboard into the pipelines run or collections created.
'Recently finished pipelin...
Brett Smith
08:23 pm Feature #5668 (New): [Workbench] Favorite projects, pipelines, collections
- Allow 'starring' pipeline instances, projects and collections.
Some pipeline runs and collections I find myself us...
Brett Smith
08:23 pm Bug #4298 (Resolved): [Workbench] Admin user should see cpu/ram/scratch capacity after clicking a...
Ward Vandewege
08:22 pm Bug #5667 (New): [Workbench] Indicate related pipeline instances
- Conflate pipeline rus with the same input.
While debugging a pipeline I am often running the same pipeline with th...
Brett Smith
08:21 pm Bug #5666 (Resolved): [Workbench] Job "failed" label and "Cancel" button need more distinction
- For a running job, the 'cancel' button looks too much like the 'failed' button.
I have to look at it twice to real...
Brett Smith
08:20 pm Bug #5665 (New): [Workbench] Link to log from pipeline and/or job summary page
- Show log collection at the pipeline level, job level or somewhere else featured prominently without having to go in... Brett Smith
07:53 pm Bug #5607 (Closed): trying docker installation again
Ward Vandewege
07:52 pm Bug #5606: trying docker installation again
Hi Albert,
We've merged several fixes to our docker containers (specifically, bug #4752 has been closed).
Could...
Ward Vandewege
07:42 pm Task #5664 (Resolved): Review 5642-crunch-job-swap-limits-wip
Brett Smith
07:41 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
5642-crunch-job-swap-limits-wip is up for review with to implement the fix suggested above. I tested it in Docker, w... Brett Smith
05:18 pm Bug #5642 (In Progress): [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit o...
Brett Smith
04:02 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
Did some more testing on my desktop. Even Docker 1.5 exhibits the kill behavior.
Using @--memory-swap=-1@ is docu...
Brett Smith
07:38 pm Bug #5663 (Resolved): [Documentation] Use "...puts rand()..." instead of "rake secret" in apiserv...
-apps/workbench/config/application.yml.example should put "foobar" into secret_token, instead of "~"- "rake secret" s... Nancy Ouyang
06:56 pm Revision 0ae2871e (arvados): 4685: Add arv-keepdocker --download, used by task bootstrapping scri...
Peter Amstutz
06:49 pm Revision 807e72e0 (arvados): 5642: crunch-job uses higher memory limit when running few tasks.
This gives a task all of the node's RAM when it's the only task
running this round, which is more in line with user e...
Brett Smith
06:49 pm Revision 8f238ab3 (arvados): 5642: Explicitly make all swap available under Docker in crunch-job.
Without this, Docker 1.2 through 1.5 send subprocesses SIGKILL if they
exceed the memory limit. Refer to #5642 for a...
Brett Smith
06:03 pm Revision 50843fcf (arvados): 5493: minor refactoring
Radhika Chippada
05:57 pm Bug #5662 (New): [FUSE] cd/ls sometimes takes too long on su92l
... Abram Connelly
04:03 pm Bug #5653 (Resolved): [SDKs] arv-copy of Pipeline Template did not copy all branches required to ...
Copying Pipeline Template tb05z-p5p6p-wp8680agywvi2fo (which has two steps, each using a different branch of the sgut... Sarah Guthrie
03:58 pm Revision 5ea2ee64 (arvados): Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada
03:56 pm Revision 6fe9234c (arvados): 5365: Do not link to job, log, output in pipeline instance if the us...
Disable Log tab and show tooltip in such a scenario.
Working in manual testing. Integration test updates are on the way.
Radhika Chippada
03:46 pm Revision e4ea50a9 (arvados): 4685: Adding "job executive" to cwl_job.
Peter Amstutz
03:11 pm Revision 672107d3 (arvados-dev): Be consistent in our package and binary naming:
arv-git-httpd becomes arvados-git-httpd
No issue #
Ward Vandewege
03:11 pm Revision 672107d3 (arvados): Be consistent in our package and binary naming:
arv-git-httpd becomes arvados-git-httpd
No issue #
Ward Vandewege
03:02 pm Bug #5652 (Resolved): [SDKs] There is no way to silence arv-put and arv-get
On successful upload, 'arv-put' spits out a message of the form "Collection saved ...". There is no way to silence t... Abram Connelly
02:32 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Reviewing commit:949e725
The changes are good. Since you're taking days off, I've gone ahead and merged the branc...
Brett Smith
02:29 pm Revision 2d56bd2e (arvados): Merge branch '5416-repo-dir-is-uuid'
Refs #5416. Brett Smith
02:19 pm Task #5651 (New): Fix reported scaling factor for failed jobs (see notes)
For example, su92l-d1hrv-wo4tw2o83t7o0h8, where the scaling factor (and compute time used by the failed job) keeps in... Ward Vandewege
01:56 pm Task #5641 (In Progress): Review 5416-repo-dir-is-uuid
Brett Smith
03:06 am Revision 2b08bead (arvados): 4685: Working on alternate arv-cwl-job replacement for classic crunc...
Peter Amstutz
02:02 am Task #5649 (New): [Workbench] We need better job graphs, less spaghetti

Our job graphs are not useful. Here's an example for a job with just 8 tasks:
!20150402-job-graphs.png!
This ...
Ward Vandewege
12:15 am Revision 9186a081 (arvados-dev): 5416: Terminate connections on the configured test database (not...
Tom Clegg

04/02/2015

09:37 pm Revision bcd68a65 (arvados): 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...
Brett Smith
09:26 pm Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
Another solution -- edit the text in the "welcome to ARvados" box that says "You are accessing public data." right no... Nancy Ouyang
06:46 pm Feature #5647 (Resolved): [Workbench] Log-in on anonymous redirects to google sign-in with no war...
tl;dr: Clicking on Login on topnav takes me to google login and this could potentially be very confusing if it's my v... Nancy Ouyang
09:16 pm Revision 935416f8 (arvados): 4685: Working on CWL job runner.
Peter Amstutz
07:45 pm Bug #5365 (In Progress): [Workbench] Do not link to objects that are not readable by current user
Radhika Chippada
07:41 pm Feature #5370 (Resolved): [Workbench] If anonymous config is enabled, logged-out workbench homepa...
Radhika Chippada
07:25 pm Bug #4752 (Resolved): [Docker] Make websockets work, probably by using passenger standalone inste...
Applied in changeset arvados|commit:1a4d0158373902cac889ce5409fcae447d4a68d6. Peter Amstutz
07:18 pm Bug #4752: [Docker] Make websockets work, probably by using passenger standalone instead of apache.
4752-docker-websockets LGTM, but please pull before you merge; I added one commit to the branch. Ward Vandewege
02:28 pm Bug #4752: [Docker] Make websockets work, probably by using passenger standalone instead of apache.
A few more changes for you to review:
* Fix compute node containers to restart correctly.
* Fix git server hostna...
Peter Amstutz
07:23 pm Revision 1a4d0158 (arvados): Merge branch '4752-docker-websockets' closes #4752
Peter Amstutz
07:18 pm Task #5619 (Resolved): Review 4752-docker-websockets
Ward Vandewege
02:28 pm Task #5619 (In Progress): Review 4752-docker-websockets
Peter Amstutz
07:17 pm Revision 8e76f934 (arvados): Make arvdock abort with a nice error message if docker or curl can not
be found.
refs #4752
Ward Vandewege
06:35 pm Feature #5646: [Workbench] Display duration on pipeline instance listings
^--the above picture is to show that it's very hard to tell which of the arv-run /bin/bashes on the left correspond t... Nancy Ouyang
06:34 pm Feature #5646 (New): [Workbench] Display duration on pipeline instance listings
I could not find my pipeline, and wasn't sure if it was in Home project or some other project.
I have a _ton_ of ...
Nancy Ouyang
06:27 pm Feature #5645 (Resolved): [Workbench] Social media optimize anonymous collections/projects/pipelines
!SEO-arvados-facebook.png!
everyone wants to share their cool datasets on social media, right? :)
This is how G...
Nancy Ouyang
06:13 pm Task #5644 (Resolved): Review 5626-git-server-hostname
Radhika Chippada
02:33 pm Task #5644 (In Progress): Review 5626-git-server-hostname
Peter Amstutz
02:25 pm Task #5644 (Resolved): Review 5626-git-server-hostname
Peter Amstutz
05:01 pm Bug #5426 (Resolved): [Workbench] Large downloads through workbench fail
Ward Vandewege
05:01 pm Task #5503 (Resolved): Deploy "proxy_buffer off;" on /collections/download
Ward Vandewege
04:05 pm Bug #5626 (Resolved): [API] Configuration option to set git server hostname
Applied in changeset arvados|commit:8053949c0bd853f9e6d342dbda504766bd3120a1. Peter Amstutz
03:31 pm Bug #5626: [API] Configuration option to set git server hostname
Peter,
Thanks for the updated tests. Just one more comment about the test.
* Can you also verify the push url in ...
Radhika Chippada
02:34 pm Bug #5626: [API] Configuration option to set git server hostname
Peter,
Took a quick look at this update.
* Is it possible to write tests? Toggle the config setting and do a get ...
Radhika Chippada
02:21 pm Bug #5626 (In Progress): [API] Configuration option to set git server hostname
Peter Amstutz
04:02 pm Revision 8053949c (arvados): Merge branch '5626-git-server-hostname' closes #5626
Peter Amstutz
04:01 pm Revision b3d9b57e (arvados): 5626: Expand test to check both positive and negative cases a bit pe...
Peter Amstutz
02:38 pm Revision 05fab15b (arvados): 5626: Add test for git_hostname configuration option.
Peter Amstutz
02:24 pm Revision 9eaccd03 (arvados): 4752: Websockets works. Fix compute node containers to restart corr...
git server hostname. Arvdock waits for API/workbench to be ready before telling
the user to go to workbench.
Peter Amstutz
02:40 am Revision b439ab78 (arvados): 5416: Browse git repository contents in workbench.
Tom Clegg
02:40 am Revision 4ae0927c (arvados): 5416: Fix comment.
Tom Clegg

04/01/2015

10:28 pm Revision dbbc879d (arvados): 5416: Browse git repository contents in workbench.
Tom Clegg
10:24 pm Revision b62aa0b5 (arvados): 5416: Fix comment.
Tom Clegg
09:43 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
We tested out the original problem job with a Docker 1.5 package, and it failed the same way. An upgrade by itself w... Brett Smith
09:20 pm Bug #5642 (Resolved): [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on c...
You can reproduce this outside Crunch, using any Docker image:... Brett Smith
09:36 pm Bug #4752: [Docker] Make websockets work, probably by using passenger standalone instead of apache.
LGTM, thanks! Ward Vandewege
01:53 pm Bug #4752 (In Progress): [Docker] Make websockets work, probably by using passenger standalone in...
Peter Amstutz
09:36 pm Task #5619 (Resolved): Review 4752-docker-websockets
Ward Vandewege
07:35 pm Task #5619 (In Progress): Review 4752-docker-websockets
Ward Vandewege
01:53 pm Task #5619 (Resolved): Review 4752-docker-websockets
Peter Amstutz
08:32 pm Bug #5606: trying docker installation again
I'm glad you're making progress!
There's a startup time of 10-15 seconds for the API server, you may be trying to ...
Peter Amstutz
03:51 pm Bug #5606: trying docker installation again
All in all, most menus require to click "Refresh" a couple of times to get working, but it is now functional.
Next...
Albert Vilella
02:58 pm Bug #5606: trying docker installation again
trying again now...... Albert Vilella
02:41 pm Bug #5606: trying docker installation again
Hi Albert, we have recently (in the past couple of days) merged some substantial improvements to the Docker container... Peter Amstutz
08:14 pm Revision 37971741 (arvados): Merge branch '5626-git-server-hostname' into 4752-docker-websockets
Peter Amstutz
08:12 pm Revision 949e7250 (arvados): 5416: Prefer repos stored locally by uuid, fall back to name. Update...
Tom Clegg
08:12 pm Task #5641 (Resolved): Review 5416-repo-dir-is-uuid
Tom Clegg
08:12 pm Task #5640 (Resolved): Use uuid instead of name as repo path in arv-git-httpd
Tom Clegg
07:39 pm Task #5640 (In Progress): Use uuid instead of name as repo path in arv-git-httpd
Tom Clegg
07:39 pm Task #5640 (Resolved): Use uuid instead of name as repo path in arv-git-httpd
Tom Clegg
07:59 pm Revision 0b990461 (arvados): 5626: Add git_hostname configuration option.
Peter Amstutz
07:55 pm Bug #5627 (Resolved): [SDKs] PySDK file.seek() default whence should be SEET_SET, not SEEK_CUR
Applied in changeset arvados|commit:fd0074f2200bc41bc63be770fffbe2446fb0cc03. Brett Smith
07:00 pm Bug #5627 (Resolved): [SDKs] PySDK file.seek() default whence should be SEET_SET, not SEEK_CUR
Heeeyyyyyy everybody, remember that time when I was grumbling about how our old seek() method had the wrong default w... Brett Smith
07:50 pm Revision fd0074f2 (arvados): 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 incor...
Brett Smith
07:38 pm Task #5639 (Resolved): Update test utils to mock pycurl instead of requests
Tom Clegg
07:37 pm Task #5638 (Resolved): Update keep client library
Tom Clegg
07:36 pm Task #5637 (Resolved): Update package dependencies
Tom Clegg
07:35 pm Task #5636 (Resolved): Fetch remote repo to internal.git if needed during job#save
Tom Clegg
07:34 pm Task #5635 (Resolved): Validate repository name as name, url, or uuid during job#save
Tom Clegg
07:34 pm Task #5634 (Resolved): Update Go SDK
Peter Amstutz
07:33 pm Task #5633 (Resolved): Update Python SDK
Peter Amstutz
07:33 pm Task #5632 (Resolved): Update API server
Peter Amstutz
07:33 pm Task #5631 (Resolved): create Jenkins pipeline
Ward Vandewege
07:33 pm Task #5630 (Resolved): Write tests
Peter Amstutz
07:33 pm Task #5629 (Resolved): Write test script
Ward Vandewege
07:33 pm Task #5628 (Resolved): Meeting about crunch strategy
Peter Amstutz
07:26 pm Bug #5535 (Resolved): [Ops] When creating new shell user accounts, check that there is not an exi...
I looked at the script, and it already does this check. Resolving. Ward Vandewege
07:13 pm Task #5561 (Resolved): Review branch: 5556-collection-show-timeout
Radhika Chippada
07:06 pm Bug #5096 (Resolved): [Workbench] Avoid passing manifest_text around the network too much when up...
Ward Vandewege
07:00 pm Bug #5626 (Resolved): [API] Configuration option to set git server hostname
In current master, the hostname for the git server is always git.(uuid_prefix).arvadosapi.com. The git server hostna... Peter Amstutz
06:59 pm Bug #5625 (Closed): [Docker] Shell container should add user accounts when login permission links...
Peter Amstutz
06:58 pm Story #5624 (New): [API] [Workbench] [Performance] Use object caching to improvement performance ...
Use a "memcached" like architecture to cache objects retrieved / created / updated to reduce the amount of data trans... Radhika Chippada
06:57 pm Feature #4717: [API] [SDKs] Read-only flag on keep_services table as hint to clients not to try t...
Noted #5414 as a "check for conflicts if 5414 isn't merged yet" reminder. Tom Clegg
06:29 pm Story #5623 (Resolved): [Crunch] Specify Crunch2 features and APIs
broad constraints
* support CWL
* support other workflow runners like Queue
* multiple jobs can share nodes
* reu...
Tom Clegg
06:17 pm Bug #5417: [Workbench] Show error condition / refuse to start a pipeline instance if some inputs ...
Detecting it early in a-r-p-i sounds worthwhile too, but I think it's more urgent for _Workbench_ to detect this cond... Tom Clegg
03:10 pm Bug #5417: [Workbench] Show error condition / refuse to start a pipeline instance if some inputs ...
From reading the subject line and the existing a-r-p-i code combined, I'm guessing what we want is that, before it cr... Brett Smith
05:38 pm Bug #5418: [Workbench] Make the brand/root link unclickable when not logged in
I'm curious about the thought process behind this, right now if a first time user is coming in through an anonymous p... Nancy Ouyang
05:34 pm Feature #5375: [workbench] Enable in-browser preview for text files in collections
Looks great! I guess I wasn't very clear, but I'd find it very helpful for Workbench to display a few lines from the ... Nancy Ouyang
05:04 pm Feature #5622 (Resolved): [Workbench] Fix timeout when generating long "list of collections with ...
The pathological case is the empty block, for example:
https://workbench.qr1hi.arvadosapi.com/collections/d41d8c...
Ward Vandewege
04:08 pm Revision d318cc5c (arvados): 4752: Fix failing setup by polling for API server to come up.
Peter Amstutz
03:48 pm Revision 715bd31a (arvados): 5414: Add TestGetWithLocalServiceHint.
Tom Clegg
03:48 pm Revision df7b3255 (arvados): 5414: Clean up Locator / MakeLocator() API.
Tom Clegg
03:42 pm Story #5621 (New): [Documentation] Improve SDK documentation
Today on IRC, sguthrie asked "how can I get the full path of a file in an arvados collection?" and Brett answered (in... Radhika Chippada
03:16 pm Task #5608 (Resolved): Review branch: 5493-getting-started-modal (without the actual html in place)
Radhika Chippada
03:15 pm Bug #5420 (Resolved): [Workbench] Checkbox selections in collections page is wrong when using bac...
Applied in changeset arvados|commit:5781ff2dc48f95b7554259e0210272e7de2d883b. Radhika Chippada
02:50 pm Bug #5420: [Workbench] Checkbox selections in collections page is wrong when using back button
Brett said:
> I'm not so sure the page is being reloaded.
I verified by looking at workbench and api server logs ...
Radhika Chippada
03:09 pm Feature #5247 (Resolved): [Documentation] (recurring) Refresh user documentation
Radhika Chippada
03:08 pm Revision 5781ff2d (arvados): closes #5420
Merge branch '5420-collection-checkbox-selections' Radhika Chippada
02:50 pm Task #5564 (Resolved): Review branch: 5420-collection-checkbox-selections
Radhika Chippada
02:40 pm Bug #5620 (Resolved): [Workbench] Collection#show page search filter is neither cleared nor appli...
* Using Safari or Chrome, access https://workbench.4xphq.arvadosapi.com/collections/4xphq-4zz18-gbv4fbtq6sdvzpd . You... Radhika Chippada
02:38 pm Revision 53aa570d (arvados): 4752: Update documentation related to docker
Peter Amstutz
02:32 pm Revision 2d723078 (arvados): 5420: remove search box autocomplete off update so that this can be ...
Radhika Chippada
02:23 pm Revision 58a4f7eb (arvados): Merge branch 'master' into 5420-collection-checkbox-selections
Radhika Chippada
02:15 pm Feature #4253 (Resolved): [API] Users can create their own arvados-hosted git repositories
Applied in changeset arvados|commit:17014a715c21dd85a02c34b807b8c362c8706cf1. Brett Smith
02:10 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
4253-gitolite-migration-wip LGTM Ward Vandewege
05:47 am Feature #4253: [API] Users can create their own arvados-hosted git repositories
Brett Smith wrote:
> Moving the username check is great. My thinking about splitting the / check is that, if we jus...
Tom Clegg
02:13 pm Revision 17014a71 (arvados): Merge branch '4253-gitolite-migration-wip'
Closes #4253, #5617. Brett Smith
02:13 pm Revision 2a2de566 (arvados): 4253: Add script to migrate existing Gitolite installations.
Brett Smith
02:10 pm Task #3243 (Resolved): add keepproxy
Peter Amstutz
02:09 pm Task #5617 (Resolved): Review 4253-gitolite-migration-wip
Ward Vandewege
02:07 pm Feature #5613: [Docker] Store postgres and gitolite data in a separate data volume from API conta...
I started looking at some of the data directories in the api_server container that would need to be kept separately f... Peter Amstutz
01:56 pm Task #5442 (Resolved): Further define requirements (Peter/Ward)
Ward Vandewege
01:51 pm Revision 156f4973 (arvados): 4752: Use passenger standalone for API server instead of passenger a...
Peter Amstutz
01:50 pm Task #5605 (Resolved): Review 4253-user-repos-wip
Applied in changeset arvados|commit:13abe637d1c33935496df30fdc62417e24e04536. Brett Smith
01:45 pm Revision 13abe637 (arvados): Merge branch '4253-user-repos-wip'
Refs #4253. Closes #5605. Brett Smith
01:43 pm Revision 35a47705 (arvados): 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 g...
Brett Smith
01:43 pm Revision 39b48294 (arvados): 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 en...
Brett Smith
01:43 pm Revision 5af08542 (arvados): 4253: Add Workbench interface to create repositories.
Commit includes contributions from Tom Clegg. Brett Smith
01:42 pm Revision fd3278f5 (arvados): 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 usern...
Brett Smith
01:15 pm Bug #5612 (Resolved): [Docker] Can't run crunch jobs after stopping and restarting containers.
Applied in changeset arvados|commit:384a67905e6d8cfdee305244c7f163e229f8ab84. Peter Amstutz
01:09 pm Revision 384a6790 (arvados): Merge branch '5612-munge-docker-cleanup' closes #5612
Peter Amstutz

03/31/2015

09:37 pm Bug #5612: [Docker] Can't run crunch jobs after stopping and restarting containers.
5612-munge-docker-cleanup LGTM Ward Vandewege
08:42 pm Bug #5612 (In Progress): [Docker] Can't run crunch jobs after stopping and restarting containers.
Peter Amstutz
03:16 pm Bug #5612 (Resolved): [Docker] Can't run crunch jobs after stopping and restarting containers.
Peter Amstutz
09:36 pm Task #5618 (Resolved): Review 5612-munge-docker-cleanup
Ward Vandewege
09:15 pm Task #5618 (Resolved): Review 5612-munge-docker-cleanup
Peter Amstutz
09:13 pm Revision 9cebd15a (arvados): 5612: Wrap munge with startup script that cleans up /var/run/munge o...
sockets and pidfiles. Can now run jobs after stopping and restarting
containers.
Peter Amstutz
09:05 pm Task #5617 (Resolved): Review 4253-gitolite-migration-wip
Diff it against @update-gitolite.rb@—there's a lot of shared code. Brett Smith
09:02 pm Revision 749c0d9f (arvados): 4253: Add script to migrate existing Gitolite installations.
Brett Smith
08:51 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
commit:a89c721 is good to merge. Thank you. Brett Smith
07:49 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Brett: thanks for your patience, the third comment above uncovered a bug in code which was uncovered once the test is... Radhika Chippada
05:29 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Reviewing commit:1f5a673.
* The changes to ApplicationController are no longer needed now that the modal is includ...
Brett Smith
02:23 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Brett: Made all the suggested updates, except the placement of Next and Prev buttons. When these buttons are placed u... Radhika Chippada
08:47 pm Bug #5502 (Resolved): [Node Manager] Add local SSD to compute nodes on GCP
Ward Vandewege
08:45 pm Task #5576 (Resolved): Have Packer run get-meta-data.py before arvados-compute-ping-controller.rb
Ward Vandewege
07:55 pm Revision 8b95d2e5 (arvados): Merge branch 'master' into 5420-collection-checkbox-selections
Radhika Chippada
07:40 pm Revision 11ad4d96 (sso-provider): 5412: Add support for authentication through LDAP.
Peter Amstutz
07:37 pm Task #5616 (Resolved): Review 5412-ldap-support
Peter Amstutz
07:36 pm Task #5446 (Resolved): Use LDAP OmniAuth gem
Peter Amstutz
07:35 pm Feature #5412 (In Progress): [SSO] Support LDAP-only configuration
Peter Amstutz
07:28 pm Revision a89c721e (arvados): 5493: one more stale update
Radhika Chippada
07:21 pm Revision e3c562df (arvados): 5493: test uncovered an issue with getting_started_shown handling; f...
Radhika Chippada
07:00 pm Feature #5414: [Keep] Use data stored remotely (not in local keepstore)
Review comments:
* Mostly looks good and I was able to follow the updates towards the syntax and comment updates. ...
Radhika Chippada
05:32 pm Feature #5414: [Keep] Use data stored remotely (not in local keepstore)
Comments on https://arvados.org/projects/arvados/wiki/Keep_S3_gateway
Does @POST /collection@ use the API token of...
Peter Amstutz
06:51 pm Revision 17379ed7 (arvados): Merge branch 'master' into 5493-getting-started-modal
Radhika Chippada
06:22 pm Story #5615 (New): [Documentation] Pipeline/job Log tabs should link to (new) doc page(s) about h...
Examples wrt graphs
* How do I know I'm using swap / don't have enough RAM? (And how do I fix it?)
* How do I know ...
Tom Clegg
04:25 pm Bug #5614 (New): [Workbench] 504 error returned when trying to create a large new collection
URL creating the timeout:
https://workbench.tb05z.arvadosapi.com/combine_selected?action_data={%22current_project_uu...
Sarah Guthrie
03:35 pm Task #5603 (In Progress): Review 5414-keep-service-hints
Peter Amstutz
03:31 pm Revision c6bc1e96 (arvados): 4253: Even stricter about accepted repository names during setup.
Brett Smith
03:30 pm Task #5480 (Resolved): Update Workbench repository management UI
Brett Smith
03:29 pm Feature #5613 (Closed): [Docker] Store postgres and gitolite data in a separate data volume from ...
Store data separately from code. Add a "arvdock update" command that downloads new application images, but keeps the... Peter Amstutz
03:29 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
Thanks for the improvements. I have rebased on top of master to account for #5416 and squash some of your commits. ... Brett Smith
03:22 pm Revision 898bbe80 (arvados): 4253: Even stricter about accepted repository names during setup.
Brett Smith
03:20 pm Bug #5539 (Resolved): [Docker] UX improvements
Applied in changeset arvados|commit:3353ab9554dc5dfa647dd767b7b2623adcf753ab. Peter Amstutz
03:18 pm Revision 3353ab95 (arvados): Merge branch '5539-better-docker' closes #5539
Peter Amstutz
03:17 pm Bug #5425 (Resolved): [Crunch] SLURM Node failure
Re-ran the original job, which completed successfully. Marking this as resolved. Peter Amstutz
03:14 pm Revision 8be6352f (arvados): 4253: Use same repo name logic whether or not user already existed b...
Tom Clegg
03:14 pm Revision 8c7fb5f1 (arvados): 4253: Merge Repository permission requirements of #4253 and #5416.
Brett Smith
03:14 pm Revision cd28c9db (arvados): 4253: Add tests for renaming repos.
Brett Smith
03:14 pm Revision 9a6c3a5b (arvados): 4253: Add Workbench interface to create repositories.
Brett Smith
03:13 pm Story #5257 (Resolved): [CWL] write draft 2 spec
https://common-workflow-language.github.io/#/ Peter Amstutz
03:12 pm Task #5270 (Resolved): write Draft 2 spec
Peter Amstutz
03:12 pm Task #5443 (Resolved): Discuss CWL integration plan (Tom/Peter)
Peter Amstutz
01:56 pm Revision 1f5a6730 (arvados): Merge branch 'master' into 5493-getting-started-modal
Radhika Chippada
01:55 pm Revision 4108d902 (arvados): 5493: improve test to verify Next button disables when last page is ...
Radhika Chippada
01:23 pm Revision 920a201e (arvados): 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 usern...
Brett Smith
01:23 pm Revision dbf4d66b (arvados): 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 en...
Brett Smith
01:23 pm Revision b68feeee (arvados): 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 g...
Brett Smith
01:51 am Revision 15303f9c (arvados): 5493: getting_started modal is served from layout html
Radhika Chippada
12:34 am Task #5487 (In Progress): Click job script_name to see source code (plain)
Tom Clegg

03/30/2015

10:26 pm Task #5488 (Resolved): Review 5416-arv-git-httpd
Tom Clegg
10:25 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
Comments @ commit:7ca7892, accompanied by commits on 4253-user-repos-wip (which you're welcome to modify/rebase/rejec... Tom Clegg
08:07 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
4253-user-repos-wip now at commit:7ca7892 with the Workbench interface added. Brett Smith
10:05 pm Revision d66803ae (arvados): 4253: Add tests for renaming repos.
Tom Clegg
09:12 pm Revision ea103bd3 (arvados): 4253: Add .git suffix as input-group-addon.
Tom Clegg
09:11 pm Revision 585a8655 (arvados): 4253: Clear modal state when [re]opening.
Tom Clegg
08:42 pm Revision 0ce47259 (arvados): 4253: Use same repo name logic whether or not user already existed b...
Tom Clegg
08:42 pm Revision ebd5b4a2 (arvados): 4253: Bikeshed error messages.
Tom Clegg
08:10 pm Revision 7ca7892c (arvados): 4253: Fixup repository UI with note about clone delay.
Brett Smith
08:06 pm Revision 5ec73064 (arvados): 4253: Add Workbench interface to create repositories.
Brett Smith
07:57 pm Revision 40ee9916 (arvados): Merge branch '5416-arv-git-httpd' refs #5416
Tom Clegg
07:57 pm Revision 40ee9916 (arvados-dev): Merge branch '5416-arv-git-httpd' refs #5416
Tom Clegg
07:56 pm Revision db36b8ad (arvados): Merge branch '5416-arv-git-httpd' refs #5416
Tom Clegg
07:42 pm Revision 7a54e370 (arvados): 5493: do not show "Public pipelines and datasets" link in help menu ...
Radhika Chippada
07:15 pm Revision b0a3771f (arvados): 5493: update tests to use updated fixture active_no_prefs_profile_no...
Radhika Chippada
06:28 pm Revision 27106389 (arvados): 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 g...
Brett Smith
05:38 pm Task #5576 (In Progress): Have Packer run get-meta-data.py before arvados-compute-ping-controller.rb
Ward Vandewege
05:13 pm Task #5576 (Resolved): Have Packer run get-meta-data.py before arvados-compute-ping-controller.rb
Ward Vandewege
12:15 am Task #5576 (In Progress): Have Packer run get-meta-data.py before arvados-compute-ping-controller.rb
This is still an issue on the latest su92l compute node. Brett Smith
05:14 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Radhika Chippada wrote:
> Some review comments. Several of these are trivial and please feel free to ignore if you p...
Tom Clegg
02:49 am Feature #5416: [API] Clone git repositories without using an SSH private key
Some review comments. Several of these are trivial and please feel free to ignore if you prefer.
* Install guide u...
Radhika Chippada
05:03 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Radhika Chippada wrote:
> * The curoverse welcome page is updated (and manually tested locally) in curoverse-private...
Brett Smith
04:52 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Radhika Chippada wrote:
> * The workbench dialog is implemented in arvados repository branch 5493-getting-started-mo...
Brett Smith
05:00 pm Revision d843787b (arvados): 5416: Merge branch 'master' into 5416-arv-git-httpd
Tom Clegg
05:00 pm Revision 38bc4c0e (arvados): 5416: Improve variable names & filenames. Report original error if g...
Tom Clegg
05:00 pm Revision ce4e75d0 (arvados): 5416: Add permission-denied tests.
Tom Clegg
04:10 pm Revision f9c00088 (arvados-dev): fix minor bugly in perms
reminder: bugly = bug that makes something look ugly :) Sitaram Chamarty
03:56 pm Task #5608 (In Progress): Review branch: 5493-getting-started-modal (without the actual html in p...
Brett Smith
01:16 pm Task #5608 (Resolved): Review branch: 5493-getting-started-modal (without the actual html in place)
This is to review the wiring of getting_started modal into workbench navigation. The modal does not yet contain the a... Radhika Chippada
03:51 pm Task #5605 (In Progress): Review 4253-user-repos-wip
Tom Clegg
03:44 pm Bug #5420: [Workbench] Checkbox selections in collections page is wrong when using back button
Radhika Chippada wrote:
> Implementation notes:
>
> * Adding id to checkboxes resolved the issue in /collections ...
Brett Smith
03:23 pm Task #5564 (In Progress): Review branch: 5420-collection-checkbox-selections
Brett Smith
03:06 pm Revision 6c6a37bf (arvados): 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 en...
Brett Smith
03:04 pm Revision 2c65feef (arvados): 4253: Fixup crunch-dispatch again.
Brett Smith
02:38 pm Feature #5414: [Keep] Use data stored remotely (not in local keepstore)
5414-keep-service-hints branch @ commit:9e91179:
* Support @+K@uuid@ in Python library
* Support @+K@uuid@ and @+...
Tom Clegg

03/29/2015

10:37 pm Task #5555 (Resolved): Update documentation for new repository names (e.g., 'you/you')
Brett Smith
10:36 pm Revision 2013ac24 (arvados): 4253: Fixup documentation.
Brett Smith
10:29 pm Task #5479 (Resolved): Update repository permission rules
Brett Smith
08:33 pm Bug #5607 (Closed): trying docker installation again
Installed via the docker installation on Sun 29 March 2015 on an Ubuntu 14.04.2 laptop with docker 1.5. The logs don'... Albert Vilella
08:33 pm Bug #5606 (New): trying docker installation again
Installed via the docker installation on Sun 29 March 2015 on an Ubuntu 14.04.2 laptop with docker 1.5. The logs don'... Albert Vilella
06:26 pm Revision dd274916 (arvados): 4253: Fixup crunch-dispatch.
Brett Smith
05:50 pm Revision f71727b4 (arvados): 4253: Fixup repository documentation.
Brett Smith
05:46 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
4253-user-repos-wip is up for review. Following our Gitolite changes, this implements the necessary changes on the A... Brett Smith
05:43 pm Task #5605 (Resolved): Review 4253-user-repos-wip
Brett Smith
05:40 pm Revision 75feaad8 (arvados): 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 usern...
Brett Smith
05:29 pm Feature #3818: [API] Discovery document schema should include whether field on resource is writab...
I started going down this path to try to address an issue I was encountering in #4253. I eventually found out that W... Brett Smith
01:26 pm Revision 1f225f2c (arvados): 5493: add pager-count where text such as "1 of 10" is shown.
Radhika Chippada
03:25 am Bug #5604 (Rejected): [Workbench] Fiddlesticks when going back from collection#show to collection...
* Go to /collections page
* Enter text (for example, alice in staging)
* Click on the Show icon to the left of ...
Radhika Chippada
01:58 am Task #5603 (Resolved): Review 5414-keep-service-hints
Tom Clegg
01:58 am Task #5458 (Resolved): Update keep clients to heed proxy-uuid hints
Tom Clegg
12:31 am Revision 9e911791 (arvados): 5414: Add client support for Keep service hints.
Also, some incidental improvements in nearby code:
* Consistent logging in keepproxy, with one reusable logging stat...
Tom Clegg

03/28/2015

07:19 am Revision 90c7763b (arvados): 5414: Add client support for Keep service hints.
Tom Clegg

03/27/2015

11:45 pm Revision dd532a66 (arvados): Merge branch 'master' into 5493-getting-started-modal
Radhika Chippada
11:44 pm Revision e59bc286 (arvados): 5493: remove the helper method update_getting_started_shown_user_pre...
Radhika Chippada
09:45 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Implementation notes:
* The workbench dialog is implemented in arvados repository branch 5493-getting-started-moda...
Radhika Chippada
09:27 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Update: *Modal* with pre/next buttons now on branch by Radhika. I will implement HTML content for model over the next... Nancy Ouyang
12:07 am Feature #5493 (In Progress): [Workbench] Add "Getting Started" modal inside Workbench
Radhika Chippada
09:16 pm Revision d176328c (arvados): Merge branch '5502-node-manager-gce-ssd-wip'
Refs #5502. Brett Smith
08:52 pm Revision 7ec30c76 (arvados): 5493: add test for the getting_started help menu item.
Radhika Chippada
06:42 pm Story #5585 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
Ward Vandewege
06:38 pm Feature #5582 (New): [API] [Workbench] Add read-only ("locked") flag to projects
Tom Clegg
06:19 pm Bug #3249 (Resolved): [Workbench] middle click in ssh-key box closes the entire dropdown when a n...
There's no SSH box in that dropdown any more! Tom Clegg
06:16 pm Feature #5414 (In Progress): [Keep] Use data stored remotely (not in local keepstore)
Tom Clegg
06:16 pm Bug #5474 (Resolved): [Workbench] WebsocketTest#test_live_log_charting is not reliable
Tom Clegg
06:11 pm Story #5547 (Resolved): [CWL] Fix cwltool packaging
Peter Amstutz
06:10 pm Task #5574 (Resolved): Add an at-boot script to Packer GCE images to format local SSD and mount i...
Ward Vandewege
05:29 pm Task #5574 (In Progress): Add an at-boot script to Packer GCE images to format local SSD and moun...
Ward Vandewege
06:10 pm Bug #5502: [Node Manager] Add local SSD to compute nodes on GCP
5502-node-manager-gce-ssd-wip LGTM Ward Vandewege
05:29 pm Bug #5502: [Node Manager] Add local SSD to compute nodes on GCP
5502-compute-cleanups-wip LGTM thanks! Ward Vandewege
06:09 pm Task #5577 (Resolved): Review 5502-node-manager-gce-ssd-wip
Ward Vandewege
05:51 pm Revision 663d0245 (arvados): 5493: update user_profile test to expect getting_started modal for u...
also, add one more user scenario where prefs exists with getting_started_shown but no profile. Radhika Chippada
05:30 pm Story #5554: [API] Delete crunch job log messages from logs table after the jobs finish
Radhika Chippada wrote:
> While addressing #5534 (Log tab takes too long to load ...), I noticed that the pipeline i...
Tom Clegg
05:29 pm Task #5576 (Resolved): Have Packer run get-meta-data.py before arvados-compute-ping-controller.rb
Ward Vandewege
01:51 pm Task #5576 (In Progress): Have Packer run get-meta-data.py before arvados-compute-ping-controller.rb
Ward Vandewege
05:28 pm Task #5580 (Resolved): Review puppet branch 5502-compute-cleanups-wip
Ward Vandewege
05:23 pm Task #5580 (Resolved): Review puppet branch 5502-compute-cleanups-wip
Brett Smith
03:42 pm Task #5579 (Resolved): Review puppet branch 4253-user-git-repos-wip
Ward Vandewege
02:30 pm Task #5579 (In Progress): Review puppet branch 4253-user-git-repos-wip
Ward Vandewege
01:56 pm Task #5579 (Resolved): Review puppet branch 4253-user-git-repos-wip
Brett Smith
03:41 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
Brett Smith wrote:
> Ward Vandewege wrote:
> > * arv = Arvados.new( { :suppress_ssl_warnings => false } )
> >
...
Ward Vandewege
03:25 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
Ward Vandewege wrote:
> * arv = Arvados.new( { :suppress_ssl_warnings => false } )
>
> Since you added code to ...
Brett Smith
02:30 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
reviewing 4253-user-git-repos-wip:
* arv = Arvados.new( { :suppress_ssl_warnings => false } )
Since you added...
Ward Vandewege
01:39 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
Ward Vandewege wrote:
> reviewing 4253-gitolite3-wip:
>
> * is it necessary to call the 'gitolite setup' exec on ...
Brett Smith
01:35 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
reviewing 4253-gitolite3-wip:
* is it necessary to call the 'gitolite setup' exec on every run?
otherwise, LGTM
Ward Vandewege
01:54 pm Revision 1c186394 (arvados): Merge branch 'master' into 5420-collection-checkbox-selections
Radhika Chippada
01:52 pm Revision b10a9487 (arvados): 5493: (thanks to tom) modal paging is awesome.
Radhika Chippada
01:37 pm Task #5578 (Resolved): Review Puppet branch 4253-gitolite3-wip
Ward Vandewege
01:35 pm Task #5578 (In Progress): Review Puppet branch 4253-gitolite3-wip
Ward Vandewege
01:35 pm Task #5578 (Resolved): Review Puppet branch 4253-gitolite3-wip
Ward Vandewege
01:30 pm Task #5578 (In Progress): Review Puppet branch 4253-gitolite3-wip
Ward Vandewege
01:25 am Revision 53fac68b (arvados): 5493: fix a bug in user profile handling where any pre-existing pref...
Radhika Chippada

03/26/2015

10:05 pm Task #5578 (Resolved): Review Puppet branch 4253-gitolite3-wip
Brett Smith
07:07 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Suggestion for @app/assets/javascripts/modal_pager.js@... Tom Clegg
02:22 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
h4. Implementation notes / details
No notification bar ("new here?" etc). Instead, show the modal itself if it has...
Tom Clegg
06:55 pm Revision 5380c722 (arvados): 5493: wiring for 'getting started' popup
Radhika Chippada
06:44 pm Task #5574: Add an at-boot script to Packer GCE images to format local SSD and mount it to /tmp
The new Packer image prepared for this boots fine, but doesn't actually do anything with the attached storage. Brett Smith
02:55 pm Task #5574 (Resolved): Add an at-boot script to Packer GCE images to format local SSD and mount i...
The disk is at @/dev/disk/by-id/google-FOO@, where @FOO@ is a string we can specify at node creation time.
/tmp is...
Brett Smith
05:59 pm Task #5575 (Resolved): Teach Node Manager to specify a full disk list on node creation
Brett Smith
04:35 pm Task #5575 (In Progress): Teach Node Manager to specify a full disk list on node creation
Brett Smith
03:24 pm Task #5575 (Resolved): Teach Node Manager to specify a full disk list on node creation
Disk list should look roughly like:... Brett Smith
05:58 pm Bug #5502: [Node Manager] Add local SSD to compute nodes on GCP
5502-node-manager-gce-ssd-wip is up for review. It manually specifies full information about disks that should be at... Brett Smith
01:16 pm Bug #5502 (In Progress): [Node Manager] Add local SSD to compute nodes on GCP
Brett Smith
05:55 pm Task #5577 (Resolved): Review 5502-node-manager-gce-ssd-wip
See #5502 comments for background. Brett Smith
05:31 pm Revision 5dfdd042 (arvados): 5502: Node Manager attaches a local SSD to GCE compute nodes.
This is the best option to provide temporary working space for compute
work on GCE.
Brett Smith
04:29 pm Revision b8261deb (arvados): 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 nam...
Brett Smith
04:19 pm Task #5576 (Resolved): Have Packer run get-meta-data.py before arvados-compute-ping-controller.rb
The latter needs the former to install the ping URL file before it can do anything. The current setup works, but it ... Brett Smith
01:15 pm Task #5478 (Resolved): Update repository name rules
Brett Smith

03/25/2015

11:05 pm Bug #5556 (Resolved): [Workbench] Timeout error on collection#show for a collection with large ma...
Applied in changeset arvados|commit:46b124cc766e4e35e40c1c3e2c1b388816aa682a. Radhika Chippada
07:59 pm Bug #5556: [Workbench] Timeout error on collection#show for a collection with large manifest text
Brett wrote:
> The new test confirms that toggling the new configuration setting doesn't break the API client. How...
Radhika Chippada
05:54 pm Bug #5556: [Workbench] Timeout error on collection#show for a collection with large manifest text
Reviewing commit:655469d
The new test confirms that toggling the new configuration setting doesn't break the API c...
Brett Smith
02:15 pm Bug #5556 (In Progress): [Workbench] Timeout error on collection#show for a collection with large...
Radhika Chippada
05:50 am Bug #5556: [Workbench] Timeout error on collection#show for a collection with large manifest text
Workbench with profiling enabled shows the logs#index API call taking longer than anything else, too.
I'm guessing...
Tom Clegg
11:00 pm Revision 46b124cc (arvados): closes #5556
Merge branch '5556-collection-show-timeout' Radhika Chippada
08:13 pm Bug #5565 (Resolved): [Workbench] Show (anonymous-appropriate) breadcrumbs when rendering layout ...
As an anonymous user is navigating through a public project, navigating to a collection or pipeline instance results ... Radhika Chippada
07:47 pm Revision d80a6ec2 (arvados): Merge branch 'master' into 5556-collection-show-timeout
Radhika Chippada
07:34 pm Task #5557 (Resolved): Review branch: 5247-anonymous-doc
Radhika Chippada
05:10 pm Task #5557 (In Progress): Review branch: 5247-anonymous-doc
Brett Smith
07:05 pm Task #5248 (Resolved): [Documentation] Add public projects (anonymous access) to documentation.
Applied in changeset arvados|commit:4f6b424e682892109740f6cb6b8f1af2612e7536. Radhika Chippada
06:59 pm Revision 4f6b424e (arvados): refs #5247
closes #5248
Merge branch '5247-anonymous-doc'
Radhika Chippada
06:58 pm Revision 5faa0d43 (arvados): 5247: couple more caption updates.
Radhika Chippada
06:51 pm Feature #5247: [Documentation] (recurring) Refresh user documentation
Radhika Chippada wrote:
> Brett: made all the suggested updates. As for the last comment, I left the Advanced tab sl...
Brett Smith
06:21 pm Feature #5247: [Documentation] (recurring) Refresh user documentation
Brett: made all the suggested updates. As for the last comment, I left the Advanced tab slide as is because once I ex... Radhika Chippada
05:30 pm Feature #5247: [Documentation] (recurring) Refresh user documentation
Reviewing commit:b01a47b
* The intro paragraph says, "By visiting this project, you can see what an Arvados projec...
Brett Smith
06:26 pm Revision a1a9b820 (arvados): Merge branch 'master' into 5556-collection-show-timeout
Radhika Chippada
06:19 pm Revision a7b60f7e (arvados): 5247: some caption updates.
Radhika Chippada
05:48 pm Revision 24584338 (arvados): 5416: Fix overly sensitive error message regexp.
Tom Clegg
05:37 pm Revision 90198dc6 (arvados): Merge branch 'master' into 5247-anonymous-doc
Radhika Chippada
05:32 pm Task #5561 (In Progress): Review branch: 5556-collection-show-timeout
Brett Smith
02:20 pm Task #5561 (Resolved): Review branch: 5556-collection-show-timeout
Radhika Chippada
05:30 pm Bug #5534 (Resolved): [Workbench] Log tab takes too long to load with large logs
Applied in changeset arvados|commit:8ddb457318d535fadad9a5554e2944cec96b17df. Radhika Chippada
03:53 pm Bug #5534: [Workbench] Log tab takes too long to load with large logs
LGTM Peter Amstutz
05:30 pm Story #3762 (Resolved): [Keep] Process entries on the current "delete" list.
Applied in changeset arvados|commit:0d1971f04c8f0674ff8d94bae5dbb7f6b94e7f5f. Radhika Chippada
03:53 pm Story #3762: [Keep] Process entries on the current "delete" list.
LGTM Peter Amstutz
05:26 pm Revision 8ddb4573 (arvados): closes #5534
Merge branch '5534-limit-log-lines' Radhika Chippada
05:25 pm Revision d81ed360 (arvados): Merge branch 'master' into 5534-limit-log-lines
Radhika Chippada
05:24 pm Revision 0d1971f0 (arvados): closes #3762
Merge branch '3762-delete-list-worker' Radhika Chippada
05:23 pm Revision 659a8c75 (arvados): Merge branch 'master' into 3762-delete-list-worker
Radhika Chippada
05:18 pm Task #5564 (Resolved): Review branch: 5420-collection-checkbox-selections
Radhika Chippada
05:15 pm Revision abd56447 (arvados): Merge branch 'master' into 5420-collection-checkbox-selections
Radhika Chippada
05:15 pm Revision a230c411 (arvados): 5420: address checkbox selection caching issue with Safari and Chrome.
Radhika Chippada
05:14 pm Bug #5420: [Workbench] Checkbox selections in collections page is wrong when using back button
Implementation notes:
* Adding id to checkboxes resolved the issue in /collections page (verified before and after...
Radhika Chippada
03:07 pm Bug #5420 (In Progress): [Workbench] Checkbox selections in collections page is wrong when using ...
Radhika Chippada
05:06 pm Task #5444 (Resolved): Confirm gitolite integration plan looks OK
Settled through in-office conversation. We know the way forward. Brett Smith
03:55 pm Bug #5562 (Resolved): [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
When there are lots of keep clients on one node sending or receiving lots of data to the same keep server on another ... Peter Amstutz
03:55 pm Task #5512 (Resolved): Review 4253-user-usernames-wip
Applied in changeset arvados|commit:febb804129f39963722e530a394f36367220d4b5. Brett Smith
03:53 pm Task #5551 (Resolved): Review branch: 5534-limit-log-lines
Peter Amstutz
03:51 pm Revision febb8041 (arvados): Merge branch '4253-user-usernames-wip'
Refs #4253. Closes #5512. Brett Smith
03:51 pm Task #5537 (Resolved): Review 3762-delete-list-worker
Peter Amstutz
03:48 pm Revision 50be38a0 (arvados): Added a comment to volume Delete() about race condition.
Peter Amstutz
03:21 pm Revision 9cb7b087 (arvados): 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. ...
Brett Smith
03:21 pm Revision 9aa11569 (arvados): 4253: Clean up some user setup methods.
As much as possible, use more methods provided by Rails, rather than
reimplementing them ourselves.
Brett Smith
03:21 pm Revision ff8721dd (arvados): 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 valida...
Brett Smith
03:18 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
commit:fa2abe9 of 4253-user-usernames-wip LGTM Peter Amstutz
02:17 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
Peter Amstutz wrote:
> I'm getting an error running the migration. Maybe what's happening is that after ActiveRecor...
Brett Smith
01:42 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
I'm getting an error running the migration. Maybe what's happening is that after ActiveRecord::RecordNotUnique is ra... Peter Amstutz
03:02 pm Revision 655469d6 (arvados): 5556: add test to invoke collection#show with and without include_ac...
Radhika Chippada
02:16 pm Revision fa2abe96 (arvados): 4253: Fixup migration by having Rails check for duplicate usernames.
Brett Smith
02:16 pm Revision 4fce5c64 (arvados): 5556: Added select() to @logs in CollectionsController#show to avoid...
Also, added Accept-Encoding request header in workbench request to api server. Radhika Chippada
05:31 am Bug #5560 (New): [DRAFT] [API] Good API for accessing the old_ and new_attributes in Logs table p...
Problems with the @old_attributes@ and @new_attributes@ hashes in the properties hash:
* They don't look quite close...
Tom Clegg

03/24/2015

09:37 pm Revision 3d4ac757 (arvados-dev): run-tests.sh should advertise the availability of services/arv-g...
refs #5416 Ward Vandewege
09:33 pm Task #5552 (Resolved): Review 5539-better-docker
Ward Vandewege
08:15 pm Task #5552 (In Progress): Review 5539-better-docker
Ward Vandewege
02:34 pm Task #5552 (Resolved): Review 5539-better-docker
Peter Amstutz
09:33 pm Bug #5539: [Docker] UX improvements
Reviewing 5539-better-docker: LGTM
Ward Vandewege
08:53 pm Revision 8505cb40 (arvados): Documentation: installation pages improvements. Be clear about the
purpose of each installation method, and its limitations.
No issue #
Ward Vandewege
08:23 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Indeed, it seems BasicAuth() is new in Go 1.4. Added BasicAuth compatibility shim for go1.3 in commit:1f3874e. Now at... Tom Clegg
04:55 pm Feature #5416: [API] Clone git repositories without using an SSH private key
reviewing 5416-arv-git-httpd
# git.curoverse.com/arvados.git/services/arv-git-httpd
/tmp/tmp.o64n3HhKy5/src/git.c...
Ward Vandewege
08:22 pm Revision 452dace2 (arvados): 5416: Merge remote-tracking branch 'origin/5416-arv-git-httpd' into ...
Tom Clegg
08:20 pm Revision d1ad9601 (arvados): 5416: gofmt formatting changes.
Tom Clegg
08:19 pm Revision 1f3874e8 (arvados): 5416: Add BasicAuth compatibility shim for go1.3.
Tom Clegg
07:29 pm Feature #5513 (Resolved): Node manager should always have one node idle
Done! Tom Clegg
07:23 pm Feature #5494: [Documentation] Run an uncommitted script straight from a working directory using ...
http://doc.arvados.org/user/topics/running-pipeline-command-line.html looks rather out of date and doesn't address th... Tom Clegg
06:36 pm Feature #5247: [Documentation] (recurring) Refresh user documentation
About 5247-anonymous-doc branch implementation:
The anonymous documentation is added in the 'Getting started' guid...
Radhika Chippada
02:51 pm Feature #5247 (In Progress): [Documentation] (recurring) Refresh user documentation
Radhika Chippada
06:34 pm Task #5557 (Resolved): Review branch: 5247-anonymous-doc
Radhika Chippada
06:28 pm Revision b01a47b2 (arvados): 5247: white space
Radhika Chippada
06:27 pm Revision 923077ab (arvados): 5247: anonymous access documentation
Radhika Chippada
04:38 pm Task #5508 (Closed): Make sure repository fetch_url is properly updated on rename
This is going to become a non-issue because we're getting rid of the URL columns. Brett Smith
03:38 pm Bug #4953 (Resolved): [Workbench] [dup] Time out error for renaming a collection with a lot (300+...
This issue as such is resolved by #5218, where the manifest_text is not sent to server when only a name (or descripti... Radhika Chippada
03:28 pm Bug #5556 (Resolved): [Workbench] Timeout error on collection#show for a collection with large ma...
Viewing this collection results in api server timeout error. In the last one week, I saw timeout errors at least 75% ... Radhika Chippada
03:25 pm Task #5555 (Resolved): Update documentation for new repository names (e.g., 'you/you')
Brett Smith
03:18 pm Story #5257 (In Progress): [CWL] write draft 2 spec
Peter Amstutz
03:18 pm Story #5554: [API] Delete crunch job log messages from logs table after the jobs finish
While addressing #5534 (Log tab takes too long to load ...), I noticed that the pipeline instance tb05z-d1hrv-lx5w1pn... Radhika Chippada
03:11 pm Story #5554 (Resolved): [API] Delete crunch job log messages from logs table after the jobs finish
After a job completes, the full job log is written to Keep, so it isn't necessary to leave the (possibly incomplete) ... Radhika Chippada
03:18 pm Task #5270 (In Progress): write Draft 2 spec
Peter Amstutz
03:18 pm Task #5443 (In Progress): Discuss CWL integration plan (Tom/Peter)
Peter Amstutz
03:15 pm Task #5509 (Resolved): Review 5425-set-docker-memory-limits
Peter Amstutz
02:50 pm Task #5248 (In Progress): [Documentation] Add public projects (anonymous access) to documentation.
Radhika Chippada
02:40 pm Task #5249 (Resolved): Write up implementation summary on wiki
Tom Clegg
02:40 pm Task #5507 (Resolved): Review 5198-remote-link-ctrl-click
Tom Clegg
02:36 pm Task #3682 (Resolved): Implement TrashCollector
Implemented as RunPullWorker go routine. Radhika Chippada
02:32 pm Revision e97d70a1 (arvados): 5539: Require that the user update resolv.conf, and use FQDN (api.de...
workbench.dev.arvados) to refer to services more consistently. Peter Amstutz
02:19 pm Bug #5549 (Rejected): [Workbench] [Duplicate] Files tab doesn't update after upload
Duplicate of #4770 Radhika Chippada
01:21 pm Bug #5549 (Rejected): [Workbench] [Duplicate] Files tab doesn't update after upload
Peter Amstutz
02:12 pm Task #5532 (Resolved): make sure the get.arvados.org script downloads the keepproxy image too
Ward Vandewege
02:12 pm Feature #5529 (Resolved): [Docker] Add keepproxy to the docker images
Ward Vandewege
02:03 pm Task #5551 (Resolved): Review branch: 5534-limit-log-lines
Radhika Chippada
02:01 pm Bug #5534 (In Progress): [Workbench] Log tab takes too long to load with large logs
This pipeline instance is still running as of this writing, so far running for 1 day and 14 hours and 5+ minutes. So ... Radhika Chippada
01:58 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
Peter Amstutz wrote:
> Disallowing dots (periods), dashes, and underscores in usernames seems a bit harsh. Is there...
Brett Smith
01:54 pm Revision aa9dc786 (arvados): The easy-docker-install method should also get the keepproxy and sso
docker images.
closes #5529
Ward Vandewege
01:54 pm Revision aa9dc786 (arvados-dev): The easy-docker-install method should also get the keepproxy and...
docker images.
closes #5529
Ward Vandewege
01:49 pm Revision a329f06e (arvados): 5534: When a pipeline has long running jobs with hundreds of thousan...
fetching all those lines. Limiting the number of log lines retrieved helped resolve this issue. Using limit size of 2... Radhika Chippada
01:30 pm Bug #5536 (Resolved): [Keepproxy] keepproxy should retry on DiscoverKeepServers() failure or emp...
Applied in changeset arvados|commit:e809173d733bc78ce7877f6ed9711b29fd7cee0e. Peter Amstutz
01:21 pm Bug #5536: [Keepproxy] keepproxy should retry on DiscoverKeepServers() failure or empty list
5536-retry-discover-servers LGTM Ward Vandewege
01:30 pm Revision 70ab42cb (arvados): Merge branch 'master' into 5539-better-docker
Peter Amstutz
01:29 pm Revision e809173d (arvados): Merge branch '5536-retry-discover-servers' closes #5536
Peter Amstutz
01:21 pm Task #5542 (Resolved): Review 5536-retry-discover-servers
Ward Vandewege
02:36 am Revision 3f99a8c6 (arvados): 5539: Retry keepproxy if it quits (this happens when restarting the ...
the api server isn't ready yet, so need to keep trying). Peter Amstutz
02:08 am Story #5548 (Resolved): [CWL/OPS] Jenkins runs cwltool tests
Peter Amstutz
02:08 am Story #5547 (Resolved): [CWL] Fix cwltool packaging
See https://github.com/common-workflow-language/common-workflow-language/issues/28
For some reason, "python setup....
Peter Amstutz

03/23/2015

09:12 pm Revision 78691191 (arvados): 5539: Arvados-in-Docker improvements
* arvdock start now restarts existing containers instead of deleting them. Use arvdock reset to delete the container... Peter Amstutz
09:11 pm Bug #5539 (In Progress): [Docker] UX improvements
Peter Amstutz
04:04 pm Bug #5539 (Resolved): [Docker] UX improvements
* Along with... Peter Amstutz
08:54 pm Task #5532 (In Progress): make sure the get.arvados.org script downloads the keepproxy image too
Ward Vandewege
12:19 am Task #5532 (Resolved): make sure the get.arvados.org script downloads the keepproxy image too
Ward Vandewege
08:49 pm Revision 5cdd9c17 (arvados-dev): Merge branch '5529-build-and-test-keepproxy-docker-image'
refs #5529 Ward Vandewege
08:49 pm Revision 5cdd9c17 (arvados): Merge branch '5529-build-and-test-keepproxy-docker-image'
refs #5529 Ward Vandewege
08:49 pm Revision 65ecef65 (arvados-dev): Make sure to also push the keepproxy and sso images to the Docke...
refs #5529 Ward Vandewege
08:49 pm Revision 65ecef65 (arvados): Make sure to also push the keepproxy and sso images to the Docker re...
refs #5529 Ward Vandewege
08:46 pm Task #5531 (Resolved): make sure the keepproxy image is built by jenkins and is uploaded to the d...
Ward Vandewege
12:18 am Task #5531 (Resolved): make sure the keepproxy image is built by jenkins and is uploaded to the d...
Ward Vandewege
08:44 pm Task #5533 (Resolved): review 5529-add-keepproxy-docker-image
Ward Vandewege
12:21 am Task #5533 (Resolved): review 5529-add-keepproxy-docker-image
Ward Vandewege
08:15 pm Bug #5518: [SDKs] arvados not defined in arvados.util
found again here: qr1hi-8i9sb-b599bwcqo43r1uc
my current workaround is to use sdk version 3598c3003a7987cca5c0536b...
Bryan Cosca
08:06 pm Revision 2e59e0a4 (arvados): Merge branch '5529-add-keepproxy-docker-image'
refs #5529 Ward Vandewege
08:06 pm Revision 67328f09 (arvados): Merge branch 'master' into 5529-add-keepproxy-docker-image
Ward Vandewege
08:04 pm Feature #5529: [Docker] Add keepproxy to the docker images
commit:8cda7f9 LGTM Peter Amstutz
05:40 pm Feature #5529: [Docker] Add keepproxy to the docker images
There seem to be some DNS issues:... Peter Amstutz
12:17 am Feature #5529 (In Progress): [Docker] Add keepproxy to the docker images
Ward Vandewege
12:16 am Feature #5529 (Resolved): [Docker] Add keepproxy to the docker images
Ward Vandewege
06:10 pm Revision c1b4ee5b (arvados): Merge branch '5524-crunch-temp-keep-errors' closes #5524
Peter Amstutz
06:10 pm Bug #5524 (Resolved): [Crunch] Add "arvados.errors.Keep" to list of magic strings in crunch-job t...
Applied in changeset arvados|commit:c1b4ee5b62630d6df3037955b68aa77ec3ee1f5a. Peter Amstutz
05:58 pm Bug #5524 (In Progress): [Crunch] Add "arvados.errors.Keep" to list of magic strings in crunch-jo...
Peter Amstutz
06:08 pm Revision bf207e24 (arvados): 5524: Match magic string arvados.errors.Keep as likely part of an ex...
backtrace and mark task as temporary failure. Peter Amstutz
05:54 pm Revision 879ba08f (arvados): 5536: Keepproxy retry keep server discovery on error or empty list.
Peter Amstutz
05:51 pm Task #5542 (Resolved): Review 5536-retry-discover-servers
Peter Amstutz
05:50 pm Revision df9e166a (arvados): Merge pull request #1 from curoverse/master
pulling from upstream Joshua C. Randall
05:49 pm Bug #5536 (In Progress): [Keepproxy] keepproxy should retry on DiscoverKeepServers() failure or ...
Peter Amstutz
01:30 pm Bug #5536 (Resolved): [Keepproxy] keepproxy should retry on DiscoverKeepServers() failure or emp...
Ward Vandewege
05:47 pm Revision 1fea1b7a (arvados): Merge branch '5425-set-docker-memory-limits' refs #5425
Peter Amstutz
05:46 pm Bug #5198 (Resolved): [Workbench] Middle clicking on Run this pipeline brings fiddlesticks
Tom Clegg
01:47 pm Bug #5198: [Workbench] Middle clicking on Run this pipeline brings fiddlesticks
Tom said:
>> This comment: “but there's no ‘copy link address’ option in the right-click menu” … I saw this in right...
Radhika Chippada
05:51 am Bug #5198: [Workbench] Middle clicking on Run this pipeline brings fiddlesticks
Radhika Chippada wrote:
> Branch looked good overall. Some of my observations:
>
> * Ctrl-click on pipeline inst...
Tom Clegg
05:46 pm Bug #5541 (New): [Workbench] Buttons should have consistent ctrl-click and right-click behavior
See #5198 notes
On ctrl-click,
* some buttons do nothing
* some buttons open a dialog or do whatever they would ...
Tom Clegg
05:37 pm Bug #5425: [Crunch] SLURM Node failure
Tom Clegg wrote:
> This is suboptimal, but it is a step toward using a single worker node to run multiple [users']...
Peter Amstutz
05:33 pm Bug #5425: [Crunch] SLURM Node failure
I see. Docker 1.2 defaults to limiting swap to 2x given @--memory@, but doesn't yet have the @--memory-swap=-1@ optio... Tom Clegg
05:00 pm Bug #5425: [Crunch] SLURM Node failure
The code in 5425-set-docker-memory-limits lgtm @ commit:c96d48a.
However, I've tried some tests locally and settin...
Tom Clegg
04:42 pm Bug #5425: [Crunch] SLURM Node failure
Conservative memory limits will cause jobs to run unnecessarily slowly:
* when a worker runs 4 tasks, 3 of them fini...
Tom Clegg
03:11 pm Bug #5425: [Crunch] SLURM Node failure
Some notes relating to 5425-set-docker-memory-limits
This uses @docker run --memory=xxx@. Based on some experimen...
Peter Amstutz
05:01 pm Task #5509 (In Progress): Review 5425-set-docker-memory-limits
Tom Clegg
04:39 pm Feature #5540 (New): [Crunch] Contain all job/task containers in a memory-limiting cgroup
Even with #5425, it could improve worker node stability -- and allow some memory oversubscription for task processes ... Tom Clegg
04:24 pm Revision 88056329 (arvados): Merge branch 'master' into 3762-delete-list-worker
Radhika Chippada
04:20 pm Story #3762: [Keep] Process entries on the current "delete" list.
* Removed all the new code for API discovery and instead using permission_ttl. Per our discussion with Tom, defaultTr... Radhika Chippada
02:17 pm Story #3762: [Keep] Process entries on the current "delete" list.
Reviewing 3762-delete-list-worker commit:fed6d3b
The cached discovery document should part of the ArvadosClient s...
Peter Amstutz
04:11 pm Revision f565fb6f (arvados): 3762: create NewWorkQueue instances of pullq and trashq in handers_t...
it is expected that keepstore or the tests will create these objects and handlers should not have to. Radhika Chippada
04:01 pm Revision 7f28788a (arvados): 3762: undo the api server discovery document update. trash worker ca...
Radhika Chippada
03:29 pm Feature #5538 (Resolved): [SDK] Add retry support to Go arvadosclient
ArvadosClient doesn't retry errors. Add a "Retries" field to ArvadosClient and update ArvadosClient.CallRaw() to per... Peter Amstutz
02:54 pm Revision bedc4bf7 (arvados): Merge branch '5198-remote-link-ctrl-click' refs #5198
Tom Clegg
02:35 pm Revision b01138f2 (arvados): Merge branch 'master' of git.curoverse.com:arvados into 3762-delete-...
Radhika Chippada
02:19 pm Bug #5500 (Resolved): [Crunch] Detect temporary error conditions
Peter Amstutz
02:18 pm Task #5537 (In Progress): Review 3762-delete-list-worker
Peter Amstutz
02:18 pm Task #5537 (Resolved): Review 3762-delete-list-worker
Peter Amstutz
01:52 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
Disallowing dots (periods), dashes, and underscores in usernames seems a bit harsh. Is there a particular reasoning ... Peter Amstutz
01:29 pm Bug #5535 (Resolved): [Ops] When creating new shell user accounts, check that there is not an exi...
The script that needs modification is in the puppet tree at
./modules/arvados-shell-server/templates/usr-local-arv...
Peter Amstutz
01:05 pm Revision 23721458 (arvados): Merge branch '5318-git-sharing-note' closes #5318
Peter Amstutz
01:05 pm Bug #5318 (Resolved): [Workbench] Make note of lag time when changing git permissions
Applied in changeset arvados|commit:23721458d7ec8c44c4b54f45eb7d2a4e6d7cdce1. Peter Amstutz
01:02 pm Bug #5318: [Workbench] Make note of lag time when changing git permissions
I get what you're saying, but I don't really have time to fiddle with it more, so I'm merging as is. Thanks. Peter Amstutz
01:02 pm Task #5505 (Resolved): Review 5318-git-sharing-note
Peter Amstutz
12:57 pm Task #5512 (In Progress): Review 4253-user-usernames-wip
Peter Amstutz
12:52 pm Bug #5534 (Resolved): [Workbench] Log tab takes too long to load with large logs
With a very long running pipeline, like tb05z-d1hrv-lx5w1pngtl2poj9, when you click on the "Log" tab, it spins for a ... Peter Amstutz
05:52 am Revision 8b1d7833 (arvados): 5198: Merge branch 'master' into 5198-remote-link-ctrl-click
Tom Clegg
05:46 am Revision 17efed0c (arvados): 5198: Update comment.
Tom Clegg
12:21 am Revision 8cda7f9c (arvados): Add a keepproxy docker image
refs #5529 Ward Vandewege
12:18 am Task #5530 (Resolved): add keepproxy to arvdock and the build infrastructure
Ward Vandewege
12:17 am Task #5530 (Resolved): add keepproxy to arvdock and the build infrastructure
Ward Vandewege

03/22/2015

06:02 pm Revision d8326579 (arvados): Go SDK improvements:
- keepclient now respects the ARVADOS_API_HOST_INSECURE environment
variable
- arvadosclient and keepclient accept...
Ward Vandewege
03:16 pm Task #5516 (Resolved): Review 5276-job-graph-phantom-tooltip
Tom Clegg
06:30 am Bug #5276 (Resolved): [Workbench] Log graph pop up shows when there is no log graph
Applied in changeset arvados|commit:6381b9e85f278b0c8cb45ffccd89ca1b1bc4d3ee. Anonymous

03/21/2015

08:37 pm Revision 6381b9e8 (arvados): Merge branch '5276-job-graph-phantom-tooltip' closes #5276
Tom Clegg
08:19 pm Revision df9955d7 (arvados): 5276: Merge branch 'master' into 5276-job-graph-phantom-tooltip
Tom Clegg
08:19 pm Revision 5cb7bacb (arvados): 5276: Name log fixtures. Fix over-sensitive test.
Tom Clegg
02:06 pm Feature #5375 (Resolved): [workbench] Enable in-browser preview for text files in collections
Radhika Chippada
02:03 pm Feature #5375 (In Progress): [workbench] Enable in-browser preview for text files in collections
Also added javascript and rtf application types to the list of white-listed applications. Radhika Chippada
10:50 am Feature #5375 (Resolved): [workbench] Enable in-browser preview for text files in collections
Applied in changeset arvados|commit:10d3f91d4b5619172dd5d8fbf3e8aa863b673e2f. Radhika Chippada
02:04 pm Task #5497 (Resolved): Review branch: 5375-preview-collection-text-files
Radhika Chippada
01:54 pm Revision a51029fa (arvados): refs #5375
Merge branch '5375-preview-collection-text-files' Radhika Chippada
01:32 pm Revision 3c3d04e7 (arvados): 5375: added javascript and rtf application types to white-listed app...
Radhika Chippada
10:44 am Revision 10d3f91d (arvados): closes #5375
Merge branch '5375-preview-collection-text-files' Radhika Chippada
10:42 am Revision 1d20cb1d (arvados): 5375: small updates on comments
Radhika Chippada
03:14 am Revision 2fdfdc0a (arvados): 5375: and add the new test file
Radhika Chippada
03:11 am Revision cb152be8 (arvados): 5375: move the mime type tests into a new collections_helper_test.
Radhika Chippada
03:01 am Revision d9561b01 (arvados): Merge branch 'master' into 5375-preview-collection-text-files
Radhika Chippada
02:59 am Revision fed6d3b2 (arvados): Merge branch 'master' into 3762-delete-list-worker
Radhika Chippada
02:58 am Revision 6c14ca8f (arvados): 3762: Expose Discovery func in arvadosclient. Use Discovery to get d...
Radhika Chippada

03/20/2015

09:16 pm Revision a307f4b9 (arvados): 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...
Brett Smith
09:01 pm Bug #5352: [Crunch] Dispatcher not handling node allocation failures
su92l is running multiple crunch-dispatch --job instances. When there is a race condition and multiple crunch-jobs g... Peter Amstutz
08:21 pm Feature #5375: [workbench] Enable in-browser preview for text files in collections
At commit:4a8dc95, I just have one organizational thought. "Following Rails convention":http://guides.rubyonrails.or... Brett Smith
06:38 pm Feature #5375: [workbench] Enable in-browser preview for text files in collections
Brett, thanks for the review comments. I addressed all the comments. (I was being lazy about the new fixture pdf; now... Radhika Chippada
08:00 pm Bug #5381: [Crunch] Node went away unexpectedly during pipeline run.
Is there a minimum idle time a node must have reached in order to get killed off by node manager during its shutdown ... Tom Clegg
07:56 pm Revision 2ca0934c (arvados): Merge branch 'master' into 3762-delete-list-worker
Radhika Chippada
07:55 pm Feature #5459: [Crunch] Job logs include node-level resource usage statistics (cpu, ram, swap, etc)
Could be done from crunch-job by running a "crunchstat ... sleep 2^30" process on each node at the beginning of the j... Tom Clegg
07:51 pm Feature #5459: [Crunch] Job logs include node-level resource usage statistics (cpu, ram, swap, etc)
This is in addition to (and hopefully in the same format as) the per-task-container stats already provided by crunchs... Tom Clegg
07:46 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Last page of modal should have direct link to not just doc.arvados.org but also the port-a-pipeline step-by-step tuto... Nancy Ouyang
07:37 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Mockup of navbar with #5370 quickfix, link to wiki page https://arvados.org/projects/arvados/wiki/Public_Pipelines_an... Nancy Ouyang
07:45 pm Story #5471 (Rejected): [Workbench] Remove ActiveRecord dependency
Tom Clegg
05:57 pm Story #5471: [Workbench] Remove ActiveRecord dependency
I assume the issue here is that the installer is forced to @apt-get install sqlite3@ or something like that. Maybe we... Tom Clegg
07:45 pm Task #5440: [Documentation] Revert doc-to-homepage
4. Remove "/start" section entirely for now
5. Add port-a-pipeline into the "/user" section
Nancy Ouyang
07:42 pm Feature #5495: [Workbench] Change "recent pipelines" to curated selection of "public pipelines"
Quickfix -- see mockup https://arvados.org/issues/5493#note-2 , essentially don't change workbench dashboard for now,... Nancy Ouyang
07:41 pm Bug #5474 (Feedback): [Workbench] WebsocketTest#test_live_log_charting is not reliable
Tom Clegg
07:41 pm Bug #5474: [Workbench] WebsocketTest#test_live_log_charting is not reliable
*Could* be fixed already in 5276-job-graph-phantom-tooltip in #5276 Tom Clegg
07:32 pm Feature #5370: [Workbench] If anonymous config is enabled, logged-out workbench homepage should l...
!mockup-safepage.png! re-upload with crop Nancy Ouyang
07:21 pm Feature #5370: [Workbench] If anonymous config is enabled, logged-out workbench homepage should l...
I think a quickfix to get us to release is to add a link to a wiki page with a manually curated listing public pipel... Nancy Ouyang
07:28 pm Bug #5515 (Feedback): Job failure due to 'arv-put' 'ConnectionError'?
Tom Clegg
07:20 pm Bug #5515: Job failure due to 'arv-put' 'ConnectionError'?
This would have been interpreted as a temporary failure by crunch-job if:
# arv-put caught KeepWriteError and exited...
Tom Clegg
07:25 pm Bug #5524 (Resolved): [Crunch] Add "arvados.errors.Keep" to list of magic strings in crunch-job t...
Make sure not to trigger this behavior on any "failed write, about to retry" warning messages given by the keep clien... Tom Clegg
07:09 pm Bug #5523: [Crunch] crunchstat should not report errors during normal timing races
Would be good to have more detail - job ID or log fragment.
We could probably start by changing that message to sa...
Tom Clegg
06:05 pm Bug #5523 (New): [Crunch] crunchstat should not report errors during normal timing races
Container stat files appear and disappear in normal operation. In the "normal" cases, such events should not be logge... Peter Amstutz
07:04 pm Revision 4a8dc955 (arvados): 5375: update the fixture pdh with the value got from keep put.
Radhika Chippada
06:30 pm Revision 2606f4df (arvados): 5375: improved mime_types initializer. enhance collections_helper to...
update config param name, value, and comment. add .seq, which is another supported extension of fasta to test. Radhika Chippada
06:08 pm Revision 7e5416c8 (arvados): Merge branch '5319-collection-pdh-fix-performance-2-wip'
Refs #5319. Brett Smith
06:06 pm Revision 1d0aef8f (arvados): 5319: Improve collection PDH fix performance with LIKE searches.
PostgreSQL regexp searches use a lot of RAM, and these queries run out
of RAM on qr1hi. Prefer LIKE queries, which u...
Brett Smith
03:46 pm Bug #5521 (Closed): [Workbench] Slow download speed from browser
From a customer: "We tried downloading both output files and noticed two things: 1: While the speed when uploading is... Bryan Cosca
03:30 pm Revision 03e8ba64 (arvados): Merge branch 'master' into 5375-preview-collection-text-files
Radhika Chippada
03:30 pm Story #3762 (In Progress): [Keep] Process entries on the current "delete" list.
Radhika Chippada
03:27 pm Revision ac037435 (arvados): 3762: Run trash worker. Add tests to test the trash worker.
Radhika Chippada
01:39 pm Bug #5276: [Workbench] Log graph pop up shows when there is no log graph
Tom Clegg wrote:
> Brett Smith wrote:
> > I think it should be possible to use @using_wait_time(0) do … end@
>
>...
Brett Smith

03/19/2015

10:32 pm Bug #5276: [Workbench] Log graph pop up shows when there is no log graph
Brett Smith wrote:
> I think it should be possible to use @using_wait_time(0) do … end@
Good point. Fixed, commit...
Tom Clegg
09:08 pm Bug #5276: [Workbench] Log graph pop up shows when there is no log graph
Reviewing commit:ea344b06, and I just have one pithy test style comment. Where you test against @page.evaluate_scrip... Brett Smith
10:23 pm Revision a6ea5019 (arvados): 5276: Use using_wait_time 0 instead of evaluate_script.
Tom Clegg
10:12 pm Revision ab9955f1 (arvados): 5276: Reveal and update the log graph as soon as the first data point
arrives, rather than waiting for the redraw timer.
Return an empty hover tooltip for the placeholder data point. (Th...
Tom Clegg
08:28 pm Bug #5518 (Resolved): [SDKs] arvados not defined in arvados.util
I came across this error message in qr1hi-8i9sb-nuqmxt87gvnq47e:
3/19/2015 4:00:18 PM compute2 1 task-print 0 File...
Bryan Cosca
08:18 pm Task #5516 (In Progress): Review 5276-job-graph-phantom-tooltip
Brett Smith
06:27 pm Task #5516 (Resolved): Review 5276-job-graph-phantom-tooltip
Tom Clegg
06:26 pm Revision ea344b06 (arvados): 5276: Reveal and update the log graph as soon as the first data poin...
ather than waiting for the redraw timer. Tom Clegg
06:26 pm Task #5489 (Resolved): Reproduce or find plausible explanation
Tom Clegg
05:59 pm Bug #5515 (Feedback): Job failure due to 'arv-put' 'ConnectionError'?
pipeline instance tb05z-d1hrv-ojcxrzlohzyir4r fails from what looks like a 'ConnectionError' from 'arv-put':... Abram Connelly
05:54 pm Feature #5514 (Closed): Workbench enhancements
Here is a list of enhancmenets and annoyances in workbench that I have:
- Show log collection at the pipeline leve...
Abram Connelly
05:08 pm Revision b4e040f6 (arvados): 5276: Improve job log graph tests.
* Run tests as a non-admin user. (This just needed an update in the
log simulator to insert the logs with the same ...
Tom Clegg
05:05 pm Feature #5513 (Resolved): Node manager should always have one node idle
Of course this could be a money thing, but it would be nice if there was an idle node at all times, even if something... Bryan Cosca
04:24 pm Revision 52f124ea (arvados): 5276: Remove redundant test teardown.
Tom Clegg
04:21 pm Bug #5318: [Workbench] Make note of lag time when changing git permissions
The code at commit:4e72d37 is fine, but the text seems kind of easy to miss. I wonder if we could maybe hook into th... Brett Smith
04:10 pm Task #5505 (In Progress): Review 5318-git-sharing-note
Brett Smith
04:03 pm Task #5512 (Resolved): Review 4253-user-usernames-wip
Brett Smith
04:03 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
4253-user-usernames-wip is up for review. It implements the "Assign usernames" part of this story, and then uses tha... Brett Smith
04:00 pm Task #5477 (Resolved): Assign usernames
Brett Smith
03:56 pm Revision fa92aa4a (arvados): 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. ...
Brett Smith
03:55 pm Revision 1a3c91dc (arvados): 4253: Clean up some user setup methods.
As much as possible, use more methods provided by Rails, rather than
reimplementing them ourselves.
Brett Smith
03:53 pm Revision ee46c18d (arvados): 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 valida...
Brett Smith
03:48 pm Feature #5511: [Workbench] Workbench should support viewing VCF files
I would like to view a vcf :) Bryan Cosca
03:48 pm Feature #5511 (New): [Workbench] Workbench should support viewing VCF files
Bryan Cosca
03:15 pm Bug #5285 (Resolved): [SDKs] arv-run-pipeline-instance does not use 'settings.conf' file like oth...
Applied in changeset arvados|commit:4925686f6aa7214568ebd60be3acaa49dbf9dd1a. Peter Amstutz
02:54 pm Bug #5285: [SDKs] arv-run-pipeline-instance does not use 'settings.conf' file like other 'arv' tools
commit:a578a05 is good to merge. Thanks. Brett Smith
03:12 pm Revision 4925686f (arvados): Merge branch '5285-arpi-use-settings' closes #5285
Peter Amstutz
03:11 pm Feature #5510 (New): [DRAFT] [Crunch] User can configure task retries
For some of our long running jobs, we're finding that we get new types of transient failures that are not identified ... Peter Amstutz
03:10 pm Bug #5506 (Closed): arv-copy issue with moving pathomap template
Not a bug in arv-copy. The fetch_url of the repository record was not updated when the repository was renamed. This... Peter Amstutz
03:08 pm Task #5504 (Resolved): Review 5285-arpi-use-settings
Peter Amstutz
02:50 pm Task #5504 (In Progress): Review 5285-arpi-use-settings
Brett Smith
02:52 pm Revision c96d48a6 (arvados): 5425: Set memory limit on container as a fraction of total system me...
allocated to task each when invoking Docker. Peter Amstutz
02:49 pm Bug #5425 (In Progress): [Crunch] SLURM Node failure
Peter Amstutz
02:49 pm Task #5509 (Resolved): Review 5425-set-docker-memory-limits
Peter Amstutz
02:47 pm Feature #5375: [workbench] Enable in-browser preview for text files in collections
Reviewing commit:a9c8f2d
There should be a one-to-one mapping between file formats, and MIME types. Several diffe...
Brett Smith
02:29 pm Bug #5198: [Workbench] Middle clicking on Run this pipeline brings fiddlesticks
Branch looked good overall. Some of my observations:
* Ctrl-click on pipeline instance “Re-run options” is workin...
Radhika Chippada
01:49 pm Task #5508 (Closed): Make sure repository fetch_url is properly updated on rename
This is an existing bug in the API server. Brett Smith
01:41 pm Task #5497 (In Progress): Review branch: 5375-preview-collection-text-files
Brett Smith
01:20 pm Task #5507 (In Progress): Review 5198-remote-link-ctrl-click
Radhika Chippada
06:45 am Task #5507 (Resolved): Review 5198-remote-link-ctrl-click
Tom Clegg
12:48 pm Task #5456 (Resolved): Review branch: 5418-brand-unclickable-anonymous
Radhika Chippada
12:48 pm Task #5450 (Resolved): Add test case for looking up a record by created_at, using the exact times...
Radhika Chippada
07:29 am Revision ed807a40 (arvados-dev): openssh 6.8 compat
Sitaram Chamarty
06:45 am Task #5498 (Resolved): Prohibit accidentally ctrl-clickable remote links
Tom Clegg
05:50 am Revision 165a594b (arvados): 5198: Remove href attributes from remote:true links to prevent ctrl-...
Tom Clegg
03:59 am Feature #5416: [API] Clone git repositories without using an SSH private key
Added tests, install docs, and discovery doc support; now at commit:b4f4cbf on 5416-arv-git-httpd.
There's a 5416-...
Tom Clegg

03/18/2015

09:25 pm Bug #5506: arv-copy issue with moving pathomap template
qr1hi-tpzed-tkobql3098tyycn has manage access to bryan.coscamasonancestry. bryan.cosca-mason-ancestry was name change... Bryan Cosca
09:23 pm Bug #5506 (Closed): arv-copy issue with moving pathomap template
arv-copy --src qr1hi --dst su92l --dst-git-repo bcosc --project-uuid su92l-tpzed-6ujvgnhlbkp7abw qr1hi-p5p6p-fe2l3h8x... Bryan Cosca
06:44 pm Revision 4e72d379 (arvados): 5318: Add note on sharing page for repository object about lag time ...
Peter Amstutz
06:42 pm Bug #5285 (In Progress): [SDKs] arv-run-pipeline-instance does not use 'settings.conf' file like ...
Peter Amstutz
06:41 pm Task #5505 (Resolved): Review 5318-git-sharing-note
Peter Amstutz
06:36 pm Revision a578a055 (arvados): 5285: Remove cruft made redundant by Ruby SDK
Peter Amstutz
06:33 pm Task #5504 (Resolved): Review 5285-arpi-use-settings
Peter Amstutz
06:20 pm Bug #5318 (In Progress): [Workbench] Make note of lag time when changing git permissions
Updating this story to add a note to Workbench that there is a lag time on updating git permissions. Peter Amstutz
06:07 pm Task #5503 (In Progress): Deploy "proxy_buffer off;" on /collections/download
Peter Amstutz
06:07 pm Task #5503 (Resolved): Deploy "proxy_buffer off;" on /collections/download
Peter Amstutz
05:59 pm Bug #5502 (Resolved): [Node Manager] Add local SSD to compute nodes on GCP
Node manager, on GCP, should add one local SSD slice to compute nodes
https://cloud.google.com/compute/docs/disk...
Peter Amstutz
05:52 pm Revision 1ed0df4d (arvados): Merge branch '5500-crunch-temporary-failure' refs #5500
Peter Amstutz
05:52 pm Bug #5426 (In Progress): [Workbench] Large downloads through workbench fail
Peter Amstutz
05:51 pm Task #5501 (Resolved): Review 5500-crunch-temporary-failure
Peter Amstutz
05:32 pm Task #5501 (In Progress): Review 5500-crunch-temporary-failure
Tom Clegg
04:20 pm Task #5501 (Resolved): Review 5500-crunch-temporary-failure
Peter Amstutz
05:48 pm Revision a239e2db (arvados): 5500: Add TASK_TEMPFAIL constant. shell_or_die always exits non-zer...
Peter Amstutz
05:47 pm Bug #5500: [Crunch] Detect temporary error conditions
commit:a239e2d LGTM, thanks Tom Clegg
05:44 pm Bug #5500: [Crunch] Detect temporary error conditions
All done. Now at commit:a239e2db534cc36aa8c3e08077383d84bf6ba8e8 Peter Amstutz
05:31 pm Bug #5500: [Crunch] Detect temporary error conditions
At commit:3365d47
* @$tempfail@ should probably be called @$exitcode@: it doesn't actually signify tempfail unless i...
Tom Clegg
04:19 pm Bug #5500 (In Progress): [Crunch] Detect temporary error conditions
Peter Amstutz
04:18 pm Bug #5500 (Resolved): [Crunch] Detect temporary error conditions
tb05z-8i9sb-2e16dypy0eg7m59... Peter Amstutz
04:23 pm Revision 3365d47a (arvados): 5500: Add SLURM "Communication connection failure" to pattern of tem...
failures. "pip install" failure returns temporary error status (111) so the
task can be retried.
Peter Amstutz
03:55 pm Bug #5499 (Duplicate): [SDKs] arv-copy fails to create collection after copying many blocks
arv-copy --src qr1hi --dst su92l --dst-git-repo bcosc --project-uuid su92l-j7d0g-s10d0ru68kdzgve qr1hi-p5p6p-hu2ep9hu... Bryan Cosca
03:26 pm Task #5498 (In Progress): Prohibit accidentally ctrl-clickable remote links
Tom Clegg
03:26 pm Task #5498 (Resolved): Prohibit accidentally ctrl-clickable remote links
Tom Clegg
03:20 pm Feature #5375 (In Progress): [workbench] Enable in-browser preview for text files in collections
Radhika Chippada
02:18 pm Feature #5375: [workbench] Enable in-browser preview for text files in collections
Notes about implementation:
* The gem mime_types supports 1868 mime types. The data file is within the gem. It is ...
Radhika Chippada
03:19 pm Task #5497 (Resolved): Review branch: 5375-preview-collection-text-files
Radhika Chippada
03:13 pm Revision a9c8f2dd (arvados): 5375: white space
Radhika Chippada
03:04 pm Revision f75e2ecb (arvados): 5375: enhance the mime_types initializer to add a new type only when...
Radhika Chippada
02:44 pm Revision f5ed1dba (arvados): 5319: Improve collection PDH fix performance with LIKE searches.
PostgreSQL regexp searches use a lot of RAM, and these queries run out
of RAM on qr1hi. Prefer LIKE queries, which u...
Brett Smith
02:04 pm Revision c3604c1c (arvados): 5375: after much hair pulling, found the syntax to replace MIME::Typ...
Radhika Chippada
01:50 pm Revision f2d1eec0 (arvados): More tweaks for the manual install prerequisites doc page.
refs #5416 Ward Vandewege
01:45 pm Revision f46eed2a (arvados): Merge branch 'master' into 5375-preview-collection-text-files
Radhika Chippada
01:44 pm Revision 6a13c4e4 (arvados): refs #5383
Merge branch '5383-api-db-current-time' Radhika Chippada
01:41 pm Revision 44823f31 (arvados): Merge branch 'master' into 5383-api-db-current-time
Radhika Chippada
01:38 pm Revision 9917d9ee (arvados): 5383: Add back Time.parse(). Without it the value returned would be ...
and with Time.parse it would be 2015-03-18 09:37:11 -0400, which is the same as Time.now. Radhika Chippada
01:36 pm Bug #5496 (New): [SDKs] PySDK test_rewrite_on_empty_file is not reliable
From "build 1393":https://ci.curoverse.com/job/arvados-api-server/1393/console:... Brett Smith
01:31 pm Revision 25520da7 (arvados): Add git.uuid.local.domain to the manual install prerequisites page on
the overview of hostnames.
refs #5416
Ward Vandewege
01:09 pm Task #5488 (In Progress): Review 5416-arv-git-httpd
Ward Vandewege
12:57 pm Revision b38fea18 (arvados): Merge branch '5313-node-manager-node-naming-tag-wip'
Refs #5313. Closes #5434, #5467. Brett Smith
12:56 pm Revision fff9d822 (arvados): 5313: Node Manager has cloud-specific logic to get node FQDNs.
On AWS, we put compute nodes' FQDN in the name field. On GCE, we
can't do that: it can't contain dots. Add a node_f...
Brett Smith
01:15 am Bug #5383 (Resolved): [API] API server should always retrieve current time from database, never T...
Applied in changeset arvados|commit:18148ec24bf63ec3353a2cd38f6f07c460037db2. Radhika Chippada
12:58 am Bug #5383: [API] API server should always retrieve current time from database, never Time.now()
Brett wrote:
> The story suggests that it'd be ideal to have the database set these times when the INSERT or UPDATE ...
Radhika Chippada
01:10 am Revision 3c191493 (arvados): Merge branch 'master' into 5375-preview-collection-text-files
Radhika Chippada
01:08 am Revision 18148ec2 (arvados): closes #5383
Merge branch '5383-api-db-current-time' Radhika Chippada
12:58 am Task #5472 (Resolved): Review branch: 5383-api-db-current-time
Radhika Chippada
12:50 am Revision 3606f69d (arvados): 5383: better test assertion
Radhika Chippada
12:44 am Revision beebf2cb (arvados): Merge branch 'master' into 5383-api-db-current-time
Radhika Chippada
12:42 am Revision fe6bad60 (arvados): 5375: add test to verify that collection#show page enalbles / disabl...
Radhika Chippada

03/17/2015

11:34 pm Revision 12540bb0 (arvados): 5375: add some of the mime types not supported by mime_types gem to ...
Radhika Chippada
08:53 pm Support #5461: following manual install instructions on laptop
... Davide Fiorentino lo Regio
04:28 pm Support #5461: following manual install instructions on laptop
### Sorry, again now with pre tags:... Albert Vilella
04:27 pm Support #5461: following manual install instructions on laptop
### See below script as it is now
#/bin/bash
# Install dependencies
sudo apt-get install \
bison build-esse...
Albert Vilella
08:52 pm Feature #5495 (New): [Workbench] Change "recent pipelines" to curated selection of "public pipeli...
See attached screenshot.
This a quickfix.
We should include a "public pipelines" and "public collections" panels...
Nancy Ouyang
08:42 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Mockup of modal attached.
!{width:50%}mockup-workbench-intro.png!:mockup-workbench-intro.png
Nancy Ouyang
08:41 pm Feature #5493 (Resolved): [Workbench] Add "Getting Started" modal inside Workbench
1) Workbench should be self-explanatory & guide first time-users through discovering key features. Solution: Add moda... Nancy Ouyang
08:41 pm Feature #5494 (New): [Documentation] Run an uncommitted script straight from a working directory ...
There should be a way to avoid having to commit a change to my git repo in order to run an updated pipeline. It would... Bryan Cosca
08:17 pm Feature #5492: [Workbench] Add "home project" link to the "my account" dropdown
Mockup attached. Nancy Ouyang
07:38 pm Feature #5492 (Resolved): [Workbench] Add "home project" link to the "my account" dropdown
Tom Clegg
07:20 pm Story #5438 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
https://arvados.org/blogs/31 Brett Smith
07:10 pm March development review: Keeping a good thing going
Sometimes when we plan our sprints, we like to leave a little time for users to try out new features and give us feed... Brett Smith
06:53 pm Feature #5035: [Documentation] Document the minimum docker image / Dockerfile that can be used to...
... Tom Clegg
06:38 pm Bug #5491 (Closed): Job dies for no apparant reason
Bug in my code. Abram Connelly
06:36 pm Bug #5491 (Closed): Job dies for no apparant reason
I tried running a pipeline on tb05z and it was unable to start. Looking at the logs I see some errors of the form:
...
Abram Connelly
06:05 pm Bug #5383: [API] API server should always retrieve current time from database, never Time.now()
commit:ff04973 looks great, thanks. Just a couple of small background things.
The story suggests that it'd be ide...
Brett Smith
05:53 pm Revision 01916041 (arvados): gofmt cleanup.
Misha Zatsman
05:35 pm Revision a1a1aed7 (arvados): When copying a collection that already exists on the destination, fetch
manifest text from the destination in order to create a new collection with the
correct signing tokens. closes #5475
Peter Amstutz
05:35 pm Bug #5475 (Resolved): [API] arv-copy 403
Applied in changeset arvados|commit:a1a1aed711dec0676575bd914cbe1356f7c0bb03. Peter Amstutz
04:14 pm Bug #5490 (Resolved): [Crunch] Job should not be reused when docker tag _or_ arvados sdk version ...
I updated the 'arvados_sdk_version' in my pipeline and ran the pipeline. The first two jobs in the pipeline got re-u... Abram Connelly
03:41 pm Task #5489 (In Progress): Reproduce or find plausible explanation
Tom Clegg
03:41 pm Task #5489 (Resolved): Reproduce or find plausible explanation
Tom Clegg
03:39 pm Task #5488 (Resolved): Review 5416-arv-git-httpd
Tom Clegg
03:39 pm Task #5487 (Resolved): Click job script_name to see source code (plain)
Tom Clegg
03:38 pm Task #5486 (Resolved): Add arv-git-httpd to run_test_servers
Tom Clegg
03:36 pm Task #5485 (Resolved): Add install docs
Tom Clegg
03:36 pm Task #5485 (Resolved): Add install docs
Tom Clegg
03:36 pm Task #5469 (Resolved): Make arv-git-http server
Tom Clegg
03:36 pm Revision b4f4cbf7 (arvados): 5416: Add arv-git-httpd to install docs, api config, and discovery doc.
Tom Clegg
03:01 pm Revision a00ef863 (arvados-dev): 5416: Add --retry flag: when a test suite fails, prompt to try t...
Tom Clegg
03:01 pm Revision a00ef863 (arvados): 5416: Add --retry flag: when a test suite fails, prompt to try that ...
Tom Clegg
03:00 pm Revision 3c0d0df8 (arvados-dev): 5416: Add arv-git-httpd.
Tom Clegg
03:00 pm Revision 3c0d0df8 (arvados): 5416: Add arv-git-httpd.
Tom Clegg
02:57 pm Revision ad69cab0 (arvados): 5416: Merge branch 'master' into 5416-git-auth-token
Tom Clegg
02:57 pm Revision ff04973b (arvados): 5383: minor test assertion updates
Radhika Chippada
02:57 pm Revision 7521d023 (arvados): 5416: Add path variants test. Skip cloning arvados repo when not nee...
Tom Clegg
02:53 pm Revision 29dd4393 (arvados): Merge branch 'master' into 5383-api-db-current-time
Radhika Chippada
02:51 pm Revision 8efc8d84 (arvados): 5383: add one more test that updates an object twice and verifies th...
Radhika Chippada
02:33 pm Bug #5481 (New): [Workbench] Pipeline instance page does not automatically refresh when pipeline ...
for example: qr1hi-d1hrv-1wk60qdgnjobbnl
!pipelineinstancerefresh.gif!
Bryan Cosca
02:33 pm Revision 2507d473 (arvados): 5383: remove unused include statement from log_test (it is now the s...
Radhika Chippada
02:32 pm Feature #4253: [API] Users can create their own arvados-hosted git repositories
(10:28:02 AM) Me: Real quick, on 4253: how do you feel about generating usernames from VM login permissions rather th... Brett Smith
01:16 pm Feature #4253 (In Progress): [API] Users can create their own arvados-hosted git repositories
Brett Smith
02:30 pm Bug #5476 (Resolved): [SDK] Python KeepClient retry fixes
Applied in changeset arvados|commit:d8abf0b06cc38a1e1030e04966d0cb616eae8c2e. Peter Amstutz
01:26 pm Bug #5476: [SDK] Python KeepClient retry fixes
On further testing (and a brief chat with Brett) it is actually correctly not retrying servers for which it has gotte... Peter Amstutz
01:09 pm Bug #5476 (Resolved): [SDK] Python KeepClient retry fixes
# If a PUT fails due to at least one connection timeout error, it should increase the connection timeout in subsequen... Peter Amstutz
02:28 pm Revision d8abf0b0 (arvados): Merge branch '5476-connect-timeout-scale' closes #5476
Peter Amstutz
02:27 pm Revision b63b1c67 (arvados): 5383: postgres current_timestamp is the start of transaction and clo...
Radhika Chippada
02:27 pm Revision c190374a (arvados): 5476: Describe timeout behavior if KeepClient.__init__ docstring.
Peter Amstutz
02:09 pm Revision 471dd5bf (arvados): 5476: Better implementation of connection timeout scaling. Updated ...
for current_timeout. Peter Amstutz
01:37 pm Revision f78b9c58 (arvados): 5476: Increase connection timeout when retrying keep get and put.
Peter Amstutz
01:29 pm Task #5480 (Resolved): Update Workbench repository management UI
* On manage account page (at least for now)
* Add new repository -> dialog box (or inline, if easier)
** Show note...
Brett Smith
01:29 pm Task #5479 (Resolved): Update repository permission rules
* User can create a repository with owner_uuid==current_user.uuid but not with any other owner_uuid (unless current_u... Brett Smith
01:29 pm Task #5478 (Resolved): Update repository name rules
* Repository with name=bar, owned by user with username=foo, is "{base}/foo/bar.git"
* name cannot be null.
* {owne...
Brett Smith
01:28 pm Task #5477 (Resolved): Assign usernames
Add "username" attribute to users table.
* Can be null.
* Unique.
* Starts with alpha. Contains only alphanum.
* ...
Brett Smith

03/16/2015

11:38 pm Bug #5383: [API] API server should always retrieve current time from database, never Time.now()
Brett said:
>> Error tokens never go to the database, they're just generated, sent to the client, and logged for c...
Radhika Chippada
08:10 pm Bug #5383: [API] API server should always retrieve current time from database, never Time.now()
Reviewing commit:79a18f2e
I think we need some clarification on this story from Tom. I know the subject says "alw...
Brett Smith
03:41 pm Bug #5383: [API] API server should always retrieve current time from database, never Time.now()
Notes about the implementation:
* Added db_current_time library method
* Replaced all occurrences of Time.now i...
Radhika Chippada
03:35 pm Bug #5383 (In Progress): [API] API server should always retrieve current time from database, neve...
Radhika Chippada
11:16 pm Revision b0c5270a (arvados): 5383: revert db_current_time back to Time.now in application_control...
Radhika Chippada
11:07 pm Revision b5c40a03 (arvados): 5383: revert back db_current_time update to Time.now in api scripts ...
Radhika Chippada
10:35 pm Revision 50e9e555 (arvados): 5383: update db_current_time to return date with more precision. Upd...
Radhika Chippada
09:41 pm Revision 32926d65 (arvados): Merge branch 'master' into 5383-api-db-current-time
Radhika Chippada
09:25 pm Bug #5207 (Resolved): [API] Collection expires_at should be a full timestamp, not just a date.
Applied in changeset arvados|commit:ae8ed6d9d0e5231379564beedc08c812352b7043. Anonymous
07:12 pm Bug #5207: [API] Collection expires_at should be a full timestamp, not just a date.
commit:9a38a7c is good to merge. Thanks. Brett Smith
09:19 pm Revision ae8ed6d9 (arvados): Merge branch '5207-expires-at-time' closes #5207
Tom Clegg
09:18 pm Task #5457 (Resolved): Review 5207-expires-at-time
Tom Clegg
07:04 pm Task #5457 (In Progress): Review 5207-expires-at-time
Brett Smith
09:17 pm Revision b93018f0 (arvados): 5416: Allow users with repo write permission to update modified_at.
Tom Clegg
08:42 pm Revision 8e1a8322 (arvados): Added a couple helper methods to remove boilerplate from unittests, ...
Misha Zatsman
08:27 pm Revision c1068991 (arvados): 5416: Add integration tests.
Tom Clegg
07:30 pm Revision aabde5c5 (arvados): Merge branch 'master' into 5383-api-db-current-time
Radhika Chippada
07:14 pm Task #5472 (In Progress): Review branch: 5383-api-db-current-time
Brett Smith
03:36 pm Task #5472 (Resolved): Review branch: 5383-api-db-current-time
Radhika Chippada
07:00 pm Revision e3f359d1 (arvados): Merge branch '5448-crunch-job-task-fixes' refs #5448
Peter Amstutz
06:44 pm Revision 290ddb6f (arvados): Added some tests.
Misha Zatsman
06:31 pm Revision b1233abc (arvados): Cleaned up test.
Misha Zatsman
06:11 pm Bug #5475 (Resolved): [API] arv-copy 403
... Peter Amstutz
06:10 pm Revision f09da35e (arvados): Fixed bug in BlockSet.ToCollectionIndexSet.
Lots of unittests in summary_test.go. Misha Zatsman
06:05 pm Story #5438 (In Progress): [Documentation] (recurring) Write blog post in first three days of sprint
Brett Smith
05:52 pm Revision 382924ca (arvados): 5448: Clean up old cid files during job start.
Peter Amstutz
05:28 pm Bug #5474 (Resolved): [Workbench] WebsocketTest#test_live_log_charting is not reliable
From "build 1384":https://ci.curoverse.com/job/arvados-api-server/1384/console:... Brett Smith
04:41 pm Revision 9877c891 (arvados): Merge branch '5319-collection-pdh-fix-performance-wip'
Refs #5319. Brett Smith
04:41 pm Revision 4f3b7339 (arvados): 5319: Improve performance of Collection PDH fix migration.
* Use PostgreSQL's native regular expression search to limit the
number of records we pull through ActiveRecord.
* ...
Brett Smith
04:24 pm Revision 79a18f2e (arvados): Merge branch 'master' into 5383-api-db-current-time
Radhika Chippada
04:21 pm Revision 610d9aea (arvados): 5383: blob.rb uses db_current_time as well. since it is using static...
Radhika Chippada
03:35 pm Task #5450 (In Progress): Add test case for looking up a record by created_at, using the exact ti...
Radhika Chippada
03:26 pm Revision c3074f48 (arvados): 5448: Fix cid file cleanup.
Peter Amstutz
03:20 pm Revision 68483f1b (arvados): 5383: add test that creates an object and does a lookup using that o...
Radhika Chippada
03:06 pm Bug #5373 (In Progress): [Docker] Web Application Could not be Started
Neelam,
Can you please let me know what action you're taking to receive that error message? The message most like...
Brett Smith
02:47 pm Revision 1321195a (arvados): 5448: Add --all to "docker images" because it turns out it doesn't l...
Peter Amstutz
02:23 pm Revision cb7c9d8d (arvados): 5313: Fixup comment to explain why update_arvados_node doesn't retry.
Brett Smith
02:18 pm Revision d16e54da (arvados): Merge branch 'master' from github.com/daftano. No issue #
Tom Clegg
02:18 pm Revision eb68ddf0 (arvados): 5416: Add options to docs.
Tom Clegg
02:09 pm Revision df05c25b (arvados): 5319: Improve performance of Collection manifest fixing migration.
* Use PostgreSQL's native regular expression search to limit the
number of records we pull through ActiveRecord.
* ...
Brett Smith
01:58 pm Revision 50325416 (arvados-dev): Add python-backports.ssl-match-hostname to the list of python pa...
we debianize. It's a dependency for libcloud 0.17.
Fix a typo.
No issue #
Ward Vandewege
01:58 pm Revision 50325416 (arvados): Add python-backports.ssl-match-hostname to the list of python packages
we debianize. It's a dependency for libcloud 0.17.
Fix a typo.
No issue #
Ward Vandewege
01:52 pm Revision 00c2e9b2 (arvados): Merge branch 'master' into 5383-api-db-current-time
Radhika Chippada
01:51 pm Revision 94d2af98 (arvados): 5383: use db current time in place of Time.now
Radhika Chippada
01:40 pm Revision b306eb48 (arvados): 5448: Don't create new tasks if $main::success is defined. Add fail...
to cidfile and delete cidfile in reapchildren() to fix Docker cidfile collision. Peter Amstutz
01:40 pm Story #5471 (Rejected): [Workbench] Remove ActiveRecord dependency
Users are required to install a database when setting up workbench, even though workbench doesn't use a database. Ca... Peter Amstutz
01:10 pm Bug #4158 (Resolved): [Workbench] Display more Node details to non-administrators
Applied in changeset arvados|commit:a9b4a906124081439326fedc1a1e73fae9c2f40b. Peter Amstutz
01:09 pm Revision fcd19228 (arvados): Merge branch 'install-doc-uuid-prefix' no issue #
Peter Amstutz
01:08 pm Revision a9b4a906 (arvados): Merge branch '4158-fix-compute-node-detail' closes #4158
Peter Amstutz
11:38 am Revision 9f112e10 (arvados): Update install-workbench-app.html.textile.liquid
Add libsqlite3-dev dependency David
11:22 am Revision dc94a5b5 (arvados): Update install-workbench-app.html.textile.liquid
Remove sudo because to run sudo you need to have it already installed
Add git to download sources from github
David

03/14/2015

06:39 am A quick fix: Migrating Google login from OpenID to OAuth2
Perhaps you have a web application that uses OpenID to authenticate Google users. That will stop working on April 20,... Tom Clegg

03/13/2015

10:16 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Work-in-progress 5416-git-auth-token at commit:16421a1 status:
* Works in my dev environment
* Has no tests yet
...
Tom Clegg
10:04 pm Revision 16421a1a (arvados): 5416: arv-git-httpd provides HTTP access to git repositories, using ...
Tom Clegg
09:31 pm Revision f1bb6330 (arvados): 5034: Update Workbench integration tests.
A lot of tests started failing because
* they were looking for the string "content hash" to assert they were
on a ...
Brett Smith
09:17 pm Task #5469 (In Progress): Make arv-git-http server
Tom Clegg
09:17 pm Task #5469 (Resolved): Make arv-git-http server
Tom Clegg
09:17 pm Task #5453 (Resolved): Look into authenticating git-http with arvados tokens
Tom Clegg
08:35 pm Story #5468 (New): [SDKs] Refactor arv-get/put/copy into the Python "arv" wrapper using common ex...
Examples
* Exit 111 after a transient error like KeepWriteError
Tom Clegg
07:25 pm Task #5452 (Resolved): Review 5034-workbench-collection-summary-wip
Applied in changeset arvados|commit:71c4fdc3352ad5ca34c2f260fe43fa1150868a04. Brett Smith
07:25 pm Feature #5034 (Resolved): [Workbench] Show content statistics/summary (total size, number of file...
Applied in changeset arvados|commit:71c4fdc3352ad5ca34c2f260fe43fa1150868a04. Brett Smith
07:12 pm Feature #5034: [Workbench] Show content statistics/summary (total size, number of files) at top o...
Radhika Chippada wrote:
> * Can we add glyphicon-copy next to the Collection uuid and content address elements? (I w...
Brett Smith
07:08 pm Feature #5034: [Workbench] Show content statistics/summary (total size, number of files) at top o...
Brett:
* Ok with #5415 to improve UI
* Can we add glyphicon-copy next to the Collection uuid and content addre...
Radhika Chippada
06:51 pm Feature #5034: [Workbench] Show content statistics/summary (total size, number of files) at top o...
Radhika Chippada wrote:
> Brett, looks great. Just a few minor suggestions.
>
> * The comment says “Render local ...
Brett Smith
07:25 pm Task #5027 (Resolved): [Workbench] Improve Content Address/UUID display on Collection page
Applied in changeset arvados|commit:71c4fdc3352ad5ca34c2f260fe43fa1150868a04. Brett Smith
07:17 pm Revision 1e54d655 (arvados): 5034: Update Workbench Gemfile post-merge.
Refs #5034. Brett Smith
07:16 pm Revision 71c4fdc3 (arvados): Merge branch '5034-workbench-collection-summary-wip'
Closes #5027, #5034, #5452. Brett Smith
07:14 pm Revision 2f27d8fa (arvados): 5034: Improve Workbench collection display.
* Display the UUID, and make it auto-select for easy copying.
* Do the same for the portable data hash, and call it t...
Brett Smith
07:14 pm Revision 1bda9759 (arvados): 5034: Add Keep::Manifest#files_size to Ruby SDK.
Brett Smith
06:45 pm Revision ad4c4cf2 (arvados): 5034: Fixups from code review.
Brett Smith
05:59 pm Revision cd1109ef (arvados): 5313: Node Manager has cloud-specific logic to get node FQDNs.
On AWS, we put compute nodes' FQDN in the name field. On GCE, we
can't do that: it can't contain dots. Add a node_f...
Brett Smith
03:24 pm Revision a7f93242 (arvados): Merge branch '5211-improved-top-navbar'
closes #5211 Ward Vandewege
03:24 pm Bug #5211 (Resolved): [Documentation] Top Navbar of docs homepage not suitable for small window
Ward Vandewege
03:24 pm Task #5441 (Resolved): review 5211-improved-top-navbar
Ward Vandewege
03:24 pm Revision 6e066d1a (arvados): Merge branch 'master' into 5211-improved-top-navbar
Ward Vandewege
03:23 pm Revision a0f20c7a (arvados): Typo fix and gofmt fix.
Peter Amstutz
03:23 pm Revision e893c4e1 (arvados): Remove reference to as yet non-existant compute node setup page.
Refs #5211 Ward Vandewege
03:06 pm Revision 40d408b3 (arvados): refs #3761
Merge branch '3761-pull-list-worker' Radhika Chippada
02:54 pm Revision 995af457 (arvados): 3761: We do not need to MakeArvadosClient to create the pullq worker...
Radhika Chippada
02:43 pm Revision f3e7d405 (arvados): Add note to application.default.yml and installation documentation that
uuid_prefix must be exactly 5 characters. Peter Amstutz
02:31 pm Revision 8e362300 (arvados-dev): allow repo symlinks while still being paranoid...
I don't like "find -L" in a security program. Period. If you MUST keep some
of your repos somewhere else, you'll ne...
Sitaram Chamarty
02:20 pm Support #5461: following manual install instructions on laptop
Hi avilella, your site prefix is too long. It needs to be 5 characters and "barfoo" is 6. Peter Amstutz
02:16 pm Support #5461: following manual install instructions on laptop
Same content as above but properly quoted with pre tag:
Trying to install arvados locally on an Ubuntu laptop. Det...
Albert Vilella
02:12 pm Support #5461 (New): following manual install instructions on laptop

Trying to install arvados locally on an Ubuntu laptop. Details below:
http://doc.arvados.org/install/install-man...
Albert Vilella
02:15 pm Revision 09970b42 (arvados): 4158: Compute node details are in properties, not info
Peter Amstutz
02:12 pm Bug #4158 (In Progress): [Workbench] Display more Node details to non-administrators
Peter Amstutz
02:02 pm Feature #5459 (New): [Crunch] Job logs include node-level resource usage statistics (cpu, ram, sw...
Peter Amstutz
08:07 am Revision f30c4a2b (arvados-dev): lineup the info display fields
Sitaram Chamarty
12:52 am Revision 8786e256 (arvados-dev): perms: list available roles, plus several other changes...
(much thanks to Tony Finch!)
- show valid roles and their access rights, for the given repo ("-lr")
- check a ro...
Sitaram Chamarty

03/12/2015

09:44 pm Feature #5416: [API] Clone git repositories without using an SSH private key
It's easy to tell git to send your API token as an HTTP authentication password:
git config --global credentia...
Tom Clegg
05:00 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Client side plan:
* Implement git-credentials glue (and probably add a bit of config advice on the Manage Account pa...
Tom Clegg
03:57 pm Feature #5416 (In Progress): [API] Clone git repositories without using an SSH private key
Tom Clegg
09:00 pm Feature #5034: [Workbench] Show content statistics/summary (total size, number of files) at top o...
2¢: I'm inclined to defer as much as possible of the UI-tweaking to #5415. Tom Clegg
07:30 pm Feature #5034: [Workbench] Show content statistics/summary (total size, number of files) at top o...
Forgot to say this in my previous comment. The summary information is taking quite some space in the collection#show ... Radhika Chippada
06:24 pm Feature #5034: [Workbench] Show content statistics/summary (total size, number of files) at top o...
Brett, looks great. Just a few minor suggestions.
* _show_autoselect_text.html
** The comment says “Render local...
Radhika Chippada
02:22 pm Feature #5034: [Workbench] Show content statistics/summary (total size, number of files) at top o...
5034-workbench-collection-summary-wip is up for review. Some notes about the story implementation.
Tom Clegg wrot...
Brett Smith
08:17 pm Revision 40d04a66 (arvados): Merge branch 'patch-1' from github.com/daftano. No issue #
Tom Clegg
06:25 pm Task #5452 (In Progress): Review 5034-workbench-collection-summary-wip
Radhika Chippada
02:17 pm Task #5452 (Resolved): Review 5034-workbench-collection-summary-wip
See "story note-8":https://arvados.org/issues/5034#note-8 for implementation discussion. Brett Smith
04:30 pm Bug #5211: [Documentation] Top Navbar of docs homepage not suitable for small window
LGTM, but it exposes an existing bug which you should probably fix:
In #4186, commit:ed4105d added a link to insta...
Tom Clegg
04:22 pm Task #5441 (In Progress): review 5211-improved-top-navbar
Tom Clegg
04:10 pm Bug #5418 (Resolved): [Workbench] Make the brand/root link unclickable when not logged in
Applied in changeset arvados|commit:2f9de559616c21a8f5672017abd13d7319a05196. Radhika Chippada
03:56 pm Bug #5418: [Workbench] Make the brand/root link unclickable when not logged in
LGTM @ commit:5aff810
Just a formatting nitpick: "<code class="ruby">text:Rails.configuration.site_name.downcase</...
Tom Clegg
03:18 pm Bug #5418 (In Progress): [Workbench] Make the brand/root link unclickable when not logged in
Radhika Chippada
04:07 pm Revision a6852b55 (arvados): Use postgresql options to reduce questions
-S set new role to not be a superuser
-R disable the creation of more new roles for the new role
David
04:07 pm Revision 2f9de559 (arvados): closes #5418
Merge branch '5418-brand-unclickable-anonymous' Radhika Chippada
04:07 pm Revision c6b4fe59 (arvados): Merge branch 'master' into 5418-brand-unclickable-anonymous
Radhika Chippada
04:05 pm Revision bcfd9a00 (arvados): 5418: fix assert formatting
Radhika Chippada
03:57 pm Story #5098 (In Progress): [Keep] Design: using Arvados to browse, and run jobs on, input data th...
Tom Clegg
03:52 pm Task #5456 (In Progress): Review branch: 5418-brand-unclickable-anonymous
Tom Clegg
03:09 pm Task #5456 (Resolved): Review branch: 5418-brand-unclickable-anonymous
Radhika Chippada
03:42 pm Revision 9a38a7c6 (arvados): 5207: Change expires_at column type from date to datetime.
Tom Clegg
03:42 pm Task #5458 (Resolved): Update keep clients to heed proxy-uuid hints
Tom Clegg
03:41 pm Task #5457 (Resolved): Review 5207-expires-at-time
Tom Clegg
03:41 pm Task #5455 (Resolved): Migration
Tom Clegg
03:07 pm Task #5455 (In Progress): Migration
Tom Clegg
03:07 pm Task #5455 (Resolved): Migration
Tom Clegg
03:40 pm Feature #5104 (Resolved): [SDKs] Add Ruby SDK methods for manipulating collection contents (renam...
Applied in changeset arvados|commit:36f6241516d81c726bb7439650cf6ec56e6d6525. Brett Smith
03:28 pm Feature #5104: [SDKs] Add Ruby SDK methods for manipulating collection contents (rename, delete, ...
commit:cfb2585 LGTM Peter Amstutz
03:35 pm Revision 36f62415 (arvados): Merge branch '5104-ruby-sdk-collections-wip'
Closes #5104, #5423. Brett Smith
03:33 pm Revision 3a38dfbc (arvados): 5104: Add Collection class to the Ruby SDK.
This provides an interface to do filesystem-like operations on a tree
expressed in a manifest. It currently supports...
Brett Smith
03:33 pm Revision 5fd7a6b9 (arvados): 5104: Refactor Ruby SDK test infrastructure into sharable module.
Brett Smith
03:28 pm Task #5423 (Resolved): Review 5104-ruby-sdk-collections-wip
Peter Amstutz
03:07 pm Task #5454 (New): Prototype keep-to-s3 gateway
Tom Clegg
03:06 pm Revision 5aff8103 (arvados): 5418: topnav brand name is clickable only when user is logged in.
Radhika Chippada
03:06 pm Task #5453 (In Progress): Look into authenticating git-http with arvados tokens
Tom Clegg
02:46 pm Task #5453 (Resolved): Look into authenticating git-http with arvados tokens
Tom Clegg
02:39 pm Revision f8e19785 (arvados): 5034: Fixup typo.
Brett Smith
02:15 pm Revision 705c3f77 (arvados): 5034: Improve Workbench collection display.
* Display the UUID, and make it auto-select for easy copying.
* Do the same for the portable data hash, and call it t...
Brett Smith
02:15 pm Revision f1d26c2b (arvados): 5034: Add Keep::Manifest#files_size to Ruby SDK.
Brett Smith
01:54 pm Bug #5451 (New): [Documentation] Fix Go SDK comments so they look reasonable in godoc
The example given at "doc.arvados.org&rarr;SDKs&rarr;Go":http://doc.arvados.org/sdk/go/index.html should move into th... Tom Clegg
01:36 pm Revision 20f3649b (arvados): Fix arv-normalize regression. refs #5145 refs #4823
Peter Amstutz
09:36 am Revision 32324738 (arvados): Update prerequisites
Remove sudo because to run sudo you should already have to have it installed
Add git to download sources from github
David

03/11/2015

09:20 pm Revision 593e8c87 (arvados): refs #5145
Merge branch '5145-combine-collections-repeated-filenames' Radhika Chippada
08:37 pm Bug #5425: [Crunch] SLURM Node failure
Set memory limit per docker container. (total memory / number of tasks)
Peter Amstutz
08:36 pm Revision 0f3960f8 (arvados): 5145: include manifest text in assert error message to identify the ...
Radhika Chippada
08:26 pm Bug #5420: [Workbench] Checkbox selections in collections page is wrong when using back button
Hopefully we just need to add a unique @id@ to each checkbox, so the browser doesn't have to assume the "first two ch... Tom Clegg
08:22 pm Bug #5426: [Workbench] Large downloads through workbench fail
The bug appears to be in our code. Workbench does a fork (IO.popen) to call arv-get and streams the files. Nginx says... Ward Vandewege
02:47 pm Bug #5426: [Workbench] Large downloads through workbench fail
Thoughts
* Could this be a proxy issue? (Try bypassing nginx and downloading from Workbench directly, from inside th...
Tom Clegg
08:21 pm Task #5450 (Resolved): Add test case for looking up a record by created_at, using the exact times...
cf. #5381 Tom Clegg
08:15 pm Bug #5298 (Feedback): [SDKs] Should CollectionReader.all_streams() iterate lines in the manifest,...
Tom Clegg
08:14 pm Bug #5298: [SDKs] Should CollectionReader.all_streams() iterate lines in the manifest, or "logica...
Will update documentation with the existing behavior and note that the method is deprecated (#5449) Peter Amstutz
08:10 pm Bug #5298: [SDKs] Should CollectionReader.all_streams() iterate lines in the manifest, or "logica...
It's intended to preserve the streams as given in the manifest. It certainly makes sense that that's not the desired ... Tom Clegg
08:12 pm Task #5449 (New): Update examples to use new Python Collection SDK and add deprecation notes to o...
Peter Amstutz
07:59 pm Feature #5375: [workbench] Enable in-browser preview for text files in collections
+1 Brett's suggestion of looking up MIME type and considering a file "viewable" if
* its content type is "text/*" or...
Tom Clegg
07:54 pm Task #5027 (In Progress): [Workbench] Improve Content Address/UUID display on Collection page
Brett Smith
07:49 pm Task #5446 (Resolved): Use LDAP OmniAuth gem
Peter Amstutz
07:49 pm Task #5445 (Resolved): Update FUSE to use new SDK
Peter Amstutz
07:32 pm Task #5444 (Resolved): Confirm gitolite integration plan looks OK
Tom Clegg
07:24 pm Task #5270 (New): write Draft 2 spec
Peter Amstutz
07:24 pm Task #5443 (Resolved): Discuss CWL integration plan (Tom/Peter)
Peter Amstutz
07:19 pm Task #5280 (Closed): Review 5246-update-urllib3
Ward Vandewege
07:19 pm Task #5386 (Resolved): Review branch: 5145-combine-collections-repeated-filenames
Ward Vandewege
07:18 pm Task #5430 (Resolved): Review branch: 5304-include-nulls-when-notequal-filter
Radhika Chippada
03:33 pm Task #5430 (In Progress): Review branch: 5304-include-nulls-when-notequal-filter
Brett Smith
07:12 pm Task #5442 (Resolved): Further define requirements (Peter/Ward)
Peter Amstutz
07:00 pm Bug #5145 (Resolved): [Workbench] Combining collections should separate files with identical name...
Applied in changeset arvados|commit:00c9cd4ecab3683d95118ab9d68310ac5069e9f6. Radhika Chippada
06:43 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
commit:b0cf100 looks good to me. Peter Amstutz
04:20 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
Peter, thanks for the regexp lesson. Addressed all three items. Thanks. Radhika Chippada
06:48 pm Task #5432 (Resolved): Review branch: 4426-search-documentation
Radhika Chippada
03:53 pm Task #5432 (In Progress): Review branch: 4426-search-documentation
Peter Amstutz
06:45 pm Bug #4426 (Resolved): [Documentation] Support searching documentation
Applied in changeset arvados|commit:15442761cb6747628b83c54840f7d2f658bdcf2c. Radhika Chippada
06:44 pm Revision 00c9cd4e (arvados): closes #5145
Merge branch '5145-combine-collections-repeated-filenames' Radhika Chippada
06:43 pm Revision 5645698b (arvados): 4426: Adjust styling for search button on search box
Peter Amstutz
06:39 pm Revision bf213b63 (arvados): A series of changes to the top nav bar to make it more compact.
Refs #5211 Ward Vandewege
06:38 pm Task #5441 (Resolved): review 5211-improved-top-navbar
Ward Vandewege
06:38 pm Revision e8d8093c (arvados): Merge branch 'master' into 5145-combine-collections-repeated-filenames
Radhika Chippada
06:29 pm Revision 15442761 (arvados): closes #4426
Merge branch '4426-search-documentation' Radhika Chippada
06:29 pm Revision 09c24107 (arvados): Merge branch 'master' into 4426-search-documentation
Radhika Chippada
06:25 pm Feature #5439: [Tests] Provide a docker image, based on puppet/packer process, that can run the e...
"Quickly" means all dependencies are installed: for example,
* Go, ruby, python, virtualenv, passenger
* the only t...
Tom Clegg
06:16 pm Feature #5439 (New): [Tests] Provide a docker image, based on puppet/packer process, that can run...
This should reduce the prerequisites for a new developer / dev box to just "docker installed & working".
Tom Clegg
06:25 pm Task #5440 (Resolved): [Documentation] Revert doc-to-homepage
1. Title -> Arvados | Documentation
2. Top left link: Arvados -> Arvados Docs
3. Top right link: Developer Site -> ...
Nancy Ouyang
06:21 pm Bug #5211 (In Progress): [Documentation] Top Navbar of docs homepage not suitable for small window
Ward Vandewege
06:04 pm Revision 0c68efd3 (arvados): 4426: convert the search icon to a button
Radhika Chippada
06:00 pm Revision 3e157b65 (arvados): Add missing re import to PySDK arvfile module.
No issue #. Brett Smith
05:48 pm Story #5438 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
Ward Vandewege
05:39 pm Revision 57b96147 (arvados): Merge branch 'master' into 4426-search-documentation
Radhika Chippada
05:38 pm Revision bef8e622 (arvados): 4426: name attribute is needed for google search
Radhika Chippada
04:10 pm Bug #5304 (Resolved): [API] filters incorrectly exclude results for records with null value in fi...
Applied in changeset arvados|commit:83c0e051c3611b021d7f0e2ea58d10c67c92698d. Radhika Chippada
04:02 pm Bug #5304: [API] filters incorrectly exclude results for records with null value in filtered field
Commit:c68037a looks great. Go ahead and merge. Thanks. Brett Smith
04:07 pm Revision b0cf1004 (arvados): Merge branch 'master' into 5145-combine-collections-repeated-filenames
Radhika Chippada
04:07 pm Revision 07cba228 (arvados): 5145: small updates
Radhika Chippada
03:53 pm Revision 83c0e051 (arvados): closes #5304
Merge branch '5304-include-nulls-when-notequal-filter' Radhika Chippada
03:52 pm Revision dfcb25e5 (arvados): Merge branch 'master' into 5304-include-nulls-when-notequal-filter
Radhika Chippada
03:35 pm Story #3761 (Resolved): [Keep] Process entries on the current pull list.
Applied in changeset arvados|commit:ed0ed73d8bdd94dc04c93a1a2bc9f82ad45f6dcf. Radhika Chippada
03:32 pm Story #3761: [Keep] Process entries on the current pull list.
commit:80c3b98 LGTM Peter Amstutz
02:28 pm Story #3761: [Keep] Process entries on the current pull list.
Peter, I updated DiscoverKeepServers to return service_roots and used it. Also added the test. Thanks. Radhika Chippada
03:33 pm Task #5346 (Resolved): Review branch: 3761-pull-list-worker
Peter Amstutz
03:24 pm Task #5422 (Resolved): Review branch: 5374-hide-collection-checkboxes-anonymous
Radhika Chippada
03:23 pm Task #5424 (Resolved): Review branch: 5190-no-hyphens-in-repo-names
Radhika Chippada
03:21 pm Feature #5104: [SDKs] Add Ruby SDK methods for manipulating collection contents (rename, delete, ...
Peter Amstutz wrote:
> LGTM with import_manifest made private per discussion on IRC.
>
> And a test for @dst_coll...
Brett Smith
03:21 pm Revision ed0ed73d (arvados): closes #3761
Merge branch '3761-pull-list-worker' Radhika Chippada
03:14 pm Revision cfb2585c (arvados): Fixups from code review.
Brett Smith
03:14 pm Revision 60501a83 (arvados): Merge branch 'master' into 5145-combine-collections-repeated-filenames
Radhika Chippada
02:38 pm Task #5275 (Resolved): Specify desired behavior
Tom Clegg
02:13 pm Revision 80c3b989 (arvados): 3761: Expand DiscoverKeepServers method to return service_roots and ...
Radhika Chippada
01:32 pm Revision 6a983720 (arvados): Merge branch 'master' into 3761-pull-list-worker
Radhika Chippada
01:31 pm Revision a37e37c9 (arvados): 3761: add a test with invalid data manager token and expect the item...
Radhika Chippada
01:27 am Task #4341 (Resolved): Make the manual installation documentation more complete.
Ward Vandewege
01:27 am Support #4186 (Resolved): [Documentation] Install documentation improvements
Ward Vandewege
01:26 am Support #5252 (Resolved): [Support] Fix bugs and write tests (second half)
Ward Vandewege

03/10/2015

10:10 pm Task #5432 (Resolved): Review branch: 4426-search-documentation
Radhika Chippada
10:08 pm Revision e8ced6e0 (arvados): Merge branch 'master' into 4426-search-documentation
Radhika Chippada
10:08 pm Revision 26ad23e1 (arvados): 4426: add google search in doc topnav
Radhika Chippada
09:14 pm Feature #5297: [Workbench] Enable users to share with any other user
One way to reconcile "I can share with anyone I want" with "I'm invisible to some users" features is an out-of-band "... Tom Clegg
09:00 pm Feature #5104: [SDKs] Add Ruby SDK methods for manipulating collection contents (rename, delete, ...
LGTM with import_manifest made private per discussion on IRC.
And a test for @dst_coll.cp_r(".", ".", src_coll)@
Peter Amstutz
05:28 pm Feature #5104: [SDKs] Add Ruby SDK methods for manipulating collection contents (rename, delete, ...
Tom Clegg wrote:
> Brett Smith wrote:
> > Ruby also has "@FileUtils::cp_r@, which does not have that limit":http://...
Brett Smith
08:20 pm Task #5178 (Resolved): Review sigint branch on arvados-dev
Applied in changeset arvados-dev|commit:6c6ca86bfa400d880d051fd87c7c1fb9b8905114. Anonymous
08:16 pm Revision 6c6ca86b (arvados): Merge branch 'sigint' closes #5178
Tom Clegg
08:16 pm Revision 6c6ca86b (arvados-dev): Merge branch 'sigint' closes #5178
Tom Clegg
08:11 pm Story #4783 (Resolved): [CWL] Implement CWL prototype workflow runner
Peter Amstutz
08:11 pm Task #5431 (Resolved): Implement workflow runner and add tests
Peter Amstutz
08:11 pm Task #5431 (Resolved): Implement workflow runner and add tests
Peter Amstutz
08:10 pm Bug #5182 (Resolved): [Workbench] CORS error uploading via browser - better JS error handling needed
Applied in changeset arvados|commit:855a790d7be3ff345f04226bde3719fb90e6d9a5. Anonymous
08:02 pm Bug #5182: [Workbench] CORS error uploading via browser - better JS error handling needed
Tom,
* The error message are SO MUCH better now. They are quite readable and helpful now. Thanks.
* Regarding "...
Radhika Chippada
07:44 pm Bug #5182: [Workbench] CORS error uploading via browser - better JS error handling needed
Radhika Chippada wrote:
> Review comments:
>
> Just a couple minor text suggestions.
>
> * This error message ...
Tom Clegg
04:44 pm Bug #5182: [Workbench] CORS error uploading via browser - better JS error handling needed
Review comments:
Just a couple minor text suggestions.
* This error message seems too technical: “A network err...
Radhika Chippada
03:12 pm Bug #5182 (In Progress): [Workbench] CORS error uploading via browser - better JS error handling ...
Tom Clegg
02:32 pm Bug #5182: [Workbench] CORS error uploading via browser - better JS error handling needed
Three improvements in 5182-cors-error-reporting:
* By design, browsers make the "CORS headers do not permit this r...
Tom Clegg
08:09 pm Story #3761: [Keep] Process entries on the current pull list.
@GetKeepServices()@ should use @keepclient.DiscoverKeepServers()@ (or at least @arvadosclient.Call()@) instead of rei... Peter Amstutz
03:29 pm Story #3761: [Keep] Process entries on the current pull list.
* Added integration tests for pull worker. These are starting the api server and keep servers using arvadostest.run_s... Radhika Chippada
08:06 pm Revision 855a790d (arvados): Merge branch '5182-cors-error-reporting' closes #5182
Tom Clegg
08:03 pm Bug #4426 (In Progress): [Documentation] Support searching documentation
Radhika Chippada
08:03 pm Task #5427 (Resolved): Review 5182-cors-error-reporting
Radhika Chippada
04:27 pm Task #5427 (In Progress): Review 5182-cors-error-reporting
Radhika Chippada
02:06 pm Task #5427 (Resolved): Review 5182-cors-error-reporting
Tom Clegg
08:02 pm Revision 7b264271 (arvados): Merge branch 'master' into sigint
Conflicts:
jenkins/run-tests.sh
Tom Clegg
08:02 pm Revision 7b264271 (arvados-dev): Merge branch 'master' into sigint
Conflicts:
jenkins/run-tests.sh
Tom Clegg
07:55 pm Bug #5073 (Resolved): [Documentation] List known limitations of docker install at doc.arvados.org...
Applied in changeset arvados|commit:07618b6828e179f39df2918f4f8a2d8f59d2c6d9. Anonymous
07:31 pm Bug #5073: [Documentation] List known limitations of docker install at doc.arvados.org/install
5073-docker-limitations LGTM Ward Vandewege
07:52 pm Revision 07618b68 (arvados): Merge branch '5073-docker-limitations' closes #5073
Tom Clegg
07:47 pm Bug #5105 (Resolved): [Workbench] AJAX content loaders should not follow a redirect to the welcom...
Tom Clegg
07:06 pm Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
commit:2d0dd74f is good to merge. Thanks. Brett Smith
06:59 pm Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
Brett Smith wrote:
> That sounds good, and I feel better about this assertion knowing it. A comment to that effect ...
Tom Clegg
05:47 pm Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
Tom Clegg wrote:
> I wanted to check for @"html html"@ or @"body body"@ but the browser seems to automatically colla...
Brett Smith
03:42 pm Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
Brett Smith wrote:
> Reviewing commit:6058d8a. The branch looks great, this is all pretty small potatoes.
>
> * ...
Tom Clegg
07:46 pm Task #5390 (Resolved): Review 5105-ajax-redirect
Tom Clegg
07:46 pm Revision ebbe2d75 (arvados): Merge branch '5105-ajax-redirect' closes #5105
Tom Clegg
07:44 pm Revision fc79e9d9 (arvados): 5182: Tweak error messages.
Tom Clegg
07:31 pm Task #5429 (Resolved): Review 5073-docker-limitations
Ward Vandewege
07:31 pm Task #5429 (In Progress): Review 5073-docker-limitations
Ward Vandewege
06:38 pm Task #5429 (Resolved): Review 5073-docker-limitations
Tom Clegg
06:50 pm Revision 2d0dd74f (arvados): 5105: Clarify "no double-layout" asserts. Remove redundant "not on w...
Tom Clegg
06:46 pm Task #5430 (Resolved): Review branch: 5304-include-nulls-when-notequal-filter
Radhika Chippada
06:44 pm Revision c68037a9 (arvados): 5304: include nulls in resutls when filter operator is "!="
Radhika Chippada
06:38 pm Revision 56907cb9 (arvados): 5073: Document docker limitations. Bring "overview" up to the top of...
Tom Clegg
06:38 pm Revision 5fba915c (arvados): 5073: Update ruby version to 2.1.5
Tom Clegg
06:38 pm Task #5262 (Resolved): Update install doc page
Tom Clegg
06:22 pm Feature #5034 (In Progress): [Workbench] Show content statistics/summary (total size, number of f...
Brett Smith
06:13 pm Bug #5304 (In Progress): [API] filters incorrectly exclude results for records with null value in...
Radhika Chippada
06:04 pm Revision 341344e1 (arvados-dev): 5313: Build a .deb for the PyCrypto Python package.
libcloud's GCE driver requires this, so building it supports deploying
Node Manager on GCE. Refs #5313.
Brett Smith
06:04 pm Revision 341344e1 (arvados): 5313: Build a .deb for the PyCrypto Python package.
libcloud's GCE driver requires this, so building it supports deploying
Node Manager on GCE. Refs #5313.
Brett Smith
05:24 pm Revision dad9a13b (arvados): 5104: Implement code review feedback.
Brett Smith
03:40 pm Revision bc25cf11 (arvados): 5105: Better assertion for tab-loading error display.
Tom Clegg
03:17 pm Revision fed95824 (arvados): 5105: Restore previous token in an ensure block.
Tom Clegg
03:09 pm Story #5428 (New): [Tests] Enhance keep testing to support signed locators.
Background:
Currently run_test_servers.py does not support enabling Keep permission signatures when invoked via co...
Radhika Chippada
02:06 pm Task #5272 (Resolved): Detect CORS failure and display error message
Tom Clegg
02:06 pm Task #5419 (Resolved): Document how to set CORS headers on nginx proxy
Tom Clegg
01:42 pm Revision ede1e367 (arvados): 3761: Working!!!!
Radhika Chippada
01:23 pm Bug #5426 (Resolved): [Workbench] Large downloads through workbench fail
Right around 1 GiB, this download fails (notice that it fails at two different positions, but the same position the l... Peter Amstutz
12:57 pm Bug #4956 (Resolved): [API] cannot create collections with very large manifests
Peter Amstutz
12:55 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
Radhika Chippada wrote:
> * normalized = normalized.gsub(/\d+:\d+:(#{Regexp.quote manifest_file})/) {|s| uniq_file}
...
Peter Amstutz
07:06 am Revision 572a7497 (arvados): 5182: Silently skip Angular initialization if injector() returns null.
This happens occasionally during tests, and seems benign (except that
our tests demand an empty debug console).
Tom Clegg
07:00 am Revision 8c473f08 (arvados): 5182: Improve error reporting in uploader.
Missing CORS headers (and network errors which force the browser to
assume CORS headers are missing) are reported as ...
Tom Clegg
03:19 am Revision edc5c5d8 (arvados): 3761: a little refactoring
Radhika Chippada
02:53 am Revision 5744e0bd (arvados): Merge branch 'master' into 3761-pull-list-worker
Radhika Chippada
02:53 am Revision 3e39701d (arvados): 3761: need at least 1 replica
Radhika Chippada
02:31 am Revision 017f264a (arvados): 5145: revert back fixture update and instead add a new fixture for t...
Radhika Chippada

03/09/2015

09:22 pm Feature #5104: [SDKs] Add Ruby SDK methods for manipulating collection contents (rename, delete, ...
Brett Smith wrote:
> I like the principle that our SDKs should feel native to the language they're in, but the fact ...
Tom Clegg
08:18 pm Feature #5104: [SDKs] Add Ruby SDK methods for manipulating collection contents (rename, delete, ...
Tom Clegg wrote:
> Brett Smith wrote:
> > Another way to put it is, the Ruby SDK currently implements @rsync -r@, w...
Brett Smith
08:05 pm Feature #5104: [SDKs] Add Ruby SDK methods for manipulating collection contents (rename, delete, ...
Brett Smith wrote:
> Another way to put it is, the Ruby SDK currently implements @rsync -r@, while the Python SDK im...
Tom Clegg
06:38 pm Feature #5104: [SDKs] Add Ruby SDK methods for manipulating collection contents (rename, delete, ...
Thanks Peter. I'm writing up some of the in-office discussion about API considerations for Tom's benefit.
Peter A...
Brett Smith
05:52 pm Feature #5104: [SDKs] Add Ruby SDK methods for manipulating collection contents (rename, delete, ...
h2. Comments
For consistency with the Python SDK terminology, consider using the term "segments" instead of "range...
Peter Amstutz
09:04 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
* normalized = normalized.gsub(/\d+:\d+:(#{Regexp.quote manifest_file})/) {|s| uniq_file}
This is resulting in rem...
Radhika Chippada
06:34 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
... Peter Amstutz
08:57 pm Revision f747bc4a (arvados): 5145: better pattern matching for manifest text files
Radhika Chippada
07:10 pm Bug #5190 (Resolved): [Workbench] Tell admins not to put hyphens in repository names
Applied in changeset arvados|commit:cab38660eec30ff5d4e023f5d607d783ffd91785. Radhika Chippada
07:04 pm Bug #5190: [Workbench] Tell admins not to put hyphens in repository names
Yes, we decided to just inform the admin users to not use hyphens and not really address the actual gitolite issue. T... Radhika Chippada
06:50 pm Bug #5190: [Workbench] Tell admins not to put hyphens in repository names
Alternately (if the story was de facto updated without updating the story description) the text at least needs to be ... Peter Amstutz
06:47 pm Bug #5190: [Workbench] Tell admins not to put hyphens in repository names
The description says
"The API server should validate the name to ensure that only valid repository names can be se...
Peter Amstutz
07:08 pm Revision 42efffec (arvados): Merge branch 'master' into 5145-combine-collections-repeated-filenames
Radhika Chippada
07:07 pm Bug #5352: [Crunch] Dispatcher not handling node allocation failures
Doing a dummy commit ('dirtying' the git repo) and re-running the pipeline looks to work. Abram Connelly
04:57 pm Bug #5352: [Crunch] Dispatcher not handling node allocation failures
It's hard to be sure but I think this issue gets triggered when a job/pipeline fails for some reason and then the nex... Abram Connelly
07:04 pm Revision cab38660 (arvados): closes #5190
Merge branch '5190-no-hyphens-in-repo-names' Radhika Chippada
07:02 pm Revision c11612fd (arvados): 5190: updated tooltip
Radhika Chippada
07:00 pm Bug #5374 (Resolved): [workbench] Anonymous collection -- ineffectual checkboxes
Applied in changeset arvados|commit:349983851afa2bce63fbff33933d33a5ba13b8eb. Radhika Chippada
06:52 pm Bug #5374: [workbench] Anonymous collection -- ineffectual checkboxes
LGTM Peter Amstutz
06:40 pm Bug #5374: [workbench] Anonymous collection -- ineffectual checkboxes
If the user can't select anything, we should probably hide the "selection" dropdown entirely. Peter Amstutz
06:55 pm Revision ef09ad4c (arvados): Merge branch 'master' into 5190-no-hyphens-in-repo-names
Radhika Chippada
06:55 pm Revision 34998385 (arvados): closes #5374
Merge branch '5374-hide-collection-checkboxes-anonymous' Radhika Chippada
06:50 pm Revision de828286 (arvados): Merge branch 'master' into 5374-hide-collection-checkboxes-anonymous
Radhika Chippada
06:43 pm Revision e6c2f09b (arvados): Merge branch 'master' into 5374-hide-collection-checkboxes-anonymous
Radhika Chippada
06:42 pm Revision eb1b1a9e (arvados): 3761: get keep services
Radhika Chippada
06:41 pm Task #5424 (In Progress): Review branch: 5190-no-hyphens-in-repo-names
Peter Amstutz
06:36 pm Task #5422 (In Progress): Review branch: 5374-hide-collection-checkboxes-anonymous
Peter Amstutz
06:20 pm Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
Reviewing commit:6058d8a. The branch looks great, this is all pretty small potatoes.
* I wonder about the negativ...
Brett Smith
05:59 pm Revision 4d71b77b (arvados): 5182: Advise adding CORS headers to proxy error responses.
Tom Clegg
05:00 pm Task #5390 (In Progress): Review 5105-ajax-redirect
Brett Smith
04:12 pm Revision efd59dbd (arvados): 5319: Include CurrentApiClient in migration model.
Needed to use system_user_uuid. Refs #5319. Brett Smith
03:47 pm Task #5389 (Resolved): Review 5261-project-description
Tom Clegg
03:40 pm Task #5369 (Resolved): Review 5319-fix-hinted-collection-hashes-wip
Applied in changeset arvados|commit:19656a41f019488120f950b06ecf9e19074b11a3. Brett Smith
03:40 pm Bug #5319 (Resolved): [API] Portable data hash mismatches for collections with location hints (+K)
Applied in changeset arvados|commit:19656a41f019488120f950b06ecf9e19074b11a3. Brett Smith
03:31 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
Thanks. LGTM Peter Amstutz
03:29 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
Peter Amstutz wrote:
> I noticed that it doesn't actually update the contents of @manifest_text@. Is that intention...
Brett Smith
01:12 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
I noticed that it doesn't actually update the contents of @manifest_text@. Is that intentional or an oversight?
@...
Peter Amstutz
03:35 pm Revision 19656a41 (arvados): Merge branch '5319-fix-hinted-collection-hashes-wip'
Closes #5319, #5369. Brett Smith
03:32 pm Revision 2a610a9d (arvados): 5319: Add API migration for manifests with bad portable data hashes.
Refer to #5319 for background discussion and rationale. The migration
ensures that collections are still addressable...
Brett Smith
03:32 pm Revision cf3a1032 (arvados): 5319: Fix incorrect portable_data_hash in test fixture.
Brett Smith
03:04 pm Bug #5425 (Resolved): [Crunch] SLURM Node failure
I have seen repeated SLURM node failures when re-running Sally's killer job of doom. We should find out why.
http...
Peter Amstutz
02:00 pm Task #5423 (In Progress): Review 5104-ruby-sdk-collections-wip
Peter Amstutz
01:42 pm Revision 2ae40cbb (arvados): Merge branch 'master' into 3761-pull-list-worker
Radhika Chippada
01:40 pm Task #5419 (In Progress): Document how to set CORS headers on nginx proxy
Tom Clegg
01:35 pm Feature #5261 (Resolved): [Workbench] Show project description in its own tab
Applied in changeset arvados|commit:633660dcd81d4ddea5c0a55a7731af35c4586052. Anonymous
01:30 pm Revision 633660dc (arvados): Merge branch '5261-project-description' closes #5261
Tom Clegg
12:43 pm Story #4783 (In Progress): [CWL] Implement CWL prototype workflow runner
Peter Amstutz
12:42 pm Story #5257 (New): [CWL] write draft 2 spec
Peter Amstutz
07:11 am Bug #5373: [Docker] Web Application Could not be Started
Brett Smith wrote:
> Neelam,
>
> Can you please let me know what process you used to upgrade and restart the Dock...
neelam yadav
04:10 am Revision 8f4c794c (arvados): 5261: Fix DST transition bug: browser timezone != test suite timezone.
Tom Clegg
03:37 am Revision 44690743 (arvados): 5105: report issue was not working in chrome. added remotipart which...
Radhika Chippada

03/08/2015

11:38 pm Task #5424 (Resolved): Review branch: 5190-no-hyphens-in-repo-names
Radhika Chippada
11:37 pm Bug #5190 (In Progress): [Workbench] Tell admins not to put hyphens in repository names
Radhika Chippada
11:36 pm Revision ca111ab9 (arvados): 5190: tell user to not use hyphens in tooltip for repository name ed...
Radhika Chippada
09:14 pm Task #5423 (Resolved): Review 5104-ruby-sdk-collections-wip
Brett Smith
09:13 pm Task #5107 (Resolved): Add collections#rename and collections#delete methods to Ruby SDK
Brett Smith
09:13 pm Task #5109 (Resolved): Add "import files from another collection" API to Ruby SDK
Brett Smith
09:13 pm Task #5108 (Resolved): Implement internal representation for collections in Ruby SDK (analogous t...
Brett Smith
09:12 pm Revision 64046fa6 (arvados): 5104: Add Collection class to the Ruby SDK.
This provides an interface to do filesystem-like operations on a tree
expressed in a manifest. It currently supports...
Brett Smith
07:03 pm Revision 1df8b462 (arvados): 5261: Merge branch 'master' into 5261-project-description
Tom Clegg
07:03 pm Revision 1fa86a46 (arvados): 5261: Change placeholder text from "New group" to "New project"
Tom Clegg
04:31 pm Task #5422 (Resolved): Review branch: 5374-hide-collection-checkboxes-anonymous
Radhika Chippada
04:30 pm Bug #5374 (In Progress): [workbench] Anonymous collection -- ineffectual checkboxes
Discussed with Tom. We will hide the checkboxes in anonymous view for collection#show page. Radhika Chippada
04:25 pm Revision aa50f466 (arvados): 5374: in collection show page, hide checkboxes for anonymous user view.
Radhika Chippada
03:50 pm Revision 81baf362 (arvados): 3761: integration test WIP
Radhika Chippada
01:47 am Bug #5215 (Resolved): [Workbench] When a pipeline is run using "output_name = false," the job out...
Tom confirmed that using "output_name = false" does not result in marking the output collections as expired. They are... Radhika Chippada
01:38 am Bug #5420 (Resolved): [Workbench] Checkbox selections in collections page is wrong when using bac...
* Go to "/collections" page
* Select one or more collections; let's say you selected collection 1 and 2
* Use t...
Radhika Chippada
12:22 am Revision 560ceadf (arvados): 3761: (WIP) add integration test for pull_worker
Radhika Chippada
 

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