Activity

From 02/16/2015 to 03/17/2015

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): 5416: Add --retry flag: when a test suite fails, prompt to try that ...
Tom Clegg
03:01 pm Revision a00ef863 (arvados-dev): 5416: Add --retry flag: when a test suite fails, prompt to try t...
Tom Clegg
03:00 pm Revision 3c0d0df8 (arvados): 5416: Add arv-git-httpd.
Tom Clegg
03:00 pm Revision 3c0d0df8 (arvados-dev): 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): 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-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
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 cf3a1032 (arvados): 5319: Fix incorrect portable_data_hash in test fixture.
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
03:04 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

03/07/2015

03:30 am Task #5419 (Resolved): Document how to set CORS headers on nginx proxy
Tom Clegg

03/06/2015

10:24 pm Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
Tom Clegg wrote:
> Just noticed that I still didn't fix the "report issue" feature enough to actually submit the use...
Tom Clegg
10:11 pm Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
Just noticed that I still didn't fix the "report issue" feature enough to actually submit the user-entered text/info.... Tom Clegg
02:50 am Bug #5105 (In Progress): [Workbench] AJAX content loaders should not follow a redirect to the wel...
Tom Clegg
02:49 am Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
Coincidentally, #5261 revealed a related bug, and fixed it with a general "don't respond to XHR with 302" change (com... Tom Clegg
10:23 pm Revision 6058d8a2 (arvados): 5105: Include form data with report_issue request.
Tom Clegg
10:03 pm Bug #5365: [Workbench] Do not link to objects that are not readable by current user
Generally, Workbench should not link to objects that are not readable.
In the specific case of the Log tab, when t...
Tom Clegg
09:35 pm Bug #5211: [Documentation] Top Navbar of docs homepage not suitable for small window
Debatably the problem is that there are too many top nav elements.
Suggest
* Merge the nearly-useless "Admin Guid...
Tom Clegg
09:32 pm Bug #5179: [Workbench] [SDKs] Incorrect collection display when stream has entries with subdirect...
Best fix for this is probably to use the new SDK from #5104. Tom Clegg
09:23 pm Bug #5304: [API] filters incorrectly exclude results for records with null value in filtered field
Agreed. The SQL way of thinking (NULL == 1 is false, and NULL <> 1 is also false) seems confusing enough to be worth ... Tom Clegg
09:15 pm Bug #5235: [Workbench] Pipeline instance "Re-run with latest" button occasionally returns Not fou...
Any clues in our workbench access/Rails logs? Tom Clegg
09:13 pm Bug #5198 (In Progress): [Workbench] Middle clicking on Run this pipeline brings fiddlesticks
Tom Clegg
09:09 pm Bug #5318 (Feedback): [Workbench] Make note of lag time when changing git permissions
Tom Clegg
08:57 pm Bug #5418 (Resolved): [Workbench] Make the brand/root link unclickable when not logged in
Tom Clegg
08:43 pm Bug #5215 (In Progress): [Workbench] When a pipeline is run using "output_name = false," the job ...
Tom Clegg
08:22 pm Bug #5417 (Resolved): [Workbench] Show error condition / refuse to start a pipeline instance if s...
Tom Clegg
08:19 pm Revision f54333c8 (arvados): 3761: update GetContent function to use read_content test data info.
Radhika Chippada
07:57 pm Feature #5261: [Workbench] Show project description in its own tab
* Agree with you about "editing description". Let's not worry about it at this time.
* I do not like "Read me" for...
Radhika Chippada
06:30 pm Feature #5261: [Workbench] Show project description in its own tab
Radhika Chippada wrote:
> * The “Name” of the project is only shown in the Summary tab.
Fixed. &rarr; commit:9b3c...
Tom Clegg
04:36 pm Feature #5261: [Workbench] Show project description in its own tab
* The new Summary tab displays Name and Description (partial: 'name_and_description’). This needs to be split into tw... Radhika Chippada
02:50 am Feature #5261 (In Progress): [Workbench] Show project description in its own tab
Tom Clegg
07:49 pm Feature #5416 (Resolved): [API] Clone git repositories without using an SSH private key
Tom Clegg
07:31 pm Feature #5415 (New): [Workbench] Improve presentation of anonymously-viewed collections (via both...
Features wanted
* "wget-friendly" page should have a link -- which wget/curl tools know not to follow -- to the regu...
Tom Clegg
07:26 pm Feature #5414 (Closed): [Keep] Use data stored remotely (not in local keepstore)
Tom Clegg
07:21 pm Revision 2a4c56d2 (arvados): 3761: move test assertions from teardown method into performTest fun...
Radhika Chippada
07:05 pm Support #5252 (In Progress): [Support] Fix bugs and write tests (second half)
Ward Vandewege
07:05 pm Feature #5104 (In Progress): [SDKs] Add Ruby SDK methods for manipulating collection contents (re...
Brett Smith
07:04 pm Feature #5297: [Workbench] Enable users to share with any other user
The current setup makes it possible to have a multi-tenant site, where disjoint sets of users don't see one another. ... Tom Clegg
07:01 pm Bug #5320 (Closed): [Docker] SLURM does not start reliably on API server
Tom Clegg
06:57 pm Feature #5118 (In Progress): [OPS] Use packer to generate docker images for our various services
Ward Vandewege
06:42 pm Feature #5413 (New): [DRAFT] [API/SSO] Use externally-defined (e.g., LDAP) groups as permission g...
If groups/permissions have already been encoded in another system, it should be possible to import or use them direct... Tom Clegg
06:39 pm Feature #5412 (Resolved): [SSO] Support LDAP-only configuration
Included:
* Admin configures SSO to use _only_ LDAP strategy
Not included:
* Support Google and LDAP logins from...
Tom Clegg
06:05 pm Revision 8c19d0da (arvados): 5261: Rename Summary tab to Description.
Tom Clegg
05:47 pm Revision 9b3c1e96 (arvados): 5261: Move project name from Summary tab back to heading area.
Tom Clegg
04:37 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
Peter Amstutz wrote:
> General comment: my understanding is that best practices for migrations to modify the tables ...
Brett Smith
04:36 pm Revision cea7dc41 (arvados): 5319: Fixup migration UUID generation code.
Brett Smith
04:22 pm Revision 18cc8023 (arvados): 5319: Migration fixups from code review.
Brett Smith
02:33 pm Task #5389 (In Progress): Review 5261-project-description
Radhika Chippada
02:32 pm Task #5386 (In Progress): Review branch: 5145-combine-collections-repeated-filenames
Peter Amstutz
02:28 pm Story #3761: [Keep] Process entries on the current pull list.
In @Pull()@, @KeepClient.Arvados.ApiToken@ needs to be set to match the value from @GenerateRandomApiToken()@.
@pu...
Peter Amstutz
01:54 pm Feature #5391 (New): [SDK] Go KeepClient offers a "read block" API that recovers from transmissio...
As an optimization, the Go keep client uses @HashCheckingReader@ which computes the hash incrementally and only repor... Peter Amstutz
02:50 am Task #5266 (Closed): Detect various AJAX errors and ensure fail handler runs
Tom Clegg
02:50 am Task #5265 (Closed): Add tests for redirect, timeout, and error
Tom Clegg
02:38 am Revision db1542b9 (arvados): 5105: Skip database reset where we use a mock instead of the real API.
Tom Clegg
02:34 am Revision 797d78f4 (arvados): 5105: Remove unnecessary self.included/class_eval stuff.
Tom Clegg
02:01 am Task #5390 (Resolved): Review 5105-ajax-redirect
Tom Clegg

03/05/2015

11:58 pm Revision d554f6e4 (arvados): 5105: Really call the report_issue action, instead of fetching "/",
when the "send" button is clicked. Tom Clegg
11:38 pm Revision 878b0ff6 (arvados): 5105: Move displaced comment.
Tom Clegg
11:38 pm Revision 4e98958d (arvados): 5105: Add API stub helpers and basic ArvadosApiClient unit tests.
Tom Clegg
11:38 pm Revision 470e9c16 (arvados): 5105: Treat not-logged-in AJAX requests as errors, instead of redire...
Tom Clegg
11:38 pm Revision 630b5256 (arvados): 5105: Tidy up test case.
Tom Clegg
11:16 pm Revision a9fdae7d (arvados): 5104: Refactor Ruby SDK test infrastructure into sharable module.
Brett Smith
11:07 pm Story #3761: [Keep] Process entries on the current pull list.
Peter, addressed all your feedback and the tests are much more readable now. I also made the GetContent and PutConten... Radhika Chippada
10:59 pm Revision c7200a36 (arvados): 3761: Improve the tests to RunTestPullWorker for each test and verif...
Add a test that puts two items on the queue and verifies that old item is overwritten by the new item. Radhika Chippada
10:46 pm Revision 130511ce (arvados): 5105: Treat not-logged-in AJAX requests as errors, instead of redire...
Tom Clegg
10:43 pm Task #5266 (In Progress): Detect various AJAX errors and ensure fail handler runs
Tom Clegg
10:20 pm Revision 2b8a6158 (arvados): 5105: Move displaced comment.
Tom Clegg
09:56 pm Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
!5105-tab-logged-out.png! Tom Clegg
09:12 pm Revision a882872e (arvados): 3761: verify ReadContent and PutContent outputs.
Radhika Chippada
09:12 pm Bug #5388: [Crunch] Jobs do not re-run with latest docker image if job is unchanged but docker im...
I should mention that I'm submitting the job via the CLI tool 'arv-run-pipeline-instance':... Abram Connelly
09:00 pm Bug #5388 (Resolved): [Crunch] Jobs do not re-run with latest docker image if job is unchanged bu...
I successfully ran a job with a docker image of my own making called 'arvados/dax-node'. I did not alter the job but... Abram Connelly
09:10 pm Task #5265 (In Progress): Add tests for redirect, timeout, and error
Tom Clegg
09:07 pm Task #5389 (Resolved): Review 5261-project-description
Tom Clegg
08:09 pm Revision 1c6d77f9 (arvados): 5261: Fix {redirect_to @object} usage.
Tom Clegg
07:56 pm Feature #5387 (New): [DRAFT] [Workbench] Improve provenance/used-by graphs so they are legible ev...
It seems really jumbled here: qr1hi-4zz18-5pcbxfehz0md08h
I think this could use some reworking to make it easier ...
Bryan Cosca
07:43 pm Revision 314b31df (arvados): 3761: include names in test data initializations
Radhika Chippada
07:39 pm Revision 31778296 (arvados): 5105: Add API stub helpers and basic ArvadosApiClient unit tests.
Tom Clegg
07:39 pm Task #5385 (Resolved): Update tests
Tom Clegg
02:52 pm Task #5385 (In Progress): Update tests
Tom Clegg
02:52 pm Task #5385 (Resolved): Update tests
Tom Clegg
07:38 pm Revision 86801538 (arvados): 5261: Redirect to destination project's Collections tab when copying...
Tom Clegg
07:37 pm Task #5263 (Resolved): Add API mocking facility
Tom Clegg
02:52 pm Task #5263 (In Progress): Add API mocking facility
Tom Clegg
07:07 pm Revision 57991d19 (arvados): 5261: When redirecting during an AJAX request, send the target URI in
a JSON object {"href":"..."} instead of responding 302.
This lets us use "redirect_to X" to mean "send the user to p...
Tom Clegg
06:58 pm Revision d0583fc9 (arvados): 5261: Update tests.
Tom Clegg
06:31 pm Revision a798ad3d (arvados): 3761: log errors in RunPullWorker instead of Pull method.
Radhika Chippada
04:37 pm Revision a69c06d2 (arvados): 3761: pass keepClient to Pull method
Radhika Chippada
03:35 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
* Updated combine action to handle duplicate names by appending a number to the file name being repeated.
* Combin...
Radhika Chippada
03:28 pm Task #5386 (Resolved): Review branch: 5145-combine-collections-repeated-filenames
Radhika Chippada
03:20 pm Revision 7699440a (arvados): Merge branch 'master' into 3761-pull-list-worker
Radhika Chippada
02:52 pm Task #5347 (Resolved): Rearrange projects#show layout
Tom Clegg
02:38 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
General comment: my understanding is that best practices for migrations to modify the tables directly using SQL, inst... Peter Amstutz
02:27 pm Revision b5c6c474 (arvados): 5145: add tests to verify combine collections with duplicate filenames
Radhika Chippada
02:17 pm Task #5369 (In Progress): Review 5319-fix-hinted-collection-hashes-wip
Peter Amstutz

03/04/2015

11:00 pm Feature #5384 (New): [DRAFT] [Workbench] Improve display of pipelines and jobs
screenshots attached. Cleaner, but ctrl-f doesn't work easily on the whole pipeline.
It's kind of a trade-off betwe...
Nancy Ouyang
09:40 pm Bug #5383 (Resolved): [API] API server should always retrieve current time from database, never T...
If possible, the created_at and modified_at timestamps should be set by putting CURRENT_TIMESTAMP() in the SQL statem... Tom Clegg
09:38 pm Revision d67d6c4e (arvados): Merge branch 'master' into 5145-combine-collections-repeated-filenames
Radhika Chippada
09:31 pm Revision fc1d010f (arvados): 5145: while combining colletions, append an integer for any duplicat...
Radhika Chippada
09:28 pm Feature #5382 (New): [Documentation] arvados VM simulator, demonstrating how it looks to use Arva...
Example: https://divshot.com
* No need to interact with the real world at all. Not intended as a way to actually get...
Tom Clegg
09:00 pm Bug #5381 (New): [Crunch] Node went away unexpectedly during pipeline run.
In pipeline 4xphq-d1hrv-rfu9kj37vmke3dh the first two jobs use compute9, then compute9 goes away unexpectedly before ... Peter Amstutz
07:51 pm Task #5376 (New): [workbench] wget link or download-all link in public collections
Should be present by default & link should be logical .
https://workbench.qr1hi.arvadosapi.com/collections/qr1hi-4...
Nancy Ouyang
07:49 pm Revision 6ba419ef (arvados): 5261: Move project name and description into a Summary tab.
Reduce tab font size to reduce chances of word-wrapping tabs. Tom Clegg
07:45 pm Feature #5375 (New): [workbench] Enable in-browser preview for text files in collections
The magnifying class should be enabled --
Just displaying the first 100kb is fine.
https://github.com/github/lin...
Nancy Ouyang
07:20 pm Bug #5374 (Resolved): [workbench] Anonymous collection -- ineffectual checkboxes
Either the checkboxes should not exist, or you should be able to say "select/deselect all" and "download selected"
...
Nancy Ouyang
07:19 pm Story #5257 (In Progress): [CWL] write draft 2 spec
Peter Amstutz
07:19 pm Task #5270 (In Progress): write Draft 2 spec
Peter Amstutz
07:13 pm Revision fcad01c9 (arvados): Merge branch '4956-limit-request-size' refs #4956
Peter Amstutz
07:13 pm Revision 5fbc413c (arvados): 4956: Mark monkey patching methods as internal
Peter Amstutz
07:11 pm Task #5366 (Resolved): Review 4956-limit-request-size
Peter Amstutz
04:52 pm Task #5366 (In Progress): Review 4956-limit-request-size
Tom Clegg
07:05 pm Revision 068189e8 (arvados): 4956: Refactor http request patching used in Python SDK.
Test_request_too_large uses published size instead of hardcoded size. Make
note that user must configure upstream we...
Peter Amstutz
07:03 pm Task #5367 (Resolved): Review 5246-urllib3-workaround
Peter Amstutz
03:17 pm Task #5367 (In Progress): Review 5246-urllib3-workaround
Brett Smith
06:16 pm Task #5347 (In Progress): Rearrange projects#show layout
Tom Clegg
06:14 pm Bug #4956: [API] cannot create collections with very large manifests
The test in @sdk/python/tests/test_api.py@ would be a bit more stable if it looked up the request limit in the discov... Tom Clegg
05:05 pm Bug #5246 (Resolved): [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError...
Applied in changeset arvados|commit:3979c83819a07b544aa4a0510bbeb58d1c92905a. Peter Amstutz
04:58 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
commit:b434a3a8 is good to merge. Thanks. Brett Smith
04:57 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
Brett Smith wrote:
> Reviewing commit:0b4ad564. I'm fine with the fix in principle.
>
> The version-parsing code...
Peter Amstutz
03:12 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
Reviewing commit:0b4ad564. I'm fine with the fix in principle.
The version-parsing code isn't rich enough. As on...
Brett Smith
05:03 pm Revision 3979c838 (arvados): Merge branch '5246-urllib3-workaround' closes #5246
Peter Amstutz
04:59 pm Revision b434a3a8 (arvados): 5246: Use pkg_resources.parse_version to test urllib3 version string...
Debian 8 specifically in comment. Peter Amstutz
04:40 pm Bug #5043 (Resolved): [Crunch] accept arbitrarily long stderr lines in crunchstat
Applied in changeset arvados|commit:a04ea95e79c60ed2a54eaec5b5c2e235fe39ef9a. Anonymous
04:32 pm Bug #5043: [Crunch] accept arbitrarily long stderr lines in crunchstat
Tom Clegg wrote:
> It's not just luck: the Go log library also guarantees "each logging operation makes a single c...
Peter Amstutz
04:36 pm Revision a04ea95e (arvados): Merge branch '5043-crunchstat-long-lines' closes #5043
Tom Clegg
04:36 pm Task #5360 (Resolved): Review 5043-crunchstat-long-lines
Tom Clegg
04:06 pm Bug #5145 (In Progress): [Workbench] Combining collections should separate files with identical n...
Radhika Chippada
02:43 pm Bug #5373: [Docker] Web Application Could not be Started
Neelam,
Can you please let me know what process you used to upgrade and restart the Docker containers? I think th...
Brett Smith
07:32 am Bug #5373 (Closed): [Docker] Web Application Could not be Started
On upgrading docker images, i am getting below error:
Web application could not be started
could not connect ...
neelam yadav
12:09 am Revision 5b380960 (arvados-dev): prevent info leak when gitolite-shell is used as $SHELL...
The error message is explicitly the same as you get when you do send in an
invalid git/gitolite command; this is by d...
Sitaram Chamarty

03/03/2015

11:02 pm Feature #5370 (Resolved): [Workbench] If anonymous config is enabled, logged-out workbench homepa...
Right now, if you go to curover.se/pathomap and then click on the top navbar "curoverse beta", you get to "welcome to... Nancy Ouyang
11:01 pm Task #5369 (Resolved): Review 5319-fix-hinted-collection-hashes-wip
Brett Smith
11:00 pm Revision 0b9975ce (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
10:50 pm Feature #5368 (Closed): [Workbench] job scripts accessible in some way
I have attached a screenshot of exactly what someone expected to be clickable (highlighted in orange). Nancy Ouyang
10:50 pm Bug #5352: [Crunch] Dispatcher not handling node allocation failures
For some jobs that I run, the state from workbench shows 'failed' even while the job/pipeline is still running and pr... Abram Connelly
10:36 pm Revision e58abe50 (arvados): 5319: Fix incorrect portable_data_hash in test fixture.
Brett Smith
10:03 pm Revision 0b4ad564 (arvados): 5246: Add urllib3 workaround, along with a note why it is necessary.
Peter Amstutz
10:00 pm Task #5323 (Resolved): Find another workaround
Peter Amstutz
09:49 pm Task #5323 (In Progress): Find another workaround
Peter Amstutz
10:00 pm Task #5367 (Resolved): Review 5246-urllib3-workaround
Peter Amstutz
09:48 pm Task #5355 (Resolved): Review branch: 5349-timestamp-error-for-running-pipeline
Tom Clegg
04:12 pm Task #5355 (In Progress): Review branch: 5349-timestamp-error-for-running-pipeline
Tom Clegg
09:42 pm Bug #5043: [Crunch] accept arbitrarily long stderr lines in crunchstat
Peter Amstutz wrote:
> > Also: Get rid of the "log channel" and use Go's own logging library instead: it guarantees ...
Tom Clegg
07:43 pm Bug #5043: [Crunch] accept arbitrarily long stderr lines in crunchstat
I took some time to beat on this a little bit. Tested this way:... Peter Amstutz
04:06 pm Bug #5043: [Crunch] accept arbitrarily long stderr lines in crunchstat
5043-crunchstat-long-lines at commit:508bcab includes
Accept arbitrarily long lines on stderr. Split long stderr l...
Tom Clegg
02:36 am Bug #5043 (In Progress): [Crunch] accept arbitrarily long stderr lines in crunchstat
Tom Clegg
09:24 pm Revision 78387b4f (arvados): 4956: Add maximum request size checking to http_request patch in api...
Raises MediaUploadSizeError if the request is too big. Peter Amstutz
09:21 pm Task #5357 (Resolved): Advertise configurable request size limit in discovery doc (default 128MiB)
Peter Amstutz
04:28 pm Task #5357 (In Progress): Advertise configurable request size limit in discovery doc (default 128...
Peter Amstutz
09:21 pm Task #5358 (Resolved): In Python SDK, check each request's size against discovered limit
Peter Amstutz
04:28 pm Task #5358 (In Progress): In Python SDK, check each request's size against discovered limit
Peter Amstutz
09:21 pm Task #5366 (Resolved): Review 4956-limit-request-size
Peter Amstutz
09:16 pm Bug #5365: [Workbench] Do not link to objects that are not readable by current user
curover.se/pathomap > SNP-Annotation-justmap > uuid > log Nancy Ouyang
09:07 pm Bug #5365 (Resolved): [Workbench] Do not link to objects that are not readable by current user
h2. Specific examples to fix
(copied from note-3)
In the specific case of the Log tab, when the log data is not...
Nancy Ouyang
09:06 pm Revision f1589a6f (arvados): 5043: Remove errant +1 from error message.
Tom Clegg
08:40 pm Story #3761: [Keep] Process entries on the current pull list.
Radhika Chippada wrote:
> Peter,
> Addressed all the review comments. Some details / exceptions:
>
> * I used ...
Peter Amstutz
06:35 pm Story #3761: [Keep] Process entries on the current pull list.
Peter,
Addressed all the review comments. Some details / exceptions:
* I used "SignLocator" instead of "MakePermS...
Radhika Chippada
08:40 pm Bug #5349 (Resolved): [Workbench] Pipeline Template error: no implicit conversion of ActiveSuppor...
Applied in changeset arvados|commit:912699d40991706b279aa6f9ed51991ea9250001. Radhika Chippada
06:53 pm Bug #5349: [Workbench] Pipeline Template error: no implicit conversion of ActiveSupport::TimeWith...
Added a test in commit:4393148 that passes with commit:a1d70a2 but not without it. Using @Time.parse(current_job[:cre... Tom Clegg
08:33 pm Revision 912699d4 (arvados): closes #5349
Merge branch '5349-timestamp-error-for-running-pipeline' Radhika Chippada
07:56 pm Revision 10a83d8c (arvados): 5349: update test to use a new fixture.
Radhika Chippada
06:48 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
Radhika Chippada wrote:
> Scenario 1: Two files from two different directories of a Collection are combined. The fil...
Tom Clegg
06:24 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
There are two distinct scenarios here.
* Scenario 1: Two files from two different directories of a Collection are ...
Radhika Chippada
06:21 pm Revision 4393148a (arvados): 5349: Add test to protect bugfix in a1d70a2116673ac46f4946115bdb5048...
Tom Clegg
05:59 pm Revision ba386628 (arvados): Merge branch 'master' into 5349-timestamp-error-for-running-pipeline
Radhika Chippada
05:57 pm Revision eced957a (arvados): 3761: Pass pullq to RunPullWorker
Radhika Chippada
05:26 pm Revision ca7460bc (arvados): Merge branch 'master' into 3761-pull-list-worker
Radhika Chippada
05:26 pm Revision 8ba8aece (arvados): 3761: pass keepclient as an arg to RunPullWorker
Radhika Chippada
05:16 pm Revision 7e814093 (arvados): Merge branch '5322-sso-manual-account-doc' closes #5322
Peter Amstutz
05:15 pm Feature #5322 (Resolved): [SSO] Support adding users with email/password based login at rails con...
Applied in changeset arvados|commit:7e814093e36dd6fc96353584c2c0797f4654f317. Peter Amstutz
03:18 pm Feature #5322: [SSO] Support adding users with email/password based login at rails console
Reviewing 5322-sso-manual-account-doc:
I pushed a few more small changes onto this branch to make the hostname nam...
Ward Vandewege
05:15 pm Bug #5305 (Resolved): Arv-copy issues
Applied in changeset arvados|commit:6cd3b6fb1c143017c6bca4db899c8c6ddd237572. Peter Amstutz
04:33 pm Bug #5305: Arv-copy issues
Reviewing commit:8356273.
Peter Amstutz wrote:
> Brett Smith wrote:
> > * The new name-finding heuristics in cop...
Brett Smith
04:20 pm Bug #5305: Arv-copy issues
Brett Smith wrote:
> Reviewing commit:ae41687
>
> * All the new API calls need to respect args.retries. Effectiv...
Peter Amstutz
05:13 pm Revision 6cd3b6fb (arvados): Merge branch '5305-arv-copy-fixes' closes #5305
Peter Amstutz
05:10 pm Task #5360 (In Progress): Review 5043-crunchstat-long-lines
Peter Amstutz
02:35 am Task #5360 (Resolved): Review 5043-crunchstat-long-lines
Tom Clegg
05:10 pm Revision 2365c0eb (arvados): Fixed SafeApi -> ThreadSafeApiCache refs #4823
Peter Amstutz
05:10 pm Task #5341 (Resolved): Review 5305-arv-copy-fixes
Peter Amstutz
05:06 pm Revision a380fd23 (arvados): Fix arv-mount use arvados.config.settings() to initialize ThreadSafe...
refs #4823 Peter Amstutz
04:42 pm Revision 1d45536f (arvados): 5305: Remove erroneous comment
Peter Amstutz
04:39 pm Revision 4d26f92c (arvados): 4956: Add 'maxRequestSize' to discovery document
Peter Amstutz
04:22 pm Revision 83562734 (arvados): 5305: Added num_retries to all execute() calls. Refactored
collection-name-choosing logic to be easier to follow. Peter Amstutz
04:20 pm Task #5314 (Resolved): 5309-keepproxy-panic
Peter Amstutz
04:20 pm Task #4893 (Resolved): Review 4823-python-sdk-writable-collection-api
Peter Amstutz
04:05 pm Revision b887df48 (arvados): Merge branch 'master' into 3761-pull-list-worker
Radhika Chippada
04:05 pm Revision ba032ff9 (arvados): 3761: improved tests with delays
Radhika Chippada
03:56 pm Revision 508bcab6 (arvados): 5043: Split long stderr lines rather than consume unlimited memory.
Tom Clegg
03:19 pm Task #5337 (Resolved): Review 5322-sso-manual-account-doc
Ward Vandewege
03:17 pm Task #5337 (In Progress): Review 5322-sso-manual-account-doc
Ward Vandewege
03:18 pm Revision b3bccdb7 (arvados): Follow the naming conventions for hostnames; add SSO server as a
public-facing service that requires an SSL certificate.
refs #5322
Ward Vandewege
03:10 pm Revision 116d6fd6 (arvados): Merge branch '5313-node-manager-gce-fixups2-wip'
Refs #5313. Brett Smith
03:09 pm Revision e2ab0a12 (arvados): 5313: Rely more on datacenter constructor in Node Manager GCE driver.
When initialized with a datacenter argument, the GCE libcloud driver
acts a lot more like the EC2 one. Many listings...
Brett Smith
03:09 pm Revision d3b57b61 (arvados): 5313: Revert Node Manager's GCE boot disk destroy code.
After upgrading to libcloud>=0.16, it's redundant to create a node
with ex_disk_auto_delete=True, then destroy the no...
Brett Smith
02:57 pm Revision 74b568d3 (arvados): Update arvados-fuse dependency on python sdk refs #4823
Peter Amstutz
02:55 pm Feature #4823 (Resolved): [SDKs] Good Collection API for Python SDK
Applied in changeset arvados|commit:bb19e060336c4e734b3e1922c5be3c4b40ff7da8. Peter Amstutz
02:48 pm Task #5308 (Resolved): Decide on explicit, documented limits on maximum manifest size, maximum AP...
Peter Amstutz
02:34 pm Revision bb19e060 (arvados): Merge branch '4823-python-sdk-writable-collection-api' closes #4823
Peter Amstutz
02:34 pm Revision 256068ed (arvados): 4823: Docstring and comment fixes.
Peter Amstutz
02:35 am Revision 46558e7b (arvados): 5043: Use Go's log package to serialize writes. Lose logChan.
Tom Clegg
02:35 am Task #5274 (Resolved): Avoid parsing tokens in child's stderr
Tom Clegg
02:35 am Task #5273 (Resolved): Add test
Tom Clegg
02:09 am Revision 753d0ef6 (arvados): 3761: code refactoring
Radhika Chippada

03/02/2015

10:11 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
Brett Smith wrote:
> The longer-term plan is for Workbench to ignore objects that expire in the future (showing them...
Tom Clegg
08:12 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
Tom Clegg wrote:
> A migration that _changes_ the PDH values would make the old/broken PDH unfindable, which means e...
Brett Smith
07:16 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
Yes, PDH should stay the same when the hints change (e.g., when the data comes and goes from different storage system... Tom Clegg
03:07 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
+1 to doing a migration. It should probably include updating the PDH of the collection in pipelines templates. Peter Amstutz
10:02 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Reviewing commit:c691e44.
Peter Amstutz wrote:
> Brett Smith wrote:
> > h2. Code issues
> >
> > * FUSE's test...
Brett Smith
08:59 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Brett Smith wrote:
> Reviewing commit:63b03a3. We're coming down the home stretch. I expect this to be my last top...
Peter Amstutz
09:54 pm Task #5358 (Resolved): In Python SDK, check each request's size against discovered limit
Hopefully, the existing authentication header monkey-patch will solve most of the mystery of how to hook into google-... Tom Clegg
09:52 pm Task #5357 (Resolved): Advertise configurable request size limit in discovery doc (default 128MiB)
Tom Clegg
09:11 pm Revision a5b7c827 (arvados): Merge branch 'master' into 3761-pull-list-worker
Radhika Chippada
09:10 pm Bug #5349: [Workbench] Pipeline Template error: no implicit conversion of ActiveSupport::TimeWith...
* This issue is happening for pipelines in Running state. It is due to a recent update to handle start_at timestamp i... Radhika Chippada
08:14 pm Bug #5349 (In Progress): [Workbench] Pipeline Template error: no implicit conversion of ActiveSup...
Radhika Chippada
04:09 pm Bug #5349: [Workbench] Pipeline Template error: no implicit conversion of ActiveSupport::TimeWith...
Refreshing a running pipeline instance page reproduces this /sometimes/ Bryan Cosca
03:32 pm Bug #5349: [Workbench] Pipeline Template error: no implicit conversion of ActiveSupport::TimeWith...
I can see the normal pipeline instance page now, -but I cannot cancel any jobs. I can pause though.-
Edit: Was on ...
Bryan Cosca
03:20 pm Bug #5349: [Workbench] Pipeline Template error: no implicit conversion of ActiveSupport::TimeWith...
qr1hi-d1hrv-07ek396rvbutqjb is one instance that shows the problem, qr1hi-d1hrv-kd3498krej4o6ln is another. Bryan Cosca
03:19 pm Bug #5349 (Resolved): [Workbench] Pipeline Template error: no implicit conversion of ActiveSuppor...
I clicked on re-run with latest on instance: qr1hi-d1hrv-idj2c7bhyqmhjcs. The pipeline queued for a few seconds and t... Bryan Cosca
09:06 pm Task #5355 (Resolved): Review branch: 5349-timestamp-error-for-running-pipeline
Radhika Chippada
09:04 pm Revision 9d879418 (arvados): 5349: Reverted "Time.iso8601(current_job[:created_at]" back to "curr...
Radhika Chippada
08:51 pm Revision c691e44f (arvados): 4823: More fixes and cleanups.
* Renamed SynchronizedCollectionBase to RichCollectionBase
* Renamed arvapi parameter of one_task_per_input_file to a...
Peter Amstutz
08:35 pm Bug #5309 (Resolved): [Keep] Keepproxy panic
Applied in changeset arvados|commit:f2674d147238c963e055a448e94e962fe2e76619. Peter Amstutz
07:23 pm Bug #5309: [Keep] Keepproxy panic
At commit:979c134 on 5309-keepproxy-panic
This (in keepproxy_test.go) looks like an accidentally-not-deleted debug...
Tom Clegg
08:31 pm Revision f2674d14 (arvados): Merge branch 'origin-5309-keepproxy-panic' closes #5309
Peter Amstutz
08:22 pm Revision 0e656d5a (arvados): 5309: Add comment about testing for content-length error bug.
Peter Amstutz
08:20 pm Support #5251 (Resolved): [Support] Fix bugs and write tests (first half)
Knocking down story points to balance out bugs brought onto this sprint. Brett Smith
07:42 pm Revision 61508b80 (arvados): 5043: Accept long stderr lines from crunch tasks.
Tom Clegg
07:36 pm Task #5286 (Resolved): Review 4601-openid-migrate-to-oauth2 (sso-provider)
Ward Vandewege
07:15 pm Task #5351 (Resolved): Review 4751-node-manager-stricter-node-pairing-wip
Applied in changeset arvados|commit:6be95f5c3a2fcbe6321bba52c20393060e33e637. Brett Smith
05:03 pm Task #5351 (In Progress): Review 4751-node-manager-stricter-node-pairing-wip
Peter Amstutz
04:28 pm Task #5351 (Resolved): Review 4751-node-manager-stricter-node-pairing-wip
Brett Smith
07:15 pm Bug #4751 (Resolved): [Node Manager] Can erroneously pair cloud nodes with stale Arvados node rec...
Applied in changeset arvados|commit:6be95f5c3a2fcbe6321bba52c20393060e33e637. Brett Smith
06:24 pm Bug #4751: [Node Manager] Can erroneously pair cloud nodes with stale Arvados node records
I feel like this came up in an earlier code review (discussing the pitfalls of reusing computed node records generall... Peter Amstutz
03:46 pm Bug #4751: [Node Manager] Can erroneously pair cloud nodes with stale Arvados node records
Moving to current sprint because it came up again during science support, and it's likely to become more pressing now... Brett Smith
07:08 pm Revision 6be95f5c (arvados): Merge branch '4751-node-manager-stricter-node-pairing-wip'
Closes #4751, #5351. Brett Smith
07:07 pm Revision 212b5870 (arvados): 4751: Node Manager considers ping times for stricter node pairing.
Because the pairing decision is currently based on IP address alone,
Node Manager will occasionally pair a cloud node...
Brett Smith
07:07 pm Revision 3e5f2c7f (arvados): Merge branch '5313-node-manager-gce-fixes-wip'
Closes #5313, #5350. Brett Smith
07:05 pm Bug #5305: Arv-copy issues
Reviewing commit:ae41687
* All the new API calls need to respect args.retries. Effectively, calling @.execute()@ ...
Brett Smith
06:37 pm Revision 149eb0da (arvados): 3761: use SignLocator
Radhika Chippada
05:52 pm Story #5353 (Resolved): [Node Manager] Support multiple node sizes and boot new nodes correctly f...
Correct me if I'm wrong but if we're in the cloud, we're able to pick out the specs that we want on each node, in ord... Bryan Cosca
04:58 pm Bug #5352 (Resolved): [Crunch] Dispatcher not handling node allocation failures
Pipeline instance su92l-d1hrv-wqa83p9taz3tvmf failed for the second job in it's two job pipeline.
From the logs, t...
Abram Connelly
04:47 pm Task #5314 (In Progress): 5309-keepproxy-panic
Tom Clegg
04:36 pm Story #3761: [Keep] Process entries on the current pull list.
It would be a clearer if @RunPullWorker@ took the @WorkQueue@ object instead of a channel.
In pull_worker.go:27 th...
Peter Amstutz
04:30 pm Task #5341 (In Progress): Review 5305-arv-copy-fixes
Brett Smith
04:27 pm Revision 2475b1d9 (arvados): 4751: Node Manager considers ping times for stricter node pairing.
Because the pairing decision is currently based on IP address alone,
Node Manager will occasionally pair a cloud node...
Brett Smith
03:37 pm Revision 70f2a361 (arvados): 5313: Node Manager's GCE driver destroys boot disks reliably.
This more closely matches the behavior of the EC2 driver, which we
want.
* Upgrade to libcloud 0.16, which adds an e...
Brett Smith
03:29 pm Revision a8ac3926 (arvados): 5313: Rename Node Manager's `user-data` GCE tag to `arv-ping-url`.
`user-data` is an EC2-specific name. `arv-ping-url` more clearly
describes what's in it.
Brett Smith
03:09 pm Task #5346 (In Progress): Review branch: 3761-pull-list-worker
Peter Amstutz
01:58 pm Task #5346 (Resolved): Review branch: 3761-pull-list-worker
Radhika Chippada
03:01 pm Task #5273 (In Progress): Add test
Tom Clegg
03:00 pm Task #5347 (Resolved): Rearrange projects#show layout
Tom Clegg
02:30 pm Revision 8c01f630 (arvados): Be consistent in the naming of the arvados-data-manager package and ...
No issue # Ward Vandewege
02:30 pm Revision 8c01f630 (arvados-dev): Be consistent in the naming of the arvados-data-manager package ...
No issue # Ward Vandewege
01:57 pm Revision c50da8ea (arvados): Build arvados-data-manager deb.
No issue # Ward Vandewege
01:57 pm Revision c50da8ea (arvados-dev): Build arvados-data-manager deb.
No issue # Ward Vandewege

02/28/2015

02:36 am Revision a56406d7 (arvados): Added lots of unit tests.
Switched collections.ReadCollections.BlockToCollectionIndex to collections.ReadCollections.BlockToCollectionIndices s... Misha Zatsman

02/27/2015

08:50 pm Task #5280 (Feedback): Review 5246-update-urllib3
Peter Amstutz
08:31 pm Bug #5310 (Resolved): [SDK] arv-copy breaks when copying by PDH and multiple collections have the...
Further arv-copy work at #5305 Peter Amstutz
08:30 pm Task #5341 (Resolved): Review 5305-arv-copy-fixes
Peter Amstutz
08:30 pm Task #5324 (Resolved): Fix copy issues
Peter Amstutz
08:27 pm Bug #5304: [API] filters incorrectly exclude results for records with null value in filtered field
I note this code in record_filters.rb:... Brett Smith
08:17 pm Bug #5327: [SDK] CLI tools should catch socket errors like "Connection refused"
And this may be out of scope, but given that patterns are starting to emerge in our tools, it doesn't seem totally un... Brett Smith
08:16 pm Bug #5327: [SDK] CLI tools should catch socket errors like "Connection refused"
I feel like it would be helpful to define a bigger picture strategy for catching and reporting SDK exceptions in our ... Brett Smith
03:57 pm Bug #5327 (New): [SDK] CLI tools should catch socket errors like "Connection refused"
Common SDK errors like "connection refused" should be reported to the user in a friendly fashion instead of resulting... Peter Amstutz
08:14 pm Revision ae416879 (arvados): 5305: Add heuristics to choose name when collection is referenced by...
Peter Amstutz
08:11 pm Bug #5318: [Workbench] Make note of lag time when changing git permissions
Bryan,
Can you please clarify what you mean when you say you "granted them owner access?" If you created the repo...
Brett Smith
07:27 pm Revision 32a14171 (arvados): Merge branch 'master' into 3761-pull-list-worker
Radhika Chippada
07:27 pm Revision afd38976 (arvados): 3761: additional tests
Radhika Chippada
07:25 pm Task #5306 (Resolved): Review 5283-crunch-collation-safety-wip
Applied in changeset arvados|commit:62fea2a463eb0d8c3aef84a56ba84561a196666b. Brett Smith
07:25 pm Bug #5283 (Resolved): [Crunch] crunch-job apparently died while collating job's output
Applied in changeset arvados|commit:62fea2a463eb0d8c3aef84a56ba84561a196666b. Brett Smith
03:02 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
commit:a61b22a LGTM. Please merge. Peter Amstutz
07:23 pm Revision 62fea2a4 (arvados): Merge branch '5283-crunch-collation-safety-wip'
Closes #5283, #5306. Brett Smith
07:22 pm Revision 679e083d (arvados): 5283: Log more crunch-job output handling.
Requested during code review. Brett Smith
07:20 pm Revision 0e4de53a (arvados): 5283: crunch-job doesn't use freeze logic after a job fails.
If the job has failed permanently, we want to go through all the
end-of-job logic. Previously, we were getting sidet...
Brett Smith
07:20 pm Revision eab3fd07 (arvados): 5283: Improve reliability of crunch-job output collation.
* Check the results of all pipe opens, exit statuses, and writes.
Log any problems.
* Have fetch_block return undef...
Brett Smith
07:16 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Reviewing commit:63b03a3. We're coming down the home stretch. I expect this to be my last top-to-bottom review of t... Brett Smith
07:03 pm Revision d0ea98ec (arvados): 5305: Handle collection pdh for docker image
Peter Amstutz
04:56 pm Story #3761 (In Progress): [Keep] Process entries on the current pull list.
Radhika Chippada
04:43 pm Revision c3be77dc (arvados): 5322: Add documentation to "install SSO" section. (Possibly this sh...
into the admin guide, the admin guide is kind of useless right now.) Peter Amstutz
04:41 pm Task #5337 (Resolved): Review 5322-sso-manual-account-doc
Peter Amstutz
04:40 pm Task #5325 (Resolved): document for ops
Peter Amstutz
04:39 pm Feature #5322 (In Progress): [SSO] Support adding users with email/password based login at rails ...
Peter Amstutz
04:12 pm Revision cb9fbffa (arvados): 3761: Run pull list worker, which processes pull reqests from the list.
Radhika Chippada
03:27 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
What happens if a user who is not so clever with Python does something like this? (I think it does the right thing, ... Peter Amstutz
02:57 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
Something to look at for inspiration:
http://swift-lang.org/main/
The gist is it Swift is a "parallel scripting...
Peter Amstutz
03:10 pm Feature #4601 (Resolved): [SSO] Migrate OpenId users to OAuth/Google+
Applied in changeset sso-provider|commit:08542a178c1bc11c222dee6b4202c731f96ade77. Peter Amstutz
03:09 pm Revision 08542a17 (sso-provider): Merge branch '4601-openid-migrate-to-oauth2' closes #4601
Peter Amstutz

02/26/2015

10:52 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
I believe "this change is our culprit":https://arvados.org/projects/arvados/repository/revisions/75a07d8175c9ee9a1c21... Brett Smith
07:21 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
The affected collections have manifests with Keep location hints in them (@+Kqr1hi@), and the portable data hash corr... Brett Smith
06:40 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
qr1hi-4zz18-yrocuypi31jo3ru and qr1hi-4zz18-h03wet37z45z2c9 are known culprits Bryan Cosca
06:29 pm Bug #5319 (In Progress): [API] Portable data hash mismatches for collections with location hints ...
Brett Smith
04:33 pm Bug #5319: [API] Portable data hash mismatches for collections with location hints (+K)
My current workaround is to select all the files and then create a new collection, which i guess makes a new hash. an... Bryan Cosca
04:31 pm Bug #5319 (Resolved): [API] Portable data hash mismatches for collections with location hints (+K)
!portabledatahash.png! Bryan Cosca
10:07 pm Task #5325 (Resolved): document for ops
Peter Amstutz
10:07 pm Task #5324 (Resolved): Fix copy issues
Peter Amstutz
10:06 pm Task #5323 (Resolved): Find another workaround
Peter Amstutz
10:06 pm Task #5268 (Resolved): Investigate further
Peter Amstutz
10:01 pm Feature #5322 (Resolved): [SSO] Support adding users with email/password based login at rails con...
Peter Amstutz
09:58 pm Task #5286 (In Progress): Review 4601-openid-migrate-to-oauth2 (sso-provider)
Ward Vandewege
06:59 pm Revision b10c68ef (arvados): Move the licensing info out of the second column and towards the foo...
No issue # Ward Vandewege
06:49 pm Bug #4426: [Documentation] Support searching documentation
Adding something like this should do the trick:... Ward Vandewege
06:29 pm Revision 42e23bae (arvados): Merge branch '5310-arv-copy-by-pdh'
refs #5310 Ward Vandewege
06:28 pm Task #5311 (Resolved): Review 5310-arv-copy-by-pdh
Ward Vandewege
06:27 pm Task #5311 (In Progress): Review 5310-arv-copy-by-pdh
Ward Vandewege
06:27 pm Revision d22f7ca7 (arvados): Merge branch 'master' into 5310-arv-copy-by-pdh
Ward Vandewege
06:20 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Brett Smith wrote:
> Sorry, I summarized the issue too much. It's really _normalize_stream. From running the Wor...
Peter Amstutz
03:56 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Peter Amstutz wrote:
> Brett Smith wrote:
> > * My earlier comment about testing internal attributes and methods in...
Brett Smith
03:34 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Reviewing commit:cb832096
Peter Amstutz wrote:
> Brett Smith wrote:
> > I would love to clean this up, but I don...
Brett Smith
06:19 pm Revision 63b03a39 (arvados): 4823: Add flush() to ArvadosFile. Fix tests to avoid using internal...
import in _normalize_stream. Make KeepRequestError more generic (now
represents a list of "request errors" instead o...
Peter Amstutz
06:01 pm Bug #5320 (Closed): [Docker] SLURM does not start reliably on API server
For whatever reason, SLURM does not reliably start on the API server Docker image when it starts. This prevents jobs... Brett Smith
04:12 pm Revision a61b22a2 (arvados): 5283: Revert excess log tweaking.
This is unhelpful after 687beeda. Brett Smith
04:08 pm Bug #5318 (Resolved): [Workbench] Make note of lag time when changing git permissions
I created a new git repo bcosc.gatk2 using the admin account for bcosc@bu.edu, which has manage access.
git clone ...
Bryan Cosca
03:51 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
Peter Amstutz wrote:
> Brett Smith wrote:
>
> > Well, what does your pipeline do? This is expected behavior if a...
Brett Smith
03:02 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
"collated output manifest text to send to API server is $manifest_size bytes with access tokens"
Peter Amstutz
01:49 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
I'll work on fixing the bug.
Peter Amstutz wrote:
> "collated output manifest is $manifest_size bytes, including ...
Brett Smith
03:49 pm Revision 253e2855 (arvados): 5283: Fixup log message by request.
Brett Smith
03:49 pm Revision 687beeda (arvados): 5283: Fixup null output detection.
Brett Smith
03:34 pm Bug #5317 (Closed): 5316
Bryan Cosca
03:34 pm Bug #5317 (Closed): 5316
Bryan Cosca
03:06 pm Feature #5316 (New): [DRAFT] [Workbench] Browse change history for records
Based on user feedback, users of workbench would like to:
# Get a timeline of changes to records (such as a past v...
Peter Amstutz
08:02 am Bug #4232 (Resolved): [Workbench] Pipeline instances with many components should render quickly (...
Merged. Phil Hodgson
08:02 am Task #4873 (Resolved): Review 4232
Phil Hodgson
08:01 am Revision 9e111d1d (arvados): Merge branch '4232-slow-pipes-n-jobs' closes #4232
Phil Hodgson

02/25/2015

10:09 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
Brett Smith wrote:
> Well, what does your pipeline do? This is expected behavior if a task fails to set an output...
Peter Amstutz
07:50 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
Peter Amstutz wrote:
> Running a test pipeline:
>
> [...]
>
> # Why is it saying "Error retrieving '' output b...
Brett Smith
06:53 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
Running a test pipeline:... Peter Amstutz
04:59 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
Peter Amstutz wrote:
> * It's supposed to skip the task if the output is empty (@next unless exists $_->{'arvados_ta...
Brett Smith
04:36 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
* It's supposed to skip the task if the output is empty (@next unless exists $_->{'arvados_task'}->{'output'};@) but ... Peter Amstutz
03:46 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
This issue seems to be reproducible with any Crunch job that sets task output without setting success. I ran a very ... Brett Smith
02:53 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
5283-crunch-collation-safety-wip is up for review. It probably won't fix the problem, but it makes a number of relia... Brett Smith
09:42 pm Revision 979c1342 (arvados): 5309: Fix keepclient and keepproxy bugs related to error handling:
* KeepClient: Handle nil response and nil response Body from Client.Do(GET)
* KeepProxy: Only defer reader.Close() if...
Peter Amstutz
09:40 pm Task #5314 (Resolved): 5309-keepproxy-panic
Peter Amstutz
07:46 pm Revision a12247ff (arvados): 5283: Fixup more log messages.
Brett Smith
07:09 pm Revision e4c05dbe (arvados): 5310: Use c.get('name') instead of c['name']
* 'name' isn't necessarily present when obj_uuid is a PDH,
src.collections().get(uuid=obj_uuid).execute() may retur...
Peter Amstutz
07:08 pm Task #5311 (Resolved): Review 5310-arv-copy-by-pdh
Peter Amstutz
07:08 pm Bug #5310 (In Progress): [SDK] arv-copy breaks when copying by PDH and multiple collections have ...
Peter Amstutz
07:02 pm Bug #5310 (Resolved): [SDK] arv-copy breaks when copying by PDH and multiple collections have the...
Peter Amstutz
07:07 pm Bug #5309 (In Progress): [Keep] Keepproxy panic
Peter Amstutz
05:55 pm Bug #5309 (Resolved): [Keep] Keepproxy panic
2015-02-25_17:00:26.64334 2015/02/25 17:00:26 204.238.141.200: GET 8028819a18d3727630fa30c81853d23f begin
2015-02-25...
Peter Amstutz
06:01 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
From requests __init__.py... Peter Amstutz
04:53 pm Revision 538f4a84 (arvados): 5283: crunch-job doesn't use freeze logic after a job fails.
If the job has failed permanently, we want to go through all the
end-of-job logic. Previously, we were getting sidet...
Brett Smith
04:53 pm Revision f90440a4 (arvados): 5283: Log more crunch-job output handling.
Requested during code review. Brett Smith
04:40 pm Task #5308 (Resolved): Decide on explicit, documented limits on maximum manifest size, maximum AP...
Peter Amstutz
04:07 pm Task #5299 (Resolved): Determine cause
Peter Amstutz
04:00 pm Task #5306 (In Progress): Review 5283-crunch-collation-safety-wip
Peter Amstutz
02:51 pm Task #5306 (Resolved): Review 5283-crunch-collation-safety-wip
Brett Smith
04:00 pm Revision cb832096 (arvados): 4823: Add arvapi parameter to one_task_per_input_file() to solve moc...
problems. Refactor Collection.copy() and add Collection.add(). Fix docstring
bugs.
Peter Amstutz
03:59 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Brett Smith wrote:
> Reviewing commit:ad69b48
>
> h2. New API stuff
>
> I think malformed manifests should alw...
Peter Amstutz
03:29 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
commit:ad76f76 is good to merge—love to see some cruft cleaned up. Thanks for sticking through this. Brett Smith
08:38 am Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
* @PipelineInstance#dependency_search@ removed
* Indeed, you surmised correctly about removing the pipeline_template...
Phil Hodgson
03:11 pm Bug #5307 (New): [Workbench] Additional settings for ssh/config from Manage Account page
!forwardagent.png!
This could use
ForwardAgent yes
ForwardX11 no
(if youre on multiple clusters)
User bcosc...
Bryan Cosca
02:50 pm Revision d70f2d85 (arvados): 5283: Improve reliability of crunch-job output collation.
* Check the results of all pipe opens, exit statuses, and writes.
Log any problems.
* Have fetch_block return undef...
Brett Smith
02:39 pm Revision 0c9dd4b5 (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
08:12 am Revision ad76f76c (arvados): Merge branch 'master' into 4232-slow-pipes-n-jobs
Phil Hodgson
08:10 am Revision acced3c4 (arvados): 4232: remove traces of no-longer-needed "dependency" code for pipeli...
Phil Hodgson
02:19 am Bug #5305: Arv-copy issues
I ran into this copying gatk3
arv-copy --src qr1hi --dst tb05z --dst-git-repo bcosc.bu --project-uuid tb05z-j7d0g-...
Bryan Cosca

02/24/2015

11:16 pm Bug #5305: Arv-copy issues
The template is not in order. My pipeline template tb05z-p5p6p-bzn8uoope28ytmo goes allelotype_run > run_lobSTR > sor... Bryan Cosca
11:13 pm Bug #5305 (Resolved): Arv-copy issues
arv-copy --src qr1hi --dst tb05z --dst-git-repo bcosc.bu --project-uuid tb05z-j7d0g-8vvizxhqnqj24rv qr1hi-p5p6p-9pkax... Bryan Cosca
10:13 pm Revision a1fc5b9e (arvados): 4823: Remove sync_mode() from Collection in favor of writable() flag.
Collection constructor raises ArgumentError() on bad manifest. Fix
assertEquals() -> assertEqual().
Peter Amstutz
10:06 pm Bug #3819 (Resolved): [Workbench] It's not possible to share a project with the 'All Users' group
Ward Vandewege
09:56 pm Bug #3819: [Workbench] It's not possible to share a project with the 'All Users' group
Turns out that the group_class field on the 'All users' group on our older installations is set to null. On newer one... Ward Vandewege
09:55 pm Bug #5304 (Resolved): [API] filters incorrectly exclude results for records with null value in fi...

There appears to be a bug in our filter code on the API side, where a call like this:
arv group list --filters...
Ward Vandewege
07:32 pm Story #5250 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
Brett Smith
07:03 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Reviewing commit:ad69b48
h2. New API stuff
I think malformed manifests should always raise ArgumentError when y...
Brett Smith
07:01 pm Bug #4956: [API] cannot create collections with very large manifests
Analysis:
There are two underlying causes here:
# CollectionWriter was used in a way that created fragmented ma...
Peter Amstutz
06:42 pm Bug #4956: [API] cannot create collections with very large manifests
Whoops.
This manifest isn't 28 MiB. It's at least two orders of magnitude larger than that. The 28 MiB manifest ...
Peter Amstutz
03:52 pm Feature #5300 (New): [DRAFT] [Workbench] Message Center
A way to communicate to users without creepily emailing them directly. Bryan Cosca
03:49 pm Task #5299 (In Progress): Determine cause
Peter Amstutz
03:48 pm Task #5299 (Resolved): Determine cause
Peter Amstutz
03:48 pm Task #5102 (Resolved): Try to reproduce
Peter Amstutz
02:25 pm Bug #3785 (Resolved): [Crunch] Job log collections should be stored with the same owner_uuid (and...
Applied in changeset arvados|commit:18ddae75beb91b0792ad34a9b4996316715e67b7. Peter Amstutz
01:19 pm Bug #3785: [Crunch] Job log collections should be stored with the same owner_uuid (and therefore ...
Peter, I understand about the testing crunch jobs. LGTM Radhika Chippada
02:22 pm Revision 18ddae75 (arvados): Merge branch '3785-job-log-collection-owner' closes #3785
Peter Amstutz
01:20 pm Task #5295 (Resolved): Review 3785-job-log-collection-owner
Radhika Chippada

02/23/2015

11:33 pm Bug #5298 (Feedback): [SDKs] Should CollectionReader.all_streams() iterate lines in the manifest,...
A user just encountered an issue where their Crunch script had surprising behavior because an input manifest defined ... Brett Smith
11:14 pm Revision a5a4f79e (arvados): Added block to collection index map. Started using collection index ...
Started running summarize() methods after reading data from disk so that we can modify the summarization code and tes... Misha Zatsman
10:49 pm Revision d3f9fad0 (arvados): Fixed bug where I wasn't copied saved data.
Computed and logged summary of replication state. Misha Zatsman
10:13 pm Bug #5235: [Workbench] Pipeline instance "Re-run with latest" button occasionally returns Not fou...
Sorry, I don't think this is related to the middle button issue. I'm not really sure how to explain it other than it ... Bryan Cosca
09:52 pm Bug #5235: [Workbench] Pipeline instance "Re-run with latest" button occasionally returns Not fou...
Bryan,
Any chance you might be middle-clicking the button? That returns a 404, and would basically make this a du...
Brett Smith
09:54 pm Bug #4956: [API] cannot create collections with very large manifests
Here's the log:... Peter Amstutz
08:24 pm Bug #4956: [API] cannot create collections with very large manifests
Was able to recreate the error. Notes:
* This is a severely degenerate manifest. There are many instances of seq...
Peter Amstutz
09:50 pm Bug #4520 (Resolved): [SDKs] arv copy should respect --project-uuid when saving destination Colle...
Applied in changeset arvados|commit:f0fe7273c1851cb93e9edd58c0b60d3590b222ed. Peter Amstutz
09:40 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Peter Amstutz wrote:
> * Updated test.
Please assert that the first put returns the right hash (so we're sure it ...
Brett Smith
09:35 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
* Don't encode manifest_text by default to avoid double-encode faults.
* Coerce unicode strings to ascii in put(). ...
Peter Amstutz
08:38 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Peter Amstutz wrote:
> Brett Smith wrote:
>
> > Please change this condition to @isinstance(data, str)@ to accept...
Brett Smith
08:16 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Brett Smith wrote:
> Please change this condition to @isinstance(data, str)@ to accept subclasses, and add a test....
Peter Amstutz
07:51 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Reviewing commit:a47dc2b
Peter Amstutz wrote:
> > * The docker_image_hash link is copied incorrectly. The name s...
Brett Smith
07:15 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Brett Smith wrote:
> Reviewing commit:74784b3.
>
> * The code to take a source collection and turn it into a coll...
Peter Amstutz
03:07 am Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Reviewing commit:74784b3.
* The code to take a source collection and turn it into a collection on dst (including n...
Brett Smith
09:49 pm Revision f0fe7273 (arvados): Merge branch '4520-arv-copy-project-uuid' closes #4520
Peter Amstutz
09:48 pm Revision 8a5790d5 (arvados): 4520: Tweak test that put(u'foo') does the right thing.
Peter Amstutz
09:47 pm Task #5238 (Resolved): Review 4520-arv-copy-project-uuid
Peter Amstutz
02:44 am Task #5238 (In Progress): Review 4520-arv-copy-project-uuid
Brett Smith
09:43 pm Bug #3785: [Crunch] Job log collections should be stored with the same owner_uuid (and therefore ...
Radhika Chippada wrote:
> Peter,
> The update to set the owner_uuid for the log itself looks good.
>
> Just a c...
Peter Amstutz
06:28 pm Bug #3785: [Crunch] Job log collections should be stored with the same owner_uuid (and therefore ...
Peter,
The update to set the owner_uuid for the log itself looks good.
Just a couple of questions.
* Is it po...
Radhika Chippada
09:41 pm Revision 6b5b6890 (arvados): Added flags to write network data and then read it back. This is use...
Unfortunately had to switch H,L fields in blockdigest from private to public, otherwise they would not be exported. Misha Zatsman
09:36 pm Revision a4bc2867 (arvados): 4520: Coerce unicode strings to ascii in put(). Use result.content ...
literal result bytes) instead result.text (returns unicode) when processing
Keep responses.
Peter Amstutz
09:10 pm Revision f387f8bb (arvados): 3785: Log tab is no longer suppressed for anonymous users.
Peter Amstutz
08:20 pm Feature #5297: [Workbench] Enable users to share with any other user
I know I did some work on the API server end to make it possible for all users to see basic information about each ot... Brett Smith
08:17 pm Feature #5297 (New): [Workbench] Enable users to share with any other user
As a user, I would like to share my pipeline with another random user, but I currently cannot because he's not in my ... Bryan Cosca
08:18 pm Bug #5285: [SDKs] arv-run-pipeline-instance does not use 'settings.conf' file like other 'arv' tools
This tool already uses the Arvados class from the Ruby SDK, which reads from the configuration file. However, it als... Brett Smith
08:17 pm Revision 7b0d3939 (arvados): 4520: manifest_text() is utf-8 encoded by default so it can be safel...
Keep. Add test that calling put() with a unicode string raises an error.
Fetching user uuid in arv-copy uses num_ret...
Peter Amstutz
08:03 pm Story #3490: [Workbench] Create and edit pipeline templates
Bryan suggested http://json.parser.online.fr/ for inspiration in the related ticket. Brett Smith
08:03 pm Feature #5291 (Closed): [Workbench] Editing pipeline templates on Workbench
Duplicates #3490. Brett Smith
03:29 pm Feature #5291 (Closed): [Workbench] Editing pipeline templates on Workbench
It would be cool to have something like this: http://json.parser.online.fr/ with the collapsible objects Bryan Cosca
07:59 pm Bug #3434: No workbench user interface for sharing collections
Not sure why we deferred this? We just got a user request for it. Brett Smith
07:44 pm Bug #5294 (Closed): [SDKs] Make arv-copy useful for copying a Docker image
Peter's doing the code parts in #4520. Documentation should be covered in #5288. Closing a duplicate of those. Brett Smith
04:42 pm Bug #5294 (Closed): [SDKs] Make arv-copy useful for copying a Docker image
It's handy to be able to copy a Docker image collection from one project to another. However, because Arvados needs ... Brett Smith
07:41 pm Revision 248d2ebb (arvados): Added BlockToReplication field to collection.ReadCollections.
Lots of other little cleanup. Misha Zatsman
07:30 pm Bug #5292 (Closed): [Node Manager] Failed to recognize busy node on qr1hi
Caused by #4751. Brett Smith
07:04 pm Bug #5292: [Node Manager] Failed to recognize busy node on qr1hi
Saw something similar with qr1hi-8i9sb-en76y3f8yrtjitc. When it entered the queue, Node Manager booted several nodes... Brett Smith
04:07 pm Bug #5292 (Closed): [Node Manager] Failed to recognize busy node on qr1hi
This morning on qr1hi, the single minimum compute node was up (qr1hi-7ekkf-09hjulgcrpxp1iw), and running a job (qr1hi... Brett Smith
07:17 pm Revision a47dc2bc (arvados): 4520: Better checking to see if collection already exists at the des...
Set args.project_uuid to default value (current user uuid) if not set on
command line to simplify code.
Peter Amstutz
06:55 pm Revision f70584ec (arvados): 4520: Bonus fix because arv-copy was giving KeepClient.put() unicode...
instead of byte strings. KeepClient will now reject that. Peter Amstutz
06:54 pm Revision b7642ef6 (arvados): 4520: Refactor code to create the collection record. Also refactore...
which creates Docker metadata links so that copying any collection which
represents a Docker image will also copy ove...
Peter Amstutz
06:23 pm Task #5295 (In Progress): Review 3785-job-log-collection-owner
Radhika Chippada
04:43 pm Task #5295 (Resolved): Review 3785-job-log-collection-owner
Peter Amstutz
06:20 pm Feature #5296 (New): [Workbench] Extend Sharing tab to collections
Right now, in workbench, projects can be shared with other users/groups in workbench but not collections. It would b... Abram Connelly
06:02 pm February development review: Sharing is caring
Once you've found an interesting result in your analysis, you don't want to keep it to yourself. You want to share i... Brett Smith
04:45 pm Revision d960e97b (arvados): 3785: Upload job log to collection with --project-uuid same owner_uu...
Peter Amstutz
04:42 pm Task #5271 (Resolved): Fix crunch-job
Peter Amstutz
03:52 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
qr1hi-8i9sb-mcla1dzm2zrpl0t is a rerun of the exact same original job, and it died the exact same way. My test must ... Brett Smith
03:50 pm Bug #5277 (Resolved): FUSE does not parse timestamps with fraction of a second
Applied in changeset arvados|commit:b5cd9c9b9b160f316f9df6dda155df8a67cb8188. Peter Amstutz
03:44 am Bug #5277: FUSE does not parse timestamps with fraction of a second
commit:98f1b83 is good to merge. I've updated arvados-dev and Jenkins to build a ciso8601 .deb to fulfill the depend... Brett Smith
03:48 pm Revision b5cd9c9b (arvados): Merge branch '5277-fuse-mtime-fix' closes #5277
Peter Amstutz
03:47 pm Task #5278 (Resolved): Review 5277-fuse-mtime-fix
Peter Amstutz
03:07 am Task #5278 (In Progress): Review 5277-fuse-mtime-fix
Brett Smith
03:44 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
If you don't have the OpenSSL wrapper that it wants to use, it will silently disable the feature. That might be what... Peter Amstutz
03:57 am Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
Peter Amstutz wrote:
> Doesn't work (default Debian packages in Jesse):
>
> * python-requests 2.4.3-4
> * python...
Brett Smith
03:35 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Brett Smith wrote:
> The whole suite of non-classes and extra @createFooCollection()@ constructor methods here is ...
Peter Amstutz
03:20 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
Reviewing commit:ad2792e
* You can remove the PipelineInstance#dependency_search method from API server as well. ...
Brett Smith
03:16 pm Revision ad69b48e (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
03:16 pm Revision 25485439 (arvados): 4823: Clean up imports in collection.py
Peter Amstutz
03:10 pm Bug #5192 (Resolved): [API] Disallow changing the name of a repository record (by non-admin users)
Both API and Workbench already disallow a non-admin user from changing a repository name.
* API: repository.rb -> ...
Radhika Chippada
03:04 pm Bug #5192 (In Progress): [API] Disallow changing the name of a repository record (by non-admin us...
Radhika Chippada
02:44 pm Revision 3070d89e (arvados): 4823: Handle edge cases of files named '.' so that the FUSE test pas...
tests for invalid manifests. Defer populating CollectionReader streams until
needed to avoid extra copy of the manif...
Peter Amstutz
03:45 am Task #5280 (In Progress): Review 5246-update-urllib3
Brett Smith
03:41 am Revision 91a75ac3 (arvados-dev): 5277: Build .deb for new ciso8601 dependency.
Refs #5277. Brett Smith
03:41 am Revision 91a75ac3 (arvados): 5277: Build .deb for new ciso8601 dependency.
Refs #5277. Brett Smith

02/21/2015

06:06 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
Branch prepared with latest master, and with what I believe are the conclusions. That is, in the end I've removed the... Phil Hodgson
01:34 pm Revision 78fc2408 (arvados-dev): authkeys file need not be 0700...
0600 is sufficient.
Caught by Christoph. I don't actually think there is any possibility of this
being used to atta...
Sitaram Chamarty
01:33 pm Revision 9cd1e373 (arvados-dev): allow gitolite-shell to be used as "$SHELL"...
Experts only; no support and no docs.
Idea courtesy "calestyo"; see mails on Feb 20 or so in this:
https://groups.go...
Sitaram Chamarty
09:21 am Revision ad2792ed (arvados): 4232: revert experimental change to using find? for each of the jobs...
Phil Hodgson
09:11 am Revision c4fa80c6 (arvados): Merge branch 'master' into 4232-slow-pipes-n-jobs
Phil Hodgson

02/20/2015

10:40 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
I created a small Perl script that fetched the failing task, and fed its output to a flattened version of create_outp... Brett Smith
08:08 pm Bug #5283 (In Progress): [Crunch] crunch-job apparently died while collating job's output
Brett Smith
03:00 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
qr1hi-8i9sb-gnwpoyq1fgc2vky is a job that's almost identical, except the Crunch script explicitly sets its task's suc... Brett Smith
10:35 pm Feature #4823: [SDKs] Good Collection API for Python SDK
The FUSE "edge cases" test revealed some awkward interactions between POSIX semantics and what's expressable in manif... Brett Smith
02:19 pm Feature #4823: [SDKs] Good Collection API for Python SDK
> * CollectionReader should fit into this hierarchy somehow. You're literally copying huge swaths of code from Colle... Brett Smith
08:58 pm Revision 93d38f3c (arvados): 4823: Fix tests broken by prior refactoring. Renamed 'api.py' to 'a...
so it wouldn't be awkwardly shadowed by the 'api' method. Peter Amstutz
08:26 pm Revision 664ca60e (arvados): make carousel arrows more obvious
Nancy Ouyang
06:29 pm Revision 62e3f155 (arvados): 4823: Refactoring. ReadOnly Collection is now CollectionReader, rep...
CollectionReader implementation (but maintains the same public API). Peter Amstutz
02:55 pm Story #5250 (In Progress): [Documentation] (recurring) Write blog post in first three days of sprint
Brett Smith
02:43 pm Bug #5288 (Resolved): [Documentation] Write user guide for arv-copy
Write a guide that walks a user through the process of starting from no configuration, and using arv-copy to copy a p... Brett Smith
02:21 pm Feature #5284: [Docker] Auto setup as much as possible for new users
Alternatively, maybe we shouldn't do any automatic user setup at all, and instead make sure the user is consistently ... Brett Smith
01:57 pm Revision 26b15b2f (sso-provider): 4601: Add indexes to enforce uniqueness on users.uuid and
authentications.[provider, uid] Peter Amstutz
03:51 am Revision 7b070ca1 (sso-provider): Merge branch '4601-openid-migrate-to-oauth2' into login_via_ema...
Peter Amstutz
03:51 am Revision 17ae8c64 (sso-provider): Add note about action mailer
Peter Amstutz
03:44 am Revision cb81985a (sso-provider): 4601: Improve configuration comments
Peter Amstutz
03:43 am Revision 71814268 (sso-provider): Local database sign up and sign in works!
Peter Amstutz
03:07 am Revision 4d479d06 (sso-provider): 4601: Generate uuid as part of creating new user record
Peter Amstutz
02:53 am Feature #4601: [SSO] Migrate OpenId users to OAuth/Google+
4601-openid-migrate-to-oauth2
* To support multiple providers, start using the "authentications" table.
** Migrat...
Peter Amstutz
02:20 am Feature #4601 (In Progress): [SSO] Migrate OpenId users to OAuth/Google+
Peter Amstutz
02:36 am Revision c9b81415 (sso-provider): 4601: Correctly create OAuth2 authentication record after findi...
authentication. Peter Amstutz
02:21 am Task #5286 (Resolved): Review 4601-openid-migrate-to-oauth2 (sso-provider)
Peter Amstutz
02:21 am Revision 551bae0f (sso-provider): 4601: Provide uuid in place of OpenId 2.0 for identity_url, for...
compatability with current master API server. Peter Amstutz
02:20 am Task #4421 (Resolved): API server can migrate users from OpenID to OpenID Connect
Peter Amstutz
02:06 am Bug #5285 (Resolved): [SDKs] arv-run-pipeline-instance does not use 'settings.conf' file like oth...
Having the file ... Abram Connelly

02/19/2015

10:13 pm Revision 20608e8c (sso-provider): 4601: Migrating user from OpenId 2.0 to OAuth2 works, new user ...
Peter Amstutz
10:04 pm Feature #5284 (New): [Docker] Auto setup as much as possible for new users
The API server Docker image is configured with auto_setup_new_users, but none of the related settings like auto_setup... Brett Smith
09:12 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Reviewing commit:f39118d. I have read more into the implementations for this round, which informs some of my discuss... Brett Smith
08:51 pm Revision f3d6ca90 (sso-provider): 4601: Migrate identity_url to authentications table.
Peter Amstutz
07:55 pm Revision 63ee2945 (sso-provider): 4601: Initial work in establishing how to get the openid_id fro...
flow to be able to do migration. Peter Amstutz
07:46 pm Revision d8856736 (arvados): Fix typo on doc homepage.
No issue # Ward Vandewege
06:58 pm Bug #5283 (Resolved): [Crunch] crunch-job apparently died while collating job's output
See qr1hi-8i9sb-ds95g67jm2jpmnd. The last line in the log says "collate", which means that we've entered @create_out... Brett Smith
06:55 pm Bug #4956: [API] cannot create collections with very large manifests
Re-ran the job and got the same error: qr1hi-8i9sb-77epylk1ecakg3a Peter Amstutz
04:07 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
For reference, the github issue for this bug was:
https://github.com/shazow/urllib3/issues/412
Peter Amstutz
03:55 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
Tracked it down. The bug is in urllib3 and is fixed in 1.10.
Peter Amstutz
03:36 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
This appears to be a requests and/or urllib3 bug. The "OpenSSL.SSL.WantWriteError" exception is a non-fatal error th... Peter Amstutz
04:00 pm Revision 71aa90b8 (arvados): 5246: Add minimum version constraint on urllib3 because of bug #5246
Peter Amstutz
03:59 pm Task #5280 (Closed): Review 5246-update-urllib3
Peter Amstutz
03:44 pm Task #5102 (In Progress): Try to reproduce
Peter Amstutz
03:33 pm Task #5268 (In Progress): Investigate further
Peter Amstutz
03:20 pm Revision 98f1b834 (arvados): 5277: Add test for mtime. Use ciso8601 module to parse arvados time...
Peter Amstutz
03:18 pm Task #5279 (Resolved): Add test and fix
Peter Amstutz
03:18 pm Task #5279 (Resolved): Add test and fix
Peter Amstutz
03:17 pm Task #5278 (Resolved): Review 5277-fuse-mtime-fix
Peter Amstutz
03:16 pm Bug #5277 (In Progress): FUSE does not parse timestamps with fraction of a second
Peter Amstutz
02:38 pm Bug #5277 (Resolved): FUSE does not parse timestamps with fraction of a second
Peter Amstutz
02:42 pm Support #5251 (In Progress): [Support] Fix bugs and write tests (first half)
Ward Vandewege
02:39 pm Revision f39118da (arvados): 4823: Revert FUSE changes unrelated to ThreadSafeApiCache
Peter Amstutz
02:32 pm Revision 0d63ac0c (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
02:32 pm Revision 27fe76f5 (arvados): 4823: Fix fuse tests for SafeApi -> ThreadSafeApiCache changes. Add...
of mtime assertions. Peter Amstutz

02/18/2015

10:51 pm Bug #5276 (Resolved): [Workbench] Log graph pop up shows when there is no log graph
!log_graph_popup_shows.gif! Bryan Cosca
09:32 pm Task #5275 (Resolved): Specify desired behavior
Tom Clegg
09:32 pm Task #5274 (Resolved): Avoid parsing tokens in child's stderr
Tom Clegg
09:31 pm Task #5273 (Resolved): Add test
Tom Clegg
09:31 pm Task #5272 (Resolved): Detect CORS failure and display error message
Use a horrible hack like timeouts if necessary. Tom Clegg
09:30 pm Task #5271 (Resolved): Fix crunch-job
Peter Amstutz
09:27 pm Task #5270 (Resolved): write Draft 2 spec
Peter Amstutz
09:26 pm Task #5268 (Resolved): Investigate further
Peter Amstutz
09:20 pm Bug #5267 (New): [Node Manager] add one integration test for node manager
Ward Vandewege
09:16 pm Task #5266 (Closed): Detect various AJAX errors and ensure fail handler runs
Tom Clegg
09:15 pm Task #5265 (Closed): Add tests for redirect, timeout, and error
Tom Clegg
09:12 pm Task #5263 (Resolved): Add API mocking facility
Tom Clegg
09:11 pm Task #5262 (Resolved): Update install doc page
Tom Clegg
09:03 pm Bug #4957: [SDKs] arv keep put blows up when trying to put a danging symlink
Tom Clegg wrote:
> Perhaps rsync's behavior in the face of IO errors is a good model to follow. "Some stuff failed a...
Ward Vandewege
09:02 pm Bug #4957: [SDKs] arv keep put blows up when trying to put a danging symlink
Perhaps rsync's behavior in the face of IO errors is a good model to follow. "Some stuff failed along the way, so exi... Tom Clegg
08:46 pm Bug #4426: [Documentation] Support searching documentation
Suggest using site:doc.arvados.org and delegating to Google search Peter Amstutz
08:43 pm Feature #5261 (Resolved): [Workbench] Show project description in its own tab
The description tab should become the leftmost tab.
This tab should be the initially displayed tab -- unless the d...
Tom Clegg
08:20 pm Feature #5260 (New): [Tests] Implement long-running keepstore services in run-tests, similar to w...
Tom Clegg
08:18 pm Feature #5259 (New): [Tests] Reduce dependency on integration tests
Tom Clegg
08:16 pm Task #5213 (Resolved): Review branch: 4759-timestamp-precision
Tom Clegg
08:16 pm Task #5221 (Resolved): Review branch: 5186-collection-with-empty-properties
Radhika Chippada
08:16 pm Task #4947 (Resolved): Provide example to science team
Peter Amstutz
08:16 pm Story #5257 (Resolved): [CWL] write draft 2 spec
Peter Amstutz
07:46 pm Feature #5256 (Resolved): [OPS] Make it possible to kick off a Jenkins build for an arbitrary com...
Ward Vandewege
07:43 pm Bug #5255 (New): [Testing] Add a new unit-test-only build step to the build pipeline, before the ...
Ward Vandewege
07:42 pm Feature #5254 (New): [Testing] Make run-tests.sh able to run only unit tests or integration tests...
Ward Vandewege
06:44 pm Support #5252 (Resolved): [Support] Fix bugs and write tests (second half)
Ward Vandewege
06:44 pm Support #5251 (Resolved): [Support] Fix bugs and write tests (first half)
Ward Vandewege
06:43 pm Story #5250 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
Ward Vandewege
06:41 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
Phil Hodgson wrote:
> Suggesting that we merge in the removal of the rendering of the "dependencies" in the API and ...
Brett Smith
06:39 pm Task #5249 (Resolved): Write up implementation summary on wiki
Tom Clegg
06:38 pm Task #5167 (Resolved): Figure out appropriate scope for first implementation
Tom Clegg
06:37 pm Feature #5072 (Resolved): [Documentation] (recurring) Refresh user documentation
Tom Clegg
06:37 pm Task #5248 (Resolved): [Documentation] Add public projects (anonymous access) to documentation.
We have a bunch of sharing features. We should have a page on the documentation site that explains them all. Ward Vandewege
06:37 pm Feature #5247 (Resolved): [Documentation] (recurring) Refresh user documentation
Ward Vandewege
06:19 pm Story #2659 (Resolved): [Workbench] Anonymous user can access publicly shared data using Workbenc...
Ward Vandewege
05:45 pm Support #5071 (Resolved): [Support] Fix bugs and write tests (second half)
Ward Vandewege
04:52 pm Revision 78ca9c5c (arvados): closes #5197
Merge branch '5197-collection-name-owner-unique' Radhika Chippada
04:48 pm Bug #5194: [Documentation] User guide doesn't link to or acknowledge new "Getting Started" section
This is great, thanks. Peter Amstutz
04:43 pm Bug #5246 (Resolved): [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError...
WTF?... Peter Amstutz
04:20 pm Revision 7383891f (arvados-dev): Reflect deploy changes in run-deploy.sh
Refs #5226 Ward Vandewege
04:20 pm Revision 7383891f (arvados): Reflect deploy changes in run-deploy.sh
Refs #5226 Ward Vandewege
03:32 pm Bug #5207: [API] Collection expires_at should be a full timestamp, not just a date.
expires_at should absolutely be a timestamp just like all the others.
Suggest a unit test that verifies every *_at...
Tom Clegg
03:31 pm Revision cbccf62a (arvados): 4759: Update Node Manager to parse new Arvados API timestamps.
Refs #4759. Brett Smith
02:43 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
so in here: qr1hi-j7d0g-0x4b08b68zanwxh
I have new collection and new collection (2)
I have foo.txt in each of them...
Bryan Cosca

02/17/2015

11:20 pm Bug #5194 (Resolved): [Documentation] User guide doesn't link to or acknowledge new "Getting Star...
Applied in changeset arvados|commit:9c8bad50218730ac2c640f8e1c00fd12f2f174e4. Anonymous
11:04 pm Bug #5194 (In Progress): [Documentation] User guide doesn't link to or acknowledge new "Getting S...
Nancy Ouyang
11:03 pm Bug #5194 (New): [Documentation] User guide doesn't link to or acknowledge new "Getting Started" ...
* I kept "finished" because hopefully they ran their first pipeline in addition to reading the guide
* fixed
* fixed
Nancy Ouyang
10:53 pm Bug #5194 (In Progress): [Documentation] User guide doesn't link to or acknowledge new "Getting S...
Radhika Chippada
10:52 pm Bug #5194: [Documentation] User guide doesn't link to or acknowledge new "Getting Started" section
Review comments:
Looks much better and clears the confusion with disconnected "Getting started" sections. Just a f...
Radhika Chippada
10:29 pm Bug #5194: [Documentation] User guide doesn't link to or acknowledge new "Getting Started" section
Note about task #5243:
This is a quick fix only.
* I disambiguated "user guide" vs "getting started" sections with...
Nancy Ouyang
11:20 pm Task #5243 (Resolved): Review branch 5194-quickfix-disambiguate-gettingstarted-sections
Applied in changeset arvados|commit:9c8bad50218730ac2c640f8e1c00fd12f2f174e4. Anonymous
10:55 pm Task #5243 (In Progress): Review branch 5194-quickfix-disambiguate-gettingstarted-sections
Radhika Chippada
10:22 pm Task #5243 (Resolved): Review branch 5194-quickfix-disambiguate-gettingstarted-sections
This is a quick fix only. I disambiguated the new "getting started" section from the "getting started" subsection in ... Nancy Ouyang
11:16 pm Revision 9c8bad50 (arvados): closes #5243, #5194 Merge branch '5194-quickfix-disambiguate-getting...
Nancy Ouyang
11:07 pm Revision efb77a42 (arvados): Merge branch '3408-production-datamanager' refs #3408
Misha Zatsman
11:06 pm Revision a5f72c4a (arvados): 5194: minor fixes
Nancy Ouyang
11:06 pm Revision f5a88673 (arvados): Merge branch 'master' into 3408-production-datamanager refs #3408
Misha Zatsman
11:02 pm Revision 83ea6e36 (arvados): Changes to allow datamanager to run indefinitely:
Logger's worker goroutine returns after final write.
minutes-between-runs flag specifies how many minutes to wait bet...
Misha Zatsman
11:00 pm Task #5222 (Resolved): Review 4138-node-manager-gce-wip
Applied in changeset arvados|commit:319503f1a8eda9fb9cea0bff038ad437e88ebeac. Brett Smith
11:00 pm Feature #4138 (Resolved): [Node Manager] Support Google Cloud Platform in node manager
Applied in changeset arvados|commit:319503f1a8eda9fb9cea0bff038ad437e88ebeac. Brett Smith
10:02 pm Feature #4138: [Node Manager] Support Google Cloud Platform in node manager
Brett Smith wrote:
> Tom Clegg wrote:
> > * services/nodemanager/doc/gce.example.cfg seems to have forked the docum...
Tom Clegg
03:44 pm Feature #4138: [Node Manager] Support Google Cloud Platform in node manager
Tom Clegg wrote:
> * services/nodemanager/doc/gce.example.cfg seems to have forked the documentation in ec2.example....
Brett Smith
10:55 pm Revision 319503f1 (arvados): Merge branch '4138-node-manager-gce-wip'
Closes #4138, #5222.
Thanks, Tim.
Brett Smith
10:49 pm Revision d32bbed0 (arvados): 4138: Revamp Node Manager driver proxying in BaseComputeNodeDriver.
Accessing attributes through a super() proxy does not invoke
__getattr__ on base classes, so the old implementation m...
Brett Smith
10:49 pm Revision c51fe8e8 (arvados): 4138: Refactor out Node Manager DriverTestMixin.
Brett Smith
10:49 pm Revision d6d290bf (arvados): 4138: Prepare Node Manager GCE driver for production.
* Set node metadata in more appropriate places.
* Bridge more differences between GCE and EC2, like the fact that
s...
Brett Smith
10:49 pm Revision 45fdc95e (arvados): 4138: general GCE fixes
* JSON credential file
** GCE credentials are delivered as a JSON string (and the key is formatted as a multi-line RS...
Tim Pierce
10:49 pm Revision af52e497 (arvados): 4138: code review feedback
Tim Pierce
10:49 pm Revision 51d417f9 (arvados): 4138: GCE fixes
The 'network_id' parameter needs to be delivered as 'location' in GCE.
The ping_url parameter is now delivered in th...
Tim Pierce
10:49 pm Revision b5249ac7 (arvados): 4138: Refactor common Node Manager driver initialization to base dri...
Brett Smith
10:49 pm Revision 9d6a6eca (arvados): 4138: support for Google Cloud Engine.
* Added:
** nodemanager/arvnodeman/computenode/drivers/gce.py
** nodemanager/doc/gce.example.cfg
** nodemanager/tests...
Tim Pierce
10:49 pm Revision 5884b7c4 (arvados): 4138: Fix noop Node Manager EC2 driver tests.
The previous tests simply instantiated the driver, then checked that a
mock method was truthy (which it will always b...
Brett Smith
10:49 pm Revision 708630d0 (arvados): 4138: Simplify Node Manager GCE credential handling.
Because libcloud's GCE driver accepts a key path as a constructor
argument, it's relatively straightforward to put al...
Brett Smith
10:49 pm Revision a6837612 (arvados): 4138: updated unit test
Corrected test_create_includes_ping_secret to account for delivering the
ping secret via metadata in GCE.
Tim Pierce
10:46 pm Feature #5245 (New): [Documentation] Show footer with date last updated
A "date last updated" footer on each doc page will help users troubleshoot if any documentation falls out of date and... Nancy Ouyang
10:19 pm Revision 95053e5f (arvados): 5194: Quickfix, disambiguated getting started and user guide section...
Nancy Ouyang
10:10 pm Story #3408: [Keep] Implement Production Data Manager
Peter Amstutz wrote:
> * The Arvados convention for timestamps is to end in "_at" so runInfo["started_at"] instead o...
Misha Zatsman
09:37 pm Revision 1713f54c (arvados): Merge branch '3408-production-datamanager' refs #3408
Misha Zatsman
09:33 pm Bug #5211: [Documentation] Top Navbar of docs homepage not suitable for small window
This happens in-between "super small" where it turns into a mobile-friendly page, and "big" when the top navbar is flat. Nancy Ouyang
09:30 pm Revision 6100a423 (arvados): More changes in response to Peter's review.
Started referencing keep servers by uuid.
Moved more logger init code into constructor call.
Switched logged timestam...
Misha Zatsman
09:23 pm Bug #5240 (Closed): Create spec of Public Project list
Bryan Cosca
09:21 pm Bug #5240 (Closed): Create spec of Public Project list
make sure descriptions are had in all collections, templates, projects, subprojects, etc. Bryan Cosca
09:22 pm Story #5239 (Closed): Create public RNA seq tuxedo pipeline
Bryan Cosca
09:21 pm Story #5239 (Closed): Create public RNA seq tuxedo pipeline
Bowtie > Tophat > cufflinks > HTSeq Bryan Cosca
09:20 pm Bug #4520 (In Progress): [SDKs] arv copy should respect --project-uuid when saving destination Co...
Peter Amstutz
09:16 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Notes:
It should now correctly respect --project-uuid for collections, templates, pipeline instances, and docker i...
Peter Amstutz
09:12 pm Task #5238 (Resolved): Review 4520-arv-copy-project-uuid
Peter Amstutz
09:12 pm Task #5114 (Resolved): Fix
Peter Amstutz
07:59 pm Task #5114 (In Progress): Fix
Peter Amstutz
09:04 pm Revision 74784b33 (arvados): 4520: tested copying, fixed bad 'properties' field
Peter Amstutz
09:02 pm Feature #5090 (Resolved): [Documentation] Add some direct links on doc.arvados.org to the most us...
Nancy Ouyang
09:01 pm Task #5196 (Resolved): Review branch 5090-doc-to-homepage
Nancy Ouyang
08:53 pm Revision 546b44cf (arvados): refs #5090 Merge branch '5090-doc-to-homepage'
Nancy Ouyang
08:16 pm Revision bef0f85f (arvados): 4520: --project-uuid now used for owner_uuid on all create() calls.
Peter Amstutz
08:10 pm Feature #5237 (New): [Workbench] Pipeline re-run dialog should offer docker image choices (latest...
Tom Clegg
07:46 pm Task #5031: Review/feedback
Wiki page is ready for another round of feedback. Brett Smith
07:45 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
I've updated "the wiki page":https://arvados.org/projects/arvados/wiki/Python_SDK with our current thinking about the... Brett Smith
06:46 pm Revision f3250432 (arvados): 3408: Merge branch 'master' into 3408-production-datamanager
Tom Clegg
06:43 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Brett Smith wrote:
>
> h2. What am I reviewing?
>
> A lot of the code in this branch is meant to provide API su...
Peter Amstutz
06:39 pm Bug #5235 (New): [Workbench] Pipeline instance "Re-run with latest" button occasionally returns N...
This has happened to me maybe 3 or so times in the last 100-200 attempts, hard to reproduce, maybe its just an intern... Bryan Cosca
06:36 pm Revision 50d3be92 (arvados): 4823: Record manifest_text response from API server. Give better na...
some tests. Peter Amstutz
06:29 pm Revision bd53829c (arvados): refs #4926 Merge branch '4926-rename-share.png'
Nancy Ouyang
05:35 pm Bug #4759 (Resolved): [API] greater than filter is treated as greater than or equals for modifica...
Applied in changeset arvados|commit:3598c3003a7987cca5c0536ba8206ec40c1c3649. Anonymous
05:07 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
Tom, that is fine. I also used "humans" in several tests earlier for the same reason. We can deal with them when we d... Radhika Chippada
05:04 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
Radhika Chippada wrote:
> One minor comment about the tests. In the python test_timestamp_inequality_filter, why use...
Tom Clegg
04:37 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
Tom, yes, I agree that "2015-02-17" should mean "2015-02-17T00:00:00.000000000Z" and all the updates look good.
On...
Radhika Chippada
06:41 am Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
4759-timestamp-precision-TC now has
commit:5517f02 4759: Add functional tests for timestamp precision.
commit:6ee...
Tom Clegg
05:16 pm Revision 20b2d6f7 (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
05:15 pm Revision 503c616f (arvados): 4823: More tests and fixes for updating and merging from remote api ...
Tests pass. Peter Amstutz
05:09 pm Bug #5233 (New): [Tests] Eliminate system globals in test suites
It should be possible to run jenkins/run-tests.sh on two source trees concurrently on the same machine (using either ... Tom Clegg
05:07 pm Revision 3598c300 (arvados): Merge branch '4759-timestamp-precision-TC' closes #4759
Tom Clegg
04:50 pm Task #5219 (Resolved): Review branch: 5096-wb-collection-name-or-desc-update
Radhika Chippada
04:11 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
Suggesting that we merge in the removal of the rendering of the "dependencies" in the API and call it a day, with the... Phil Hodgson
03:42 pm Revision 28467b48 (arvados): 4138: Fixup GCE shutdown window docs.
Brett Smith
03:38 pm Revision 37916fad (arvados): 4138: Fixup GCE boot time calculations.
Store boot time in node metadata when we create a node. Assume 0 if
that's not available.
Brett Smith
03:30 pm Bug #5220 (Resolved): [Workbench] for collections shared anonymously, do not show the 'Sharing an...
Applied in changeset arvados|commit:d54738ad3b2fde0207cf1ebbdc6f4360cd141d90. Radhika Chippada
03:16 pm Bug #5220: [Workbench] for collections shared anonymously, do not show the 'Sharing and Permissio...
I added one whitespace cleanup commit on this branch, thanks, LGTM.
Please pull in that commit and merge!
Ward Vandewege
03:25 pm Revision d54738ad (arvados): closes #5220
Merge branch '5220-no-sharing-box-for-anon-user' Radhika Chippada
03:20 pm Revision 177e076e (arvados): 4926: renamed share.png to sharing.png due to adblock on firefox
Nancy Ouyang
03:17 pm Task #5225 (Resolved): Review branch: 5220-no-sharing-box-for-anon-user
Ward Vandewege
03:15 pm Task #5225 (In Progress): Review branch: 5220-no-sharing-box-for-anon-user
Ward Vandewege
03:13 pm Revision 96e0115f (arvados): 5220: whitespace cleanup.
Ward Vandewege
02:26 pm Revision 39e2e62f (arvados): 4138: Fixup GCE config e-mail address.
Brett Smith
06:35 am Revision 5517f022 (arvados): 4759: Add functional tests for timestamp precision.
Tom Clegg
06:06 am Revision 6ee389b7 (arvados): 4759: Add test for inequality filters.
Tom Clegg
03:35 am Revision 4f8b2d75 (arvados): 4759: Ignore args to as_json.
Tom Clegg
02:36 am Task #5165 (Resolved): Review 3410-replication-attrs
Tom Clegg
12:27 am Revision fe7c0afe (arvados): 4759: add (options = nil) to time_format -> as_json method. Several ...
SELECT "logs".* FROM "logs" WHERE (logs.id >= 7) ORDER BY id asc LIMIT 20
Error publishing event: wrong number of arg...
Radhika Chippada

02/16/2015

11:59 pm Revision afa3f1f4 (arvados): 4759: do not use modified_at getter method; test passes but still ot...
Radhika Chippada
11:34 pm Bug #5220: [Workbench] for collections shared anonymously, do not show the 'Sharing and Permissio...
Notes about the update:
* I hid the "Sharing and permissions" box when anonymous access is the context.
* I sho...
Radhika Chippada
10:52 pm Bug #5220 (In Progress): [Workbench] for collections shared anonymously, do not show the 'Sharing...
Radhika Chippada
06:03 pm Bug #5220: [Workbench] for collections shared anonymously, do not show the 'Sharing and Permissio...
Brett Smith wrote:
> For background, Workbench used to be quieter in this scenario. The message was added during re...
Ward Vandewege
11:31 pm Task #5225 (Resolved): Review branch: 5220-no-sharing-box-for-anon-user
Radhika Chippada
11:30 pm Revision 58f8ab40 (arvados): 5220: do not show "Sharing and permissions" box when an anonymous us...
Radhika Chippada
10:50 pm Bug #5189 (Resolved): [Workbench] Manage account does not show repositories directly owned by user
Applied in changeset arvados|commit:1ee6ce5be0c86c1d2e903252ba2a70694be5cf31. Radhika Chippada
10:46 pm Bug #5189: [Workbench] Manage account does not show repositories directly owned by user
Thanks Brett. Merged into master after making the update. Radhika Chippada
09:35 pm Bug #5189: [Workbench] Manage account does not show repositories directly owned by user
Radhika Chippada wrote:
> Brett, I need separate lists @my_repositories (which has the list of repositories for the ...
Brett Smith
09:16 pm Bug #5189: [Workbench] Manage account does not show repositories directly owned by user
Brett, I need separate lists @my_repositories (which has the list of repositories for the links + owned repositories)... Radhika Chippada
07:12 pm Bug #5189: [Workbench] Manage account does not show repositories directly owned by user
Reviewing commit:45d8d01
This code calls @Repository.where(owner_uuid: current_user.uuid)@ twice. This can make t...
Brett Smith
04:34 pm Bug #5189 (In Progress): [Workbench] Manage account does not show repositories directly owned by ...
Radhika Chippada
10:49 pm Revision 37affe0f (arvados): Merge branch 'master' into 4759-timestamp-precision
Radhika Chippada
10:46 pm Task #5223 (Resolved): Review branch: 5189-manage-acct-shows-own-repos
Radhika Chippada
06:51 pm Task #5223 (In Progress): Review branch: 5189-manage-acct-shows-own-repos
Brett Smith
04:35 pm Task #5223 (Resolved): Review branch: 5189-manage-acct-shows-own-repos
Radhika Chippada
10:46 pm Revision 1ee6ce5b (arvados): closes #5189
Merge branch '5189-manage-acct-shows-own-repos' Radhika Chippada
10:45 pm Revision c99e40c1 (arvados): 5189: a little cleanup
Radhika Chippada
10:28 pm Revision 1578bb43 (arvados): Merge branch 'master' into 5189-manage-acct-shows-own-repos
Radhika Chippada
10:24 pm Revision 40e9d6a0 (arvados): 4759: added time_format.rb initializer
Radhika Chippada
10:13 pm Feature #4138: [Node Manager] Support Google Cloud Platform in node manager
Only a couple of comments at commit:8f28c53... with the caveat that I'm still pretty new at libcloud/nodemanager:
...
Tom Clegg
09:51 pm Revision 6cd9106d (arvados): Merge branch 'master' into 4759-timestamp-precision
Conflicts:
services/api/test/integration/collections_api_test.rb
Radhika Chippada
09:49 pm Revision 5f905666 (arvados): 4823: Add new tests for BufferBlock, BlockManager, saving, updating....
changes on variable naming. Remove splitting code from splitfastq. Peter Amstutz
09:00 pm Story #3410 (Resolved): [API] Rename collection "desired replication" attributes, add model const...
Applied in changeset arvados|commit:d87717b4ec885059183ef6d7fa6780c343338455. Anonymous
05:32 pm Story #3410 (In Progress): [API] Rename collection "desired replication" attributes, add model co...
Tom Clegg
08:28 am Story #3410: [API] Rename collection "desired replication" attributes, add model constraints
Radhika Chippada wrote:
> “args.replication is how many copies we instruct Arvados to maintain (by passing it in col...
Tom Clegg
08:58 pm Revision 87ab50f7 (arvados): 5197: needed one more udpate
Radhika Chippada
08:53 pm Revision d87717b4 (arvados): Merge branch '3410-replication-attrs' closes #3410 refs #5011
Tom Clegg
08:49 pm Revision 20abd5d5 (arvados): Merge branch 'master' into 5197-collection-name-owner-unique
Conflicts:
services/api/db/structure.sql
Radhika Chippada
08:41 pm Revision 0fd86b97 (arvados): 5197: down migration working
Radhika Chippada
08:31 pm Revision 8c629ffa (arvados): Merge branch 'master' into 5197-collection-name-owner-unique
Radhika Chippada
08:31 pm Revision a002d3ef (arvados): 5197: updated migration script
Radhika Chippada
08:02 pm Revision daaeb7a2 (arvados): Fix typo in COPYING.
No issue # Ward Vandewege
07:49 pm Revision 399366e7 (arvados): 5197: update the collection_owner_uuid_name_unique index to use expi...
Radhika Chippada
07:13 pm Revision eff37344 (arvados): 3410: Merge branch 'master' into 3410-replication-attrs
Conflicts:
services/api/test/fixtures/collections.yml
services/api/test/unit/collection_test.rb
Tom Clegg
07:07 pm Revision fb179796 (arvados): 5197: write a failing test
Radhika Chippada
07:05 pm Task #5222 (In Progress): Review 4138-node-manager-gce-wip
Tom Clegg
04:15 pm Task #5222 (Resolved): Review 4138-node-manager-gce-wip
Brett Smith
07:02 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
Replaced 4759-timestamp-precision-TC with much nicer commit:5f2d5f9.
Tom Clegg
04:42 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
It doesn't seem quite right to make the models' attribute methods start returning strings instead of ActiveSupport::T... Tom Clegg
07:00 pm Revision 5f2d5f96 (arvados): 4759: Use ISO 8601 timestamps with fractional seconds in API responses.
Tom Clegg
05:54 pm Bug #5096: [Workbench] Avoid passing manifest_text around the network too much when updating and ...
Brett, thanks for the suggestion. This is much more efficient and accomplishes the goal more effectively. I made this... Radhika Chippada
05:23 pm Bug #5096: [Workbench] Avoid passing manifest_text around the network too much when updating and ...
Reviewing commit:23c1bc6
When we're doing small updates, the new update method skips a lot of the encoding work in...
Brett Smith
05:50 pm Revision fd172dd6 (arvados): refs #5096
Merge branch '5096-wb-collection-name-or-desc-update' Radhika Chippada
05:46 pm Revision 5e003c8f (arvados): Merge branch 'master' into 5096-wb-collection-name-or-desc-update
Conflicts:
apps/workbench/test/controllers/collections_controller_test.rb
Radhika Chippada
05:42 pm Revision f842b72b (arvados): 5096: more efficient update method override.
Radhika Chippada
05:32 pm Task #5205 (Resolved): Review 5200-anonymous-download
Tom Clegg
04:35 pm Bug #5095 (Resolved): [FUSE] arv-mount takes up too much memory and occassionally crashes when li...
Applied in changeset arvados|commit:8b90f80efca772efd2697ffc70d7809c32564171. Peter Amstutz
04:20 pm Bug #5095: [FUSE] arv-mount takes up too much memory and occassionally crashes when listing large...
Peter Amstutz wrote:
> Now at commit:ef4e4a3
This is good to merge. Thanks.
Brett Smith
04:00 pm Bug #5095: [FUSE] arv-mount takes up too much memory and occassionally crashes when listing large...
Brett Smith wrote:
> Reviewing commit:4106786.
>
> * Directory uses the current time as the default mtime. Colle...
Peter Amstutz
03:54 pm Bug #5095 (In Progress): [FUSE] arv-mount takes up too much memory and occassionally crashes when...
Peter Amstutz
03:19 am Bug #5095: [FUSE] arv-mount takes up too much memory and occassionally crashes when listing large...
Reviewing commit:4106786.
* Directory uses the current time as the default mtime. CollectionDirectory overrides t...
Brett Smith
04:33 pm Revision 6ab55057 (arvados): Merge branch 'master' into 5189-manage-acct-shows-own-repos
Radhika Chippada
04:33 pm Revision 8b90f80e (arvados): Merge branch '5095-fuse-ls-takes-forever' closes #5095
Peter Amstutz
04:33 pm Task #5219 (In Progress): Review branch: 5096-wb-collection-name-or-desc-update
Brett Smith
04:33 pm Task #5216 (Resolved): Review 5095-fuse-ls-takes-forever
Peter Amstutz
02:58 am Task #5216 (In Progress): Review 5095-fuse-ls-takes-forever
Brett Smith
04:32 pm Revision 446785a1 (arvados): 4823: Notes on how the mocking works with requests.Session
Peter Amstutz
04:30 pm Bug #4464 (Resolved): [Workbench] Collections tab loads forever on a specific project
The project named in this bug now loads very quickly, so I'm marking this as closed. Admittedly there's been some fa... Brett Smith
04:29 pm Revision 45d8d010 (arvados): 5189: include owned repositories in the list of repositories returne...
Radhika Chippada
04:26 pm Revision 4b79e0e7 (arvados): 4759: Use ISO 8601 timestamps with fractional seconds in API responses.
Tom Clegg
04:12 pm Revision 8f28c530 (arvados): 4138: Prepare Node Manager GCE driver for production.
* Set node metadata in more appropriate places.
* Bridge more differences between GCE and EC2, like the fact that
s...
Brett Smith
04:12 pm Revision 82bb5282 (arvados): 4138: Revamp Node Manager driver proxying in BaseComputeNodeDriver.
Accessing attributes through a super() proxy does not invoke
__getattr__ on base classes, so the old implementation m...
Brett Smith
04:12 pm Revision 58be160a (arvados): 4138: Fix noop Node Manager EC2 driver tests.
The previous tests simply instantiated the driver, then checked that a
mock method was truthy (which it will always b...
Brett Smith
04:12 pm Revision 1e0fa596 (arvados): 4138: Refactor out Node Manager DriverTestMixin.
Brett Smith
04:12 pm Revision 650bd4ae (arvados): 4138: support for Google Cloud Engine.
* Added:
** nodemanager/arvnodeman/computenode/drivers/gce.py
** nodemanager/doc/gce.example.cfg
** nodemanager/tests...
Tim Pierce
04:12 pm Revision 6bd3ba96 (arvados): 4138: Refactor common Node Manager driver initialization to base dri...
Brett Smith
04:12 pm Revision 0d0de386 (arvados): 4138: GCE fixes
The 'network_id' parameter needs to be delivered as 'location' in GCE.
The ping_url parameter is now delivered in th...
Tim Pierce
04:12 pm Revision c2fb3f57 (arvados): 4138: code review feedback
Tim Pierce
04:12 pm Revision 36929497 (arvados): 4138: updated unit test
Corrected test_create_includes_ping_secret to account for delivering the
ping secret via metadata in GCE.
Tim Pierce
04:12 pm Revision 2b6cfad3 (arvados): 4138: general GCE fixes
* JSON credential file
** GCE credentials are delivered as a JSON string (and the key is formatted as a multi-line RS...
Tim Pierce
04:12 pm Revision 0d0a1fe0 (arvados): 4138: Simplify Node Manager GCE credential handling.
Because libcloud's GCE driver accepts a key path as a constructor
argument, it's relatively straightforward to put al...
Brett Smith
04:01 pm Revision ef4e4a34 (arvados): 5095: _mtime on collection defaults to 0 instead of time.time().
Peter Amstutz
03:59 pm Revision f22dda84 (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Conflicts:
sdk/python/tests/arvados_testutil.py
services/fuse/arvados_fuse/__init__.py
Peter Amstutz
03:49 pm Task #5213 (In Progress): Review branch: 4759-timestamp-precision
Tom Clegg
03:11 pm Revision 7b877a2b (arvados): 5095: Set _mtime when the collection object is updated.
Peter Amstutz
02:00 pm Bug #5186 (Resolved): [Workbench] Collection viewing broken for collections with empty (but non-n...
Applied in changeset arvados|commit:0cefa4c0f3c1b16884b04d6273bd8730166d69ba. Radhika Chippada
01:58 pm Bug #5186: [Workbench] Collection viewing broken for collections with empty (but non-nil) propert...
Thanks for the review feedback Brett. I removed the unnecessary statement from the collection_controller. I added a g... Radhika Chippada
03:54 am Bug #5186: [Workbench] Collection viewing broken for collections with empty (but non-nil) propert...
At commit:7ef2780
Radhika Chippada wrote:
> * My tests passed with or without "accept_attribute_as_json :properti...
Brett Smith
01:56 pm Revision 0cefa4c0 (arvados): closes #5186
Merge branch '5186-collection-with-empty-properties' Radhika Chippada
01:54 pm Revision 4c5352de (arvados): 5186: a few more test assertions.
Radhika Chippada
08:12 am Revision 11e1ee67 (arvados): 3410: Update comments.
Tom Clegg
08:12 am Revision 1e423bd9 (arvados): 3410: Fix search index so [old versions of] tests pass after down-mi...
Tom Clegg
08:11 am Revision 938338a3 (arvados): 3410: Fix overly sensitive test.
Tom Clegg
03:20 am Task #5221 (In Progress): Review branch: 5186-collection-with-empty-properties
Brett Smith
02:47 am Bug #5217 (Closed): [API] Cannot rename a new collection in a project to a previous collection na...
Duplicate of #5197. Brett Smith
 

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