Activity

From 08/19/2014 to 09/17/2014

09/17/2014

08:52 pm Task #3924 (Resolved): Write "Running tests" wiki page
Tom Clegg
08:42 pm Feature #3338: [Workbench] Show number of items in each tab of the project page.
Okay, I've created a new before_filter. I was overly concerned about before_filter ordering, which behaves as we woul... Phil Hodgson
05:41 pm Feature #3338 (New): [Workbench] Show number of items in each tab of the project page.
Reviewing commit:210d762
Unfortunately, you can't add the user_is_manager code to find_object_by_uuid, because tha...
Brett Smith
03:05 pm Feature #3338 (In Progress): [Workbench] Show number of items in each tab of the project page.
Phil Hodgson
12:27 pm Feature #3338: [Workbench] Show number of items in each tab of the project page.
Well if the only places to track changes are on deletions then the job's pretty easy, so I just did it now and commit... Phil Hodgson
09:27 am Feature #3338: [Workbench] Show number of items in each tab of the project page.
Phil Hodgson wrote:
> Now, the thing is, if we like this approach, we have to do another iteration to properly compl...
Brett Smith
08:42 pm Revision 3ef64886 (arvados): 3338: move code that sets the share_links to its own before_filter
Phil Hodgson
08:11 pm Revision a9f3e9ce (arvados): Update Gemfiles to use latest arvados gem. refs #3550
Tom Clegg
06:12 pm Task #3772 (Resolved): Review 3550-local-pipeline
Tom Clegg
06:05 pm Story #3550 (Resolved): [SDKs] arv-run-pipeline-instance supports running jobs locally using arv-...
Applied in changeset arvados|commit:dce0ccabe3d9fab6943e89dc84050793cca5b553. Anonymous
05:05 pm Story #3550: [SDKs] arv-run-pipeline-instance supports running jobs locally using arv-crunch-job
Tom Clegg wrote:
> Now at commit:2da969c
I think this is good to merge. Thanks.
Brett Smith
11:24 am Story #3550: [SDKs] arv-run-pipeline-instance supports running jobs locally using arv-crunch-job
Brett Smith wrote:
> Reviewing commit:d35d434. Earlier disclaimer about UUIDs still applies.
>
> Tom Clegg wrote...
Tom Clegg
06:01 pm Revision dce0ccab (arvados): Merge branch '3550-local-pipeline' closes #3550
Tom Clegg
06:00 pm Revision aee63d7c (arvados): 3550: Merge branch 'master' into 3550-local-pipeline
Conflicts:
sdk/cli/bin/arv-run-pipeline-instance
Tom Clegg
05:56 pm Feature #3923 (Closed): [Workbench] Use web notifications to alert user when pipelines finish
Tom Clegg
05:34 pm Revision ab7c9781 (arvados): 3699: misc improvements
* added -v/--verbose flag to enable debug output
* skip copying a src repository if it has already been copied this
...
Tim Pierce
05:26 pm Feature #3605: [Workbench] improved dashboard page
Reviewing commit:fc2096f2.
So, we just had an issue where adding a new test fixture along with a new test broke an...
Brett Smith
04:24 pm Task #3921 (Resolved): Update crunch-job
Peter Amstutz
04:24 pm Task #3920 (New): Use .utc-date data-utc-date javascript
Peter Amstutz
04:23 pm Task #3919 (Resolved): Debug streaming
Peter Amstutz
04:16 pm Bug #3882: [Workbench] fiddlesticks trying to cancel job that is already cancelled
Tom thinks this might actually be an API-side bug. Keep that in mind. Brett Smith
04:02 pm Task #3916 (Resolved): Testing
Tim Pierce
04:02 pm Task #3915 (Resolved): Implement timeout configuration settings
Tim Pierce
04:02 pm Task #3914 (Resolved): Study httplib2 and other docs
Research to identify options for setting timeout settings Tim Pierce
03:59 pm Task #3913 (Resolved): Test crunch-job log output
Tim Pierce
03:59 pm Task #3912 (Resolved): Rewrite crunch_job::Log to pipe output to arv-put
Tim Pierce
03:55 pm Bug #3910 (Closed): [SDKs] Client libraries should retry failed API requests after errors like Ga...
Clients to address:
* Ruby
* arv-run-pipeline-instance (assuming it's still not using the Ruby SDK)
* Workbench (a...
Tom Clegg
03:48 pm Task #3909 (Resolved): Add throttle logic
Peter Amstutz
03:39 pm Task #3906 (Resolved): Add state column
Peter Amstutz
03:37 pm Task #3904 (Resolved): Encode/decode filenames as utf-8
Peter Amstutz
03:26 pm Support #3823 (Resolved): [Support] Fix bugs and write tests (the second half of the sprint)
Tim Pierce
03:26 pm Task #3732 (Resolved): Fix bugs the second half of the sprint
Tim Pierce
03:20 pm Support #3902 (Resolved): [Support] Support: fix bugs and write tests second half
Tom Clegg
03:06 pm Bug #3634 (In Progress): [Workbench] Page content is the same as where you left it when navigatin...
Phil Hodgson
03:06 pm Story #3661 (In Progress): [Workbench] Add "Move" and "Copy" buttons to top of #show page for eve...
Phil Hodgson
02:43 pm Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Ah hm! My guess is that it's because it's rendered as a button instead of a Bootstrap-button-styled link. In spite of... Phil Hodgson
11:53 am Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Phil Hodgson wrote:
> Opa! The existing code for selection copying that would need to refer to this new model method...
Brett Smith
10:58 am Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
For me the buttons are properly in a row, so I can't reproduce what you saw. But I think it would be a separate issue... Phil Hodgson
10:56 am Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Opa! The existing code for selection copying that would need to refer to this new model method for us to stay DRY is ... Phil Hodgson
03:05 pm Feature #3900 (Resolved): [Workbench] Trash button on collection uses "delete" API instead of set...
The trash button for collections in Workbench should use the collections/delete API instead of changing owner_uuid to... Tom Clegg
03:04 pm Bug #3891: I/O error listing arv-mount shared directory
Could this be #3871? Brett Smith
11:18 am Bug #3891 (Resolved): I/O error listing arv-mount shared directory
Peter Amstutz
03:00 pm Story #2761 (Resolved): [Workbench] diagnostic suite runs against a production instance
Applied in changeset arvados|commit:2d04e7d3466cfbf166aecfde71dea909ad0b9119. Radhika Chippada
12:22 pm Story #2761: [Workbench] diagnostic suite runs against a production instance
LGTM, thanks! Tom Clegg
03:00 pm Revision fc2096f2 (arvados): 3605: Test queue_size method and queue_position field. Adjust "GET ...
tests for jobs controller to test that users don't see queue items for which
they do not have permissions.
Peter Amstutz
02:59 pm Task #3870 (Resolved): Review branch: 2761-diagnostic-suite
Radhika Chippada
02:58 pm Feature #3899 (Resolved): [Crunch] crunch-job and Workbench use the new job state attribute (see ...
Expected changes:
* Crunch-job reads/writes the new state attribute instead of the old success/running flags.
* Wor...
Tom Clegg
02:56 pm Story #3898 (Resolved): [API] Job model has a single state attribute that can be updated and read...
Before validation:
* If state has changed to Running, set started_at to now
* If state has changed to Failed or Com...
Tom Clegg
02:56 pm Revision 2d04e7d3 (arvados): closes #2761
Merge branch '2761-diagnostic-suite' Radhika Chippada
02:55 pm Revision 9ad5b41b (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
02:54 pm Story #3897 (New): [SDKs] Clients can specify which auth config file to load.
The usual methods by which a client authenticates to Arvados are
* ARVADOS_API_HOST, ARVADOS_API_TOKEN and ARVADOS_A...
Tim Pierce
02:33 pm Feature #3895 (Closed): set up dev ci server
Ward Vandewege
02:29 pm Feature #3894 (Resolved): [Documentation] Document the run-tests.sh program on the Hacking pages ...
Tom Clegg
02:26 pm Revision c99ba4cd (arvados): Merge branch 'update-go-sdk-documentation'
Updating Go SDK Documentation,
no issue #
Misha Zatsman
02:25 pm Support #3893 (Resolved): [Documentation] Explain in public wiki how to submit good/safe support ...
Tom Clegg
02:10 pm Revision 2df94bb0 (arvados): no issue # - fix couple more places where description is failing on ...
Radhika Chippada
01:56 pm Revision 66cba099 (arvados): 3411: fix failing tests
The FuseSharedTest requires "pipeline_with_template.pipelineInstance" on
my machine, but not on Jenkins. Puzzling.
N...
Tim Pierce
01:24 pm Feature #3892 (New): [SDKs] Install man pages for CLI tools (auto generate from the --help content)
Tom Clegg
12:27 pm Task #3883 (Resolved): Review 3411-expire-collections
Tom Clegg
12:24 pm Revision 210d762a (arvados): 3338: add a 'count-change' event that the tab panes listen for, and ...
Phil Hodgson
11:46 am Revision 21cdd100 (arvados): Merge branch '3411-expire-collections'
Refs #3411. Tim Pierce
11:45 am Revision f1603177 (arvados): 3411: added new collection fixtures owned by active_user
Tim Pierce
11:42 am Revision c51634ca (arvados): Merge branch '3187-pipeline-instance-page' into 3605-improved-dashboard
Peter Amstutz
11:38 am Revision 1431ecfb (arvados): no issue # : fix nil issue in pipeline_templates page
Radhika Chippada
11:36 am Revision a3f380f9 (arvados): 3187: Fix tests and some debug spew.
Peter Amstutz
11:30 am Revision 8c5f7a86 (arvados): 3699: code review
* More feedback when copying collections and blocks
* Drop default DEBUG log level
* Rename --project_uuid -> --proje...
Tim Pierce
11:13 am Revision 2da969cc (arvados): 3550: Fix race conditions: avoid setting running/success/finished_at
attributes until output and log have been saved. Tom Clegg
11:00 am Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
* Default logging level is still "DEBUG", that needs to be changed
* It should list which collections are being copi...
Peter Amstutz
09:53 am Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
New revision at commit:9cff4a0 renames symbolic names found in @script_version@ and @supplied_script_version@ fields ... Tim Pierce
11:00 am Story #3411 (Resolved): [API] Implement Trash behavior using collection expiration
Applied in changeset arvados|commit:517d3fca54225873d36f94083f3b7056ce271f46. Tim Pierce
10:39 am Story #3411: [API] Implement Trash behavior using collection expiration
LGTM, thanks!
Tom Clegg
10:22 am Story #3411: [API] Implement Trash behavior using collection expiration
New revision at commit:0a5f8b6
Tom Clegg wrote:
> Tim Pierce wrote:
> > > * Should also test whether not-yet-exp...
Tim Pierce
10:03 am Story #3411: [API] Implement Trash behavior using collection expiration
Tim Pierce wrote:
> > * Should also test whether not-yet-expired and expired collections can be retrieved with @get ...
Tom Clegg
10:59 am Revision 517d3fca (arvados): Merge branch '3411-expire-collections'
Closes #3411. Tim Pierce
10:59 am Bug #3890 (Resolved): [API] dots (and probably other valid characters) are being stripped from gi...
Ward Vandewege
10:57 am Revision d8f97ca4 (arvados): 3550: Fix running local job repeatedly on subsequent loop iterations.
Tom Clegg
10:51 am Revision 6f243369 (arvados): 3661: proposed change of the selection javascript to use the new cop...
Phil Hodgson
10:48 am Revision aad2f86f (arvados): 3550: Add missing .andand
Tom Clegg
10:20 am Revision 0a5f8b68 (arvados): 3411: code review feedback
* Ensure each functional test issues only one request to the controller
* $application_config['default_trash_lifetime...
Tim Pierce
10:17 am Bug #3889 (Resolved): [API] [Workbench] Refactor any functional tests that call multiple actions ...
Example: "admin can create collection with unsigned manifest".
If multiple actions are called from a functional te...
Tom Clegg
10:10 am Revision 735f1ed1 (arvados): 2761: added some comments
Radhika Chippada
10:04 am Revision 283a6c02 (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
09:52 am Task #3886 (In Progress): Review 3605-queue-position-size
Brett Smith
09:30 am Task #3886 (Resolved): Review 3605-queue-position-size
Peter Amstutz
09:49 am Revision 37ab78a4 (arvados): 3550: Add missing .andand
Tom Clegg
09:44 am Revision 9cff4a0b (arvados): 3699: bugfix (renamed repository_map -> local_repo_dir)
Tim Pierce
09:32 am Task #3888 (In Progress): Fix tests
Peter Amstutz
09:32 am Task #3888 (Resolved): Fix tests
Peter Amstutz
09:32 am Task #3887 (In Progress): Fix tests
Peter Amstutz
09:32 am Task #3887 (Closed): Fix tests
Peter Amstutz
09:31 am Task #3723 (Resolved): Implement dashboard layout at https://arvados.org/attachments/download/349...
Peter Amstutz
09:31 am Task #3863 (Resolved): Review 3605-node-info-field
Peter Amstutz
09:29 am Revision d60536bb (arvados): 3605: Add "queue_position" to jobs. Also add a route on jobs contro...
the true size of the job queue. Peter Amstutz
09:29 am Task #3860: Review 3338-tab-counts
Ball's in your court at the moment, I think, but if you decide to merge the current work as-is and want me to take a ... Brett Smith
09:13 am Revision 9e235719 (arvados): Merge branch 'master' into 3605-improved-dashboard
Conflicts:
apps/workbench/app/models/job.rb
services/api/app/models/job.rb
Peter Amstutz
09:11 am Revision 1f1963df (arvados): Merge branch '3605-node-info-field' refs #3605
Peter Amstutz
09:04 am Revision 2749cf27 (arvados): Fix test
Peter Amstutz
09:02 am Task #3729 (Resolved): Design command line
Peter Amstutz
03:14 am Revision 3c37f8e6 (arvados): Undo two hunks that I accidentally committed in 565c31196f3ccd4346c8...
no issue # Ward Vandewege
03:14 am Revision 3c37f8e6 (arvados-dev): Undo two hunks that I accidentally committed in 565c31196f3ccd43...
no issue # Ward Vandewege
01:43 am Revision 3de7432a (arvados-dev): Add some robustness in the postgresql department.
no issue # Ward Vandewege
01:43 am Revision 3de7432a (arvados): Add some robustness in the postgresql department.
no issue # Ward Vandewege
12:34 am Task #3872 (In Progress): Review 3147-py-collection-retries-wip2
Tim Pierce

09/16/2014

10:47 pm Revision 4dc656ce (arvados): 3609: Fix trimming redirect parts of the command line.
Peter Amstutz
10:45 pm Story #3705 (Resolved): [Keep] Generalize PullList module to BlockWorkList
Applied in changeset arvados|commit:4cfb296612f7b483b56c36f119ca175def706d2f. Tim Pierce
10:39 am Story #3705: [Keep] Generalize PullList module to BlockWorkList
Tim,
I am reading through these changes as a learning exercise and had a few comments.
* BlockWorkList: "BlockLis...
Radhika Chippada
10:44 pm Task #3858 (Resolved): Review 3705-keep-blockworklist
Tim Pierce
10:41 pm Revision 4cfb2966 (arvados): Merge branch '3705-keep-blockworklist'
Closes #3705. Tim Pierce
10:36 pm Revision b4d7d4a3 (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
10:35 pm Revision 787c47f7 (arvados): 2761: minor updates to diagnostics test config explanation.
Radhika Chippada
10:34 pm Story #2761: [Workbench] diagnostic suite runs against a production instance
Tom,
Updated per you feedback.
- Added "diagnostics" section in application.default.yml with a sample configurati...
Radhika Chippada
02:43 pm Story #2761: [Workbench] diagnostic suite runs against a production instance
I like having the diagnostics tests in a separate directory, but I think we should also separate them from the other ... Tom Clegg
10:34 pm Revision 87163a6e (arvados): 3705: use %v to format interface types
Tim Pierce
10:32 pm Revision 452baf1e (arvados): Fix arv-run-pipeline-instance to not crash when template is null. n...
Peter Amstutz
10:32 pm Revision 77c077a4 (arvados): 3609: Now print log messages for submitted pipeline.
Peter Amstutz
10:30 pm Revision 5e655f24 (arvados): Fix arv-run-pipeline-instance to not crash when template is null. n...
Peter Amstutz
10:09 pm Revision 82c5dcae (arvados): 3705: drop unnecessary 'items' from BlockWorkList
Tim Pierce
09:56 pm Revision 391c3551 (arvados): 3705: use helper functions in tests
Tim Pierce
09:01 pm Revision 565c3119 (arvados-dev): Only install the latest gem (i.e. the one we just built).
No issue # Ward Vandewege
09:01 pm Revision 565c3119 (arvados): Only install the latest gem (i.e. the one we just built).
No issue # Ward Vandewege
09:00 pm Revision 0d1919c4 (arvados): Fix test
Peter Amstutz
08:52 pm Revision 7cf1194b (arvados): Also build our java-bwa-samtools docker image.
no issue # Ward Vandewege
08:52 pm Revision 7cf1194b (arvados-dev): Also build our java-bwa-samtools docker image.
no issue # Ward Vandewege
07:10 pm Feature #3338: [Workbench] Show number of items in each tab of the project page.
Done, as you've recommended.
Now, the thing is, if we like this approach, we have to do another iteration to prope...
Phil Hodgson
10:57 am Feature #3338: [Workbench] Show number of items in each tab of the project page.
Reviewing commit:893f659
* You could make @tab_counts@ a little more predictable by using @contents.items_availabl...
Brett Smith
07:09 pm Revision db9ccbd2 (arvados): 3338: move the user_is_manager and shared items to the already-overr...
Phil Hodgson
07:05 pm Revision b941bb69 (arvados): 3338: fix the integration test so that it checks the on-screen colle...
rather than trying to use the fixtures which doesn't work anyway Phil Hodgson
06:40 pm Revision ec3e6558 (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
06:40 pm Revision 869c692d (arvados): 2761: update config
Radhika Chippada
06:05 pm Task #3872: Review 3147-py-collection-retries-wip2
New branch to review, at c19503e. Brett Smith
04:03 pm Task #3872: Review 3147-py-collection-retries-wip2
Taking this back for a bit to deal with some merge conflicts from a bugfix. Brett Smith
06:00 pm Revision df8ac6c1 (arvados): 3147: Add retry support to FUSE driver.
Brett Smith
06:00 pm Revision c19503ef (arvados): 3147: crunch-job retries data uploads more for longer-running jobs.
Brett Smith
06:00 pm Revision 2ffac087 (arvados): 3147: FUSE driver requires a Python SDK with retry support.
I also took out some of the older log-handling code while I was at it,
since the stricter versioning makes it unneces...
Brett Smith
06:00 pm Revision 8d3efbe3 (arvados): 3147: Add retry support to PySDK list_all utility.
Brett Smith
06:00 pm Revision cd051b59 (arvados): 3147: PySDK tests use mock>=1.0 and easier mock side_effect.
Brett Smith
06:00 pm Revision 4d066589 (arvados): 3147: Move PySDK HTTP test infrastructure to testutil.
Making this available to other test collections. Brett Smith
06:00 pm Revision f6c14d2b (arvados): 3147: Add retry support to Python CLI tools.
Brett Smith
06:00 pm Revision 434a4469 (arvados): 3147: Add retry support to PySDK Collection objects.
This required updating the FUSE driver's SafeApi object to better
imitate a real API object, now that CollectionReade...
Brett Smith
06:00 pm Revision 17dece4b (arvados): 3147: Add retry_method to the Python SDK.
This gives us a way to make retry support flexible and consistent
across SDK classes. Any class that has retryable o...
Brett Smith
06:00 pm Revision ceceb839 (arvados): 3147: Make PySDK KeepClient.get and put retry_methods.
Brett Smith
06:00 pm Revision 3b5c8cf8 (arvados): 3147: Add retry support to PySDK StreamReader classes.
Brett Smith
06:00 pm Revision 4c1de84b (arvados): 3147: Fix variable name typo.
This variable was renamed in previous branch work, but this last user
of it wasn't caught until just now.
Brett Smith
06:00 pm Revision f749765c (arvados): 3147: PySDK StreamReader instantiates a KeepClient late.
Similarly with API client instantiation in KeepClient, this helps with
testing. Refs #3693.
Brett Smith
05:54 pm Revision c49db117 (arvados): 3705: drop unnecessary current_list pointer
Tim Pierce
05:27 pm Revision 63af4052 (arvados): no issue # remove pipeline instance fixture to address failing test.
Merge branch '2875-pipeline-description' Radhika Chippada
05:26 pm Revision a6f8d9e2 (arvados): 2875: remove pipeline instance fixture and use an existing one.
Radhika Chippada
05:11 pm Bug #3831 (In Progress): [Crunch] inconsistent find_or_create behavior in pipeline runner vs job
Tom Clegg
05:10 pm Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Reviewing commit:700fcdd3
Phil Hodgson wrote:
> Alright so I've committed the idea. If we agree then perhaps the ...
Brett Smith
04:29 pm Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Alright so I've committed the idea. If we agree then perhaps the @#copies_to_projects?@ could be used in the selectio... Phil Hodgson
04:07 pm Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
You're absolutely right about that confusion. What I did to @ArvadosModel@ makes no sense and belongs in @ArvadosBase... Phil Hodgson
02:19 pm Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Phil Hodgson wrote:
> The @goes_in_projects?@ was already present in every single model already inheriting from Arva...
Brett Smith
12:14 pm Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
The @goes_in_projects?@ was already present in every single model already inheriting from ArvadosModel that is suppos... Phil Hodgson
11:44 am Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Phil,
I asked Tom about copying projects on IRC, and he remarked, "if that happened it would be very pleasing but ...
Brett Smith
09:39 am Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Thanks Radhika. There's logic to that decision - certainly until such time as it is decided that copying a project's ... Phil Hodgson
05:10 pm Bug #3877 (Resolved): [Crunch] crunch-dispatch gets large and slow after a verbose job exceeds ma...
Applied in changeset arvados|commit:91fe76f4a3f8e5f59d12343ae69d2ba5a43d8e55. Anonymous
10:40 am Bug #3877 (Resolved): [Crunch] crunch-dispatch gets large and slow after a verbose job exceeds ma...
Tom Clegg
05:04 pm Revision 91fe76f4 (arvados): Merge branch '3877-log-memory-leak' closes #3877
Tom Clegg
04:55 pm Revision 1245c795 (arvados): 2761: add diagnostics section to config
Radhika Chippada
04:54 pm Story #3411: [API] Implement Trash behavior using collection expiration
Ready for another look at commit:9d18764
Tom Clegg wrote:
> In @services/api/app/models/collection.rb@
> * I thi...
Tim Pierce
03:33 pm Story #3411: [API] Implement Trash behavior using collection expiration
In @services/api/app/models/collection.rb@
* I think the lambda style is superfluous here since the where() doesn't ...
Tom Clegg
04:52 pm Revision c8b329a7 (arvados): Combined all examples into one big, runable source file with syntax ...
Found and fixed some bugs in example code.
Added example of requesting manifest text.
Turned references to source dir...
Misha Zatsman
04:49 pm Revision 9d187640 (arvados): 3411: code review
Feedback from code review:
* Dropped unnecessary lambda from Collection.default_scope.
* Set owner_uuid of new colle...
Tim Pierce
04:36 pm Revision 19ba184b (arvados): Make sure to run apt-get update before trying to install
openjdk-7-jre-headless into the java-bwa-samtools arvados docker image.
no issue #
Ward Vandewege
04:35 pm Story #3550: [SDKs] arv-run-pipeline-instance supports running jobs locally using arv-crunch-job
Reviewing commit:d35d434. Earlier disclaimer about UUIDs still applies.
Tom Clegg wrote:
> Presumably the name s...
Brett Smith
04:08 pm Story #3550: [SDKs] arv-run-pipeline-instance supports running jobs locally using arv-crunch-job
Brett Smith wrote:
> Trying to run with a local pipeline template on shell.qr1hi, I got this crash:
Hm, seems lik...
Tom Clegg
03:16 pm Story #3550: [SDKs] arv-run-pipeline-instance supports running jobs locally using arv-crunch-job
Reviewing commit:672df7e. All the UUIDs in this comment are dedicated test UUIDs and they're OK to be public.
Try...
Brett Smith
04:30 pm Task #3879 (Resolved): Review 3877-log-memory-leak
Ward Vandewege
10:52 am Task #3879 (Resolved): Review 3877-log-memory-leak
Tom Clegg
04:23 pm Revision 700fcdd3 (arvados): 3661: add centralized method for defining whether an object can be c...
Phil Hodgson
04:22 pm Revision 454e8fd7 (arvados): 3661: removed useless method to wrong project
(fix from last commit) Phil Hodgson
04:05 pm Revision 46ad2015 (arvados): Merge branch '3878-arv-mount-block-cache' closes #3878
Peter Amstutz
04:04 pm Revision facb6375 (arvados): 3878: Remove raise debugging exception.
Peter Amstutz
04:03 pm Revision fdbf1d6a (arvados): 3699: update script_version and supplied_script_version
When copying git repositories, any script_version or
supplied_script_version in the components or jobs should be rena...
Tim Pierce
04:01 pm Revision 3babb86c (arvados): Moved file.
Misha Zatsman
04:00 pm Revision d35d4340 (arvados): 3550: Fix crash when --template loaded from local JSON file has no u...
Tom Clegg
03:59 pm Revision aa1e4c45 (arvados): 3550: Remove extraneous "to" in usage message.
Tom Clegg
03:43 pm Task #3487 (Resolved): Show all component and job details, and overall timing stats
Peter Amstutz
03:33 pm Task #3883 (In Progress): Review 3411-expire-collections
Tom Clegg
03:16 pm Task #3883 (Resolved): Review 3411-expire-collections
Tim Pierce
03:24 pm Task #3884 (Closed): Review 3605-improved-dashboard
Peter Amstutz
03:23 pm Revision 886d7eef (arvados): 3605: Automatically reload the dashboard using ajax.
Peter Amstutz
03:16 pm Task #3739 (Resolved): Add default_trash_lifetime
Tim Pierce
03:16 pm Task #3739 (In Progress): Add default_trash_lifetime
Tim Pierce
03:16 pm Task #3741 (Resolved): API server filters for trashed objects
Tim Pierce
03:16 pm Task #3741 (In Progress): API server filters for trashed objects
Tim Pierce
03:14 pm Revision 9f340593 (arvados): 3411: set default collection expiration policy
* Added default_scope to Collections restricting them to collections that
have not yet expired
* Added a default_t...
Tim Pierce
03:12 pm Bug #3882: [Workbench] fiddlesticks trying to cancel job that is already cancelled
If the problem is that the job in question was already cancelled, the "cancel" action should probably respond 200 OK. Tom Clegg
02:59 pm Bug #3882 (Resolved): [Workbench] fiddlesticks trying to cancel job that is already cancelled
This job misbehaved and is spooling tons of stdout/stderr (very slowly) to crunch-dispatch. In trying to cancel it fr... Ward Vandewege
02:49 pm Revision 46f5403f (arvados): 3878: Fix block cache sharing across threads so arv-mount uses a bou...
of memory to store block. Also fixes bug in cache management code and cleans
some exception handler error reporting.
Peter Amstutz
02:09 pm Task #3881: Review 3634-tab-state
Added review feedback to the story. Radhika Chippada
01:50 pm Task #3881 (In Progress): Review 3634-tab-state
Radhika Chippada
01:09 pm Task #3881 (Resolved): Review 3634-tab-state
Phil Hodgson
02:09 pm Bug #3634: [Workbench] Page content is the same as where you left it when navigating (back) to it...
Review feedback:
Either I do not understand the requirement or it is not working correctly.
- I went to my home...
Radhika Chippada
01:10 pm Bug #3634: [Workbench] Page content is the same as where you left it when navigating (back) to it...
Well I did a bit of research and found a gem (https://github.com/mnarayan01/bootstrap-tab-history) that seems to hand... Phil Hodgson
01:30 pm Revision 518e0fab (arvados): 3699: document required options --src and --dst
Tim Pierce
01:28 pm Revision ac22ee15 (arvados): 3699: more help text for --src and --dst options
Tim Pierce
01:21 pm Revision 677eebc8 (arvados): 3699: update --src, --dst, --dst-git-repo args
Per code review:
* Use mandatory --src and --dst flags to specify source and destination
Arvados. Each one can spe...
Tim Pierce
01:20 pm Task #3870 (In Progress): Review branch: 2761-diagnostic-suite
Tom Clegg
01:12 pm Story #3609 (In Progress): [SDKs] arv-run wrapper to interactively submit 'run-command' jobs
Peter Amstutz
01:09 pm Task #3880 (Resolved): Remember active tab panel on browser back navigation
Phil Hodgson
11:40 am Task #3880 (In Progress): Remember active tab panel on browser back navigation
Phil Hodgson
11:40 am Task #3880 (Resolved): Remember active tab panel on browser back navigation
Phil Hodgson
01:05 pm Revision 09c2c027 (arvados): 3634: add gem that handles Bootstrap tab state automagically
Phil Hodgson
01:01 pm Revision 6d5e04a7 (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
12:12 pm Task #3861 (Resolved): Review branch: 2875-pipeline-description
Radhika Chippada
10:45 am Task #3861 (In Progress): Review branch: 2875-pipeline-description
Peter Amstutz
11:36 am Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
New rev at commit:04a4fa5
* Issue helpful error message when config file cannot be opened
* Require @--dst-git-re...
Tim Pierce
11:25 am Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
Peter Amstutz wrote:
> ** With some tinkering, I was able to copy a pipeline instance successfully. However, while ...
Tim Pierce
11:08 am Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
Peter Amstutz wrote:
> 1. Not addressed
commit:34aac296 doesn't address this? I'm confused.
> 2. Not addresse...
Tim Pierce
10:43 am Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
1. Not addressed
2. Not addressed
3. Not addressed
4. Not addressed
I'm copying from my local development insta...
Peter Amstutz
11:31 am Revision 04a4fa58 (arvados): 3699: code review
* Issue helpful error message when config file cannot be opened
* Require --dst_git_repo argument
* Allow collections...
Tim Pierce
11:30 am Feature #2875 (Resolved): [Workbench] Editable description field for pipeline instances and templ...
Applied in changeset arvados|commit:4dedb0cc8921e7210ed245107b83996eb0d4e974. Radhika Chippada
11:15 am Feature #2875: [Workbench] Editable description field for pipeline instances and templates
# Collections page has name listed twice, description should go into the info panel like we discussed
# Grammar fix:...
Peter Amstutz
11:28 am Revision 4dedb0cc (arvados): closes #2875
Merge branch '2875-pipeline-description' Radhika Chippada
11:27 am Revision 642670d6 (arvados): 2875: minor text update
Radhika Chippada
11:22 am Revision bc7b64be (arvados): 2875: collection description is now textile and also the display is ...
Radhika Chippada
11:05 am Task #3852 (In Progress): Review 3661-copy-move-from-show
Brett Smith
10:44 am Task #3852 (New): Review 3661-copy-move-from-show
Peter Amstutz
10:44 am Task #3852 (In Progress): Review 3661-copy-move-from-show
Peter Amstutz
10:54 am Revision ac79a0b1 (arvados): 2875: remove junk migration lines
Radhika Chippada
10:51 am Revision 1065f68b (arvados): 3877: Fix memory leak after "log truncated" decision. Clean up code.
Tom Clegg
09:56 am Bug #3875 (New): [Workbench] Buttons and text overlap for smaller window sizes in workbench
For smaller window sizes in workbench, the text and buttons start overlapping with each. There are a few screenshots... Abram Connelly
09:13 am Task #3860 (In Progress): Review 3338-tab-counts
Brett Smith
09:10 am Support #3702 (Resolved): [Support] Fix bugs and write tests (the first half of the sprint)
Brett Smith
09:10 am Task #3730 (Resolved): Fix bugs the first half of the sprint
Brett Smith
09:01 am Task #3733 (In Progress): Write wrapper
Peter Amstutz
09:01 am Task #3729 (In Progress): Design command line
Peter Amstutz
08:32 am Bug #3147 (In Progress): [SDKs] Python clients should automatically retry failed API and Keep req...
Brett Smith
08:32 am Bug #3147 (New): [SDKs] Python clients should automatically retry failed API and Keep requests (i...
3147-py-collection-retries-wip is up for review to implement the remaining requirements in this story. A couple of p... Brett Smith
02:15 am Revision 5df584b3 (arvados): 3705: update for code review
* Changed the type of the NextItem channel from *list.Element to
interface{} (i.e. a list.Element.Value)
* Better c...
Tim Pierce

09/15/2014

10:52 pm Revision 546448eb (arvados): 3609: Collect command line arguments, uploads files, builds arv-run ...
Peter Amstutz
09:50 pm Story #3705: [Keep] Generalize PullList module to BlockWorkList
Review discussion continues at https://github.com/curoverse/arvados/pull/8/files Tom Clegg
02:09 pm Story #3705: [Keep] Generalize PullList module to BlockWorkList
Comment in block_work_list.go:
* "Close() Shuts down the manager and the worker cleanly."
** I think the phrase "...
Tom Clegg
09:44 pm Feature #2875: [Workbench] Editable description field for pipeline instances and templates
Noticed several suspicious lines like this in @services/api/db/structure.sql@ (note the timestamp):... Tom Clegg
08:58 pm Feature #3874 (New): [Crunch] "Resume job" API: clone a job and all of its tasks, reset failed ta...
Tom Clegg
08:47 pm Feature #3605 (In Progress): [Workbench] improved dashboard page
Peter Amstutz
03:11 pm Feature #3605: [Workbench] improved dashboard page
Review feedback for branch 3605-node-info-field:
Just a couple very minor comments:
* apps/workbench/app/views/...
Radhika Chippada
08:42 pm Task #3723 (In Progress): Implement dashboard layout at https://arvados.org/attachments/download/...
Peter Amstutz
08:41 pm Revision bff8478a (arvados): 3605: Getting jobs/queue_size from API server works. Fixed server-side
sorting. Date rendering improvements. Peter Amstutz
06:19 pm Revision 7faaccf2 (arvados): 3705: describe BlockWorkList flow more explicitly
Updated file comments to describe the overall data flow for a
BlockWorkList manager and worker more explicitly.
Tim Pierce
06:16 pm Task #3872 (Resolved): Review 3147-py-collection-retries-wip2
Please see "review notes on the story":https://arvados.org/issues/3147#note-25. Brett Smith
06:16 pm Task #3802 (Resolved): arv-mount exposes retry support
Brett Smith
06:16 pm Task #3735 (Resolved): Make crunch-job retry when it calls arv-put
Brett Smith
06:16 pm Revision de76145e (arvados): 3147: Add retry support to FUSE driver.
Brett Smith
06:16 pm Revision 2d09b0aa (arvados): 3147: crunch-job retries data uploads more for longer-running jobs.
Brett Smith
06:15 pm Revision 9321272a (arvados): 3147: FUSE driver requires a Python SDK with retry support.
I also took out some of the older log-handling code while I was at it,
since the stricter versioning makes it unneces...
Brett Smith
05:25 pm Revision bc206af6 (arvados): 3147: Add retry support to PySDK list_all utility.
Brett Smith
05:25 pm Revision fc50347a (arvados): 3147: Add retry support to Python CLI tools.
Brett Smith
05:24 pm Revision 2cdf77b4 (arvados): 3147: Add retry support to PySDK Collection objects.
This required updating the FUSE driver's SafeApi object to better
imitate a real API object, now that CollectionReade...
Brett Smith
04:31 pm Revision ff1f91af (arvados): 3147: PySDK StreamReader instantiates a KeepClient late.
Similarly with API client instantiation in KeepClient, this helps with
testing. Refs #3693.
Brett Smith
04:31 pm Revision c0adc047 (arvados): 3147: Move PySDK HTTP test infrastructure to testutil.
Making this available to other test collections. Brett Smith
04:31 pm Revision d4d74449 (arvados): 3147: PySDK tests use mock>=1.0 and easier mock side_effect.
Brett Smith
04:31 pm Revision f277d8e0 (arvados): 3147: Fix variable name typo.
This variable was renamed in previous branch work, but this last user
of it wasn't caught until just now.
Brett Smith
04:31 pm Revision 16325f03 (arvados): 3147: Add retry_method to the Python SDK.
This gives us a way to make retry support flexible and consistent
across SDK classes. Any class that has retryable o...
Brett Smith
04:31 pm Revision ddfc97a8 (arvados): 3147: Add retry support to PySDK StreamReader classes.
Brett Smith
04:31 pm Revision 13295e3b (arvados): 3147: Make PySDK KeepClient.get and put retry_methods.
Brett Smith
03:45 pm Bug #3817: [API] Discovery document schema does not include generated fields like job dependencies
Note - even if the discovery doc uses api_response, clients will still learn about fields that are not returned to th... Tom Clegg
03:08 pm Revision 07a3aa96 (arvados): Merge remote-tracking branch 'origin/master' into 3605-improved-dash...
Peter Amstutz
03:08 pm Revision 195b1b9f (arvados): 3605: Finally settled on a layout. Adding in remaining information ...
Peter Amstutz
02:55 pm Task #3863 (In Progress): Review 3605-node-info-field
Radhika Chippada
02:51 pm Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
New revision at commit:963c9e8. There has been a lot of diff churn here, and merges from master, (mostly around maki... Tim Pierce
02:46 pm Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Phil,
I had recently worked on move, copy, (and combine collections) for projects. The copy operation was only suppo...
Radhika Chippada
02:43 pm Revision 963c9e8f (arvados): 3699: copy collection properties, name, etc.
copy_collection now copies the original collection object from src to dst,
changing uuid/owner_uuid/ensure_unique_nam...
Tim Pierce
02:31 pm Story #3187: [Workbench] Better information and features on "show pipeline instance" page
Peter,
I may not have done a great job of reviewing any potential issues with the updates. However, I have a few com...
Radhika Chippada
02:28 pm Task #3862 (In Progress): Review 3187-pipeline-instance-page
Radhika Chippada
02:20 pm Revision f2170ad3 (arvados): 3699: report success/failure unambiguously
Tim Pierce
01:58 pm Revision e09e5737 (arvados): 3699: back out attempts to change tempfile.tempdir
Too many error conditions -- if the disk is full, have the user change
it manually with TMPDIR=/scratch
Tim Pierce
01:34 pm Bug #3871 (Resolved): [FUSE] Crashes on non-ASCII folder names
As a qr1hi admin, with a default Keep mount, trying to ls the @shared@ subdirectory, I get this backtrace:... Brett Smith
01:30 pm Revision 1ecc9b7b (arvados): 3699: typo fix
Tim Pierce
01:28 pm Revision 044d3d29 (arvados): 3699: use /scratch instead of /tmp for git copies
Tim Pierce
01:26 pm Story #3550: [SDKs] arv-run-pipeline-instance supports running jobs locally using arv-crunch-job
Peter Amstutz wrote:
> This help text is confusing:
Indeed. Changed to: "Run jobs in the local terminal session i...
Tom Clegg
01:13 pm Revision b23bcfdc (arvados): 3699: ensure unique names for new pipelines
Tim Pierce
01:11 pm Revision bc59a822 (arvados): Merge branch 'master' into 3699-arv-copy
Tim Pierce
01:09 pm Bug #3856: [Workbench] Integration tests don't run with Firefox 32/33
It appears that selenium web driver does not work with Firefox 32.
http://stackoverflow.com/questions/25646639/fir...
Radhika Chippada
01:06 pm Revision 6d84b6c8 (arvados): 3699: delete pi['uuid'] before committing
Tim Pierce
01:03 pm Revision a0e2de21 (arvados): 3699: copy_pipeline_template requires dst_git_repo
Tim Pierce
12:20 pm Revision 672df7ed (arvados): 3550: Update docs to match new flag name. Add note about job re-use.
Tom Clegg
12:06 pm Story #2761: [Workbench] diagnostic suite runs against a production instance
* Added "apps/workbench/test/diagnostics" test directory
* Added diagnostics testing configuration to application....
Radhika Chippada
12:03 pm Task #3870 (Resolved): Review branch: 2761-diagnostic-suite
Radhika Chippada
12:01 pm Revision 289f610d (arvados): Merge branch 'master' into 2761-diagnostic-suite
Conflicts:
apps/workbench/config/application.default.yml
Radhika Chippada
11:39 am Revision 565198b9 (arvados): 3699: allow pipeline instances without templates
Tim Pierce
11:27 am Revision bf243e06 (arvados): no issue # fix failing test to use selenium driver
Radhika Chippada
10:54 am Revision bf775ee6 (arvados): 2875: integration tests to verify description on pipeline templates,...
Radhika Chippada
10:53 am Task #3765 (Resolved): [Workbench] Pipeline instance #show page should not show the _current_ tem...
Radhika Chippada
10:52 am Task #3191 (Resolved): Add editable title/description fields to pipeline template and pipeline in...
Radhika Chippada
10:51 am Task #3039 (Resolved): Add description attribute to PipelineInstance model
Radhika Chippada
10:51 am Task #3868 (Resolved): Add / update integration tests to verify description for pipeline template...
Radhika Chippada
10:50 am Task #3867 (Resolved): Add description option to arv-run-pipeline-instance script
Radhika Chippada
10:48 am Revision 4dac4271 (arvados): 3699: fix inconsistent function parameters
All copy methods/functions now start with (object_to_copy, src_client,
dst_client).
Tim Pierce
10:40 am Revision c18a4746 (arvados): 3699: bug fix (return value for copy_git_repo)
Tim Pierce
10:38 am Task #3659 (Resolved): arv-put exposes retry support
Brett Smith
10:30 am Revision 9fe1eb15 (arvados): 3699: use a consistent destination branch for copy_git_repo
copy_git_repo copies commits from the source repository to a branch in
the destination named for the source repositor...
Tim Pierce
10:10 am Revision b056c28b (arvados): 3699: fix copy_git_repo
Need to specify destination branch explicitly when pushing. Tim Pierce
10:04 am Bug #3866 (Resolved): [SDK] Python KeepClient needs to construct URLs smarter
When the Python KeepClient makes a request to a Keep service, it constructs the Keep service URL with simple string c... Brett Smith
09:56 am Revision ee52a6f8 (arvados): 3699: bug fixes
Tim Pierce
09:55 am Revision 7a260be1 (arvados): 3550: Merge branch 'master' into 3550-local-pipeline
Tom Clegg
09:55 am Revision 4c4c2951 (arvados): 3550: Clarify help message, mention that there are limitations.
Tom Clegg
09:48 am Revision 9a88a95c (arvados): Updated Gemfile to pull in changes from commit:ac594f1 refs #3187
Peter Amstutz
09:44 am Revision 177a1468 (arvados): Remove projects panels from dashboard
Peter Amstutz
09:41 am Revision f91bae11 (arvados): Merge branch '3187-pipeline-instance-page' into 3605-improved-dashboard
Peter Amstutz
08:18 am Revision a6e1c4ee (arvados): 2875: render template description as textile attribte in show recent...
Radhika Chippada
08:10 am Revision 0119bfdc (arvados): 2875: add description option
Radhika Chippada

09/12/2014

08:33 pm Revision 61a24458 (arvados-dev): Fixes for the deploy stage of the build pipeline: actually upgra...
debian packages and gems.
no issue #
Ward Vandewege
08:33 pm Revision 61a24458 (arvados): Fixes for the deploy stage of the build pipeline: actually upgrade our
debian packages and gems.
no issue #
Ward Vandewege
06:15 pm Revision fcf7b077 (arvados): 2875: add initial description to pipeline instance when created usin...
Radhika Chippada
05:30 pm Revision 34aac296 (arvados): 3699: bug fixes and feedback
* added 'arv copy' front end to sdk/cli/bin/arv
* can supply --recursive for pipeline templates as well as pipeline
...
Tim Pierce
05:00 pm Story #3654 (Resolved): [Workbench] Add "combine selected collections" and "combine selected file...
Applied in changeset arvados|commit:f43a783466bf8257781bac0acfa14008b2d532a1. Radhika Chippada
09:16 am Story #3654: [Workbench] Add "combine selected collections" and "combine selected files" actions ...
1, 2. Giving the collection a name seems to pull it to the top of the project so now I can find it.
3, 4. There's...
Peter Amstutz
04:56 pm Task #3832 (Resolved): Review branch: 3654-combine-selections
Radhika Chippada
04:49 pm Revision ff9f9c7e (arvados): Merge branch 'master' into 2875-pipeline-description
Radhika Chippada
04:46 pm Revision f43a7834 (arvados): closes #3654
Merge branch '3654-combine-selections' Radhika Chippada
04:43 pm Revision b53be4b8 (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
04:41 pm Revision 45f25c3c (arvados): 2875: initial description on pipeline instance when the template has...
Radhika Chippada
04:32 pm Revision dcf5e0ce (arvados): Working on recent pipelines/collections tables
Peter Amstutz
03:52 pm Revision 90ecfcca (arvados): Merge branch 'master' into 3605-improved-dashboard
Peter Amstutz
03:52 pm Revision 63b52a3a (arvados): 3605: Dashboard compute node and pipeline status work in progress
Peter Amstutz
03:48 pm Revision 96d9f313 (arvados): Merge branch 'master' into 2875-pipeline-description
Radhika Chippada
03:46 pm Revision 4bde33a6 (arvados): 2875: set initial description on the new pipeline instance created b...
Radhika Chippada
03:20 pm Task #3658 (Resolved): PySDK Collection classes expose retry support
Brett Smith
03:20 pm Revision c78412ea (arvados): Bug fix: manifests with extra spaces
Extend the regular expression to match manifest_text to permit more than
a single space in manifest entries (seen in ...
Tim Pierce
03:15 pm Bug #3848: [SDK] Python SDK should always set proper version when built from git
Discussed in sprint planning that we want to solve this at the SDK level; i.e., customize the @egg_info@ command in @... Brett Smith
02:49 pm Bug #3782: [Workbench] Browser prompts about long-running JavaScript when trying to view a large ...
Desire quick workaround by truncating log to some reasonable size. Peter Amstutz
02:35 pm Task #3280 (Resolved): [Workbench] Collection#show preview/download buttons use wrong icons and e...
Radhika Chippada
02:34 pm Task #3280: [Workbench] Collection#show preview/download buttons use wrong icons and encourage pr...
This is being addressed as part of #3654 updates. Radhika Chippada
02:19 pm Revision e5152a25 (arvados): 3654: disable search icon collection show page rather than hide it w...
Radhika Chippada
01:26 pm Revision 132db914 (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
01:23 pm Revision 32b97aec (arvados): Merge branch 'master' into 2875-pipeline-description
Conflicts:
services/api/app/models/pipeline_instance.rb
services/api/db/structure.sql
Radhika Chippada
01:17 pm Revision a31f94b1 (arvados): 2875: add new partial to display name and description.
Radhika Chippada
01:15 pm Bug #3864 (New): [Workbench] Breadcrumb bar is covered up when top nav menu takes up multiple lines.
Peter Amstutz
10:26 am Task #3863 (Resolved): Review 3605-node-info-field
Peter Amstutz
10:25 am Revision b9ce5840 (arvados): 3605: Provide "info" field to all requesters. Filters out any keys ...
"secret" to non-admin users. Also fix fiddlesticks on workbench viewing
details for node.
Peter Amstutz
10:18 am Support #3823 (In Progress): [Support] Fix bugs and write tests (the second half of the sprint)
Tim Pierce
09:43 am Revision ac594f16 (arvados): Merge branch '3187-start-finish-timestamps-tasks-pipelines' refs #3187
Peter Amstutz
09:39 am Task #3849 (Resolved): Review 3187-start-finish-timestamps-tasks-pipelines
Ward Vandewege
09:39 am Revision 00a0690c (arvados): Fixed typo Y% -> %Y
Peter Amstutz
08:52 am Task #3862 (Resolved): Review 3187-pipeline-instance-page
Peter Amstutz
08:52 am Revision 8b9f3b87 (arvados): 3187: Text tweaks.
Peter Amstutz

09/11/2014

07:37 pm Revision 2109516c (arvados): 3654: update tests to match the selection dropdown text changes.
Radhika Chippada
07:22 pm Task #3861 (Resolved): Review branch: 2875-pipeline-description
Radhika Chippada
07:21 pm Feature #2875 (In Progress): [Workbench] Editable description field for pipeline instances and te...
Radhika Chippada
07:20 pm Revision 0cf2f356 (arvados): 2875: add description to jobs and pipeline_instances.
Radhika Chippada
07:15 pm Feature #3338: [Workbench] Show number of items in each tab of the project page.
So I like what I've done so far. To finish it off - if this approach meets with approval - we would make it so that a... Phil Hodgson
06:30 pm Revision f6ea610f (arvados): Included included file.
Misha Zatsman
06:29 pm Revision 946aeb2d (arvados): Moved code to seperate file for syntax coloring.
Switched to using arv.List instead of arv.Call. Misha Zatsman
06:19 pm Task #3860 (Resolved): Review 3338-tab-counts
Phil Hodgson
06:18 pm Revision 893f6597 (arvados): 3338: Tests that the fixture collection count for a project matches ...
Phil Hodgson
06:18 pm Task #3854 (Resolved): Implement simple, generic way to get #count for each pane
Phil Hodgson
10:07 am Task #3854 (In Progress): Implement simple, generic way to get #count for each pane
Phil Hodgson
10:07 am Task #3854 (Resolved): Implement simple, generic way to get #count for each pane
Phil Hodgson
05:49 pm Revision 451e52c2 (arvados): 3338: vital action missing from previous commit
Phil Hodgson
05:30 pm Revision 555c1e92 (arvados): 3338: System in place that allows for item counts to be displayed ne...
(Currently does not refresh itself after activities such as adding or removing items, but this is now eminently possi... Phil Hodgson
05:12 pm Revision 004e5280 (arvados): 3187: Setting dates to locale works.
Peter Amstutz
04:35 pm Task #3832: Review branch: 3654-combine-selections
Please take another look, most importantly the checkbox move logic updates in _show_files.html.erb. Thanks. Radhika Chippada
09:58 am Task #3832 (In Progress): Review branch: 3654-combine-selections
Peter Amstutz
04:19 pm Revision bc8c85ca (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
04:18 pm Revision a9619cd9 (arvados): 3654: move the checkbox to the left of the row in collection show pa...
Radhika Chippada
03:55 pm Revision 6386f2ac (arvados): Merge branch '3187-start-finish-timestamps-tasks-pipelines' into 318...
Peter Amstutz
03:54 pm Revision 35bf7a16 (arvados): 3187: Update the task start time when the task actually starts.
Peter Amstutz
03:52 pm Revision 9be97616 (arvados): 3187: Generalized reloading to reload other parts of the page in add...
just tabs. Panel reloading no longer messes up collapsable panel state. Peter Amstutz
03:01 pm Revision 8012f6cc (arvados): Fallout from #3036: the test for the checkbox value on acceptance of...
user agreement was expecting a keep hash, rather than an Arvados UUID.
This fixes accepting the user agreement (if o...
Ward Vandewege
03:01 pm Revision 2d911a46 (arvados): 3654: add a default name to newly created combined collection
Radhika Chippada
02:57 pm Task #3858 (Resolved): Review 3705-keep-blockworklist
Summary:
The pull list was previously implemented as a "PullList" type. Tom asked me to reimplement it as a generi...
Tim Pierce
02:47 pm Task #3652 (Resolved): Rewrite PullList as a BlockManager implementation
Tim Pierce
02:47 pm Task #3652 (In Progress): Rewrite PullList as a BlockManager implementation
Tim Pierce
02:47 pm Task #3752 (Resolved): Define BlockManager interfaces and types
Tim Pierce
02:44 pm Revision 577bd728 (arvados): 3705: replace pullmgr with a BlockWorkList
Tim Pierce
02:01 pm Bug #3857 (Resolved): [SDKs] Python KeepClient should use different timeouts for different operat...
Executive summary:
If an arvados.KeepClient is connecting to a Keep proxy (service_type == 'proxy'):
* The TCP c...
Brett Smith
01:38 pm Revision 35bee4f8 (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
11:57 am Bug #3856 (Closed): [Workbench] Integration tests don't run with Firefox 32/33
This might just be me, and it's almost certainly not our bug per se, but I wanted to start this bug report to keep tr... Brett Smith
11:57 am Revision a0fc519d (arvados): 3187: Tested and fixed and time calculation algorithm.
Peter Amstutz
11:21 am Revision f2bed1a9 (arvados): Clean up manifest whitespace in split-fastq.
The previous code was generating two spaces between the stream name
and block list, because it had the space from as_...
Brett Smith
10:46 am Bug #3855 (Closed): [SDK] New keep mount is very slow on initial usage
On shell nodes, I find doing some simple tasks, like changing directories and listing files, is extremely slow. Afte... Abram Connelly
10:33 am Revision 7082cec0 (arvados): 2761: update comment
Radhika Chippada
10:29 am Story #3654: [Workbench] Add "combine selected collections" and "combine selected files" actions ...
# I went to my "home" project and selected three items, and then clicked on "Selection... → Combine selections i... Peter Amstutz
10:02 am Revision 97d1d110 (arvados): 2761: input selection revisited
Radhika Chippada
09:49 am Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
# Add 'copy' subcommand to 'arv' frontend.
# Give a friendlier error message, preferably explaining that the user ne...
Peter Amstutz
09:41 am Task #3852 (Resolved): Review 3661-copy-move-from-show
Phil Hodgson
09:40 am Task #3851 (Resolved): Add one or two new integration tests for the new buttons
Phil Hodgson
09:10 am Task #3851 (In Progress): Add one or two new integration tests for the new buttons
Phil Hodgson
09:10 am Task #3851 (Resolved): Add one or two new integration tests for the new buttons
Phil Hodgson
09:37 am Revision aff3c1ad (arvados): 3661: tentative implementation of Capybara "best practice" of using ...
Phil Hodgson
09:35 am Revision ec48719c (arvados): 3661: Add a new test that ensures that the new "Copy to project" but...
Phil Hodgson
09:10 am Task #3845 (Resolved): Add the buttons and make them work
Phil Hodgson
09:04 am Task #3788 (Resolved): Review 3453-arv-list-docker-images
Peter Amstutz
09:03 am Task #3838 (In Progress): Review 3699-arv-copy
Peter Amstutz
09:03 am Task #3850 (Resolved): Add started_at and finished_at to tasks and pipelines
Peter Amstutz
09:03 am Task #3850 (Resolved): Add started_at and finished_at to tasks and pipelines
Peter Amstutz
09:02 am Task #3849 (Resolved): Review 3187-start-finish-timestamps-tasks-pipelines
Peter Amstutz
09:02 am Task #3487 (In Progress): Show all component and job details, and overall timing stats
Peter Amstutz
09:02 am Revision e7973cab (arvados): Merge branch 'master' into 3187-start-finish-timestamps-tasks-pipelines
Peter Amstutz
08:57 am Revision 08b9ee71 (arvados): 3187: Added algorithm to calculate wall clock run time from a set of...
Peter Amstutz
08:53 am Bug #3848 (Resolved): [SDK] Python SDK should always set proper version when built from git
One thing that would help debug Docker images is if the Arvados Python modules were installed with version numbers th... Brett Smith

09/10/2014

10:27 pm Revision 52ecfbd9 (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
10:26 pm Revision 9c861f63 (arvados): 2761: file path needs lookup in prevew panel
Radhika Chippada
06:27 pm Revision 0bf498cd (arvados): 3705: add BlockWorkList and unit tests
Tim Pierce
05:49 pm Story #3705 (In Progress): [Keep] Generalize PullList module to BlockWorkList
Tim Pierce
05:49 pm Task #3752 (In Progress): Define BlockManager interfaces and types
Tim Pierce
05:43 pm Bug #3847 (Resolved): [SDK] --project-uuid switch behaves strangely without = (seen in arv-keepdo...
$ arv keep docker --project-uuid qr1hi-j7d0g-593lq8oed0gymt3 --name "Docker image with crunch user" 76ca48f2d705
arv...
Sarah Guthrie
05:12 pm Revision aadca3ff (arvados): 3187: Lots of work on presentation of job details, calculating time and
concurrency factors. Peter Amstutz
05:06 pm Revision 741bf44b (arvados): Prevent PySDK CollectionReader from sending UUIDs to Keep.
No issue #. I tickled this while I was working on #3147. Ward saw
the apparent symptom come up in a Job log, so I'm...
Brett Smith
05:01 pm Revision 0313c6ef (arvados): 3187: Added queue_position field to job response.
Peter Amstutz
04:13 pm Revision b4e495d7 (arvados): 2761: test in staging.
Radhika Chippada
03:36 pm Revision 7ad2ce19 (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
03:32 pm Revision aa22ee64 (arvados): 2761: wait for the pipeline run to complete or until wait time exceeds.
Radhika Chippada
02:30 pm Bug #3846 (Resolved): [SDK] Improve timeout handling in Python KeepClient
Applied in changeset arvados|commit:4ef537243058616754efde56438a193626556bca. Brett Smith
02:08 pm Bug #3846 (In Progress): [SDK] Improve timeout handling in Python KeepClient
Brett Smith
01:45 pm Bug #3846 (Resolved): [SDK] Improve timeout handling in Python KeepClient
The Python KeepClient is impatient. If you're dealing with full 64MiB blocks, you're likely to run into timeout exce... Brett Smith
02:26 pm Revision 4ef53724 (arvados): 3846: Improve timeout handling in PySDK KeepClient.
* Catch socket errors (including timeouts) and treat them as
transient with regard to retry logic.
* Increase the d...
Brett Smith
02:11 pm Revision c2a7a5a0 (arvados): 3661: make existing tests pass
Phil Hodgson
01:47 pm Revision 5ff99015 (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
01:45 pm Revision 72da0be3 (arvados): 2761: test updates to be able to handle multiple inputs
Radhika Chippada
01:38 pm Revision b41bfad0 (arvados): 3705: add BlockWorkList
Tim Pierce
12:55 pm Bug #3842 (Resolved): [Workbench] Manifests with more than one entry for a file display the file ...
Applied in changeset arvados|commit:bafb417c531d6094697a13a7465313d1cc7c0bc9. Brett Smith
09:31 am Bug #3842 (In Progress): [Workbench] Manifests with more than one entry for a file display the fi...
Brett Smith
09:07 am Bug #3842 (Resolved): [Workbench] Manifests with more than one entry for a file display the file ...
Peter Amstutz
12:48 pm Revision 9126da70 (arvados): 3661: Added buttons for Copy and Move to the general #show page, sho...
Phil Hodgson
12:38 pm Revision bafb417c (arvados): 3842: Keep::Manifest concatenates file information from manifest.
The previous implementation failed to consider the possibility that
file information would be spread across multiple ...
Brett Smith
11:45 am Revision bdaaaf23 (arvados): 2761: load inputs dynamically
Radhika Chippada
11:00 am Revision 4b34d258 (arvados): 3699: add support for --recursive and --project_uuid
Tim Pierce
10:40 am Revision 2332fe41 (arvados): 2761: diagnostics testing config in application.yml
Radhika Chippada
10:34 am Task #3845 (Resolved): Add the buttons and make them work
Phil Hodgson
10:30 am Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
Ah! Obviously! It's @#goes_in_projects?@!
Still wonder about the copying of contents of a folder.
Phil Hodgson
09:32 am Story #3661: [Workbench] Add "Move" and "Copy" buttons to top of #show page for every kind of obj...
My first reactions after a tour:
* What "goes in folders"? Is there a definition for this currently, or should I b...
Phil Hodgson
10:20 am Task #3844 (Resolved): Agressively close PUT connections when there are no writable volumes.
Otherwise, the clients waste bandwidth and time uploading blocks which can not be saved (and only find out after the ... Ward Vandewege
10:17 am Bug #3843 (Resolved): [Crunchstat] Report CPU accounting numbers accurately.
Expected by user: same as CPU usage figures reported by top (between 0 and 400 on a 4-core node).
Currently reported...
Ward Vandewege
01:49 am Revision 513f1a70 (arvados-dev): allow gitolite.conf to be tested locally!
please see documentation in the code Sitaram Chamarty

09/09/2014

03:41 pm Bug #3840 (New): [Crunch] Clean unused code from crunch-job
Off the top of my head:
* Support for Job knobs.
* Unsupported install methods. I think the stuff about calling ...
Brett Smith
03:39 pm Revision 655d5ae8 (arvados): 3187: Record started_at and finished_at for tasks and pipelines.
Peter Amstutz
03:35 pm Revision 735d5487 (arvados): 2761: use application.yml to configure diagnostics testing
Radhika Chippada
03:23 pm Task #3839 (Resolved): Display the view icon for files in collections only when the file suffix i...
Radhika Chippada
03:20 pm Task #3839 (Resolved): Display the view icon for files in collections only when the file suffix i...
Radhika Chippada
03:19 pm Revision 9a57602c (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
03:17 pm Revision a3615da8 (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
03:16 pm Revision 960925be (arvados): 3654: display show icon for files only when the file suffix is one o...
Radhika Chippada
03:16 pm Revision b0440160 (arvados): #3830: Make crunch-job's git calls more robust.
* Check git's exit status and only continue on 0.
* Log git's exit status after optional calls.
* Always log the reso...
Brett Smith
03:00 pm Revision 3bbfa6d0 (arvados): 3699: rename repositories in copied pipeline instance
Tim Pierce
02:43 pm Revision e5ab4ce1 (arvados): 3187: Migration to add started_at and finished_at to job_tasks and p...
Peter Amstutz
02:30 pm Revision 155c3adf (arvados): 3699: typo fix
Tim Pierce
02:25 pm Task #3758 (Resolved): arv-copy works on git repos
Tim Pierce
02:25 pm Task #3838 (Resolved): Review 3699-arv-copy
Tim Pierce
02:23 pm Revision 379f500e (arvados): 3699: add copy_git_repo step to copy_pipeline_instance
Tim Pierce
01:41 pm Feature #3605: [Workbench] improved dashboard page
give some indication of how busy the cluster is, such as number of nodes busy/idle Peter Amstutz
01:40 pm Story #3187: [Workbench] Better information and features on "show pipeline instance" page
Also show queue position of queued jobs. Peter Amstutz
12:22 pm Story #3187: [Workbench] Better information and features on "show pipeline instance" page
Plan:
* Use collapsible panels for each component. Show summary at the top, user can click to expand and get deta...
Peter Amstutz
01:25 pm Revision 300729d2 (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
01:24 pm Revision 37cd4135 (arvados): Merge branch 'master' into 2761-diagnostic-suite
Radhika Chippada
01:23 pm Revision 1eedd481 (arvados): 2761: diagnostics testing
Radhika Chippada
01:20 pm Bug #3472 (Resolved): arv-keepdocker reports "no --project-uuid" error but doesn't accept --proje...
Applied in changeset arvados|commit:f467b469109e27bc18635c8952892e4c23fabd60. Anonymous
01:20 pm Feature #3453 (Resolved): [SDK] "arv keep docker" should support listing images in Keep and placi...
Applied in changeset arvados|commit:f467b469109e27bc18635c8952892e4c23fabd60. Anonymous
01:15 pm Feature #3453: [SDK] "arv keep docker" should support listing images in Keep and placing images i...
commit:83bcea2 is good to merge. Thanks. Brett Smith
11:54 am Feature #3453: [SDK] "arv keep docker" should support listing images in Keep and placing images i...
Brett Smith wrote:
> Reviewing commit:8eeb267
>
> * In @check_project_exists@:
> ** This function effectively fo...
Peter Amstutz
09:41 am Feature #3453: [SDK] "arv keep docker" should support listing images in Keep and placing images i...
Reviewing commit:8eeb267
* In @check_project_exists@:
** This function effectively forces the user to use @except...
Brett Smith
01:16 pm Story #3550: [SDKs] arv-run-pipeline-instance supports running jobs locally using arv-crunch-job
This help text is confusing:... Peter Amstutz
01:09 pm Task #3772 (In Progress): Review 3550-local-pipeline
Peter Amstutz
11:58 am Revision f467b469 (arvados): Merge branch '3453-arv-list-docker-images' closes #3453, #3472, refs...
Peter Amstutz
11:58 am Feature #3837 (Closed): [Crunch] User can easily combine output from multiple pipelines into a si...
A user who needs to run the same pipeline on many samples in different collections should have a simple mechanism to ... Tim Pierce
11:53 am Revision 83bcea2d (arvados): 3453: Rename check_project_exists to desired_project_uuid. Now rais...
catches distinct apiclient.errors.Error, ValueError errors for project not
found or invalid uuid.
Peter Amstutz
11:17 am Revision 651dc72c (arvados): 3699: fix bugs
Tim Pierce
09:28 am Bug #3586 (Resolved): [API] Job "priority" field defaults to "null", should default to "0"
Peter Amstutz
09:25 am Revision d97be42e (arvados): Merge branch '3586-job-priority' closes #3586
Peter Amstutz
09:19 am Revision 7f3ed5e2 (arvados): Merge branch 'master' into 3586-job-priority closes #3586
Peter Amstutz

09/08/2014

06:53 pm Revision 0bb834af (arvados): Added to Go SDK documentation:
* Added link to instuctions on how to develop with bleeding edge client code.
* Fixed type error in documentation.
* ...
Misha Zatsman
05:00 pm Bug #3644 (Resolved): [SDK] Fix arv-mount --tags and --groups modes to handle "home" project and ...
Applied in changeset arvados|commit:50e48820312868513b6efcafa84c6d825ac51cd4. Anonymous
03:04 pm Bug #3644: [SDK] Fix arv-mount --tags and --groups modes to handle "home" project and #3036 colle...
Tim Pierce wrote:
> OK. It's clever. I don't see any red flags in the thread locking, but I don't think I unders...
Peter Amstutz
04:59 pm Task #3804 (Resolved): Review 3644-arv-mount-projects
Peter Amstutz
04:55 pm Revision 50e48820 (arvados): Merge branch '3644-arv-mount-projects' closes #3644
Peter Amstutz
04:54 pm Revision 8eeb2671 (arvados): 3453: Refactored arv-put to remove support for name links, correctly...
ensure_name_unique to prevent name collisions. arv-keepdocker should now
correctly handle cases where the user provi...
Peter Amstutz
04:48 pm Revision ccc1d433 (arvados): 3699: define copy_git_repo
Tim Pierce
03:54 pm Revision 34110141 (arvados): 3644: Update tests broken by merge
Peter Amstutz
03:50 pm Revision d6ee8d4e (arvados): 3823: bug fixes for arvados-bcbio-nextgen.py
Refs #3823 Tim Pierce
03:47 pm Revision 91761a83 (arvados): 3823: bug fixes for arvados-bcbio-nextgen.py
Tim Pierce
03:38 pm Story #2761 (In Progress): [Workbench] diagnostic suite runs against a production instance
Radhika Chippada
03:37 pm Revision 837cb95f (arvados): 3644: Moved some common regex patterns into SDK
Peter Amstutz
03:07 pm Revision bd86112f (arvados): Merge branch 'master' into 3644-arv-mount-projects
Peter Amstutz
03:06 pm Revision be4c2feb (arvados): 3644: Restore 'tag' tests and add 'SharedDirectory' and 'HomeDirecto...
All tests should pass now. Peter Amstutz
02:20 pm Bug #3663 (Resolved): [SDKs] Python CollectionReader should return at least one byte to caller pe...
Applied in changeset arvados|commit:90fc79852a995fd8e665cf48ae20c49a9bbc78eb. Tim Pierce
02:04 pm Bug #3663: [SDKs] Python CollectionReader should return at least one byte to caller per block rea...
commit:d070454 looks good to me. Thanks. Brett Smith
02:18 pm Task #3744 (Resolved): arv-copy works on pipeline instances
Tim Pierce
02:18 pm Task #3743 (Resolved): arv-copy works on docker images
Tim Pierce
02:18 pm Task #3816 (Resolved): Review 3663-collection-reader-performance
Tim Pierce
01:45 pm Task #3816 (In Progress): Review 3663-collection-reader-performance
Stolen per IRC discussion. Brett Smith
02:06 pm Revision 90fc7985 (arvados): Merge branch '3663-collection-reader-performance'
Closes #3663. Tim Pierce
01:53 pm Revision be5ce814 (arvados): 3699: skip components which have not yet run
Tim Pierce
01:48 pm Revision 6f793d4d (arvados): 3699: test storing the empty collection (edge case)
Tim Pierce
01:39 pm Bug #3835 (Resolved): [SDKs] Python and CLI tools should give more helpful error messages after a...
Errors returned from arvados.keep.KeepClient.put are short and cryptic, e.g.:
arvados.errors.KeepWriteError: Writ...
Tim Pierce
12:08 pm Feature #3453: [SDK] "arv keep docker" should support listing images in Keep and placing images i...
Reviewing commit:b6017f4
* I wonder if it's really appropriate to unconditionally set @ensure_unique_name=True@ in...
Brett Smith
11:24 am Bug #3833: [Keep] Improve file and directory invalidation in fuse driver
The FUSE driver uses a timestamp and expiration time to determine whether to refresh directory contents from the serv... Peter Amstutz
11:18 am Bug #3833 (Resolved): [Keep] Improve file and directory invalidation in fuse driver
Peter Amstutz
11:20 am Bug #3834 (New): [Workbench] pipeline instance that is RunningOnClient should be rendered as Runn...
Running pipeline instance qr1hi-d1hrv-lh4tb4ozwupp60i on lightning-dev2, I see the status of the currently running jo... Abram Connelly
11:06 am Story #3654: [Workbench] Add "combine selected collections" and "combine selected files" actions ...
Since we do not yet have file picker and hence since it is not possible to select files from within a project, added ... Radhika Chippada
11:04 am Task #3832 (Resolved): Review branch: 3654-combine-selections
Radhika Chippada
11:03 am Task #3800 (Resolved): Add integration tests to test "Combine selected collections and files into...
Radhika Chippada
11:03 am Task #3799 (Resolved): Add integration tests to test "Combine selected collections and files into...
Radhika Chippada
11:02 am Task #3798 (Resolved): Add selection dropdown with "Combine selected collections and files into a...
Radhika Chippada
11:02 am Task #3797 (Resolved): Add selection dropdown with "Combine selected collections and files into a...
Radhika Chippada
11:02 am Task #3796 (Resolved): Add "Combine selected collections and files into a new collection" action ...
Radhika Chippada
10:56 am Revision 7e3496ab (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
10:56 am Revision b6017f4e (arvados): 3453: Add ensure_unique_name=True to collection create.
Peter Amstutz
10:56 am Revision 2b96f094 (arvados): 3654: redirection to newly created collection is now working.
Radhika Chippada
10:53 am Revision 9e9506f9 (arvados): Merge branch 'master' into 3453-arv-list-docker-images
Peter Amstutz
10:53 am Revision d43fb929 (arvados): Added create#ensure_unique_name to discovery document. "Add a subpr...
button now uses "ensure_unique_name" to avoid errors when the user creates more
than one project called "New project"...
Peter Amstutz
10:43 am Revision c6537733 (arvados): 3453: Create links and collection objects in the specified project, ...
the docker image has already been uploaded to some other project. Peter Amstutz
10:15 am Bug #3831 (Closed): [Crunch] inconsistent find_or_create behavior in pipeline runner vs job
The pipeline runner automatically adds a find_or_create = true field for jobs in the pipeline, if one does not exist.... Ward Vandewege
10:07 am Support #3702 (In Progress): [Support] Fix bugs and write tests (the first half of the sprint)
Ward Vandewege
10:01 am Task #3732 (In Progress): Fix bugs the second half of the sprint
Tim Pierce
09:15 am Bug #3822 (Resolved): [Crunch] 'arv pipeline run ...' generates 'ERROR: duplicate key value viol...
Peter Amstutz

09/06/2014

03:53 pm Revision 43d6c4e3 (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
03:51 pm Revision e386cf44 (arvados): 3654: slight update to redirect to newly created collection
Radhika Chippada
11:23 am Feature #3829 (Duplicate): [Crunch] Email notification when pipeline finishes, depending on user ...
When I'm debugging a pipeline and don't know when the job will finish, it would be nice to get a notification of some... Bryan Cosca
09:09 am Bug #3367 (Resolved): Job failure
I re-ran this job, and it worked fine now, with pwd /tmp/crunch-job when you do your ls. Ward Vandewege
04:06 am Revision f7878b7f (arvados-dev): Save a bit of time: do not install RI and RDoc for the gems we i...
during testing.
no issue #
Ward Vandewege
04:06 am Revision f7878b7f (arvados): Save a bit of time: do not install RI and RDoc for the gems we install
during testing.
no issue #
Ward Vandewege
12:36 am Revision 2e255fb4 (arvados): 3654: little cleanup around the post method
Radhika Chippada
12:15 am Revision 08b394b0 (arvados): 3654: use POST method to combine selections.
Radhika Chippada

09/05/2014

11:56 pm Bug #3828 (Resolved): [Keepproxy] insufficient error checking on "defer listener.Close()" lines i...
Ward Vandewege
05:02 pm Revision 0ac9eace (arvados): Updated Gemfile again with published package version. refs #3822
Peter Amstutz
04:52 pm Revision b60e52e0 (arvados): Merge branch '3822-ensure-unique-names' refs #3822
Conflicts:
services/api/Gemfile
services/api/Gemfile.lock
Peter Amstutz
04:48 pm Revision 15f512c3 (arvados): 3822: Updated Gemfile
Peter Amstutz
04:46 pm Revision 1c679ba6 (arvados): 3822: Fixed use of string instead of symbol in hash, added missing l...
Peter Amstutz
04:23 pm Revision 3b7e5549 (arvados): 3822: Added 'ensure_unique_name' option to #create method for API se...
choose a unique name when there is a name collision in the database.
arv-run-pipeline-instance checks to see if there...
Peter Amstutz
04:00 pm Revision 852573d6 (arvados): 3654: combine options is enabled when only data collections are sele...
Radhika Chippada
03:36 pm Revision 01f16229 (arvados-dev): Install & test Ruby SDK, then use that version for other tests.
This commit gives our Ruby SDK the same treatment as other parts of
our build process: we build and install it early,...
Brett Smith
03:36 pm Revision 01f16229 (arvados): Install & test Ruby SDK, then use that version for other tests.
This commit gives our Ruby SDK the same treatment as other parts of
our build process: we build and install it early,...
Brett Smith
03:17 pm Revision 5faed0c0 (arvados): 3654: add selection dropdown to collections page
Radhika Chippada
03:10 pm Revision e7a9c2ed (arvados): 3654: test update
Radhika Chippada
03:00 pm Revision 34081b99 (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
02:58 pm Revision a6a9e106 (arvados): 3654: add selection dropdown to collections page
Radhika Chippada
02:48 pm Story #3826 (Resolved): [Crunch] Display network activity in crunchstat
(TC) sysfs provides traffic statistics. I tried this in a docker container, after doing a few pings:... Peter Amstutz
02:46 pm Bug #2933 (Resolved): Docker build is broken
Ward Vandewege
02:45 pm Revision 9564076d (arvados): 3654: add selection dropdown to collections page
Radhika Chippada
02:39 pm Bug #3825 (Resolved): [Crunch] crunch-job should save (very) large log files without filling up t...
Instead of writing to a temporary file and then calling arv-put, pipe the log directly to an arv-put process.
Ward Vandewege
02:17 pm Bug #3824 (Resolved): [Crunch] crunch-job should create task execution environment inside docker ...
Cf. commit:a5819ec1e48fba90658fcf676ffc50c1f216d484 and commit:0eb5711ade0f74e556b0a1c10909dbf0bdecb63f
Some refac...
Ward Vandewege
02:17 pm Revision 74ac5edc (arvados): 3654: add selection dropdown to collection#show page
Radhika Chippada
02:09 pm Bug #3710 (Resolved): [Workbench] Clipboard "Combine selected collections and files into a new co...
Radhika Chippada
02:08 pm Support #3823 (Resolved): [Support] Fix bugs and write tests (the second half of the sprint)
Tim Pierce
02:03 pm Revision 8c4233da (arvados): 3654: add integration and funtional tests for combining collections ...
Radhika Chippada
01:55 pm Revision d613d109 (arvados): 3699: bug fixes
Tim Pierce
01:44 pm Bug #3644: [SDK] Fix arv-mount --tags and --groups modes to handle "home" project and #3036 colle...
Peter Amstutz wrote:
> Tim Pierce wrote:
> > Reviewing at commit:9479599:
> >
> > I want to clarify that I under...
Tim Pierce
10:49 am Bug #3644: [SDK] Fix arv-mount --tags and --groups modes to handle "home" project and #3036 colle...
Tim Pierce wrote:
> Reviewing at commit:9479599:
>
> I want to clarify that I understand the thread safety concer...
Peter Amstutz
09:54 am Bug #3644: [SDK] Fix arv-mount --tags and --groups modes to handle "home" project and #3036 colle...
Reviewing at commit:9479599:
I want to clarify that I understand the thread safety concerns here. Because llfuse e...
Tim Pierce
01:18 pm Revision 33a6cc0d (arvados): Replace all remaining references to Clinical Future with Curoverse.
no issue # Ward Vandewege
11:57 am Revision f94f97fe (arvados): 3720: Update arvados Gem versions.
Gemfiles need to be in sync with the latest commit on master.
Refs #3720.
Brett Smith
11:53 am Bug #3822 (Resolved): [Crunch] 'arv pipeline run ...' generates 'ERROR: duplicate key value viol...
When submitting a pipeline instance that hasn't changed, on a job that was successfull, with the --no-reuse flag, 'ar... Abram Connelly
11:45 am Revision 52e25652 (arvados): 3644: minor control block indentation fix.
Peter Amstutz
11:43 am Revision 3d1181ac (arvados): 3644: Changed so ctime == mtime because ctime is not creation time (...
Added atime. Tweaked timestamps behavior be a bit more useful. Peter Amstutz
11:40 am Task #3806 (Resolved): Review 3720-big-manifest-performance-wip
Applied in changeset arvados|commit:41c7f2010ebdbb76fada25a21f184e2d1f4049b3. Brett Smith
11:40 am Bug #3720 (Resolved): [API] Fetching collection record is very slow when manifest is not small.
Applied in changeset arvados|commit:41c7f2010ebdbb76fada25a21f184e2d1f4049b3. Brett Smith
11:39 am Revision 41c7f201 (arvados): Merge branch '3720-big-manifest-performance-wip'
Closes #3720, #3806. Brett Smith
11:28 am Task #3742 (Resolved): arv-copy works on collections
Tim Pierce
11:16 am Revision 0c3c1a49 (arvados): 3720: Limit Workbench file rendering for large Collections.
Rendering too many files can cause rendering to take too long, and
there's not much point because it can really strai...
Brett Smith
11:16 am Revision d95e85ac (arvados): 3720: arvados-cli Gemfile refers to gemspec.
This change helps avoid loops where you have to have arvados-cli
installed to build arvados-cli.
Brett Smith
11:16 am Revision d13ad5bb (arvados): 3720: Refactor manifest parsing from API server to Ruby SDK.
To date, the API server has been parsing manifests and returning
parsed information in the files attribute. That's c...
Brett Smith
11:16 am Revision ac80f69f (arvados): 3720: Clean up+skip Ruby SDK tests.
First I changed these to get them passing again. With that done, I
added the skip. We're not currently running thes...
Brett Smith
10:52 am Feature #3453: [SDK] "arv keep docker" should support listing images in Keep and placing images i...
Peter Amstutz wrote:
> Brett Smith wrote:
> > Reviewing commit:d770a51
> >
> > * I like the project+name additio...
Brett Smith
10:14 am Feature #3453: [SDK] "arv keep docker" should support listing images in Keep and placing images i...
Brett Smith wrote:
> Reviewing commit:d770a51
>
> * I like the project+name additions, but I'm wondering about th...
Peter Amstutz
09:34 am Feature #3453 (In Progress): [SDK] "arv keep docker" should support listing images in Keep and pl...
Peter Amstutz
10:41 am Revision d7e75068 (arvados): 3699: accept collection hash as uuid
Tim Pierce
10:16 am Revision c8de202a (arvados): 3453: Now lists images by default if called with no parameters. Fix...
timestamps on images without a 'timestamp' property. Added 'Docker image'
prefix to default name. Renamed variables...
Peter Amstutz
10:06 am Revision 1fbefb98 (arvados): 3699: add arv-copy to list of installed scripts
Tim Pierce
09:35 am Task #3788 (In Progress): Review 3453-arv-list-docker-images
Peter Amstutz
09:35 am Task #3814 (Resolved): Review 3710-combine-selections-bug
Peter Amstutz
09:24 am Story #3821 (Resolved): [Workbench] Delete and rename files in collections
The "show collection" page (for a collection that is writable by the current user) should have the following features... Peter Amstutz
09:22 am Revision e322205a (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
09:18 am Revision 80df142a (arvados): Merge branch '3710-combine-selections-bug' refs #3710
Peter Amstutz
09:15 am Revision 35e39f92 (arvados): 3710: Refactored code to reduce redundancy. Use select() to get the...
text instead of reloading each object for performance. Peter Amstutz
08:55 am Story #3820 (Closed): [Crunch] Jobs need code from multiple git repositories
The Arvados repository aims to provide useful general-purpose Crunch scripts like run-command. However, users often ... Brett Smith
08:47 am Revision fb24229e (arvados): 3644: fuse_arvados test pass.
Peter Amstutz

09/04/2014

09:51 pm Bug #3819 (Resolved): [Workbench] It's not possible to share a project with the 'All Users' group
Ward Vandewege
09:11 pm Revision ac72156a (arvados-dev): Fix environment variable setting on command line. no issue #
Peter Amstutz
09:11 pm Revision ac72156a (arvados): Fix environment variable setting on command line. no issue #
Peter Amstutz
09:10 pm Revision 5184743d (arvados): Remove name and description columns on jobs table introduced acciden...
(refs #3036). Fixed workbench so tests pass. Peter Amstutz
04:58 pm Revision fd910ade (arvados): Merge branch 'master' into 3654-combine-selections
Radhika Chippada
04:58 pm Feature #3818 (New): [API] Discovery document schema should include whether field on resource is ...
Read-only fields are:
* modified_* and created_at (which are attr_protected)
* updated_at (which should be either r...
Peter Amstutz
04:55 pm Revision 58283556 (arvados): 3710: handle the scenario where files from named collections are sel...
Radhika Chippada
04:43 pm Bug #3817 (New): [API] Discovery document schema does not include generated fields like job depen...
schema_controller.rb:87:... Peter Amstutz
04:10 pm Task #3778 (Resolved): Add a test case
Applied in changeset arvados|commit:812f2714c2908e5b427a8e37032ddcd46fb08297. Brett Smith
04:10 pm Bug #3704 (Resolved): [Workbench] Server-side search fails choosing pipeline inputs with search t...
Applied in changeset arvados|commit:812f2714c2908e5b427a8e37032ddcd46fb08297. Brett Smith
04:05 pm Revision 812f2714 (arvados): 3704: Treat project filters consistently in Workbench chooser.
Before this, a chooser that was loaded on a specific project would
return empty results if the user selected a differ...
Brett Smith
04:01 pm Bug #3720: [API] Fetching collection record is very slow when manifest is not small.
LGTM Peter Amstutz
03:27 pm Task #3806 (In Progress): Review 3720-big-manifest-performance-wip
Peter Amstutz
11:40 am Task #3806: Review 3720-big-manifest-performance-wip
Fixed in commit:a3d3ebb. Checked for other API consumers and found none. Ready for review. Brett Smith
08:33 am Task #3806: Review 3720-big-manifest-performance-wip
Found a bug that needs fixing—crunch-job relies on the files attribute too. Brett Smith
03:23 pm Task #3814 (In Progress): Review 3710-combine-selections-bug
Peter Amstutz
02:09 pm Task #3814 (Resolved): Review 3710-combine-selections-bug
Radhika Chippada
02:59 pm Bug #3663 (In Progress): [SDKs] Python CollectionReader should return at least one byte to caller...
Tim Pierce
02:59 pm Task #3745 (Resolved): Print output immediately after read
Tim Pierce
02:56 pm Task #3745 (In Progress): Print output immediately after read
Tim Pierce
02:56 pm Task #3816 (Resolved): Review 3663-collection-reader-performance
Tim Pierce
02:55 pm Revision d0704549 (arvados): 3663: update test_file_reader unit test
Because StreamFileReader.read() calls are now aligned on block
boundaries, the unit test needs to take that into acco...
Tim Pierce
02:36 pm Story #3815 (New): [SDK] arv-put supports --ignore-symlinks
arv-put boolean option @--ignore-symlinks@ (defaults to true) means that arv-put will skip any symlink it encounters.... Peter Amstutz
02:23 pm Revision 94795995 (arvados): 3644: Add --by-id to invocation of arv-mount in crunch-job to get th...
behavior as before. Peter Amstutz
02:22 pm Revision 6a0610e6 (arvados): 3644: Added choose-your-own-adventure README files to the --all and ...
directories. Regular expressions are now compiled once at the top for
efficiency and readability.
Peter Amstutz
02:06 pm Revision 2449ae26 (arvados): 3710: update the combine_selected_files_into_collection method to al...
Radhika Chippada
01:57 pm Feature #3813 (Resolved): [Workbench] add link to pipeline instance from job view page
If there is just one pipeline a job is part of, just show that pipeline when the link is clicked.
If there is more...
Ward Vandewege
01:54 pm Revision 1079c06e (arvados): 3663: StreamFileReader.read() returns just one chunk
The StreamFileReader read() call reads just a single chunk from the
input stream on each call, instead of reading as ...
Tim Pierce
01:38 pm Story #3812 (Closed): [SDKs] Clients should warn when they're expecting a newer API server
Sometimes it happens that our users have trouble because they're using client software that's written for an API serv... Brett Smith
01:32 pm Bug #3783 (Resolved): [Crunch] 'arv pipeline run --run-here ...' failed at end even though all jo...
Abram,
I confirmed that the problem was that lightning-dev2 had client software that was newer than the API server...
Brett Smith
01:31 pm Revision 0576030b (arvados): 3644: Change metafiles to .arvados#collection and .arvados#project. ...
--by-hash to be --by-id since it works with both uuids and portable data
hashes.
Peter Amstutz
01:05 pm Task #3804 (In Progress): Review 3644-arv-mount-projects
Tim Pierce
12:06 pm Bug #3710 (In Progress): [Workbench] Clipboard "Combine selected collections and files into a new...
Radhika Chippada
11:42 am Task #3767 (Resolved): Get feedback from Abram and Sasha on proposed directory hierarchy
Peter Amstutz
11:41 am Revision a3d3ebb9 (arvados): 3720: Fixup crunch-job to do its own manifest parsing.
Brett Smith
11:33 am Revision 0eb5711a (arvados): Revert 2 hunks from a5819ec1e48fba90658fcf676ffc50c1f216d484, thus
un-breaking crunch-job in two important ways:
* task stdout and stderr are propagated again
* tasks can actually ru...
Ward Vandewege
11:24 am Revision 6bb1e164 (arvados): 3699: copy docker images
A Docker image dependency is specified, for each component c in
pipeline_instance['components'], as c['job']['docker_...
Tim Pierce
11:21 am Task #3744 (In Progress): arv-copy works on pipeline instances
Tim Pierce
11:21 am Task #3743 (In Progress): arv-copy works on docker images
Tim Pierce
11:07 am Revision c90d8145 (arvados): 3654: remove "Combine selected collections and files into a new coll...
Radhika Chippada
10:59 am Revision 6b4405e3 (arvados): 3644: Add threadsafe arvados api access. arv-mount now releases llf...
lock when performing network requests. Peter Amstutz
10:55 am Revision 498f3130 (arvados): 3654: add selection dropdown to collections pages
Radhika Chippada
10:51 am Revision 0abff827 (arvados): 3644: Tweak CollectionReader manifest text regular expression to use...
match. Peter Amstutz
10:49 am Bug #3810 (Closed): [Crunch] run-command should bail when $(file) expands to a nonexistent path
I just spent some time debugging an issue where a typo in a $(file) substitution led to an unhelpful error from the p... Brett Smith
08:53 am Feature #3807 (Closed): [DRAFT] [Crunch] Tasks should be reused if marked "pure"
See [[Reusable tasks]] wiki page. Ward Vandewege

09/03/2014

06:09 pm Bug #3720: [API] Fetching collection record is very slow when manifest is not small.
3720-big-manifest-performance-wip is up for review to implement a fix for this. There have been some changes from th... Brett Smith
05:59 pm Revision b1670d8b (arvados): 3720: Limit Workbench file rendering for large Collections.
Rendering too many files can cause rendering to take too long, and
there's not much point because it can really strai...
Brett Smith
05:59 pm Task #3806 (Resolved): Review 3720-big-manifest-performance-wip
See #3720 for background. Brett Smith
05:52 pm Revision 79ad5e96 (arvados): 3720: Refactor manifest parsing from API server to Ruby SDK.
To date, the API server has been parsing manifests and returning
parsed information in the files attribute. That's c...
Brett Smith
05:36 pm Revision e1ce0f42 (arvados): 3699: added copy_pipeline_instance
Added copy_pipeline_instance, integrating copy_collection and
copy_pipeline_template. Added comments.
Tim Pierce
05:15 pm Revision 2569b6b2 (arvados): 3720: Clean up+skip Ruby SDK tests.
First I changed these to get them passing again. With that done, I
added the skip. We're not currently running thes...
Brett Smith
05:15 pm Revision b9533bd0 (arvados): 3720: arvados-cli Gemfile refers to gemspec.
This change helps avoid loops where you have to have arvados-cli
installed to build arvados-cli.
Brett Smith
04:10 pm Feature #3805 (Duplicate): [SDKs] CLI supports ARVADOS_CONFIG variable
If a user has a file @$HOME/.config/arvados/foobar.conf@ with Arvados environment variable settings, e.g.:... Tim Pierce
04:10 pm Task #3804 (Resolved): Review 3644-arv-mount-projects
Peter Amstutz
04:09 pm Task #3728 (Resolved): Handle "home" and name fields correctly.
Peter Amstutz
04:01 pm Feature #3803 (Closed): [SDKs] Add a rate limiting feature to arv-put and arv-get (like rsync's b...
This could be useful for offsite uploads to keepproxy. Ward Vandewege
03:55 pm Revision b366f855 (arvados): 3644: Tested, fixed various mount modes.
Peter Amstutz
03:35 pm Revision 33710e32 (arvados): 3654: add "combine selections" option to project#show page.
Radhika Chippada
03:32 pm Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
Tim Pierce wrote:
> Peter Amstutz wrote:
> > # I think Tom said that the uuid type map is available in the discover...
Tim Pierce
02:52 pm Story #3699 (In Progress): [SDKs] Copy a pipeline instance, along with its input and output data,...
Tim Pierce
02:52 pm Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
Peter Amstutz wrote:
> In-progress review commit:1f3035c
>
> # Consider implementing part of the 'arvados.command...
Tim Pierce
02:38 pm Story #3699: [SDKs] Copy a pipeline instance, along with its input and output data, from one arva...
In-progress review commit:1f3035c
# Consider implementing part of the 'arvados.command' module (similarly to arv-p...
Peter Amstutz
03:24 pm Revision 252d0e3c (arvados): 3644: Default mount mode now includes home, shared, by_hash, and by_...
Peter Amstutz
02:10 pm Revision 918f5ae5 (arvados): 3644: Re-added support for files with json contents of arvados objects.
Changed block size reported by getattr() use 512 byte blocks which is seems to
be necessary to get 'du' to compute th...
Peter Amstutz
01:53 pm Task #3742 (In Progress): arv-copy works on collections
Tim Pierce
01:53 pm Task #3784 (Resolved): arv-copy works on pipeline templates
Tim Pierce
01:47 pm Revision 5fcf5ebe (arvados): 3699: arv-copy supports collections
arv-copy can be passed a collection UUID. copy_collection(uuid) copies
each block in the collection from the source A...
Tim Pierce
01:42 pm Bug #3792: [Crunch] Docker daemon grows to use all RAM, then won't start new containers
I can find several Docker issues about daemon memory use ("1922":https://github.com/docker/docker/issues/1922, "5923"... Brett Smith
10:42 am Bug #3792 (Closed): [Crunch] Docker daemon grows to use all RAM, then won't start new containers
One of qr1hi's compute nodes recently got into a state where it would not start any more Docker containers, because i... Brett Smith
01:12 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
This is "Docker bug 6757":https://github.com/docker/docker/issues/6757. It was fixed by "adding a @--force-rm@ optio... Brett Smith
10:45 am Bug #3793 (Resolved): [Crunch] Docker containers not removed consistently, filling disk
When we start Docker containers for jobs, we pass the @--rm=true@ option to Docker, which should remove the container... Brett Smith
01:02 pm Task #3802 (Resolved): arv-mount exposes retry support
Brett Smith
12:58 pm Task #3801 (New): crunch-job should treat intermittent Docker failures as temporary failures
Investigate possible avenues for doing this. One possibility is inspecting Docker's stderr, the same way we do with ... Brett Smith
12:50 pm Bug #3637 (Resolved): [Workbench] Add "copy" operation to selection dropdown on projects#show tab...
Applied in changeset arvados|commit:0fdafcb846ec6bb34e4b8ae91ad62c1ccd328355. Radhika Chippada
12:46 pm Bug #3637: [Workbench] Add "copy" operation to selection dropdown on projects#show tabs. Remove c...
Radhika Chippada wrote:
> Tim, thanks for the feedback. I added one more test that checks the selection state on the...
Tim Pierce
12:17 pm Bug #3637: [Workbench] Add "copy" operation to selection dropdown on projects#show tabs. Remove c...
Tim, thanks for the feedback. I added one more test that checks the selection state on the copy action when a subproj... Radhika Chippada
10:29 am Bug #3637: [Workbench] Add "copy" operation to selection dropdown on projects#show tabs. Remove c...
Reviewing at commit:44bcabe9:
Code looks good. Can we add a test to confirm that subprojects cannot be copied bet...
Tim Pierce
09:58 am Bug #3637: [Workbench] Add "copy" operation to selection dropdown on projects#show tabs. Remove c...
The "copy" operation in the project selection drop-down is applicable only to non-project type objects. Thus, sub-pro... Radhika Chippada
12:48 pm Revision 0fdafcb8 (arvados): closes #3637
Merge branch '3637-copy-selections' Radhika Chippada
12:46 pm Task #3790 (Resolved): Review branch: 3637-copy-selections
Tim Pierce
09:45 am Task #3790 (In Progress): Review branch: 3637-copy-selections
Tim Pierce
12:45 pm Task #3800 (Resolved): Add integration tests to test "Combine selected collections and files into...
Radhika Chippada
12:45 pm Task #3799 (Resolved): Add integration tests to test "Combine selected collections and files into...
Radhika Chippada
12:43 pm Task #3798 (Resolved): Add selection dropdown with "Combine selected collections and files into a...
Radhika Chippada
12:41 pm Task #3797 (Resolved): Add selection dropdown with "Combine selected collections and files into a...
Radhika Chippada
12:40 pm Task #3796 (Resolved): Add "Combine selected collections and files into a new collection" action ...
Radhika Chippada
12:14 pm Revision 682a02f1 (arvados): 3637: add one more test that verifies that the copy action is disabl...
Radhika Chippada
11:39 am Revision cd41c68c (arvados): 3644: Collections work again, added .portable_data_hash and .manifes...
virtual files to detect if a directory is a collection. Peter Amstutz
11:38 am Bug #3789: [API] Pipeline template (temporarily?) disappears after move to project
Checking the API server logs, this is a standard "Object not found" 404, just like it looks like. The pipeline templ... Brett Smith
11:11 am Story #3795 (Closed): [Crunch/SDKs] Tasks need more retry support
crunch-job currently retries tasks under a couple of conditions:
* The task exits with the specific "temporary fai...
Brett Smith
10:47 am Bug #3794 (Resolved): [SDK] CLI unit tests cannot be run automatically
The CLI unit tests are not enabled in Jenkins and many of them are currently failing. They should be rejiggered to u... Tim Pierce
10:26 am Revision a9e8119e (arvados): 3644: HomeDirectory and ProjectDirectories work, added filename sani...
Peter Amstutz
09:47 am Story #3654 (In Progress): [Workbench] Add "combine selected collections" and "combine selected f...
Radhika Chippada
09:45 am Story #3654: [Workbench] Add "combine selected collections" and "combine selected files" actions ...
Removed "Retire clippy" from subject.
Tom and I discussed this story. According to Tom, when a pipeline needs indi...
Radhika Chippada
09:46 am Story #3791 (Resolved): [Workbench] Retire clippy. This requires some means other than clippy to ...
Radhika Chippada
09:22 am Feature #3453: [SDK] "arv keep docker" should support listing images in Keep and placing images i...
Reviewing commit:d770a51
* I like the project+name additions, but I'm wondering about the approach and defaults. ...
Brett Smith

09/02/2014

10:32 pm Revision 370d158d (arvados): 3644: Shared project list almost works, still debugging.
Peter Amstutz
06:36 pm Revision 9ec9d36e (arvados): Merge branch 'master' into 3637-copy-selections
Radhika Chippada
06:26 pm Revision 44bcabe9 (arvados): 3637: remove unwanted tab chars
Radhika Chippada
06:23 pm Task #3790 (Resolved): Review branch: 3637-copy-selections
Radhika Chippada
06:22 pm Task #3779 (Resolved): Review 3637-selection-through-chooser
Everything looked good. I reviewed, tested and merged this branch into master to allow me to continue the implementat... Radhika Chippada
06:16 pm Revision 9c81bfe7 (arvados): 3637: add integration tests for "copy", "move", and "remove" operati...
Radhika Chippada
04:57 pm Bug #3789 (Closed): [API] Pipeline template (temporarily?) disappears after move to project
arv pipeline_template create --pipeline-template "{}"
{
"href":"/pipeline_templates/qr1hi-p5p6p-pg34h6t4loles1p",
...
Bryan Cosca
04:35 pm Revision 81ead9fd (arvados): Add name and description columns back in for jobs. refs #3036
Peter Amstutz
04:16 pm Revision 04bce28b (arvados): Merge branch 'master' into 3586-job-priority
Conflicts:
services/api/db/structure.sql
Peter Amstutz
04:00 pm Revision 94982cd8 (arvados): Delete names and description columns from jobs that shouldn't be the...
jobs_owner_uuid_name_unique and pipeline_instance_owner_uuid_name_unique
indexes added by mistake. refs #3036.
Peter Amstutz
03:50 pm Task #3749 (Resolved): Review 3586-job-priority
Peter Amstutz
03:26 pm Revision 4c517008 (arvados): 3637: copy selected items
Radhika Chippada
02:56 pm Task #3788 (Resolved): Review 3453-arv-list-docker-images
Peter Amstutz
02:56 pm Revision d770a511 (arvados): 3453: Add support for --images to get a list of available images. A...
for --project-uuid to place the image and tags in the specified project. Set a
more useful name for the collection c...
Peter Amstutz
02:43 pm Revision 0e0279e2 (arvados): Merge branch 'master' into 3637-copy-selections
Conflicts:
apps/workbench/app/views/application/_choose.js.erb
apps/workbench/config/routes.rb
Radhika Chippada
02:26 pm Revision c23cb2dd (arvados): 3637: undo some of the changes to absorb Tom's updates to chooser im...
Radhika Chippada
02:07 pm Support #3787 (Resolved): [Documentation] Add a section in the User Guide about how to create, up...
Ward Vandewege
01:55 pm Revision 73988a76 (arvados): Do not blow up when running jobs in local mode.
This bug was introduced in a5819ec1e48fba90658fcf676ffc50c1f216d484
no issue #
Ward Vandewege
01:51 pm Revision 5b953c11 (arvados): refs #3637 - merge Tom's updates to chooser implementation, where se...
Merge branch '3637-selection-through-chooser' Radhika Chippada
01:51 pm Task #3786 (Resolved): [SDK] `arv edit` errors should be visible after failure, even if the edite...
Currently, when you edit a pipeline template using arv edit and receive an error the format is:
[error]
[pipeline...
Bryan Cosca
01:29 pm Revision 1f3035cf (arvados): 3699: support pipeline templates
arv-copy can work on pipeline templates. Tim Pierce
01:15 pm Bug #3770: [Workbench] Fiddlesticks in Job Log tab for unreadable Log
Split off the API/Crunch part of this bug as #3785, after confirming that it's still an issue. Brett Smith
01:14 pm Bug #3785 (Resolved): [Crunch] Job log collections should be stored with the same owner_uuid (and...
A user has permission to see a Job through a Project. They can visit the Job page just fine. However, they do not hav... Brett Smith
01:01 pm Revision a92397d6 (arvados): 3644: build_project_trees method ported from workbench, needs testing
Peter Amstutz
11:03 am Task #3784 (In Progress): arv-copy works on pipeline templates
Tim Pierce
11:03 am Task #3784 (Resolved): arv-copy works on pipeline templates
Tim Pierce
09:40 am Bug #3704: [Workbench] Server-side search fails choosing pipeline inputs with search terms
Tom's branch improves the situation, but still doesn't restore the original search behavior. Now when I go through o... Brett Smith
09:36 am Bug #3783: [Crunch] 'arv pipeline run --run-here ...' failed at end even though all jobs/tasks co...
At first glance, it looks like the CLI SDK in new enough to try to use name attributes rather than name links. I thi... Brett Smith
09:32 am Bug #3783 (Resolved): [Crunch] 'arv pipeline run --run-here ...' failed at end even though all jo...
When running pipeline instance qr1hi-d1hrv-9jrnsp198ztr0kn, I get the following error after issuing an 'arv pipeline ... Abram Connelly
09:30 am Task #3777 (Resolved): review and merge 3704-broken-filters-param
Applied in changeset arvados|commit:e74d65c872b214808d341a636662d2e6536fcde6. Brett Smith
09:03 am Task #3777 (In Progress): review and merge 3704-broken-filters-param
Brett Smith
09:26 am Revision e74d65c8 (arvados): Merge branch '3704-broken-filters-param'
Unfortunately, this does not completely fix the bug, but at least it's
an improvement. See refs #3704 for more discu...
Brett Smith
09:01 am Task #3747 (Resolved): Review 3719-improve-subst-error-reporting
Brett Smith
08:48 am Bug #3782 (Resolved): [Workbench] Browser prompts about long-running JavaScript when trying to vi...
I tried to view a large Job log (qr1hi-8i9sb-zyva8qlbfmjsnse—it takes 574 pages in Workbench). While it was loading,... Brett Smith

09/01/2014

10:33 pm Story #3781 (Resolved): [DRAFT] [Workbench] Web-based file upload
Provide a web-based way to upload files to a Keep collection.
Users who are nontechnical, unable to install arv-pu...
Peter Amstutz
05:47 pm Revision 051ee2aa (arvados): crunchstat: fix typos in comments and help/error text.
no issue # Ward Vandewege
02:05 pm Revision 3320b77f (arvados): Do not blow up when arv is called with an unrecognized argument.
Calling option_parser.educate suffices, no need for a call to
Trollop::die that fails and throws a stacktrace.
no is...
Ward Vandewege

08/29/2014

08:38 pm Story #3550: [SDKs] arv-run-pipeline-instance supports running jobs locally using arv-crunch-job
Still some bugs to work out (perhaps arv-crunch-job has regressed). On lightning-dev2:... Tom Clegg
03:50 pm Story #3550 (In Progress): [SDKs] arv-run-pipeline-instance supports running jobs locally using a...
Tom Clegg
08:11 pm Task #3779 (Resolved): Review 3637-selection-through-chooser
Tom Clegg
08:10 pm Task #3776 (Resolved): Pass selected items list through chooser to its action
Tom Clegg
06:24 pm Task #3776 (In Progress): Pass selected items list through chooser to its action
Tom Clegg
04:46 pm Task #3776 (Resolved): Pass selected items list through chooser to its action
Tom Clegg
08:06 pm Revision 0f30cd32 (arvados): 3637: Propagate checkbox selection through chooser modal, remove ses...
Tom Clegg
08:02 pm Revision a16c764a (arvados): 3637: Operate only on selections within this container, even if clip...
Tom Clegg
06:24 pm Task #3778 (Resolved): Add a test case
Tom Clegg
06:23 pm Task #3777 (Resolved): review and merge 3704-broken-filters-param
Tom Clegg
06:15 pm Task #3773 (Resolved): Reproduce and diagnose
Tom Clegg
04:00 pm Task #3773 (In Progress): Reproduce and diagnose
Tom Clegg
04:00 pm Task #3773 (Resolved): Reproduce and diagnose
Tom Clegg
06:14 pm Bug #3586: [API] Job "priority" field defaults to "null", should default to "0"
Ah, I get it (I think): the jobs_owner_uuid_name_unique and pipeline_instance_owner_uuid_name_unique indices stayed i... Tom Clegg
04:54 pm Bug #3586: [API] Job "priority" field defaults to "null", should default to "0"
This index seems to have been removed from structure.sql in commit:80cbf4d9, not sure why/how:... Tom Clegg
05:54 pm Revision 01022866 (arvados): 3704: Force params[:filters] into native format so views and helpers...
Tom Clegg
04:50 pm Task #3749 (In Progress): Review 3586-job-priority
Tom Clegg
04:35 pm Revision 72de9238 (arvados): 3644: Project and Home directory work. Added support for returning ...
timestamps on projects, collections, files. Should be update
CollectionDirectory if the underlying collection record...
Peter Amstutz
04:22 pm Feature #3775 (Resolved): [Crunch] arv-crunch-job should work in local mode with an arvados-hoste...
Currently, in local mode, repository="arvados" only works if ./arvados/.git happens to exist when crunch-job runs.
...
Tom Clegg
04:10 pm Bug #3774 (Closed): [Crunch] crunch-job tries to put non-scalar structures in the environment
Reviewing a Job log, I found this little tidbit during a Docker launch @--env=JOB_PARAMETER_COMMAND=ARRAY(0x1fbbf30)@... Brett Smith
03:51 pm Task #3772 (Resolved): Review 3550-local-pipeline
Tom Clegg
03:50 pm Task #3771 (Resolved): Add --run-jobs-here flag
Tom Clegg
03:50 pm Task #3771 (Resolved): Add --run-jobs-here flag
Tom Clegg
03:48 pm Revision 72af8e48 (arvados): 3550: Add --run-jobs-here flag to arv-run-pipeline-instance.
Run new jobs locally with arv-crunch-job instead of asking
crunch-dispatch to run them.
Tom Clegg
03:46 pm Revision 8a4691d7 (arvados): 3550: Improve startup time by removing excess api client instantiation.
Tom Clegg
03:43 pm Bug #3770 (Resolved): [Workbench] Fiddlesticks in Job Log tab for unreadable Log
A user has permission to see a Job through a Project. They can visit the Job page just fine. However, they do not h... Brett Smith
03:12 pm Task #3759 (Resolved): arv-copy authenticates to multiple Arvados instances
Tim Pierce
01:30 pm Task #3759 (In Progress): arv-copy authenticates to multiple Arvados instances
Tim Pierce
03:10 pm Revision 143bbe8d (arvados): 3699: add arv-copy
* arvados.config.load(config_file) reads config_file for Arvados
configuration settings. It returns a hash with th...
Tim Pierce
02:57 pm Bug #3769 (Resolved): [API] In crunch-dispatch, throttle by bytes_per_minute or _node_minute
crunch_limit_log_event_bytes_per_job is currently a hard-coded number in the server config. It would be much more use... Ward Vandewege
02:40 pm Feature #3768 (Closed): [SDKs] Speculatively pre-fetch data blocks while reading from a collection.
Tom Clegg
01:51 pm Task #3767 (Resolved): Get feedback from Abram and Sasha on proposed directory hierarchy
Tom Clegg
01:47 pm Task #3766 (Resolved): Send screen capture to Tom O'Keefe to get design/layout advice
Tom Clegg
12:40 pm Bug #3763 (Resolved): [Workbench] "Move selected" on collections produces error.
Applied in changeset arvados|commit:51d54eb5a828cb60005c5c2d446d375b4ff8baac. Anonymous
10:43 am Bug #3763: [Workbench] "Move selected" on collections produces error.
commit:8afd225... Looks good, and the "move" button wfm now. Please merge. Thanks! Tom Clegg
09:13 am Bug #3763 (In Progress): [Workbench] "Move selected" on collections produces error.
Peter Amstutz
09:11 am Bug #3763 (Resolved): [Workbench] "Move selected" on collections produces error.
Select a collection. Selection->Move selected will result in an error. Using "move to this project" in clippy resul... Peter Amstutz
12:37 pm Revision 51d54eb5 (arvados): Merge branch '3763-move-collections-error' closes #3763
Peter Amstutz
10:40 am Task #3764 (Resolved): Review 3763-move-collections-error
Tom Clegg
10:32 am Task #3764 (Resolved): Review 3763-move-collections-error
Peter Amstutz
10:35 am Task #3765 (Resolved): [Workbench] Pipeline instance #show page should not show the _current_ tem...
Tom Clegg
10:17 am Revision 8afd2250 (arvados): 3763: Workbench will not send attributes to API server that are nil ...
changed. Peter Amstutz

08/28/2014

08:03 pm Story #3705: [Keep] Generalize PullList module to BlockWorkList
(Updated spec to communicate with channels instead of Get and Set methods) Tom Clegg
07:24 pm Revision 7c797619 (arvados-dev): Fix $leave_temp in clear_temp() no issue #
Peter Amstutz
07:24 pm Revision 7c797619 (arvados): Fix $leave_temp in clear_temp() no issue #
Peter Amstutz
06:09 pm Story #3762 (Resolved): [Keep] Process entries on the current "delete" list.
Keep should process the file asynchronously and delete each block in it.
This is written out in more detail at the...
Tom Clegg
05:47 pm Bug #3720: [API] Fetching collection record is very slow when manifest is not small.
The vast majority of the API response time is in @as_api_object@. Here's some rough benchmarking added to my API ser... Brett Smith
03:36 pm Bug #3720: [API] Fetching collection record is very slow when manifest is not small.
This bug has both an API server component and a Workbench component. Here are the slow bits when I visit the Workben... Brett Smith
03:11 pm Bug #3720 (In Progress): [API] Fetching collection record is very slow when manifest is not small.
Brett Smith
05:12 pm Revision ef6ab39e (arvados): 3644: Working on adding timestamps
Peter Amstutz
04:30 pm Story #3761 (Resolved): [Keep] Process entries on the current pull list.
Currently, when receiving its first pull list, keepstore sets up a WorkQueue instance called pullq. At the same time ... Tom Clegg
04:30 pm Bug #3714 (Resolved): [Workbench] small bugs in "report bug on the page" feature
Applied in changeset arvados|commit:21c6d252b279c9714419bf65da07e32246572238. Radhika Chippada
04:17 pm Bug #3714: [Workbench] small bugs in "report bug on the page" feature
commit:c96deb5 looks good to me. Thank you! Brett Smith
02:03 pm Bug #3714: [Workbench] small bugs in "report bug on the page" feature
Reviewing commit:0313947
* It feels a little unfortunate that the disable code is duplicated, once in the JavaScri...
Brett Smith
04:27 pm Task #3746 (Resolved): Review branch: 3714-report-issue-issues
Radhika Chippada
01:43 pm Task #3746 (In Progress): Review branch: 3714-report-issue-issues
Brett Smith
04:25 pm Feature #3760 (New): [Workbench] When referencing an object that is not readable (e.g., deleted o...
Example (current behavior):
# Users A and B are in a group together.
# User A shares a project with user B.
# User...
Tom Clegg
04:21 pm Revision 21c6d252 (arvados): closes #3714
Merge branch '3714-report-issue-issues' Radhika Chippada
04:21 pm Revision 974f1904 (arvados): Merge branch 'master' into 3714-report-issue-issues
Radhika Chippada
04:19 pm Revision 4938505b (arvados): 3637: fix test now that "Copy selections" and "Move selections" opti...
Radhika Chippada
04:09 pm Revision 4917bb2c (arvados): 3637: remove "Copy selections" and "Move selections" options from cl...
Radhika Chippada
04:05 pm Revision 2679a9f6 (arvados): Merge branch 'master' into 3637-copy-selections
Radhika Chippada
04:03 pm Revision c96deb58 (arvados): 3714: minor updates from review feedback
Radhika Chippada
03:39 pm Revision 0368e13e (arvados): Merge branch 'master' into 3714-report-issue-issues
Radhika Chippada
03:38 pm Revision 0b007070 (arvados): 3637: refactor code for better maintenance.
Radhika Chippada
03:25 pm Revision f2d89d3e (arvados): Fix arv-put tests refs #3709
Peter Amstutz
03:20 pm Revision a3be17c5 (arvados): Merge branch 'master' into 3637-copy-selections
Radhika Chippada
03:19 pm Revision 419fb180 (arvados): 3637: add copy selected items functionality to project selection dro...
Radhika Chippada
03:11 pm Revision 701c816e (arvados): 3644: More renaming GroupDirectory to ProjectDirectory, removing nam...
Peter Amstutz
02:56 pm Task #3759 (Resolved): arv-copy authenticates to multiple Arvados instances
* Looks in @$HOME/.config/arvados/${instance}.conf@ for authentication settings.
* Prompts user for ARVADOS_API_HOST...
Tim Pierce
02:54 pm Task #3758 (Resolved): arv-copy works on git repos
Tim Pierce
02:52 pm Bug #3757 (New): [Workbench] Clicking on the show link for a 'can_login' permission link renders ...
Ward Vandewege
02:50 pm Bug #3756 (Resolved): [Workbench] As an admin user, clicking 'Show' in the user list on your own ...
Proper fix:
* Better way to ensure {"move this project to..." → Home → OK} redirects to projects#show with...
Ward Vandewege
02:50 pm Bug #3719 (Resolved): [Crunch] run-command crashes: TypeError: coercing to Unicode ... NoneType f...
Applied in changeset arvados|commit:97473ddf7cd581a048af7b6585ce3ef75ff502c0. Anonymous
02:38 pm Bug #3719: [Crunch] run-command crashes: TypeError: coercing to Unicode ... NoneType found
Reviewing commit:78317da
* In SubstitutionError, why override @__init__@ just to call the super method? You can w...
Brett Smith
09:27 am Bug #3719 (In Progress): [Crunch] run-command crashes: TypeError: coercing to Unicode ... NoneTyp...
Peter Amstutz
02:49 pm Revision 97473ddf (arvados): Merge branch '3719-improve-subst-error-reporting' closes #3719
Peter Amstutz
02:48 pm Revision 462fbba4 (arvados): 3719: Python style/wording fixes.
Peter Amstutz
02:45 pm Story #3709 (Resolved): [SDKs] arv-put should return Arvados UUID of collection by default instea...
Applied in changeset arvados|commit:4fc443bfedf165307795e2b9e6c022008b5d7639. Anonymous
02:22 pm Story #3709: [SDKs] arv-put should return Arvados UUID of collection by default instead of portab...
Reviewing commit:c59670e and it looks good to me. In case it's helpful for the future, you might find testing @mydic... Brett Smith
11:32 am Story #3709 (In Progress): [SDKs] arv-put should return Arvados UUID of collection by default ins...
Peter Amstutz
02:42 pm Revision 4fc443bf (arvados): Merge branch '3709-arv-put-print-uuid' closes #3709
Peter Amstutz
02:41 pm Revision cd9c840e (arvados): 3644: Switched around command line parameters a bit. Will default t...
now. Renamed GroupsDirectory to HomeDirectory and GroupDirectory to
ProjectDirectory.
Peter Amstutz
02:23 pm Task #3747 (In Progress): Review 3719-improve-subst-error-reporting
Brett Smith
10:09 am Task #3747 (Resolved): Review 3719-improve-subst-error-reporting
Peter Amstutz
02:23 pm Task #3754 (Resolved): Review 3709-arv-put-print-uuid
Peter Amstutz
02:09 pm Task #3754 (In Progress): Review 3709-arv-put-print-uuid
Brett Smith
01:52 pm Task #3754 (Resolved): Review 3709-arv-put-print-uuid
Peter Amstutz
01:58 pm Revision 5336eb79 (arvados): Fix nil dereference causing a fiddlesticks on the collections index ...
Peter Amstutz
01:51 pm Task #3727 (Resolved): Fix crunch-job
Peter Amstutz
11:22 am Task #3727 (In Progress): Fix crunch-job
Peter Amstutz
01:35 pm Revision c2add3a9 (arvados): Merge branch 'master' into 3709-arv-put-print-uuid
Peter Amstutz
01:33 pm Revision 050a8d39 (arvados): Complain and fail if exec() returns. No issue #
Tom Clegg
01:20 pm Bug #3751 (Resolved): [Crunch] crunchstat does not pass through its stdin to its child process
Applied in changeset arvados|commit:8350db2288e8f915bb70328e89c2717d69ba62ad. Anonymous
11:37 am Bug #3751 (Resolved): [Crunch] crunchstat does not pass through its stdin to its child process
-(Also noticed that its diagnostic message goes to stdout instead of stderr.)- (this part seems to have been user err... Tom Clegg
01:18 pm Revision 8350db22 (arvados): Pass stdin to child process. closes #3751
Tom Clegg
01:16 pm Revision 97c2c0f4 (arvados): 3751: Pass stdin to child process.
Tom Clegg
11:44 am Task #3752 (Resolved): Define BlockManager interfaces and types
Tim Pierce
11:33 am Bug #3644 (In Progress): [SDK] Fix arv-mount --tags and --groups modes to handle "home" project a...
Peter Amstutz
11:32 am Task #3728 (In Progress): Handle "home" and name fields correctly.
Peter Amstutz
11:22 am Task #3726 (Resolved): Change arv-put
Peter Amstutz
11:22 am Task #3726 (In Progress): Change arv-put
Peter Amstutz
11:20 am Revision c59670ea (arvados): 3709: arv-put now prints collection uuid by default. Add --portable...
to arv-put to get the old behavior (print PDH). Crunch-job uses arv-put
--portable-data-hash to get the PDH to put i...
Peter Amstutz
11:18 am Revision 80cbf4d9 (arvados): 3586: Migrate "priority" column so it is an integer instead of as st...
Peter Amstutz
11:06 am Revision 638c2c22 (arvados): Run given command even if src tree already installed. No issue #
Tom Clegg
10:54 am Bug #3750 (New): [Workbench] Columns displaying items on project page should be sortable
User should be able to choose whether to sort by name, by creation time, modified time, etc. Peter Amstutz
10:38 am Bug #3586 (In Progress): [API] Job "priority" field defaults to "null", should default to "0"
Peter Amstutz
10:37 am Revision 38dc6b9d (arvados): 3586: Set priority to "0" if nil. Fix test fixtures.
Peter Amstutz
10:22 am Task #3749 (Resolved): Review 3586-job-priority
Peter Amstutz
10:22 am Task #3748 (Resolved): Add migration
Peter Amstutz
10:14 am Task #3748 (Resolved): Add migration
Peter Amstutz
10:22 am Revision bf1f3980 (arvados): 3586: Set job priority column default to '0', add NOT NULL constraint.
Peter Amstutz
10:17 am Bug #3637 (In Progress): [Workbench] Add "copy" operation to selection dropdown on projects#show ...
Radhika Chippada
10:08 am Task #3721 (Resolved): Improve error reporting
Peter Amstutz
09:26 am Task #3721 (In Progress): Improve error reporting
Peter Amstutz
10:06 am Revision 78317dad (arvados): 3719: Robust-put uses run-command logger.
Peter Amstutz
10:05 am Bug #3339 (Resolved): [Workbench] Project descriptions on the dashboard should be truncated at th...
Applied in changeset arvados|commit:d1f510e7fa9f1b2656c54c1e9b3ea4e4466c9d1e. Radhika Chippada
09:45 am Bug #3339: [Workbench] Project descriptions on the dashboard should be truncated at the first par...
Radhika,
Thanks very much for these changes (commit:d199bf8). I like this branch a lot. There's just one small t...
Brett Smith
09:01 am Bug #3339: [Workbench] Project descriptions on the dashboard should be truncated at the first par...
Brett:
1. I did some refactoring and tightening of the code, and also renamed the method.
2. I removed the extr...
Radhika Chippada
10:02 am Revision 55ed403e (arvados): 3719: run-command uses its own logger instead of the default Python ...
avoid cross talk with badly behaved modules. Peter Amstutz
10:02 am Revision d1f510e7 (arvados): closes #3339
Merge branch '3339-truncate-project-descriptions' Radhika Chippada
10:01 am Revision 78f13ceb (arvados): 3339: fix typo in test
Radhika Chippada
10:01 am Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Tom Clegg wrote:
> Tim Pierce wrote:
> > @fmt.Printf("%s", foo)@ will call the @foo.String()@ method if it exists. ...
Tim Pierce
09:52 am Task #3611 (Resolved): Review 3499-home-project-docs-wip
Tom Clegg
09:51 am Task #3506 (Resolved): Help Sally/Brian/Abram
Tom Clegg
09:51 am Task #3713 (Resolved): Review 3339-truncate-project-descriptions
Tom Clegg
09:02 am Task #3713: Review 3339-truncate-project-descriptions
Pushed updates, if you would like to take another look. Radhika Chippada
09:51 am Task #3708 (Resolved): Review 3342-pipeline-output-current-project
Tom Clegg
09:48 am Revision 22954b4f (arvados): Merge branch 'master' into 3339-truncate-project-descriptions
Radhika Chippada
09:30 am Revision 7aea6d3d (arvados): Remove assertion testing for obsolete output_is_persistent field. r...
Peter Amstutz
09:29 am Revision d199bf8a (arvados): Merge branch 'master' into 3339-truncate-project-descriptions
Radhika Chippada
09:26 am Revision e32be386 (arvados): 3719: Raise more specific SubstitutionError instead of generic excep...
user syntax errors. Don't print stack trace on SubstitutionError. Peter Amstutz
09:22 am Revision 0313947c (arvados): 3714: update tests to verify that the send report button is disabled...
Radhika Chippada
09:17 am Revision 7b277922 (arvados): Merge branch 'master' into 3714-report-issue-issues
Radhika Chippada
08:53 am Revision a3755ca0 (arvados): Set Gemfile version target for arvados-cli to correct version. refs...
Peter Amstutz
08:05 am Revision 2b43d13d (arvados): 3339: some refactoring of the render textile impl. improve the test ...
Radhika Chippada

08/27/2014

05:44 pm Revision 15907a13 (arvados): Revert arvados gems to versions that actually exist. refs #3342
Tom Clegg
05:32 pm Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Tim Pierce wrote:
> @fmt.Printf("%s", foo)@ will call the @foo.String()@ method if it exists. So in the case of Pul...
Tom Clegg
05:00 pm Story #3414 (Resolved): [Keep] Keep Server accepts list of blocks to pull from other servers
Applied in changeset arvados|commit:3204b60e04bf8613858bfc4a753d7114f6ca90a3. Tim Pierce
11:50 am Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Tom Clegg wrote:
> Tim Pierce wrote:
> > New revision at commit:20fec88
> >
> > Added logging for both successfu...
Tim Pierce
10:53 am Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Tim Pierce wrote:
> New revision at commit:20fec88
>
> Added logging for both successful and unsuccessful pull re...
Tom Clegg
10:20 am Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Tom Clegg wrote:
> Handy example: http://golang.org/src/pkg/container/list/list.go
That's a great example. In fa...
Tim Pierce
10:09 am Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Handy example: http://golang.org/src/pkg/container/list/list.go Tom Clegg
05:31 pm Task #3746 (Resolved): Review branch: 3714-report-issue-issues
Small update to the report issue page to disable the submit button until problem description is entered. Radhika Chippada
05:29 pm Task #3716 (Resolved): submitting without contents in the "describe the problem" is possible, sho...
Disable the submit button until the problem description is entered. Radhika Chippada
05:26 pm Task #3716 (In Progress): submitting without contents in the "describe the problem" is possible, ...
I will disable the submit button until the user enters the problem description. Radhika Chippada
01:11 pm Task #3716 (Resolved): submitting without contents in the "describe the problem" is possible, sho...
Ward Vandewege
05:29 pm Task #3715 (Resolved): workbench and api server version always render as 6333000
6333000 was the commit hash number and it was determined that this is not an issue. Verified with other commits. Radhika Chippada
01:10 pm Task #3715 (Resolved): workbench and api server version always render as 6333000
This should be a git hash. Ward Vandewege
05:21 pm Revision d2804a5f (arvados): 3714: disable submit button until problem description is entered.
Radhika Chippada
05:17 pm Bug #3339: [Workbench] Project descriptions on the dashboard should be truncated at the first par...
Comments on commit:0fe8a55
* From an code maintainability perspective, I don't understand why it's helpful to sepa...
Brett Smith
11:41 am Bug #3339 (In Progress): [Workbench] Project descriptions on the dashboard should be truncated at...
Radhika Chippada
05:10 pm Bug #3342 (Resolved): [Crunch] Pipeline outputs not added to current project.
Applied in changeset arvados|commit:0042e4b42d9f4d3900aefc68617cb28c5a61a522. Anonymous
03:05 pm Bug #3342: [Crunch] Pipeline outputs not added to current project.
LGTM to merge. Thanks for this. Tim Pierce
02:59 pm Bug #3342: [Crunch] Pipeline outputs not added to current project.
Tim Pierce wrote:
> Reviewing at commit:7c8e8d37:
>
> apps/workbench/app/models/pipeline_instance.rb:
> * Since ...
Peter Amstutz
11:40 am Bug #3342: [Crunch] Pipeline outputs not added to current project.
Reviewing at commit:7c8e8d37:
apps/workbench/app/models/pipeline_instance.rb:
* Since each component has its own ...
Tim Pierce
05:08 pm Task #3697 (Resolved): Review 3414-keep-pull-handler
Tim Pierce
05:04 pm Revision 0042e4b4 (arvados): Merge branch '3342-pipeline-output-current-project' closes #3342
Peter Amstutz
05:03 pm Revision 3630931a (arvados): 3342: Fix syntax error in pipeline_instance.rb. Restore code in cru...
that reads manifest text from arv-get pipe. Peter Amstutz
04:59 pm Revision 3204b60e (arvados): Merge branch '3414-keep-pull-handler'
Closes #3414. Tim Pierce
04:56 pm Revision 46b3cec9 (arvados): 3414: fix log typo
%s -> %v Tim Pierce
04:53 pm Bug #3714 (In Progress): [Workbench] small bugs in "report bug on the page" feature
Radhika Chippada
01:09 pm Bug #3714 (Resolved): [Workbench] small bugs in "report bug on the page" feature
Ward Vandewege
04:52 pm Task #3713 (In Progress): Review 3339-truncate-project-descriptions
Brett Smith
12:33 pm Task #3713 (Resolved): Review 3339-truncate-project-descriptions
Radhika Chippada
04:45 pm Task #3745 (Resolved): Print output immediately after read
Tim Pierce
04:38 pm Task #3744 (Resolved): arv-copy works on pipeline instances
Tim Pierce
04:38 pm Task #3743 (Resolved): arv-copy works on docker images
Tim Pierce
04:38 pm Task #3742 (Resolved): arv-copy works on collections
Tim Pierce
04:34 pm Task #3741 (Resolved): API server filters for trashed objects
API server implicitly selects delete_at is null or delete_at > now when querying collections table (rails "default sc... Tim Pierce
04:32 pm Task #3739 (Resolved): Add default_trash_lifetime
Add default_trash_lifetime config setting to workbench config/application.default.yml
See [[Hacking Workbench]]
Tim Pierce
03:57 pm Task #3738 (New): arv-run-pipeline-instance: display workbench URI instead of the bare uuid
Tom Clegg
03:57 pm Task #3737 (New): Include workbench URI in discovery document
(the one from application.yml) Tom Clegg
03:41 pm Task #3736 (Closed): [SDKs] Document Python Crunch SDK
This includes both docstrings and illustrating the new API in the tutorial/user guide. Brett Smith
03:30 pm Task #3735 (Resolved): Make crunch-job retry when it calls arv-put
Brett Smith
03:30 pm Feature #3734 (New): [Keep] Keepstore and keepproxy support HTTP Range requests
If a request has a Range header, read only the desired portion from the data volume, and return the segment with appr... Tim Pierce
03:28 pm Task #3733 (Resolved): Write wrapper
Peter Amstutz
03:28 pm Task #3732 (Resolved): Fix bugs the second half of the sprint
Brett Smith
03:28 pm Task #3731 (Resolved): Add pipe support to run-command
Peter Amstutz
03:28 pm Task #3730 (Resolved): Fix bugs the first half of the sprint
Brett Smith
03:27 pm Task #3729 (Resolved): Design command line
Peter Amstutz
03:27 pm Task #3728 (Resolved): Handle "home" and name fields correctly.
Peter Amstutz
03:27 pm Support #3702: [Support] Fix bugs and write tests (the first half of the sprint)
We've agreed to split responsibility for this story at the sprint's halfway point. I'll take point for the first half. Brett Smith
03:26 pm Task #3727 (Resolved): Fix crunch-job
Peter Amstutz
03:26 pm Task #3726 (Resolved): Change arv-put
Peter Amstutz
03:24 pm Task #3723 (Resolved): Implement dashboard layout at https://arvados.org/attachments/download/349...
...minus the stats that don't exist like $ and rating - perhaps the top right will have room for a live-from-websocke... Peter Amstutz
03:24 pm Task #3721 (Resolved): Improve error reporting
Peter Amstutz
03:17 pm Story #3188 (Closed): [Workbench] Merge "show job" functionality into "show pipeline instance" page
Subsumed by #3187 Tom Clegg
03:16 pm Bug #3147: [SDKs] Python clients should automatically retry failed API and Keep requests (includi...
Carried forward to following sprint with 1 story point. Brett Smith
03:08 pm Story #3157: [Workbench] Admin button to download user list as CSV
A few questions:
* Do we want all of prefs or just prefs.profile? Basically, do we want to define the columns in t...
Radhika Chippada
03:06 pm Task #3650 (Resolved): Implement PullHandler
Tim Pierce
03:02 pm Bug #3720: [API] Fetching collection record is very slow when manifest is not small.
https://workbench.qr1hi.arvadosapi.com/collections/d071779966740d0f4884c17c3712a6a6+8369520 → bad gateway Tom Clegg
02:59 pm Bug #3720 (Resolved): [API] Fetching collection record is very slow when manifest is not small.
This makes nginx give up on Workbench and say "502 Bad Gateway". Tom Clegg
03:02 pm Revision 854060d1 (arvados): 3342: Handle case in PipelineInstance#friendly_link_name where
pipeline_template_uuid doesn't return a PipelineTemplate. Removed unnecessary
code from crunch-job to calculate md5 ...
Peter Amstutz
03:01 pm Bug #3719: [Crunch] run-command crashes: TypeError: coercing to Unicode ... NoneType found
Pipeline instance qr1hi-d1hrv-uwem8ll6v65vin0 .
Here is the relevant error section taken from the log:...
Abram Connelly
02:59 pm Bug #3719 (Resolved): [Crunch] run-command crashes: TypeError: coercing to Unicode ... NoneType f...
Tom Clegg
02:55 pm Feature #3467 (Closed): [Crunch] Specify human readable name for pipeline instance output
Duplicate of #3342 Tom Clegg
02:51 pm Task #3718 (Closed): Hash out desired API with science team
Address questions on the wiki from Tom and others. Show the science team different alternatives and get their input ... Brett Smith
02:51 pm Feature #3607 (Resolved): [Crunch] crunch-dispatch can go into run-pipeline-instance or dispatch ...
Tom Clegg
02:47 pm Feature #2881 (New): [OPS] Basic node manager that can start/stop compute nodes based on demand
Brett Smith
02:24 pm Revision 0fe8a55a (arvados): 3339: update test to verify textile description in my projects panel...
Radhika Chippada
02:09 pm Support #3717 (Resolved): In[Support] stalling Arvados on AWS - ubuntu14.04 with docker
Ward Vandewege
01:59 pm Support #3717: In[Support] stalling Arvados on AWS - ubuntu14.04 with docker
Hi Alla,
This is a known bug in Docker 1.2.0 -- see https://github.com/docker/docker/issues/7714. It's been fixed ...
Ward Vandewege
01:31 pm Support #3717: In[Support] stalling Arvados on AWS - ubuntu14.04 with docker
Hi there,
What version of docker are you using?
Thanks,
Ward.
Ward Vandewege
01:26 pm Support #3717 (Resolved): In[Support] stalling Arvados on AWS - ubuntu14.04 with docker
Hello,
I am getting an error and I hope you can help me
+ '[' -r etc/debian_version ']'
+ lsbDist=Debian
+ ...
Alla Bushoy
02:06 pm Story #3711 (In Progress): [Docs] Update Arvados permissions model in docs
Peter Amstutz
10:55 am Story #3711 (In Progress): [Docs] Update Arvados permissions model in docs
Merge https://arvados.org/projects/arvados/wiki/Groups_Projects_Ownership_and_Permissions_Specification with http://d... Peter Amstutz
01:46 pm Support #3505 (Resolved): [Sample pipelines] Support science team
Tom Clegg
12:32 pm Task #3681 (Resolved): Truncate project description display in dashboard at the first textile lin...
Radhika Chippada
12:31 pm Task #3680 (Resolved): Update project description display in dashboard to display textile formatt...
Radhika Chippada
12:30 pm Revision 0b3427a0 (arvados): 3339: render truncated textile descriptions in dashboard
Radhika Chippada
11:50 am Revision 902e9ebf (arvados): 3414: update comment for code review
Tim Pierce
10:38 am Task #3708 (In Progress): Review 3342-pipeline-output-current-project
Tim Pierce
09:41 am Task #3708 (Resolved): Review 3342-pipeline-output-current-project
Peter Amstutz
10:38 am Revision 7c8e8d37 (arvados): 3342: Update documentation. Add "output_name", remove "output_is_pe...
Peter Amstutz
10:17 am Bug #3710 (Resolved): [Workbench] Clipboard "Combine selected collections and files into a new co...
Trying to combine these two files results in an empty collection: d41d8cd98f00b204e9800998ecf8427e+0
e64eb06386970...
Bryan Cosca
09:56 am Story #3709 (Resolved): [SDKs] arv-put should return Arvados UUID of collection by default instea...
Users want to be able to find their collections, so we should give them the Arvados UUID of the collection object ins... Peter Amstutz
09:33 am Revision cf5ffa1f (arvados): 3342: Tweak pipeline component status rendering. Support "output_na...
to specify no output should be added to the current project. Peter Amstutz
09:07 am Revision 24c42c71 (arvados): 3342: Fix links to log files to use portable_data_hash. Remove spur...
Improve error logging. Peter Amstutz

08/26/2014

11:48 pm Task #3707 (Resolved): Ensure crunch-job task output collation can survive with all permission fe...
Tom Clegg
11:41 pm Story #3706 (Resolved): [SDKs] Remove fallback-to-keep warning from python SDK if block hash has ...
Background: Crunch job tasks can use Keep as a cache for manifest fragments, which crunch-job retrieves at the end of... Tom Clegg
11:07 pm Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Tom Clegg wrote:
> At some point (not right now) I think we can rename the PullList to something more like todo_list...
Tim Pierce
09:26 pm Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
New revision at commit:20fec88
Added logging for both successful and unsuccessful pull requests.
Renamed replic...
Tim Pierce
08:47 pm Story #3414 (In Progress): [Keep] Keep Server accepts list of blocks to pull from other servers
Tom Clegg
05:55 pm Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Priorities/requests:
* In handlers:
** Log when a "pull" request is received (at the top of PullHandler).
** If ...
Tom Clegg
05:09 pm Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Tim Pierce wrote:
> # All other servers have deleted the unreplicated blocks by the time keepstore gets around to th...
Tom Clegg
01:59 pm Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Tim Pierce wrote:
> In order for one keepstore to pull blocks from another keepstore, it will need to sign the locat...
Tom Clegg
09:31 pm Bug #3704 (In Progress): [Workbench] Server-side search fails choosing pipeline inputs with searc...
Tom Clegg
04:42 pm Bug #3704 (Resolved): [Workbench] Server-side search fails choosing pipeline inputs with search t...
Part one (fixed): In current master Workbench, when I try to select inputs for a pipeline that has search terms for i... Brett Smith
09:18 pm Revision 20fec88c (arvados): 3414: rename replicator to pull_list
Renamed replicator.Replicator to pull_list.Manager. Tim Pierce
08:50 pm Revision 6c29e762 (arvados): 3414: update for code review
Added logging for pull lists. Unsuccessful pull lists are logged with
an error, successful ones are logged with the ...
Tim Pierce
08:41 pm Task #3697 (In Progress): Review 3414-keep-pull-handler
Tom Clegg
03:18 pm Task #3697 (Resolved): Review 3414-keep-pull-handler
Tim Pierce
08:40 pm Task #3569 (Resolved): Review 3354
Tom Clegg
08:38 pm Story #3705 (Resolved): [Keep] Generalize PullList module to BlockWorkList
The lists of "blocks to delete" and "blocks to pull from other keepstores" should be maintained in a BlockWorkList ty... Tom Clegg
08:30 pm Story #3354 (Resolved): [Workbench] Render description attributes as textile
Applied in changeset arvados|commit:63330000144108862a4e2b02a7a8fa124d01163e. Anonymous
08:26 pm Revision 63330000 (arvados): Merge branch '3354-render-textile' closes #3354
Tom Clegg
08:13 pm Revision 34173202 (arvados): 3354: Merge branch 'master' into 3354-render-textile
Conflicts:
apps/workbench/app/assets/stylesheets/application.css.scss
apps/workbench/app/helpers/application_helper...
Tom Clegg
08:10 pm Bug #3627 (Resolved): [Workbench] Projects that are writable, but have root owner != current_user...
Applied in changeset arvados|commit:a942e37250873d383bd885ba0dba70c63b3c073d. Anonymous
11:46 am Bug #3627: [Workbench] Projects that are writable, but have root owner != current_user, cannot be...
Looks good to me too. Peter Amstutz
07:51 pm Revision 02cbe072 (arvados): Ensure source_version is a string, even when it consists entirely of...
Tom Clegg
07:51 pm Revision ff742a82 (arvados): Fix label for API endpoint. Re-order fields. refs #3112
Tom Clegg
07:51 pm Revision a5819ec1 (arvados): Run the task setup script inside the container (if any), instead of
running setup on the host, using bind-mount for CRUNCH_SRC, and
assuming other directories have already been set up i...
Tom Clegg
07:51 pm Revision a942e372 (arvados): Merge branch '3627-selectable-projects' closes #3627
Tom Clegg
07:41 pm Task #3670 (Resolved): Review 3627-selectable-projects
Tom Clegg
05:12 pm Revision d4c8504d (arvados): 3342: Fixing outputs
Peter Amstutz
04:53 pm Revision 2ad96e9d (arvados): 3413: add TrashHandler, package trash
Added a trash collector interface for handling the trash list from Data
Manager.
"PUT /trash" requests are routed to...
Tim Pierce
04:26 pm Support #3702 (Resolved): [Support] Fix bugs and write tests (the first half of the sprint)
This is a bucket for fixing bugs encountered by users during the sprint. Here, "fixing" includes:
* Troubleshooting ...
Tom Clegg
04:22 pm Story #3701 (Closed): [Workbench] Show current user's compute node usage over time
Tom Clegg
04:16 pm Task #3679 (In Progress): Implement TrashHandler
Tim Pierce
03:53 pm Bug #3147 (In Progress): [SDKs] Python clients should automatically retry failed API and Keep req...
Brett Smith
11:35 am Bug #3147 (Resolved): [SDKs] Python clients should automatically retry failed API and Keep reques...
Applied in changeset arvados|commit:728ee9775de422840b81827c71c7b515708620a3. Brett Smith
09:36 am Bug #3147: [SDKs] Python clients should automatically retry failed API and Keep requests (includi...
LGTM, thanks. Good to merge. Thanks for adding the 403 as an open question -- this doesn't seem urgent enough to spen... Tim Pierce
03:47 pm Revision 463aed42 (arvados): 3342: Removing remaining traces of output_is_persistent. Added code in
arv-run-pipeline-instance to create collections owned by appropriate project. Peter Amstutz
03:33 pm Revision b15e80cd (arvados): refs #3620
Merge branch '3620-admin-only-gear-menu' Radhika Chippada
03:29 pm Story #3699 (Resolved): [SDKs] Copy a pipeline instance, along with its input and output data, fr...
Use case: user can copy a pipeline instance between Arvados instances, in order to rerun a pipeline on another cluste... Tom Clegg
03:28 pm Revision 71109ef9 (arvados): 3620: correct indentation when current user is available
Radhika Chippada
03:20 pm Bug #3698 (Resolved): [Crunch] Pipeline runner should detect when "output_of" refers to a non-exi...
Peter Amstutz
03:19 pm Task #3650 (In Progress): Implement PullHandler
Tim Pierce
03:17 pm Revision b185fc94 (arvados): 3414: adding PullHandler and Replicator
Added PullHandler and a "replicator" package to handle "PUT /pull" requests.
PUT /pull requests are routed to PullHa...
Tim Pierce
02:58 pm Story #3696 (Closed): [Workbench] Improve log viewer to more effectively expose relevant informat...
When reviewing why a job has failed I find myself wading through a lot of text to get at the single line of relevance... Abram Connelly
02:50 pm Task #3690 (Resolved): Review 3642-search-for-active-only
Radhika Chippada
02:50 pm Story #3620 (Resolved): [Workbench] Display system menu (gear menu) only to admin users.
Applied in changeset arvados|commit:6e39e6e9ce10895a5405c90a0b61290ab507d16d. Radhika Chippada
02:25 pm Story #3620: [Workbench] Display system menu (gear menu) only to admin users.
Reviewing commit:3c12b61
I know this bug existed before your branch, but the diff made me notice it: list items th...
Brett Smith
02:50 pm Bug #3642 (Resolved): [Workbench] Search box should not be displayed in top-nav for non-active us...
Applied in changeset arvados|commit:9cc77c22d33ced67d04148493616320e7665a8c4. Radhika Chippada
02:36 pm Bug #3642: [Workbench] Search box should not be displayed in top-nav for non-active users.
commit:5a80356 looks good to merge. Thanks. Brett Smith
02:50 pm Task #3689 (Resolved): Review 3620-admin-only-gear-menu
Radhika Chippada
02:47 pm Revision 6e39e6e9 (arvados): closes #3620
Merge branch '3620-admin-only-gear-menu' Radhika Chippada
02:45 pm Revision 006e0adf (arvados): Merge branch 'master' into 3620-admin-only-gear-menu
Radhika Chippada
02:45 pm Revision 9cc77c22 (arvados): closes #3642
Merge branch '3642-search-for-active-only' Radhika Chippada
02:43 pm Revision 38770e0e (arvados-dev): Enhanced run-tests.sh command line supporting choosing specific ...
tests, and re-using temp directories. no issue # Peter Amstutz
02:43 pm Revision 38770e0e (arvados): Enhanced run-tests.sh command line supporting choosing specific Pyth...
tests, and re-using temp directories. no issue # Peter Amstutz
02:42 pm Revision 02d48a84 (arvados): 3620: change menu item role from presentation to menuitem for clicka...
Radhika Chippada
02:07 pm Revision 12d2dafa (arvados): 3342: Migration to remove obsolete output_is_persistent column from ...
Peter Amstutz
02:05 pm Story #3112 (Resolved): [Workbench] "Report bug on this page" and "Show version detail" buttons o...
Applied in changeset arvados|commit:183bdcd6c6b2c54f8f2558fbdb6bec974c1d16e4. Radhika Chippada
01:51 pm Story #3112: [Workbench] "Report bug on this page" and "Show version detail" buttons on each work...
Just one last thing: the 404 page template only sets @req_item_plain_text@ if there's an API error. This makes the e... Brett Smith
12:13 pm Story #3112: [Workbench] "Report bug on this page" and "Show version detail" buttons on each work...
Brett: addressed all your comments. Especially, thanks for testing that reload issue, which I should have fixed after... Radhika Chippada
11:10 am Story #3112: [Workbench] "Report bug on this page" and "Show version detail" buttons on each work...
Radhika Chippada, quoting Brett Smith, wrote:
> * General style
> ** There are several references like @Rails.confi...
Brett Smith
02:04 pm Revision 5a80356d (arvados): Merge branch 'master' into 3642-search-for-active-only
Radhika Chippada
02:00 pm Task #3608 (Resolved): Review branch: 3112-report-bug
Radhika Chippada
12:13 pm Task #3608: Review branch: 3112-report-bug
Addressed all your comments. Please take another look, if you like. Thanks. Radhika Chippada
02:00 pm Revision bd1f0b63 (arvados): Merge branch 'master' into 3620-admin-only-gear-menu
Radhika Chippada
01:57 pm Revision 183bdcd6 (arvados): closes #3112
Merge branch '3112-report-bug' Radhika Chippada
01:57 pm Revision bb564d63 (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
01:56 pm Revision 740137a2 (arvados): 3112: 404 error page default message while reporting issue
Radhika Chippada
01:51 pm Revision 4d14e702 (arvados): Fixed missing import in robust_put. no issue #
Peter Amstutz
01:20 pm Revision 4fe1bc8c (arvados): 3112: login_tests works with javascript driver
Radhika Chippada
01:14 pm Story #3695 (New): [Documentation] Replace direct job submission examples with single-component p...
Tom Clegg
01:10 pm Revision 59e5d36f (arvados): 3112: still the login_tests fails when ran in the entire suite
Radhika Chippada
12:30 pm Revision 03002e6c (arvados): 3112: removed rack_test driver and added selenium driver. still the ...
Radhika Chippada
12:10 pm Revision df8e6b95 (arvados): 3112: add scrollbar to the report issue popup
Radhika Chippada
11:42 am Revision 416d8810 (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
11:40 am Revision 536713e6 (arvados): 3112: skip filters in actions controller, instead of application con...
Radhika Chippada
11:40 am Bug #3136 (Resolved): [Crunch] Job state is stale in Workbench pipeline instance views, if the jo...
Applied in changeset arvados|commit:a17b176ea55dc3820ef1bde4b99cf33c628ffbbe. Anonymous
11:35 am Bug #3136 (New): [Crunch] Job state is stale in Workbench pipeline instance views, if the job's s...
commit:c1b0e1bd832d3c2c96e60334b96f3b6989ecd1b6 looks good. Thanks. Brett Smith
11:39 am Task #3667 (Resolved): Review 3660-project-editable
Peter Amstutz
11:36 am Task #3676 (Resolved): Review 3136-stale-pipeline-instance-display
Peter Amstutz
11:36 am Revision a17b176e (arvados): Merge branch '3136-stale-pipeline-instance-display' closes #3136
Peter Amstutz
11:32 am Revision b56386aa (arvados): 3112: no need to reload after sending report.
Radhika Chippada
11:32 am Bug #3649 (Rejected): [Crunch] 'Pipeline_instances' page shows job running when it has failed
Peter Amstutz
11:32 am Revision 728ee977 (arvados): Merge branch '3147-pysdk-retries'
Closes #3147. Brett Smith
11:32 am Revision aa1d003d (arvados): 3147: Fix unwanted integer division in KeepClient logs.
Brett Smith
11:32 am Revision 5a043a14 (arvados): 3147: Add retry support to Python SDK's KeepClient.
Brett Smith
11:32 am Revision dccec0cc (arvados): 3147: Remove old Keep signing support from Python SDK.
Per Tom. Brett Smith
11:32 am Revision adbeb30c (arvados): 3147: Add RetryLoop to the Python SDK.
This provides a general-purpose mechanism for us to retry all kinds of
operations.
Brett Smith
11:32 am Revision 440d863f (arvados): 3147: Move fake Python HTTP response generation to arvados_testutil.
Other tests can use this functionality. Brett Smith
11:32 am Revision 7f5a0caf (arvados): 3147: Add check_http_response_success to Python SDK.
Other parts of the SDK need to end loops based on the result of an
HTTP request. This function puts that logic in on...
Brett Smith
11:31 am Task #3327 (Resolved): Fix workbench display to only use the actual jobs and ignore denormalized ...
Peter Amstutz
11:28 am Task #3632 (Resolved): Review 3036-collection-uuids
Peter Amstutz
11:28 am Bug #3077 (Rejected): Add migration to convert remaining non-root collection owner_uuids to name ...
Obsoleted by #3036 Peter Amstutz
11:25 am Revision c1b0e1bd (arvados): 3136: Use map to correctly get the list of uuids. Check that there ...
record before trying to use it. Peter Amstutz
11:24 am Revision 8cba6b1d (arvados): Fix test. refs #3149
Tom Clegg
11:20 am Story #3149 (Resolved): [Workbench] Workbench infinite scroll and filter system should do filteri...
Applied in changeset arvados|commit:e21b910a307440a9d34e595673539a6e7d708e55. Anonymous
11:17 am Revision 58b6e688 (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
11:14 am Revision d5835c04 (arvados): Fix migration and api templates that rely on changes that did not en...
Tom Clegg
11:00 am Revision e21b910a (arvados): Merge branch '3149-server-side-search' closes #3149
Tom Clegg
11:00 am Revision f12350f2 (arvados): 3149: Merge branch 'master' into 3149-server-side-search
Tom Clegg
10:59 am Revision d1d0fd3c (arvados): Set up arvados env vars when running arv-normalize. No issue #
Tom Clegg
10:59 am Task #3675 (Resolved): Review 3149-server-side-search
Tom Clegg
10:57 am Bug #3342 (In Progress): [Crunch] Pipeline outputs not added to current project.
Peter Amstutz
10:50 am Story #3036 (Resolved): [API] Use regular uuids instead of content hashes to identify collections
Applied in changeset arvados|commit:61cd57499905e8e8cca07c774d1bf8c6bfa069a7. Anonymous
10:45 am Revision 61cd5749 (arvados): Merge branch '3036-collection-uuids' closes #3036
Peter Amstutz
10:43 am Revision 41a6554c (arvados): Merge branch 'master' into 3036-collection-uuids
Conflicts:
services/api/test/fixtures/groups.yml
Peter Amstutz
09:59 am Task #3580 (Resolved): Update tests
Peter Amstutz
09:36 am Task #3657 (Resolved): Review 3147-pysdk-retries-wip
Tim Pierce
08:48 am Revision f1886a6d (arvados): 3036: Fix merge conflicts. One python sdk test still fails.
Peter Amstutz
01:41 am Revision 79577fec (arvados): Move styles out of tab partial. No issue #
Tom Clegg
01:29 am Revision 7e891a82 (arvados): Propagate query params to tab panes. No issue #
Tom Clegg
12:20 am Revision 70e7bc03 (arvados): Remove uuid-guessing code from "combine selected files". refs #3504
Tom Clegg

08/25/2014

11:51 pm Revision 37d93ae5 (arvados): Do not blow up in install stage when TASK_WORK is not set. No issue #
Tom Clegg
11:26 pm Revision 376149e7 (arvados): Do not blow up when tmp directory already exists. No issue #
Tom Clegg
11:16 pm Revision 82a77663 (arvados): Merge branch '3112-report-bug' into 3642-search-for-active-only
Radhika Chippada
11:16 pm Revision 3c12b612 (arvados): Merge branch '3112-report-bug' into 3620-admin-only-gear-menu
Radhika Chippada
11:12 pm Revision ea4e4e5e (arvados): 3112: alert left justification
Radhika Chippada
11:09 pm Revision 1da134ab (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
11:09 pm Story #3149: [Workbench] Workbench infinite scroll and filter system should do filtering on serve...
Peter Amstutz wrote:
> 3149-filter-any:
>
> * Documentation update adds @any@ as an example column but doesn't ex...
Tom Clegg
11:08 pm Story #3149: [Workbench] Workbench infinite scroll and filter system should do filtering on serve...
Peter Amstutz wrote:
> 3149-server-side-search:
>
> Usability notes about search. I realize not all of these (or...
Tom Clegg
04:07 pm Story #3149: [Workbench] Workbench infinite scroll and filter system should do filtering on serve...
3149-server-side-search:
Usability notes about search. I realize not all of these (or even most of them) are dire...
Peter Amstutz
02:45 pm Story #3149: [Workbench] Workbench infinite scroll and filter system should do filtering on serve...
3149-filter-any:
* Documentation update adds @any@ as an example column but doesn't explain that it has a special ...
Peter Amstutz
10:29 pm Revision 80f6898b (arvados): 3149: Clarify comments. Stick with a-b-c data keys where possible;
when not possible, explain why not. Tom Clegg
09:54 pm Task #3674 (Resolved): Review 3149-filter-any (improve filter support in API)
Tom Clegg
11:41 am Task #3674 (In Progress): Review 3149-filter-any (improve filter support in API)
Peter Amstutz
09:50 pm Revision eba617ba (arvados): Merge branch '3149-filter-any' refs #3149
Tom Clegg
09:49 pm Bug #3692 (Resolved): [API] Eventbus filters parameter should use implicit AND (like REST filters...
Tom Clegg
09:48 pm Revision a8247beb (arvados): 3149: Explain what "any" does as a filter attribute.
Tom Clegg
09:33 pm Revision 015be614 (arvados): Fix test fixtures breaking Workbench tests. refs #3171
Tom Clegg
09:26 pm Revision 8d9ccb40 (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
09:09 pm Bug #3147: [SDKs] Python clients should automatically retry failed API and Keep requests (includi...
Tim Pierce wrote:
> Two questions, one minor, one possibly significant:
>
> * sdk/python/arvados/keep.py
> ** Th...
Brett Smith
05:48 pm Bug #3147: [SDKs] Python clients should automatically retry failed API and Keep requests (includi...
Review at commit:dca92e4
The code review advice was really helpful here. Thanks for the summary. The testing here...
Tim Pierce
08:59 pm Revision f09b538f (arvados): Do not blow up when stdout!=subprocess.PIPE. no issue #
Tom Clegg
08:58 pm Revision a46654d0 (arvados): 3147: Fix unwanted integer division in KeepClient logs.
Brett Smith
08:58 pm Revision 5d1c61fc (arvados): 3147: Fixup KeepClient comments.
Per review. Brett Smith
08:45 pm Bug #3660 (Resolved): [Workbench] Project action buttons (add subproject, add data) should appear...
Applied in changeset arvados|commit:e4382e25d68a70a107baeb257e1915972759334c. Anonymous
11:34 am Bug #3660: [Workbench] Project action buttons (add subproject, add data) should appear when proje...
The first part of this comment is directly contradicted by the last part of this comment:... Peter Amstutz
08:41 pm Revision e4382e25 (arvados): Merge branch '3660-project-editable' closes #3660
Tom Clegg
08:41 pm Revision 6f86d636 (arvados): 3660: Clarify self-contradicting comment.
Tom Clegg
08:40 pm Story #3171 (Resolved): [API] Modify permission model to allow users to see a subset of other use...
Applied in changeset arvados|commit:437725d13f8775b29ad3e279a07b0bd4b7f8d098. Anonymous
01:14 pm Story #3171: [API] Modify permission model to allow users to see a subset of other users, accordi...
(I should update http://doc.arvados.org/api/permission-model.html) Tom Clegg
10:46 am Story #3171: [API] Modify permission model to allow users to see a subset of other users, accordi...
This is exactly why I wrote https://arvados.org/projects/arvados/wiki/Groups_Projects_Ownership_and_Permissions_Speci... Peter Amstutz
12:00 am Story #3171: [API] Modify permission model to allow users to see a subset of other users, accordi...
!Screenshot_from_2014-08-24_23_59_08.png! Tom Clegg
08:35 pm Task #3665 (Resolved): Review 3171-admin-groups
Tom Clegg
10:46 am Task #3665 (In Progress): Review 3171-admin-groups
Peter Amstutz
08:34 pm Revision 5596c93b (arvados): Update Gemfile.lock. refs #3405
Tom Clegg
08:24 pm Revision 437725d1 (arvados): Merge branch '3171-admin-groups' closes #3171
Tom Clegg
08:24 pm Revision 3c54f04e (arvados): Instead of munging TASK_WORK var, mkdir -p it (and therefore JOB_WORK)
in setup script.
Without this, scripts that write to arvados.current_job().tmpdir
(i.e., JOB_WORK) fail.
No issue #
Tom Clegg
07:31 pm Revision ebf95312 (arvados): Merge branch '3112-report-bug' into 3642-search-for-active-only
Radhika Chippada
07:30 pm Revision 4194cec3 (arvados): 3620: minor test update
Radhika Chippada
07:21 pm Revision e274983c (arvados): Merge branch '3112-report-bug' into 3620-admin-only-gear-menu
Radhika Chippada
07:19 pm Revision 9115746f (arvados): 3112: move manage account testing into its own file
Radhika Chippada
06:40 pm Bug #3691 (New): [Workbench] Suppress "ajax failed" error messages when ajax fails due to browser...
In fail callbacks, check @jqxhr.readyState@ and @status == 'abort'@ to determine whether the request was terminated b... Tom Clegg
05:44 pm Task #3690 (Resolved): Review 3642-search-for-active-only
Please compare against branch 3112-report-bug (in case you review it before I merge that branch into master). Thanks. Radhika Chippada
05:43 pm Task #3689 (Resolved): Review 3620-admin-only-gear-menu
Please compare against branch 3112-report-bug branch (in case you review it before I merge that branch into master). ... Radhika Chippada
05:37 pm Task #3608: Review branch: 3112-report-bug
Brett, if you want to take another look, all updated code is pushed to 3112 branch. Thanks. Radhika Chippada
05:35 pm Story #3112: [Workbench] "Report bug on this page" and "Show version detail" buttons on each work...
Brett, addressed pretty much all of your comments. Please see your feedback (#14) for my responses inline for each en... Radhika Chippada
04:03 pm Story #3112: [Workbench] "Report bug on this page" and "Show version detail" buttons on each work...
Reviewing commit:d0c85cb
* General style
** There are several references like @Rails.configuration.varname ? Rail...
Brett Smith
05:33 pm Revision f3b66f2d (arvados): Merge branch '3112-report-bug' into 3642-search-for-active-only
Radhika Chippada
05:32 pm Revision 29b8c0c6 (arvados): Merge branch '3112-report-bug' into 3620-admin-only-gear-menu
Radhika Chippada
05:20 pm Revision 7c91d696 (arvados): 3112: update issue report routes config and some other minor test up...
Radhika Chippada
04:53 pm Revision bd9ea502 (arvados): Do not blow up with pipeline has a plain value in a script_parameter...
Tom Clegg
04:52 pm Revision 59e8a18a (arvados): 3112: fix indentation
Radhika Chippada
04:51 pm Story #3036: [API] Use regular uuids instead of content hashes to identify collections
Peter Amstutz wrote:
> > * There's another story on this sprint (#2875) that adds description to PipelineInstance. H...
Tom Clegg
04:43 pm Story #3036: [API] Use regular uuids instead of content hashes to identify collections
I'm thinking about backing out the owner/name uniqueness for jobs and pipeline instances. It seems typical that the ... Peter Amstutz
04:37 pm Story #3036 (In Progress): [API] Use regular uuids instead of content hashes to identify collections
Peter Amstutz
04:43 pm Revision 3a435857 (arvados): 3112: add some space below the submit button and alert panel
Radhika Chippada
04:37 pm Bug #3136 (In Progress): [Crunch] Job state is stale in Workbench pipeline instance views, if the...
Peter Amstutz
12:34 pm Bug #3136: [Crunch] Job state is stale in Workbench pipeline instance views, if the job's state c...
Reviewing the quick Workbench fix at commit:aa0ae05... Brett Smith
04:29 pm Revision ff2e2d7b (arvados): Merge branch 'master' into 3036-collection-uuids
Conflicts:
sdk/python/arvados/commands/put.py
services/api/app/controllers/application_controller.rb
services/api/...
Peter Amstutz
04:25 pm Revision e8c9386f (arvados): 3112: minor cleanup
Radhika Chippada
04:10 pm Story #3504 (Resolved): [SDKs] Clients are compatible with #3036
Peter Amstutz
04:10 pm Task #3653 (Resolved): Review 3171-group-membership
Peter Amstutz
10:46 am Task #3653 (In Progress): Review 3171-group-membership
Peter Amstutz
04:07 pm Task #3675 (In Progress): Review 3149-server-side-search
Peter Amstutz
04:05 pm Bug #3688 (Closed): [API] User should be able to delete a project even though dependent logs exist
... Jonathan Sheffi
03:55 pm Feature #3686 (Resolved): [Workbench] Provide a sharing tab for repositories similar to setting u...
Peter Amstutz
02:41 pm Bug #3642 (In Progress): [Workbench] Search box should not be displayed in top-nav for non-active...
Radhika Chippada
02:37 pm Revision 4dbe0b01 (arvados): Merge branch '3112-report-bug' into 3620-admin-only-gear-menu
Radhika Chippada
02:37 pm Revision 0149f366 (arvados): Merge branch '3112-report-bug' into 3642-search-for-active-only
Radhika Chippada
02:36 pm Revision c6378b0e (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
02:32 pm Revision f792be9b (arvados): 3642: display search box in topnav only to active users
Radhika Chippada
02:16 pm Revision da34478c (arvados): Merge branch '3171-group-membership' refs #3171
Tom Clegg
02:15 pm Revision 7c2d7b25 (arvados): 3171: Merge branch 'master' into 3171-group-membership
Conflicts:
services/api/test/fixtures/links.yml
Tom Clegg
02:12 pm Revision 8516f7a5 (arvados): 3171: Fix wording, update docs.
Tom Clegg
02:01 pm Story #3620 (In Progress): [Workbench] Display system menu (gear menu) only to admin users.
Radhika Chippada
01:56 pm Revision d8b8e96f (arvados): 3620: display gear menu to admin users only. update the layout tests...
Radhika Chippada
01:35 pm Feature #3448 (Resolved): [Keep] storage server records (and reports in index) the timestamp of t...
Applied in changeset arvados|commit:94b5a59631f22e4e57561a6244c24b93db77f589. Tim Pierce
01:27 pm Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
LGTM, please merge.
Tim Pierce wrote:
> > Noticed this seems odd in the test case that returns 200 despite not de...
Tom Clegg
11:00 am Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
Updates at commit:cca1529:
Tom Clegg wrote:
>
> (I notice you used "e" instead of "err" here. Is there a reason...
Tim Pierce
01:33 pm Task #3683 (Resolved): Review 3448-keep-put-timestamps
Tim Pierce
12:00 pm Task #3683 (In Progress): Review 3448-keep-put-timestamps
Tom Clegg
12:00 pm Task #3683 (Resolved): Review 3448-keep-put-timestamps
Tom Clegg
01:32 pm Task #3647 (Resolved): Add timestamp support to PUT and DELETE
Tim Pierce
01:31 pm Revision 94b5a596 (arvados): Merge branch '3448-keep-put-timestamps'
Closes #3448. Tim Pierce
01:29 pm Revision 32e4350b (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
12:09 pm Revision b67cdc3c (arvados): 3112: minor update in application layout test
Radhika Chippada
12:04 pm Revision ffabe045 (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
12:02 pm Revision 4265203e (arvados): 3112: Move profile testing out of application_layout_test.rb into it...
Radhika Chippada
12:01 pm Task #3676 (In Progress): Review 3136-stale-pipeline-instance-display
Tom Clegg
09:24 am Task #3676 (Resolved): Review 3136-stale-pipeline-instance-display
Peter Amstutz
11:59 am Task #3657 (In Progress): Review 3147-pysdk-retries-wip
Tom Clegg
11:40 am Task #3682 (Resolved): Implement TrashCollector
The Keepstore TrashCollector is a module which recycles trashable blocks asynchronously. The interface is:
The Tra...
Tim Pierce
11:39 am Revision 14f130e6 (arvados): Do not blow up in crunch-dispatch.rb: do not pass --jobs and --pipel...
arguments to Rails.
no issue #
Ward Vandewege
11:29 am Revision dac7b05f (arvados): Do not blow up in crunch-dispatch: fix syntax error. Ouch.
no issue # Ward Vandewege
11:25 am Task #3681 (Resolved): Truncate project description display in dashboard at the first textile lin...
Radhika Chippada
11:24 am Task #3680 (Resolved): Update project description display in dashboard to display textile formatt...
Once #3354 branch is merged, the project description in the dashboard should display the formatted description rather... Radhika Chippada
11:21 am Task #3679 (Resolved): Implement TrashHandler
A "PUT /trash" HTTP request should be routed to a TrashHandler:
* The TrashHandler should make sure the request co...
Tim Pierce
11:13 am Revision 245a1c2e (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
10:52 am Story #3354: [Workbench] Render description attributes as textile
Added a few integration tests to test the textile description for projects. Radhika Chippada
10:47 am Task #3667 (In Progress): Review 3660-project-editable
Peter Amstutz
10:40 am Revision cca1529c (arvados): 3448: update tests with "untouchable" volumes
Added a "Touchable" flag to MockVolume, so that we can test that
PutBlock does the right thing when Touch fails. Pre...
Tim Pierce
10:40 am Revision c28604e8 (arvados): 3354: add integration tests verify textile descriptions for projects
Radhika Chippada
10:16 am Revision 952db4ab (arvados): Merge branch 'multiple-dispatch' no issue #
Tom Clegg
10:16 am Task #3678 (Resolved): Review multiple-dispatch
Ward Vandewege
10:05 am Task #3678 (Resolved): Review multiple-dispatch
Tom Clegg
10:05 am Revision c685ee1c (arvados): crunch-dispatch can run --jobs, --pipelines, or both.
Tom Clegg
09:58 am Bug #3627: [Workbench] Projects that are writable, but have root owner != current_user, cannot be...
UI changes in this branch LGTM, but since it depends on 3660 I'm going to wait until that is merged to ok this branch. Ward Vandewege
09:58 am Task #3670 (In Progress): Review 3627-selectable-projects
Ward Vandewege
09:23 am Task #3327 (In Progress): Fix workbench display to only use the actual jobs and ignore denormaliz...
Peter Amstutz
09:23 am Revision aa0ae05d (arvados): 3136: Fetch actual job objects for use in rendering pipeline jobs.
Peter Amstutz
08:57 am Bug #3649: [Crunch] 'Pipeline_instances' page shows job running when it has failed
Duplicate of #3136 Peter Amstutz
08:51 am Revision a0b0947b (arvados): With new apiserver, after upload, arv-put prints portable data hash ...
collection uuid for compatibility with crunch. refs #3504 Peter Amstutz

08/24/2014

11:43 pm Revision 8dcb4daa (arvados): 3149: Propagate filters from remote->dialog->infinite. Fix tests.
Tom Clegg
10:46 pm Story #3149 (In Progress): [Workbench] Workbench infinite scroll and filter system should do filt...
Tom Clegg
10:43 pm Task #3675 (Resolved): Review 3149-server-side-search
Depends on 3149-filter-any branch. Tom Clegg
10:42 pm Task #3674 (Resolved): Review 3149-filter-any (improve filter support in API)
Tom Clegg
10:40 pm Revision 1a1abfc1 (arvados): 3149: Do not blow up on small devices/windows.
Tom Clegg
10:24 pm Revision b04f78ea (arvados): 3149: Do not preload results in search dialog. Let infinite scroll d...
Tom Clegg
10:24 pm Revision d12257e9 (arvados): 3149: Fix infinite scroll not updating after retry/refresh.
Tom Clegg
10:24 pm Revision c5f356f0 (arvados): 3149: Fix user-controlled filters overwriting page-controlled filters.
Tom Clegg
09:54 pm Revision c3371825 (arvados): 3149: Untabify.
Tom Clegg
09:54 pm Revision 846abbca (arvados): 3149: Propagate search string to Workbench server using filters param.
Tom Clegg
09:54 pm Revision cce04610 (arvados): 3149: Let Workbench server do all the filtering where infinite-scrol...
Tom Clegg
09:50 pm Revision 482e452a (arvados): 3149: Fix operator precedence in SQL statements built from record_fi...
Tom Clegg
09:36 pm Revision dca0abdb (arvados): 3149: Support "ilike" operator in record_filters.
Tom Clegg
08:32 pm Story #3354: [Workbench] Render description attributes as textile
A few of my observations as I experimented with this branch (in preparation to address Tom's request to add a test or... Radhika Chippada
01:24 pm Story #3354: [Workbench] Render description attributes as textile
I believe I've fixed the bug you identified Tom, and pushed the changes but, frustratingly, I am having trouble getti... Phil Hodgson
08:28 pm Task #3673 (Resolved): Clear results and refresh from server if search query is dirty and idle fo...
Tom Clegg
06:49 pm Task #3673 (In Progress): Clear results and refresh from server if search query is dirty and idle...
Tom Clegg
05:19 pm Task #3673 (Resolved): Clear results and refresh from server if search query is dirty and idle fo...
Tom Clegg
08:24 pm Revision 4c8a8c8d (arvados): 3149: Support "any" and array in filter "column" element.
Tom Clegg
06:55 pm Revision d0c85cb8 (arvados): Merge branch 'master' into 3112-report-bug
Conflicts:
services/api/config/application.default.yml
Radhika Chippada
06:45 pm Task #3672 (Resolved): Propagate search query from workbench to api server
Tom Clegg
05:40 pm Task #3672 (In Progress): Propagate search query from workbench to api server
Tom Clegg
05:18 pm Task #3672 (Resolved): Propagate search query from workbench to api server
Tom Clegg
06:30 pm Story #3153 (Resolved): [API] Configuration option to automatically set up users (VM, repository,...
Applied in changeset arvados|commit:d36525cf0f67b35e9f59a3481a3739f9ebffae29. Radhika Chippada
04:28 pm Story #3153: [API] Configuration option to automatically set up users (VM, repository, invite)
Looks good, please merge.
Thanks!
Tom Clegg
06:07 pm Revision 1ee96f5e (arvados): closes #3153
Merge branch '3153-auto-setup-user' Radhika Chippada
06:06 pm Revision df706aa3 (arvados): 3153: update the newly added vm login link to not point to the "acti...
Radhika Chippada
05:40 pm Task #3671 (Resolved): Propagate search query to workbench when requesting rows in infinite scroll
Tom Clegg
05:19 pm Task #3671 (In Progress): Propagate search query to workbench when requesting rows in infinite sc...
Tom Clegg
05:17 pm Task #3671 (Resolved): Propagate search query to workbench when requesting rows in infinite scroll
Tom Clegg
05:15 pm Revision d36525cf (arvados): closes #3153
Merge branch '3153-auto-setup-user' Radhika Chippada
05:14 pm Revision 2ba51ef3 (arvados): Merge branch 'master' into 3153-auto-setup-user
Radhika Chippada
04:28 pm Task #3643 (Resolved): Review branch: 3153-auto-setup-user
Tom Clegg
04:24 pm Task #3670 (Resolved): Review 3627-selectable-projects
Note: reported bugfix is actually in 3660. Tom Clegg
04:24 pm Task #3669 (Resolved): Grey out unselectable projects in the chooser
Tom Clegg
02:57 pm Task #3669 (In Progress): Grey out unselectable projects in the chooser
Tom Clegg
04:24 pm Revision d95bc29a (arvados): 3627: Add hover highlight to Home project on dashboard.
Tom Clegg
04:19 pm Revision f45666be (arvados): 3627: Really make Home project selectable in project chooser.
Tom Clegg
04:11 pm Revision 12d4dfd4 (arvados): 3627: More consistent icons/headings in projects dropdown and chooser.
Tom Clegg
04:10 pm Revision 0b7ca85a (arvados): 3627: Grey out unselectable projects in chooser.
Tom Clegg
04:05 pm Revision a77dee1d (arvados): Fix user agreements page when no signatures needed. Add tests. No is...
Tom Clegg
02:57 pm Task #3575 (Resolved): [Workbench] "Home" project should have hover highlight like other projects
Tom Clegg
02:57 pm Revision 4dc0af33 (arvados): 3627: "My Projects" is now called "Home" and is always selectable in...
Tom Clegg
02:38 pm Bug #3627 (In Progress): [Workbench] Projects that are writable, but have root owner != current_u...
Tom Clegg
02:35 pm Revision 3c013388 (arvados): Fix disabled Continue button on user agreements page. No issue #
Tom Clegg
01:08 pm Revision 59b7bfcd (arvados): 3354: ordinary Textile link markup was no longer working - fixed by ...
Phil Hodgson
01:07 pm Revision 179ba8f1 (arvados): 3354: Rename render_content_from_database helper to render_markup, a...
Phil Hodgson
11:49 am Revision dca92e41 (arvados): 3147: Fixup KeepClient's RetryLoop use.
Switch to RetryLoop, and use the loop end logic better. Brett Smith
11:43 am Revision 4f749c94 (arvados): 3147: Fixup RetryLoop.
Having HTTPRetryLoop separate is unnecessary. Brett Smith
08:31 am Revision 661d0cfa (arvados): 3112: trailing white space
Radhika Chippada
08:11 am Revision 8a10f2ec (arvados): 3112: report issue success event handling working in 404 error page.
Radhika Chippada
12:12 am Revision 8cc7bf36 (arvados): 3112: update report_issue.js to confine event handling to report iss...
Radhika Chippada

08/23/2014

09:20 pm Task #3669 (Resolved): Grey out unselectable projects in the chooser
Tom Clegg
09:20 pm Task #3668 (Resolved): Confirm fixed by 3660 branch
Tom Clegg
09:20 pm Task #3668 (Resolved): Confirm fixed by 3660 branch
Tom Clegg
09:18 pm Task #3667 (Resolved): Review 3660-project-editable
Tom Clegg
09:18 pm Task #3666 (Resolved): Fix "is it editable?" detection for top buttons on project page
Tom Clegg
08:04 pm Task #3666 (In Progress): Fix "is it editable?" detection for top buttons on project page
Tom Clegg
08:04 pm Task #3666 (Resolved): Fix "is it editable?" detection for top buttons on project page
Tom Clegg
09:14 pm Revision ef3a7bc7 (arvados): 3660: Show add/run buttons if project is writable.
Hide move/delete buttons if move is impossible. Tom Clegg
08:03 pm Task #3565 (Resolved): Implement admin "add user to group" and "create/rename groups" interface
Tom Clegg
05:08 pm Task #3565 (In Progress): Implement admin "add user to group" and "create/rename groups" interface
Tom Clegg
08:03 pm Task #3665 (Resolved): Review 3171-admin-groups
Tom Clegg
08:02 pm Bug #3660 (In Progress): [Workbench] Project action buttons (add subproject, add data) should app...
Tom Clegg
08:00 pm Revision 050e18ef (arvados): 3171: Add administrator UI for toggling user<->role permissions.
Tom Clegg
06:22 pm Revision 12dd8631 (arvados): Merge branch 'master' into 3153-auto-setup-user
Radhika Chippada
05:06 pm Task #3564 (Resolved): Design appropriate "join group" interface
Tom Clegg
04:13 pm Bug #3663 (Resolved): [SDKs] Python CollectionReader should return at least one byte to caller pe...
The manifest format makes it possible to describe a single file consisting of a small amount of data from each of man... Tom Clegg
03:32 pm Revision b9020f29 (arvados): 3153: minor test updates: rename the variable "active_recipients" as...
Radhika Chippada
03:23 pm Story #3153: [API] Configuration option to automatically set up users (VM, repository, invite)
I also went back and tested Ward's theory that only one message is available during the test run. This is not true. W... Radhika Chippada
11:35 am Story #3153: [API] Configuration option to automatically set up users (VM, repository, invite)
Tom:
1. "use the existing setup_repo_vm_links method instead of replicating its functionality" : Yes, you are righ...
Radhika Chippada
03:17 pm Revision 9bb0d767 (arvados): 3153: update tests to look for new user created message also when an...
Radhika Chippada
01:19 pm Revision a39032f9 (arvados): 3153: when new_users_are_active config param is set, even blackliste...
Radhika Chippada
11:07 am Revision 523627b6 (arvados): Merge branch '3153-auto-setup-tests' into 3153-auto-setup-user
Radhika Chippada
11:00 am Revision 33b9b5e6 (arvados): 3153: change variable name in test from valid_username to ok_to_auto...
Radhika Chippada
10:50 am Revision 38f75fbc (arvados): 3153: directly invoke setup method during auto-setup
Radhika Chippada

08/22/2014

11:04 pm Story #3153: [API] Configuration option to automatically set up users (VM, repository, invite)
In services/api/app/models/user.rb would it be better to set ... Tom Clegg
04:17 pm Story #3153: [API] Configuration option to automatically set up users (VM, repository, invite)
Tom, I see your logic for generating unique username now. Reverted my while loop with count. Reassigning the review t... Radhika Chippada
10:46 pm Revision 195c3401 (arvados): 3153: Add integration tests.
Tom Clegg
07:08 pm Story #3661 (Resolved): [Workbench] Add "Move" and "Copy" buttons to top of #show page for every ...
Tom Clegg
06:49 pm Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
Noticed this seems odd in the test case that returns 200 despite not deleting any data. Shouldn't we expect copies_de... Tom Clegg
05:33 pm Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
Tim Pierce wrote:
> > I think @func (v *UnixVolume) Delete@ in @volume_unix.go@ is still missing its error checking ...
Tom Clegg
01:57 pm Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
at commit:c15f086:
Tom Clegg wrote:
> Tim Pierce wrote:
> > Updated with error checking. Also added a rudimenta...
Tim Pierce
11:06 am Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
Tim Pierce wrote:
> Updated with error checking. Also added a rudimentary unit test case to TestDeleteHandler.
L...
Tom Clegg
06:37 pm Bug #3660 (Resolved): [Workbench] Project action buttons (add subproject, add data) should appear...
Tom Clegg
06:11 pm Story #3354: [Workbench] Render description attributes as textile
Radhika also pointed out that we should provide some hint to the user that it's possible to use Textile here. Perhaps... Tom Clegg
06:09 pm Story #3354: [Workbench] Render description attributes as textile
Just noticed the regular hyperlink style doesn't seem to work. Is this caused by the Arvados UUID link feature, or so... Tom Clegg
05:04 pm Task #3608: Review branch: 3112-report-bug
Please take another look. Except for confining event handling to modal window, all the rest of your comments / sugges... Radhika Chippada
05:03 pm Story #3112: [Workbench] "Report bug on this page" and "Show version detail" buttons on each work...
Tom, addressed all your comments. Please take another look. Thanks. Radhika Chippada
04:59 pm Story #3036 (New): [API] Use regular uuids instead of content hashes to identify collections
Tom Clegg wrote:
> At commit:d08c3a5...
>
> @sdk/python/arvados/commands/put.py@
> * I think it would be neater ...
Peter Amstutz
04:51 pm Revision ed949940 (arvados): Accomodate otherwise valid user-supplied portable data hashes with n...
hint, as provided by crunch. Peter Amstutz
04:38 pm Task #3659 (Resolved): arv-put exposes retry support
Probably through a simple @--retries@ switch. Brett Smith
04:37 pm Task #3658 (Resolved): PySDK Collection classes expose retry support
Brett Smith
04:35 pm Bug #3147: [SDKs] Python clients should automatically retry failed API and Keep requests (includi...
3147-pysdk-retries-wip is up for review. This adds retry support to KeepClient, which is the lowest-level part of th... Brett Smith
04:31 pm Task #3657 (Resolved): Review 3147-pysdk-retries-wip
Brett Smith
04:30 pm Revision 5632bb3b (arvados): 3147: Remove old Keep signing support from Python SDK.
Per Tom. Brett Smith
04:30 pm Revision 66eb1f64 (arvados): 3147: Add retry support to Python SDK's KeepClient.
Brett Smith
04:30 pm Revision aead1339 (arvados): 3147: Add check_http_response_success to Python SDK.
Other parts of the SDK need to end loops based on the result of an
HTTP request. This function puts that logic in on...
Brett Smith
04:30 pm Revision 3e24c544 (arvados): 3147: Move fake Python HTTP response generation to arvados_testutil.
Other tests can use this functionality. Brett Smith
04:30 pm Revision a4359d15 (arvados): 3147: Add RetryLoop to the Python SDK.
This provides a general-purpose mechanism for us to retry all kinds of
operations.
Brett Smith
04:30 pm Revision 51334e82 (arvados): 3147: Add HTTPRetryLoop to the Python SDK.
Brett Smith
04:22 pm Revision 3f94855e (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
04:17 pm Task #3643: Review branch: 3153-auto-setup-user
Updated unique username logic per your suggestion. Please take another look. Thanks. Radhika Chippada
04:14 pm Revision 8f46cb4a (arvados): Merge branch 'master' into 3036-collection-uuids
Peter Amstutz
04:13 pm Task #3623 (Resolved): Review branch: 3188-remove-selected-button
Radhika Chippada
03:57 pm Task #3623 (In Progress): Review branch: 3188-remove-selected-button
Tom Clegg
04:10 pm Revision d68db5e4 (arvados): Reject empty fields in job creation filters. no issue #
Peter Amstutz
04:10 pm Bug #3183 (Resolved): [Workbench] In project view, when "Remove selected" button is used in the "...
Applied in changeset arvados|commit:db88e7487f1fca50e00c5fc004e67b922a41ad29. Radhika Chippada
04:03 pm Bug #3183: [Workbench] In project view, when "Remove selected" button is used in the "Selected" d...
LGTM, thanks. (But I noticed the branch is called 3188 but the story is 3183) Tom Clegg
04:09 pm Revision f5783fd9 (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
04:08 pm Revision db88e748 (arvados): closes #3183
Merge branch '3188-remove-selected-button' Radhika Chippada
04:05 pm Revision b6487d67 (arvados): Merge branch 'master' into 3188-remove-selected-button
Radhika Chippada
04:02 pm Revision c808c34d (arvados): 3153: fix the while loop logic.
Radhika Chippada
03:54 pm Revision 44064fd5 (arvados): Improve error checking a bit on find_commit_range for bad revisions ...
repositories. no issue # Peter Amstutz
03:51 pm Revision f1081424 (arvados): 3112: reload current location when error report modal is closing. ot...
Radhika Chippada
03:31 pm Revision 23ba171b (arvados): 3112: modal is shown by js
Radhika Chippada
03:22 pm Revision d85ec3b1 (arvados): Display first file in collection if name field is nil or empty. refs...
Peter Amstutz
02:45 pm Story #3656 (Resolved): [SDKs] "arv create object_type" should create a new object and then open ...
Tom Clegg
02:42 pm Task #3655 (Resolved): [SDKs] "arv edit" should not fail just because some special attribute (whi...
Possible ways to improve:
* Do not include unchanged attributes in the "update" API call.
** This fixes the bug onl...
Tom Clegg
02:23 pm Bug #3098 (Rejected): arv-mount refers to projects as "groups", doesn't mount the root group, doe...
duplicate of #3644 Tom Clegg
01:59 pm Revision 68c3fbc9 (arvados): Change 'expire_time' column to 'expires_at' for consistency with oth...
columns. Peter Amstutz
01:56 pm Revision 0bbd1138 (arvados): Display first file in collection if name field is nil or empty. refs...
Peter Amstutz
01:52 pm Revision c15f0864 (arvados): 3448: unit tests, bug fixes
UnixVolume.Delete tests the return status of lockfile (oops, left out of
previous commit)
New unit/integration tests...
Tim Pierce
01:49 pm Revision a73e2817 (arvados): 3112: ajax event handling on form not working. reverting back to doc...
Radhika Chippada
01:39 pm Story #3654 (Resolved): [Workbench] Add "combine selected collections" and "combine selected file...
Tom Clegg
01:37 pm Story #3171 (In Progress): [API] Modify permission model to allow users to see a subset of other ...
Tom Clegg
01:25 pm Revision 4dd469c1 (arvados): Merge branch 'master' into 3036-collection-uuids
Peter Amstutz
01:21 pm Task #3653 (Resolved): Review 3171-group-membership
Tom Clegg
01:21 pm Task #3564 (In Progress): Design appropriate "join group" interface
Tom Clegg
01:21 pm Task #3563 (Resolved): Write tests
Tom Clegg
01:21 pm Task #3562 (Resolved): Change permission model
Tom Clegg
11:58 am Revision 5674ba0e (arvados): 3171: Do not use select param for database lookup during create/dest...
Tom Clegg
11:58 am Revision a3b9c187 (arvados): 3171: Skip find_object_by_uuid during :create action.
Tom Clegg
11:56 am Revision 62d9e76a (arvados): 3171: Add fixtures to make Workbench tests pass under new permission...
Tom Clegg
11:56 am Task #3631 (Resolved): Review 3504-clients-compatible-with-3036
Peter Amstutz
11:56 am Task #3507 (Resolved): Update clients to permit arvados uuids for Collections
Peter Amstutz
09:16 am Task #3507 (In Progress): Update clients to permit arvados uuids for Collections
Peter Amstutz
11:22 am Revision 12850612 (arvados): 3036: Move manifest_text validation into Collection model. Change
uuids_for_docker_image to find_all_for_docker_image which returns Collection
objects instead of uuids. Remove unused...
Peter Amstutz
11:14 am Revision d9cfb1a3 (arvados): 3153: when exsiting repository name or vm login link is used as user...
Radhika Chippada
11:09 am Revision 9624ed09 (arvados): 3153: when deriving unique name, look for all can_login links, not j...
Radhika Chippada
10:30 am Revision c005c5ab (arvados): Merge branch 'master' into 3153-auto-setup-user
Radhika Chippada
10:30 am Revision 1b4f261c (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
10:29 am Revision 7a27da09 (arvados): 3112: limit ajax event handling only to the report form
Radhika Chippada
09:58 am Revision 1966eff7 (arvados): Merge branch '3504-clients-compatible-with-3036' refs #3504
Peter Amstutz
09:44 am Story #3504: [SDKs] Clients are compatible with #3036
All that looks good, and I haven't found any further problems. Thanks! Tom Clegg
09:05 am Story #3504: [SDKs] Clients are compatible with #3036
commit:da8b740
# Removed tag rendering code from project rows.
# Merged a few small fixes from 3036
# Tests pass
Peter Amstutz
09:17 am Task #3580 (In Progress): Update tests
Peter Amstutz
09:16 am Task #3580 (Resolved): Update tests
Peter Amstutz
09:16 am Task #3509 (Resolved): Links to collections in workbench render the "name" field sensibly
Peter Amstutz
09:16 am Task #3579 (Resolved): Update test fixtures
Peter Amstutz
09:16 am Task #3581 (Resolved): Update workbench
Peter Amstutz
09:16 am Task #3578 (Resolved): Write db migration
Peter Amstutz
09:16 am Task #3503 (Resolved): Document intended behavior and design for projects, collections and permis...
Peter Amstutz
09:16 am Task #3502 (Resolved): Document expectations for content addressing
Peter Amstutz
09:15 am Task #3614 (Resolved): Review 3441-python-keep-log-level
Peter Amstutz
09:07 am Revision 86c4b60b (arvados): Merge remote-tracking branch 'remotes/origin/3504-clients-compatible...
Conflicts:
apps/workbench/app/views/projects/_show_contents_rows.html.erb
Peter Amstutz
08:48 am Revision cb07b236 (arvados): 3036: Always select "id" column unless distinct = true. Include uuid =
portable_data_hash when requesting collection by uuid. Changed test fixture
"owned_by_aproject_with_no_name" to be a...
Peter Amstutz
08:44 am Revision da8b7405 (arvados): 3504: Don't create stand-in "name" links for post #3036 apiserver
Peter Amstutz
08:44 am Revision 66e40806 (arvados): 3504: Support copy and moving collections on new apiserver
Peter Amstutz
08:42 am Revision fe76288c (arvados): 3504: Don't create stand-in "name" links for post #3036 apiserver
Peter Amstutz
08:35 am Revision e951b096 (arvados): 3504: Back out tags on project rows. Revisit in a later story.
Peter Amstutz

08/21/2014

11:14 pm Revision 3ef0016f (arvados): 3171: Update tests to conform to new permission behavior.
Obey "select" parameter during #show too, not just #index. Tom Clegg
08:16 pm Revision 42a27c7c (arvados): 3171: Do not follow permission graph through a User, unless permissi...
Tom Clegg
08:12 pm Revision 77954799 (arvados): 3171: Outdent giant "if ... else return self" construct.
Tom Clegg
07:15 pm Task #3562 (In Progress): Change permission model
Tom Clegg
07:00 pm Revision e386d206 (arvados): 3448: add error checking in volume.Touch()
Add error checking that was erroneously left out of previous commit.
Refs #3448.
Tim Pierce
06:54 pm Revision ce9c2266 (arvados): 3153: trailing white space
Radhika Chippada
06:40 pm Task #3652 (Resolved): Rewrite PullList as a BlockManager implementation
Keepstore should be able to fulfill a pull list asynchronously: once a pull list has been received, send it to a goro... Tim Pierce
06:26 pm Story #3651 (Resolved): Running programs from Keep
Currently there are three basic ways to run programs:
- Create a Docker image with your program installed and ru...
Abram Connelly
06:25 pm Task #3650 (Resolved): Implement PullHandler
The PullHandler should be called for any "PUT /pull" request.
It expects the request body to be a JSON object enco...
Tim Pierce
06:25 pm Revision 562a420a (arvados): 3153: return nil if no unique username can be derived from an email ...
Radhika Chippada
06:20 pm Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
Another issue to clarify: if keepstore tries every server on the list for a particular block, and every one of the se... Tim Pierce
06:01 pm Story #3414: [Keep] Keep Server accepts list of blocks to pull from other servers
In order for one keepstore to pull blocks from another keepstore, it will need to sign the locator. How can it do th... Tim Pierce
05:33 pm Bug #3147: [SDKs] Python clients should automatically retry failed API and Keep requests (includi...
This story has an interesting interaction with Keep GET requests. The SDK's current algorithm for that is: Make a li... Brett Smith
05:14 pm Story #3504: [SDKs] Clients are compatible with #3036
(If it's not already removed) I think this is obsolete now in projects.css.scss... Tom Clegg
04:54 pm Story #3504: [SDKs] Clients are compatible with #3036
At commit:73bbd41...
* The "add tag" button doesn't actually work on the projects#show&rarr;collections tab. I thi...
Tom Clegg
03:11 pm Story #3504: [SDKs] Clients are compatible with #3036
Tom Clegg wrote:
> The changes to the links view etc. are harmless, I'm just asking for the following change, to a...
Peter Amstutz
02:07 pm Story #3504: [SDKs] Clients are compatible with #3036
Peter Amstutz wrote:
> Agreed that the links index page is not very nice. However I'm going to leave the code it be...
Tom Clegg
12:07 pm Story #3504: [SDKs] Clients are compatible with #3036
Tom Clegg wrote:
> At commit:2769713
>
> Workbench
> * Reviving tags might be a good idea in general but please ...
Peter Amstutz
05:11 pm Revision a9c59725 (arvados): 3036: Most workbench tests pass.
Peter Amstutz
05:10 pm Revision 5d651aff (arvados): 3504: Support copy and moving collections on new apiserver
Peter Amstutz
04:50 pm Revision 1acc76ca (arvados): 3112: change submit button text
Radhika Chippada
04:46 pm Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
Updated at commit:e386d20
Tom Clegg wrote:
> Looking at commit:dc2bf5c
>
> This looks much closer, thanks.
> ...
Tim Pierce
04:32 pm Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
Looking at commit:dc2bf5c
This looks much closer, thanks.
Noticed a couple of things
* Need error checking on ...
Tom Clegg
04:15 pm Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
Tim Pierce wrote:
> > * "GetBlock() in handlers.go should accept an additional argument indicating whether it should...
Tom Clegg
03:34 pm Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
Ready for another look: commit:dc2bf5c
Tom Clegg wrote:
> At commit:56d36387
>
> In handlers.go, we call GetBl...
Tim Pierce
02:39 pm Feature #3448: [Keep] storage server records (and reports in index) the timestamp of the most rec...
At commit:56d36387
In handlers.go, we call GetBlock(), which walks through some/all of the volumes looking for the...
Tom Clegg
02:11 pm Feature #3448 (In Progress): [Keep] storage server records (and reports in index) the timestamp o...
Tim Pierce
04:43 pm Revision 3616a539 (arvados): 3448: add error checking
Code review comments in https://arvados.org/issues/3448#note-9
* volume.Touch() must fail if the file cannot be lock...
Tim Pierce
04:33 pm Revision 1080ec93 (arvados): 3448: unit tests for deleting new blocks
Added cases to TestDeleteHandler to test that blocks newer than
-permission_ttl will not be removed from the volume e...
Tim Pierce
04:22 pm Revision cdb8b00d (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
04:15 pm Story #3153: [API] Configuration option to automatically set up users (VM, repository, invite)
Went ahead and added the loop counter with 10000 iterations. Please do let me know if you have any suggestions about ... Radhika Chippada
03:18 pm Story #3153: [API] Configuration option to automatically set up users (VM, repository, invite)
Tom, all suggestions are applied. Please take another look.
I have one concern about deriving unique username. Ass...
Radhika Chippada
04:00 pm Revision 043ff05c (arvados-dev): Declare empty variables up top to avoid bash parsing errors. no...
Peter Amstutz
04:00 pm Revision 043ff05c (arvados): Declare empty variables up top to avoid bash parsing errors. no iss...
Peter Amstutz
03:55 pm Revision dc2bf5c8 (arvados): 3448: code review comments.
Extend GetBlock() to optionally update the file modification time, so
PUT operations can update the timestamp of an e...
Tim Pierce
03:43 pm Revision c5ec75ee (arvados): 3153: use loop with counter than while(true) to derive unique username
Radhika Chippada
03:20 pm Bug #3649 (Rejected): [Crunch] 'Pipeline_instances' page shows job running when it has failed
I believe I cancelled the second and last job (but I can't quite remember, sorry) in the pipeline qr1hi-d1hrv-aa011c9... Abram Connelly
03:09 pm Revision 73bbd418 (arvados): 3504: Remove link to links index page on tags. Add comment to
CollectionsController#choose. Adjust column width in collections file table. Peter Amstutz
03:08 pm Revision 48956dad (arvados): 3504: Remove link to links index page on tags. Add comment to
CollectionsController#choose. Adjust column width in collections file table. Peter Amstutz
02:52 pm Revision 1f438358 (arvados): 3153: update tests to check for existing repo name
Radhika Chippada
02:49 pm Revision a3a84c13 (arvados): 3504: Don't set owner_uuid redundantly.
Peter Amstutz
02:45 pm Revision a131e0cc (arvados): 3036: Use preload_objects to fetch owner_uuids in the controller ins...
Peter Amstutz
02:44 pm Revision 5b7762f1 (arvados): 3036: Use preload_objects to fetch owner_uuids in the controller ins...
Peter Amstutz
02:25 pm Revision 12e80e52 (arvados): 3448: minor bugfixes
Refs #3448. Tim Pierce
02:21 pm Revision d7e56bd7 (arvados): Permit setting environment variables on command line. Added workben...
apiserver_test and cli_test variables to provide parameters to the respective
rake tests. no issue #
Peter Amstutz
02:21 pm Revision d7e56bd7 (arvados-dev): Permit setting environment variables on command line. Added wor...
apiserver_test and cli_test variables to provide parameters to the respective
rake tests. no issue #
Peter Amstutz
02:11 pm Task #3647 (In Progress): Add timestamp support to PUT and DELETE
Tim Pierce
02:11 pm Task #3647 (Resolved): Add timestamp support to PUT and DELETE
* PUT requests should update the modification time of a block on success. (The Volume interface should provide a volu... Tim Pierce
02:10 pm Revision 754d8543 (arvados): 3171: Add tests for desired behavior. Start using FactoryGirl.
Tom Clegg
02:06 pm Story #3646 (New): [Workbench] Toggle enable_job_reuse flag using pipeline instance show/edit/run...
Tom Clegg
01:56 pm Revision 0a658f81 (arvados): 3153: username regexp is updated
Radhika Chippada
01:55 pm Revision 56d36387 (arvados): 3448: check block timestamp before DELETE
volume.Delete locks the target file and checks the timestamp before
proceeding. If the file is newer than permission_...
Tim Pierce
01:23 pm Revision 0b10fae7 (arvados): Be smarter about cleanup in crunch-job after a job finishes. This sh...
resolve the problem of the many leftover stale mount points.
no issue #
Ward Vandewege
01:21 pm Revision 1e30d46f (arvados): Merge branch 'master' into 3153-auto-setup-user
Radhika Chippada
01:19 pm Revision 7153f887 (arvados): 3153: update regexp, email message
Radhika Chippada
12:13 pm Revision 6403b872 (arvados): Merge remote-tracking branch 'refs/remotes/origin/3504-clients-compa...
Conflicts:
sdk/python/arvados/commands/put.py
sdk/python/tests/test_arv_put.py
Peter Amstutz
12:13 pm Revision 112d4229 (arvados): 3504: Set owner_uuid when creating collection (will set owner_uuid o...
on old apiserver, and set owner of collection object directly on new
apiserver.)
Peter Amstutz
11:39 am Revision e8670f2a (arvados): 3504: Set the capybara driver explicitly so tests pass again.
Peter Amstutz
11:04 am Revision f16be173 (arvados): Merge remote-tracking branch 'origin/master' into 3504-clients-compa...
Peter Amstutz
11:03 am Revision 897e6cc8 (arvados): 3504: Fixed preload_links_for_objects to use @objects.to_a. Fix col...
page to restore link names. Remove obsolete tests for "persist" button. Tweak
pipeline instance tests.
Peter Amstutz

08/20/2014

10:08 pm Revision 953f5e01 (arvados): Merge branch 'master' into 3153-auto-setup-user
Radhika Chippada
10:06 pm Revision 1e7906c1 (arvados): 3112: move ajax event handling into a separate js file
Radhika Chippada
07:53 pm Task #3563 (In Progress): Write tests
Tom Clegg
07:44 pm Bug #3441 (Resolved): [SDKs] arv-put (if not in debug mode) should not print an error message whe...
Tom Clegg
07:34 pm Bug #3645 (Resolved): [Keep] Rename -permission-key-file to -blob-signing-key-file for clarity an...
Tom Clegg
07:21 pm Revision 327681d1 (arvados-dev): Unset ARVADOS_ variable from the environment before running test...
Peter Amstutz
07:21 pm Revision 327681d1 (arvados): Unset ARVADOS_ variable from the environment before running tests. ...
Peter Amstutz
07:18 pm Story #3153: [API] Configuration option to automatically set up users (VM, repository, invite)
At commit:347d974...
@services/api/app/models/user.rb@
* In @auto_setup_new_user@, check @Rails.configuration.aut...
Tom Clegg
06:38 pm Revision 63fedb56 (arvados): 3112: use jquery syntax for find buttons
Radhika Chippada
05:37 pm Revision 28d5074c (arvados): 3112: and it would help if that said partial is committed :)
Radhika Chippada
05:26 pm Revision ecc16570 (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
05:23 pm Revision 45f82943 (arvados): 3112: use partial to report error
Radhika Chippada
05:17 pm Task #3643 (In Progress): Review branch: 3153-auto-setup-user
Tom Clegg
03:47 pm Task #3643 (Resolved): Review branch: 3153-auto-setup-user
Branch ready for review. Radhika Chippada
05:10 pm Revision 7c78bea1 (arvados): 3504: Use preload_links_for_objects in projects_controller. Use
self[:portable_data_hash] in collection.rb to avoid recursive definition of
.uuid and .portable_data_hash. Revert ch...
Peter Amstutz
04:42 pm Revision 96fefe23 (arvados): Fix run_test_server Keep blob filename handling.
No issue #. Brett Smith
04:33 pm Revision c732e3d3 (arvados): 3504: CollectionReader accepts arvados object collection uuids. 'ar...
owner_uuid when collection is created. Fixed indentation. Peter Amstutz
04:18 pm Revision e8566e29 (arvados): 3036: Fix arv-put to write name/owner of collections object directly...
'name' field is present on the returned object. Python SDK tests pass. Peter Amstutz
04:15 pm Revision b9eb0404 (arvados): 3036: Commented out failing FUSE tests. Fixed uuids on fixtures to ...
prefix. Made events.py less noisy. Peter Amstutz
04:11 pm Bug #3644 (Resolved): [SDK] Fix arv-mount --tags and --groups modes to handle "home" project and ...
See notes from Brett.
Possible hierarchy:...
Peter Amstutz
04:08 pm Revision 9beaaf14 (arvados): 2800: run_test_server only uses tests/tmp for real Python tests.
tests/tmp is not available for Go tests.
This fixes a bug introduced in da01d7e1.
No issue #.
Brett Smith
04:05 pm Revision cf9e7751 (arvados): Update "standard objects" page to reflect change from keep_disks to
keep_services, and add some sanity checks. No issue # Tom Clegg
03:54 pm Revision 3e443d57 (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
03:51 pm Revision 17f836f3 (arvados): Add libpcre3-dev dependency. Sort package names in apt-get install c...
No issue # Tom Clegg
03:33 pm Revision 347d974a (arvados): Merge branch 'master' into 3153-auto-setup-user
Radhika Chippada
03:29 pm Revision 518d15a5 (arvados): 3153: update the new user email to include a phrase saying the user ...
Radhika Chippada
03:12 pm Revision 8598092d (arvados): 2800: Delay API client creation in Python CollectionReader.
This more closely matches prior behavior, and is necessary to make the
Keep tests pass. See included comments for de...
Brett Smith
03:04 pm Revision 5d8e0b2c (arvados): Treat success=true exitcode!=0 as success when collating output,
just like we did when we decided the task completed. No issue # Tom Clegg
02:36 pm Revision a44040a0 (arvados): 3153: tests with duplicate username
Radhika Chippada
02:20 pm Task #3639 (Resolved): Review 2800-pysdk-no-global-keep-client-wip
Applied in changeset arvados|commit:05bea2c50474edeb9d0e3fb8daaf838b58ea9a54. Brett Smith
09:55 am Task #3639 (Resolved): Review 2800-pysdk-no-global-keep-client-wip
Brett Smith
02:20 pm Bug #2800 (Resolved): [Crunch] Remove global state in Python SDK
Applied in changeset arvados|commit:05bea2c50474edeb9d0e3fb8daaf838b58ea9a54. Brett Smith
09:55 am Bug #2800: [Crunch] Remove global state in Python SDK
2800-pysdk-no-global-keep-client-wip is up for review to deprecate the global Keep client. Brett Smith
02:18 pm Revision 05bea2c5 (arvados): Merge branch '2800-pysdk-no-global-keep-client-wip'
Closes #2800, #3639. Brett Smith
02:18 pm Revision 40d92dda (arvados): 2800: Use local KeepClients in Python SDK tests.
This improves test isolation, and demonstrates the preferred way to
use the API.
Brett Smith
02:18 pm Revision f05bc096 (arvados): 2800: Remove global state from KeepClient.
This commit makes it possible to build and use a KeepClient that isn't
influenced by changes in outside state. Chang...
Brett Smith
02:18 pm Revision 1afe2c7b (arvados): 2800: Improve spec conformance of Python SDK KeepLocator.
* Require size to immediately follow digest.
* Accept all valid hints.
Brett Smith
02:18 pm Revision 327e1768 (arvados): 2800: Migrate from Keep to KeepClient in the Python SDK.
Brett Smith
02:18 pm Revision f6e6e018 (arvados): 2800: Introduce config.flag_is_true() to Python SDK.
Brett Smith
02:18 pm Revision da01d7e1 (arvados): 2800: Make run_test_server put Keep tempfiles in tests/tmp/.
Brett Smith
02:18 pm Revision e17db6aa (arvados): 2800: Use dedicated logger in Python SDK api module.
Brett Smith
02:18 pm Revision 3b9b5c14 (arvados): 2800: Introduce TestCaseWithServers to Python SDK.
This is a subclass of unittest.TestCase. It looks for specific class
variables to launch supporting Arvados servers ...
Brett Smith
02:09 pm Story #3036: [API] Use regular uuids instead of content hashes to identify collections
At commit:d08c3a5...
@sdk/python/arvados/commands/put.py@
* I think it would be neater to provide @owner_uuid@ up...
Tom Clegg
11:43 am Revision 78b4e097 (arvados): Merge branch 'master' into 3153-auto-setup-user
Radhika Chippada
11:40 am Revision 9074f3f3 (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
11:39 am Revision d3be53db (arvados): 3112: update config param names for report notification
Radhika Chippada
11:25 am Bug #3642 (Resolved): [Workbench] Search box should not be displayed in top-nav for non-active us...
Radhika Chippada
11:20 am Revision 35a3223e (arvados): Merge branch '3499-home-project-docs-wip'
Closes #3516. Refs #3499. Brett Smith
11:20 am Task #3516 (Resolved): Update docs
Applied in changeset arvados|commit:35a3223ee35279c04552d5d3d372998711a956ab. Brett Smith
11:19 am Story #3499: [Workbench] Objects owned directly by user are visible on a "home" project
Radhika Chippada wrote:
> - In the newly added selection image "workbench-move-selected.png", I think it would be mo...
Brett Smith
11:07 am Story #3499: [Workbench] Objects owned directly by user are visible on a "home" project
Brett, everything looks great now, but for the one concern below.
- In the newly added selection image "workbench-...
Radhika Chippada
10:33 am Story #3499: [Workbench] Objects owned directly by user are visible on a "home" project
Radhika,
All these suggestions are great. I've pushed a new commit to incorporate everything you suggested.
Ra...
Brett Smith
08:07 am Story #3499: [Workbench] Objects owned directly by user are visible on a "home" project
Review feed back for the 3499-doc branch:
1. api-tokens.html.textile.liquid
In the sentence “Click on the link ...
Radhika Chippada
11:18 am Revision 1a2947bd (arvados): 3499: Update Keep tutorial for recent UI changes.
Brett Smith
11:18 am Revision 57c56fea (arvados): 3499: Update pipeline tutorial for recent UI changes.
Brett Smith
11:18 am Revision 33755fab (arvados): 3499: Improve style consistency throughout docs.
* Capitalize Dashboard.
* Article use: "access Workbench," "access the Dashboard."
* Bold references to Workbench U...
Brett Smith
11:08 am Task #3611: Review 3499-home-project-docs-wip
Brett, added one last comment to the story. Thanks. Radhika Chippada
08:10 am Task #3611: Review 3499-home-project-docs-wip
Added review comments to the story. Radhika Chippada
10:51 am Revision e398326f (arvados): Merge branch 'master' into 3112-report-bug
Radhika Chippada
10:45 am Story #3640 (New): [SDKs] Add runtime option to SDKs (esp Python and arv-mount) to use a filesyst...
Background:
arv-mount has a block cache, which improves performance when the same blocks are read multiple times. ...
Tom Clegg
10:35 am Bug #3610 (Resolved): [Workbench] pipeline_instances#show's Components tab clobbers the websocket...
Applied in changeset arvados|commit:de3b2f9a31e7d6df9fb53fff149f5ee43d1664d0. Anonymous
10:10 am Bug #3610: [Workbench] pipeline_instances#show's Components tab clobbers the websocket log viewer...
LGTM, please merge. Ward Vandewege
10:32 am Revision 84027468 (arvados): 3499: First round of review updates.
Brett Smith
10:31 am Revision e824ef36 (arvados): Merge branch 'master' into 3112-report-bug. Also, break search testi...
Conflicts:
apps/workbench/app/controllers/application_controller.rb
apps/workbench/config/application.default.yml
...
Radhika Chippada
10:10 am Revision de3b2f9a (arvados): Merge branch '3610-pipeline-log-refresh' closes #3610
Tom Clegg
10:10 am Task #3636 (Resolved): Review 3610-pipeline-log-refresh
Ward Vandewege
09:55 am Task #3621 (Resolved): Review 2800-pgs branch
Brett Smith
09:49 am Bug #3638 (New): [Workbench] [Draft] When moving a job or pipeline between projects, outputs and ...
Tom Clegg
09:47 am Revision c84954c1 (arvados): 2800: Introduce TestCaseWithServers to Python SDK.
This is a subclass of unittest.TestCase. It looks for specific class
variables to launch supporting Arvados servers ...
Brett Smith
09:47 am Revision 5e303407 (arvados): 2800: Use dedicated logger in Python SDK api module.
Brett Smith
09:47 am Revision 4d716aad (arvados): 2800: Use local KeepClients in Python SDK tests.
This improves test isolation, and demonstrates the preferred way to
use the API.
Brett Smith
09:47 am Revision 13fe1f60 (arvados): 2800: Make run_test_server put Keep tempfiles in tests/tmp/.
Brett Smith
09:47 am Revision 4a2f470d (arvados): 2800: Migrate from Keep to KeepClient in the Python SDK.
Brett Smith
09:23 am Bug #3261: [Keep] arv-put fails if permission system is enabled
* Bug: CollectionWriter.finish() (as used by well-behaved crunch scripts, but not crunch-job) threw away its permissi... Tom Clegg
09:22 am Bug #3637 (Resolved): [Workbench] Add "copy" operation to selection dropdown on projects#show tab...
trying to move d0e8e7747e288e2778b25e70890e95cd+499 to project qr1hi-j7d0g-qhf708xb2s7cow2 didn't work. Bryan Cosca
09:04 am Revision a3222e35 (arvados): Merge branch 'master' into 3354-render-textile
Conflicts (resolved):
apps/workbench/app/controllers/application_controller.rb
Phil Hodgson
08:32 am Revision 7283c472 (arvados): 2800: Remove global state from KeepClient.
This commit makes it possible to build and use a KeepClient that isn't
influenced by changes in outside state. Chang...
Brett Smith

08/19/2014

10:10 pm Revision d08c3a56 (arvados): 3036: Fix arv-put to write name/owner of collections object directly...
'name' field is present on the returned object. Python SDK tests pass. Peter Amstutz
10:09 pm Revision 57d7ce9d (arvados): 3036: Fix #updating collection objects. Fixed database seed for emp...
Peter Amstutz
09:09 pm Task #3587 (Resolved): Review 3505-virtual-work-dir
Tom Clegg
09:00 pm Task #3636 (Resolved): Review 3610-pipeline-log-refresh
Tom Clegg
08:59 pm Task #3635 (Resolved): Stop clobbering live listener with tab-load event every time it hears an e...
Tom Clegg
08:59 pm Task #3635 (Resolved): Stop clobbering live listener with tab-load event every time it hears an e...
Tom Clegg
08:57 pm Revision e13874a4 (arvados): 3610: Move live log display into its own tab, avoid clobbering with ...
* PipelineInstances#show gets a Log tab dedicated to the live log
window, rather than hiding it below the component...
Tom Clegg
08:26 pm Revision 9336a8a8 (arvados): Fix failure detection for python tests. No issue #
Tom Clegg
08:26 pm Revision 9336a8a8 (arvados-dev): Fix failure detection for python tests. No issue #
Tom Clegg
07:09 pm Bug #3610 (In Progress): [Workbench] pipeline_instances#show's Components tab clobbers the websoc...
Tom Clegg
07:07 pm Bug #3634 (Resolved): [Workbench] Page content is the same as where you left it when navigating (...
Page content can be updated by Javascript and AJAX, but if it is, and one navigates away, and then uses the browser b... Tom Clegg
07:04 pm Revision 79df4374 (arvados-dev): Install py test deps even if py tests fail. Make docs skippable....
Tom Clegg
07:04 pm Revision 79df4374 (arvados): Install py test deps even if py tests fail. Make docs skippable. No ...
Tom Clegg
06:20 pm Story #3504: [SDKs] Clients are compatible with #3036
At commit:2769713
Workbench
* Reviving tags might be a good idea in general but please resist further creep in th...
Tom Clegg
05:58 pm Bug #3344 (Resolved): [Workbench] Cannot [figure out how to] rename a collection created by arv-p...
Sally reports in IRC that the fix in #3421 was sufficient. Brett Smith
05:32 pm Task #3611 (In Progress): Review 3499-home-project-docs-wip
Radhika Chippada
05:30 pm Revision 01463a6f (arvados): Merge branch 'master' into 3153-auto-setup-user
Radhika Chippada
05:29 pm Revision 171cb08d (arvados): 3153: auto-setup user during creation.
Radhika Chippada
03:29 pm Feature #3633 (Closed): [Workbench] Compare pipeline templates, similar to the existing pipeline ...
Ward Vandewege
02:22 pm Revision 346ebae2 (arvados): Merge branch 'skip-args'
no issue # Ward Vandewege
02:22 pm Revision 346ebae2 (arvados-dev): Merge branch 'skip-args'
no issue # Ward Vandewege
01:57 pm Revision 0bcd962d (arvados-dev): ssh-authkeys: update authkeys when keydir is present but empty
When ~/.gitolite/keydir is present but empty, and someone runs 'gitolite
trigger POST_COMPILE', gitolite does not cle...
Sitaram Chamarty
01:19 pm Revision cbe594f5 (arvados): 3036: Fix merge mistakes in collection_controller.
Peter Amstutz
11:37 am Revision b1942917 (arvados): 3036: Fixed migration to migrate modified_by_client_uuid and
modified_by_user_uuid (because modified_by isn't a column, whoops). Also fills
in in useless updated_at column becau...
Peter Amstutz
11:36 am Revision 1a0a58c4 (arvados): Merge branch 'master' into 3036-collection-uuids
Conflicts:
services/api/app/controllers/arvados/v1/collections_controller.rb
services/api/app/models/collection.rb
Peter Amstutz
11:08 am Task #3631 (In Progress): Review 3504-clients-compatible-with-3036
Tom Clegg
11:07 am Task #3631 (Resolved): Review 3504-clients-compatible-with-3036
Tom Clegg
11:08 am Task #3632 (In Progress): Review 3036-collection-uuids
Tom Clegg
11:07 am Task #3632 (Resolved): Review 3036-collection-uuids
Tom Clegg
11:07 am Revision 67c0a6e0 (arvados): 3036: Updated migration to set modified_at instead of updated_at, ad...
Peter Amstutz
11:05 am Revision 27697133 (arvados): Merge branch 'master' into 3504-clients-compatible-with-3036
Peter Amstutz
10:42 am Story #3112: [Workbench] "Report bug on this page" and "Show version detail" buttons on each work...
(continued)
* After a little more thought about the vertical space problem: perhaps all we need to do is put @over...
Tom Clegg
10:21 am Revision 1e243a79 (arvados): 2800: Introduce config.flag_is_true() to Python SDK.
Brett Smith
10:21 am Revision b56f5fa9 (arvados): 2800: Improve spec conformance of Python SDK KeepLocator.
* Require size to immediately follow digest.
* Accept all valid hints.
Brett Smith
09:40 am Revision 289e5d15 (arvados): 3504: Fix collection chooser. Fix generic link render to use uuid i...
else is available. Fix tags for objects other than collections. Peter Amstutz
08:54 am Bug #3629 (New): [Workbench] Display timestamps in user's local timezone using class="localized-t...
Most places in workbench display the raw timestamps from the database, which are stored in UTC. This is inconvenient... Peter Amstutz
 

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