Activity

From 04/06/2015 to 05/05/2015

05/05/2015

10:54 pm Bug #3843 (Resolved): [Crunchstat] Report CPU accounting numbers accurately.
Fixed by 3b0de2173e005deacc22d083a4aea23f9a648865 during #3826. Tom Clegg
09:16 pm Bug #5915 (Resolved): [Workbench] Sharing link for public collection still renders after sharing ...
To replicate: Go to https://workbench.qr1hi.arvadosapi.com/collections/download/qr1hi-4zz18-7zk4muy5grnaqpv/4qji0cfum... Nancy Ouyang
08:47 pm Bug #5913: [Workbench] Should validate that a job's repository actually exists before rendering t...
The pipeline failed because I gave the incorrect repository ('abram' as opposed to 'abram/gffpairwiseconcordance'). ... Abram Connelly
08:31 pm Bug #5913 (New): [Workbench] Should validate that a job's repository actually exists before rende...
When trying to access my repository @abram/gffpairwiseconcordance@ from pipeline su92l-d1hrv-ctxni10ap6vztks I get a ... Abram Connelly
08:37 pm Revision 2e270dde (sso-provider): 5829: Add missing erb partial for rendering buttons for links t...
service actions. Peter Amstutz
08:35 pm Revision 92e4fb52 (sso-provider): 5829: Redirect to :user_return_to after login.
Peter Amstutz
08:35 pm Story #5914 (New): [DRAFT] Provide one clear way for users to get data from an external source in...
h2. Background
Users frequently want to work with data available from public sites. It's important that it be eas...
Brett Smith
08:20 pm Feature #4456: [Workbench] Provide more feedback about when a queued job is likely to start.
Possible ways/places to present this information:
* Pipeline instance #show → Components
** If component state...
Tom Clegg
02:56 pm Feature #4456: [Workbench] Provide more feedback about when a queued job is likely to start.
Some system states that could be translated to a start-time prediction:
* All worker nodes are busy. Nodemanager wil...
Tom Clegg
08:10 pm Revision e3298ea0 (sso-provider): 5829: Add application.yml to .gitignore
Peter Amstutz
08:05 pm Revision 9cd526a5 (sso-provider): 5829: Committed application.yml by accident.
Peter Amstutz
08:03 pm Revision 4e2319ce (arvados): 4467: add "select all" and "unselect all" buttons to project contents.
Radhika Chippada
07:58 pm Revision 3f69ca6a (sso-provider): 5829: Registration and account management of built-in accounts ...
Peter Amstutz
07:45 pm Bug #5905: [SDKs] Improve certificate validation in Python SDK
I removed this recently (#5562) from source:sdk/python/arvados/keep.py in commit:7ab494e42b35b3769a326a16b7e90f1d2014... Tom Clegg
07:40 pm Feature #5735 (Resolved): [Workbench] Edit box for project description should be bigger
Applied in changeset arvados|commit:cb41817568900d52d3768a91f703f04696f6b702. Radhika Chippada
07:29 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Converted tiptitle to nonhtml_option. Radhika Chippada
06:58 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Reviewing commit:6e10831. This seems really great. Thanks for sticking it through. Just one small thing from here:... Brett Smith
06:19 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Brett: added a new "nonhtml_options" parameter to render_editable_attribute method definition and moved all the btn* ... Radhika Chippada
07:35 pm Revision cb418175 (arvados): closes #5735
Merge branch '5735-edit-description-box-size' Radhika Chippada
07:30 pm Task #5891 (Resolved): Review branch: 5735-edit-description-box-size
Radhika Chippada
07:26 pm Revision 8ac0683e (arvados): 5735: move tiptitle into nonhtml_options
Radhika Chippada
07:02 pm Bug #5713: [FUSE] File access sometimes takes too long on su92l
... Abram Connelly
06:23 pm Story #5781 (In Progress): [API] [DRAFT] Provide API methods for manipulating and combining colle...
Radhika Chippada
06:23 pm Bug #5842: [Node Manager] Too many nodes being started
Here's a log snippet that just happened that I think supports my hypothesis. We start just as a new cloud node comes... Brett Smith
06:16 pm Revision 6e10831b (arvados): Merge branch 'master' into 5735-edit-description-box-size
Radhika Chippada
06:12 pm Revision fe7d9a6c (arvados): 5735: add comment
Radhika Chippada
06:09 pm Bug #5909 (Closed): Cannot see output collection from workbench
Trying to access the output collection of the second portion of the job https://workbench.su92l.arvadosapi.com/pipel... Abram Connelly
05:53 pm Revision bd2023d1 (arvados): 5735: add a new nonhtml_options parameter to render_editable_attribu...
which can be used to pass any non data-* custom attributes that are useful in
customizing the rendering of the editab...
Radhika Chippada
05:16 pm Revision e89c415a (sso-provider): 5829: Add registration page with email confirmation. Use consi...
various login pages. Peter Amstutz
04:54 pm Bug #5908: [Workbench] collection#show performing too many unnecessary API server requests when a...
I pointed my workbench to qr1hi api server and accessed /collections/qr1hi-4zz18-zn1m6s2le7dqjfs. I noticed in the wo... Radhika Chippada
04:37 pm Bug #5908 (Closed): [Workbench] collection#show performing too many unnecessary API server reques...
Radhika Chippada
04:16 pm Story #5837 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
Brett Smith
04:14 pm April development review: Workbench makes it easy
Over the last month, we've made it easier than ever to get started with Arvados. You'll literally see the results as... Brett Smith
03:34 pm Task #5880 (Resolved): Review 5724-blob-signature-ttl
Tom Clegg
03:20 pm Revision 49ab94b9 (sso-provider): Merge branch 'login_via_email_and_password'
Peter Amstutz
03:19 pm Revision f1b13f48 (sso-provider): 5829: Better login pages for regular login and LDAP.
Peter Amstutz
02:58 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
Peter Amstutz wrote:
> commit:4dc84fd
>
> * Per office conversation, remove @if self.images.any_users(): return@ f...
Brett Smith
02:56 pm Bug #5907 (New): [SDKs] PySDK's internal decorators lose method metadata
Try, e.g., @pydoc arvados.collection.Collection.copy@. The arguments aren't named on the method signature, even thou... Brett Smith
02:38 pm Bug #5906 (New): [API] crunch-dispatch should mark a job failed when its repository cannot be fet...
h2. Development story
If you build a pipeline that refers to a remote repository that cannot be fetched (e.g., typ...
Abram Connelly
02:24 pm Revision df5a73a8 (arvados): 3793: Fixups from code review.
Brett Smith

05/04/2015

11:59 pm Revision 7d12bf89 (arvados): 5735: use data- for button text and button class custom attributes.
Radhika Chippada
11:11 pm Revision cb55d2c0 (arvados): 5735: exclude btn* attributes from span tag.
Radhika Chippada
10:02 pm Bug #5905 (Closed): [SDKs] Improve certificate validation in Python SDK
h2. Development story
Many users are seeing a warning from urllib3 letting them know that certificates can't actua...
Abram Connelly
09:18 pm Bug #5842: [Node Manager] Too many nodes being started
Theory: this is caused or exacerbated by a gap in time between when nodes ping Arvados and when they're resumed in SL... Brett Smith
09:05 pm Bug #5724 (Resolved): [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on def...
Applied in changeset arvados|commit:9d4bc458b767e4c05024dfe02207283745e1ba06. Tom Clegg
08:21 pm Bug #5724: [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on default_trash_...
Radhika Chippada wrote:
> Comments with the latest in branch (da57a997):
>
> * Since you are renaming variables, ...
Tom Clegg
04:25 pm Bug #5724: [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on default_trash_...
Comments with the latest in branch (da57a997):
* Since you are renaming variables, I was wondering if we want to c...
Radhika Chippada
02:17 pm Bug #5724: [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on default_trash_...
Comments for branch 5724-blob-signature-ttl at 6fc44a6:
Should the comment at line 234 in application.default.yml ...
Radhika Chippada
09:00 pm Bug #5898: [Tests] Race condition in test_KeepProxyTest1 (tests.test_keep_client.KeepProxyTestCas...
Suggest a wait loop in run_test_servers.py→_start_keep() and _start_keep_proxy() that waits up to X milliseconds... Tom Clegg
03:31 pm Bug #5898 (Resolved): [Tests] Race condition in test_KeepProxyTest1 (tests.test_keep_client.KeepP...
Tom Clegg
08:46 pm Revision 9d4bc458 (arvados): Merge branch '5724-blob-signature-ttl' closes #5724
Tom Clegg
08:39 pm Bug #5902: [Workbench] collection#show is unresponsive for a large collection
Also, this collection might have been copied from tb05z and might not have any provenance in terms of pipelines creat... Abram Connelly
08:37 pm Bug #5902: [Workbench] collection#show is unresponsive for a large collection
UPDATE: The project name looks to be not owned by be but by Sally Guthrie (I see it under her directory on the keep m... Abram Connelly
08:34 pm Bug #5902 (New): [Workbench] collection#show is unresponsive for a large collection
When trying to view collection su92l-4zz18-qww94nsw428dm7o, it bogs down Firefox and eventually brings up a 'Warning:... Abram Connelly
08:24 pm Bug #5901 (New): [API] Improve performance of large requests in parallel
Attached are two files. The first is a simple Python script that uses threads to fetch the same collection object fr... Brett Smith
08:17 pm Task #5891 (In Progress): Review branch: 5735-edit-description-box-size
Brett Smith
07:59 pm Task #5891 (Resolved): Review branch: 5735-edit-description-box-size
Radhika Chippada
03:18 pm Task #5891 (In Progress): Review branch: 5735-edit-description-box-size
Brett Smith
08:16 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Reviewing commit:e146ad3. The changes address the previous issues, so thanks much for that.
The span tag is gener...
Brett Smith
08:00 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Thanks Brett. Yes, limiting the inline css config to description is a good idea and I made those updates. Radhika Chippada
03:34 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Reviewing commit:13e4bac
The new CSS will set 98% width for any inline X-Editable component. I'm concerned that t...
Brett Smith
07:50 pm Revision e146ad30 (arvados): Merge branch 'master' into 5735-edit-description-box-size
Radhika Chippada
07:48 pm Revision 71ebe5f5 (arvados): 5735: use the inline css for description only so that any future inl...
Radhika Chippada
05:27 pm Feature #5900 (Closed): [SDK] Implement arvados.gettaskparam(*args) to match arvados.getjobparam(...
Since get_task_param_mount and get_job_param_mount both exist, it would be useful to also have the ability to get bot... Sarah Guthrie
05:10 pm Task #5881 (Resolved): Review 5752-arv-copy-preserve-docker-timestamps-wip
Applied in changeset arvados|commit:73c9a44b85ba72e881c5133422fcabe3f1322142. Brett Smith
03:18 pm Task #5881 (In Progress): Review 5752-arv-copy-preserve-docker-timestamps-wip
Tom Clegg
05:10 pm Bug #5752 (Resolved): [SDKs] Fix unreliable image timestamp recording in arv keep docker
Applied in changeset arvados|commit:73c9a44b85ba72e881c5133422fcabe3f1322142. Brett Smith
03:23 pm Bug #5752: [SDKs] Fix unreliable image timestamp recording in arv keep docker
commit:c19ed0b lgtm, thanks Tom Clegg
05:07 pm Revision 73c9a44b (arvados): Merge branch '5752-arv-copy-preserve-docker-timestamps-wip'
Closes #5752, #5881. Brett Smith
05:07 pm Revision 83164dbf (arvados): 5752: arv-copy preserves properties of docker_image links.
The properties include the image_timestamp, which tells Arvados when
the source image was created, rather than the co...
Brett Smith
04:28 pm Revision 47f4f1b2 (arvados): Merge branch 'master' into 5735-edit-description-box-size
Radhika Chippada
04:19 pm Task #5880 (In Progress): Review 5724-blob-signature-ttl
Radhika Chippada
03:40 pm Revision ffadd5d8 (arvados): Merge branch '5787-run-command-checkin' refs #5787
Peter Amstutz
03:30 pm Bug #5893 (Resolved): [Workbench] Fix unreliable repository browsing
Applied in changeset arvados|commit:eb3303340c51d13512397c3d83c955af9f516f47. Tom Clegg
03:11 pm Bug #5893: [Workbench] Fix unreliable repository browsing
commit:6fcd070 is good to merge. Thanks. Brett Smith
03:24 pm Revision b02d9627 (arvados): 5787: Change caught_error to last_error in vwd.py to return last exc...
Peter Amstutz
03:23 pm Task #5894 (Resolved): Review 5893-helper-stdin
Tom Clegg
02:14 pm Task #5894 (In Progress): Review 5893-helper-stdin
Brett Smith
03:19 pm Task #5869 (Resolved): Review 3145-missing-content-length-error
Peter Amstutz
03:18 pm Revision eb330334 (arvados): Merge branch '5893-helper-stdin' closes #5893
Tom Clegg
03:07 pm Bug #5897 (Closed): [FUSE] Catch and recover from any API client exceptions
#5896 caused an API client error (timeout) to be raised in arv-mount. This exception was ultimately uncaught, and ca... Brett Smith
03:04 pm Bug #5896 (New): [FUSE] Ensure all I/O errors properly distinguish "not found" and other API errors
A user is trying to work with a collection so large that, as of now, the API server can't return it—nginx returns a 5... Brett Smith
03:03 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
commit:4dc84fd
* Per office conversation, remove @if self.images.any_users(): return@ from @clean_images()@ since ...
Peter Amstutz
02:57 pm Revision eb03fb3a (arvados): Merge branch '5724-blob-signature-ttl' commit '6fc44a6' refs #5724
Tom Clegg
02:55 pm Task #5879 (Resolved): Review 5724-blob-signature-ttl at 6fc44a6
Tom Clegg
02:12 pm Task #5879 (In Progress): Review 5724-blob-signature-ttl at 6fc44a6
Radhika Chippada
02:49 pm Task #5895 (Resolved): Ensure vwd.checkin doesn't accidentally commit (or otherwise mess up) when...
see #5787 Tom Clegg
02:45 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Peter Amstutz wrote:
> You're right. Now the task will fail on IOError or OSError (but it will still try to write a...
Tom Clegg
02:27 pm Revision 066efa83 (arvados): 5724: Update reference to keepstore flag, now -blob-signature-ttl.
Tom Clegg
01:27 pm Task #5868 (Resolved): Review 5562-pycurl-upload
Peter Amstutz
01:10 pm Bug #5562 (Resolved): [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
Applied in changeset arvados|commit:fc16c2ebbb92d9b0e52b6435b717f26b9680c7e6. Peter Amstutz
01:07 pm Revision fc16c2eb (arvados): Merge branch '5562-pycurl-upload' closes #5562
Peter Amstutz

05/03/2015

02:07 pm Revision 8bef6711 (arvados-dev): (minor) fix typo
Tony Xue

05/02/2015

06:59 am Task #5894 (Resolved): Review 5893-helper-stdin
Tom Clegg
06:58 am Bug #5893 (In Progress): [Workbench] Fix unreliable repository browsing
Tom Clegg
06:51 am Bug #5893 (Resolved): [Workbench] Fix unreliable repository browsing
Sometimes, after getting 401 from arv-git-httpd and asking the credential helper for a password, git exits non-zero i... Tom Clegg
06:49 am Revision e343f081 (arvados): 5416: Remove "disable repo browsing with git2" stuff.
git2 is no longer unreliable, now that we know the silent failures
meant "git credential helpers must consume their s...
Tom Clegg
06:49 am Revision 6fcd0706 (arvados): 5893: Remove "disable repo browsing with git2" stuff.
git2 is no longer unreliable, now that we know the silent failures
meant "git credential helpers must consume their s...
Tom Clegg
06:41 am Revision 57d5f07d (arvados): 5416: Remove "disable repo browsing with git2" stuff.
git2 is no longer unreliable, now that we know the silent failures
meant "git credential helpers must consume their s...
Tom Clegg
06:41 am Revision 33b41435 (arvados): 5893: Use git credential helpers for arv-git-httpd tests. Fix workbe...
The sporadic "git exited 128" errors -- very common in git2 and rare
in git1 -- seem to have been caused by git getti...
Tom Clegg
06:41 am Revision 33235ab1 (arvados): 5416: Use git credential helpers for arv-git-httpd tests. Fix workbe...
The sporadic "git exited 128" errors -- very common in git2 and rare
in git1 -- seem to have been caused by git getti...
Tom Clegg
06:41 am Revision c311c447 (arvados): 5416: gofmt fixes. Fix some logs to print as strings, not byte arrays.
Tom Clegg
06:41 am Revision 32254a99 (arvados): 5893: Add realm="git" to WWW-Authenticate header, cf. rfc2617
Tom Clegg
06:41 am Revision 49a76fac (arvados): 5893: gofmt fixes. Fix some logs to print as strings, not byte arrays.
Tom Clegg
06:41 am Revision 42b4e23e (arvados): 5416: Add realm="git" to WWW-Authenticate header, cf. rfc2617
Tom Clegg
06:34 am Revision 00121a24 (arvados): 5416: Remove "disable repo browsing with git2" stuff.
git2 is no longer unreliable, now that we know the silent failures
meant "git credential helpers must consume their s...
Tom Clegg
06:17 am Revision 0f1d3aca (arvados): 5416: Use git credential helpers for arv-git-httpd tests. Fix workbe...
The sporadic "git exited 128" errors -- very common in git2 and rare
in git1 -- seem to have been caused by git getti...
Tom Clegg
06:09 am Revision c0a80b0a (arvados): 5416: gofmt fixes. Fix some logs to print as strings, not byte arrays.
Tom Clegg
06:07 am Revision 9019ae81 (arvados): 5416: Add realm="git" to WWW-Authenticate header, cf. rfc2617
Tom Clegg
12:25 am Support #5833 (In Progress): Cannot get Arvados installed
Ward Vandewege
12:17 am Bug #5748: [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
This doesn't appear to be related to r/o disks, I have seen it happen on tb05z as well, where all disks can be writte... Ward Vandewege

05/01/2015

09:35 pm Story #5837 (In Progress): [Documentation] (recurring) Write blog post in first three days of sprint
Brett Smith
06:15 pm Story #5837: [Documentation] (recurring) Write blog post in first three days of sprint
Stealing per discussion. Brett Smith
09:24 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
commit:bde53a1 LGTM, thanks Tom Clegg
09:15 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Tom Clegg wrote:
> Now at commit:0a87aad
>
> typo "necessay" in vwd.py
Fixed.
> > Also catches exceptions n...
Peter Amstutz
08:47 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Now at commit:0a87aad
typo "necessay" in vwd.py
> Also catches exceptions now.
Hm. This looks like "if can't...
Tom Clegg
06:44 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Tom Clegg wrote:
> Looking at commit:f6fcf9f on 5787-run-command-checkin
>
> The checkin docstring says "Symlinks...
Peter Amstutz
05:34 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Looking at commit:f6fcf9f on 5787-run-command-checkin
The checkin docstring says "Symlinks into the keep mount in ...
Tom Clegg
09:07 pm Revision 8b689efa (arvados): 5787: Fix syntax error
Peter Amstutz
09:02 pm Revision 5b970a6c (arvados): 5787: Error writing output will cause task to fail. Tweak documenta...
Peter Amstutz
08:55 pm Task #5871 (Resolved): Review 5834-api-max-response-size-wip
Applied in changeset arvados|commit:e8f91c87ef238ddf6bd96914a196d2d90825e8ee. Brett Smith
06:50 pm Task #5871 (In Progress): Review 5834-api-max-response-size-wip
Peter Amstutz
08:55 pm Bug #5834 (Resolved): [API] Be careful about memory usage when responding to collections#index qu...
Applied in changeset arvados|commit:e8f91c87ef238ddf6bd96914a196d2d90825e8ee. Brett Smith
08:18 pm Bug #5834: [API] Be careful about memory usage when responding to collections#index queries
commit:f87f91c
per the spec:
"max_response_size should be documented in application.default.yml with a note tha...
Peter Amstutz
08:49 pm Revision e8f91c87 (arvados): Merge branch '5834-api-max-response-size-wip'
Closes #5834, #5871. Brett Smith
08:48 pm Task #5859 (Resolved): Update default config, add to discovery doc
Tom Clegg
08:45 pm Revision 3f51fa48 (arvados): 5834: Limit how much manifest text data API server will load for index.
This prevents situations where clients cause the API server to balloon
in memory use by requesting an index including...
Brett Smith
08:21 pm Task #5857 (In Progress): Review 3793-clean-docker-images-wip
Peter Amstutz
08:07 pm Bug #5892 (Closed): [Workbench] collections#index returns 504 Gateway Timeout
504 Gateway Time-out
nginx/1.6.2
Tried 3x on https://workbench.su92l.arvadosapi.com/collections
qr1hi seems to...
Nancy Ouyang
08:06 pm Task #5867 (Resolved): Review branch: 4458-breadcrumbs-in-small-screens
Radhika Chippada
02:21 pm Task #5867 (In Progress): Review branch: 4458-breadcrumbs-in-small-screens
Brett Smith
08:06 pm Task #5858 (Resolved): Review branch: 5843-subproject-deletion-owner-name-constraint
Radhika Chippada
01:40 pm Task #5858 (In Progress): Review branch: 5843-subproject-deletion-owner-name-constraint
Brett Smith
08:04 pm Feature #5735 (In Progress): [Workbench] Edit box for project description should be bigger
Radhika Chippada
07:54 pm Feature #5735: [Workbench] Edit box for project description should be bigger
Notes about the update:
* The edit button for project description is now displayed on top of textarea; uses btn-pr...
Radhika Chippada
07:55 pm Task #5891 (Resolved): Review branch: 5735-edit-description-box-size
Radhika Chippada
07:43 pm Revision 13e4bacf (arvados): 5735: use inline editing for project description x-editable textarea.
Radhika Chippada
06:43 pm Revision 0a87aad4 (arvados): 5787: Write files that are pointed to by symlinks that are outside o...
Catch exceptions. Update documentation. Peter Amstutz
06:10 pm Bug #5752: [SDKs] Fix unreliable image timestamp recording in arv keep docker
After investigation, arv-copy seems like a more likely culprit. I found a family of images on su92l which all had th... Brett Smith
06:07 pm Task #5881 (Resolved): Review 5752-arv-copy-preserve-docker-timestamps-wip
Brett Smith
06:07 pm Revision c19ed0b4 (arvados): 5752: arv-copy preserves properties of docker_image links.
The properties include the image_timestamp, which tells Arvados when
the source image was created, rather than the co...
Brett Smith
05:36 pm Task #5880 (Resolved): Review 5724-blob-signature-ttl
Tom Clegg
05:35 pm Task #5879 (Resolved): Review 5724-blob-signature-ttl at 6fc44a6
Tom Clegg
05:15 pm Task #5877 (In Progress): Review 5787-run-command-checkin
Tom Clegg
03:35 pm Task #5877 (Resolved): Review 5787-run-command-checkin
Peter Amstutz
03:54 pm Bug #5835 (Closed): [SDK] arv-copy breaks with namespaced git repository names
Peter reports at standup that this was a problem in his local deployment and not an arv-copy bug. Brett Smith
03:40 pm Bug #4458 (Resolved): [Workbench] Replace e-mail address in menu bar with user icon and make sure...
Applied in changeset arvados|commit:91c467665ad493108b69c660d5424c77cce5668f. Radhika Chippada
03:33 pm Bug #4458: [Workbench] Replace e-mail address in menu bar with user icon and make sure bread crum...
commit:02676af9 is good to merge. Thanks. Brett Smith
03:36 pm Revision 91c46766 (arvados): closes #4458
Merge branch '4458-breadcrumbs-in-small-screens' Radhika Chippada
03:35 pm Bug #5878 (Closed): [Workbench] PipelineInstancesTest#test_Create_and_run_a_pipeline is not reliable
One run gave me this error:... Brett Smith
03:35 pm Revision 6a7271ad (arvados): Merge branch 'master' into 4458-breadcrumbs-in-small-screens
Radhika Chippada
03:27 pm Revision f6fcf9f5 (arvados): 5787: Copy to the right destination name, add docstring, fix syntax ...
Peter Amstutz
03:22 pm Bug #5876 (Closed): [Docker] Needs smarter dependency ordering when restarting existing containers
I did this:
* I had a functional Docker cluster going with @arvdock start@.
* I stopped it with @arvdock stop@.
...
Brett Smith
02:35 pm Bug #5875 (Closed): [Workbench] Mobile menus lack contrast (gray text on aubergine)
Brett Smith
02:34 pm Bug #5875 (Closed): [Workbench] Mobile menus lack contrast (gray text on aubergine)
See "this screenshot":https://arvados.org/attachments/download/520/4458-lack-of-dashboard.png from #4458. I think we... Brett Smith
02:34 pm Bug #5874 (New): [Workbench] Mobile menus lack contrast (gray text on aubergine)
See "this screenshot":https://arvados.org/attachments/download/520/4458-lack-of-dashboard.png from #4458. I think we... Brett Smith
02:32 pm Revision 1281ecab (arvados): 5787: run-command uploading uses new collection API and supports sym...
Peter Amstutz
02:30 pm Bug #5843 (Resolved): [Workbench] Undeleteable sub-project
Applied in changeset arvados|commit:ee8d5b171e2c30ddc3fe829ba4388778e6a78b27. Radhika Chippada
02:20 pm Bug #5843: [Workbench] Undeleteable sub-project
commit:ec359b6 is good to merge. Thanks. Brett Smith
02:26 pm Revision ee8d5b17 (arvados): closes #5843
Merge branch '5843-subproject-deletion-owner-name-constraint' Radhika Chippada
02:26 pm Revision f81a5a1a (arvados): Merge branch 'master' into 5843-subproject-deletion-owner-name-const...
Radhika Chippada
01:44 pm Support #5833: Cannot get Arvados installed
This is what I get:
tcp 0 0 127.0.1.1:53 0.0.0.0:* LISTEN -
...
Darshan Singh
07:13 am Revision da57a997 (arvados): 5724: gofmt fixes.
Tom Clegg
07:11 am Revision 5bf77ec1 (arvados): 5724: Rename -permission-* flags to -blob-sign* to match apiserver. ...
Tom Clegg
04:59 am Revision 6fc44a67 (arvados): 5724: Add blobSignatureTtl to discovery doc. Add config comment/expl...
Tom Clegg

04/30/2015

10:24 pm Task #5871 (Resolved): Review 5834-api-max-response-size-wip
Brett Smith
10:23 pm Revision f87f91cb (arvados): 5834: Limit how much manifest text data API server will load for index.
This prevents situations where clients cause the API server to balloon
in memory use by requesting an index including...
Brett Smith
09:41 pm Revision 085bacc5 (arvados): 5493: fixed colorspace leading to yellow gif
Nancy Ouyang
09:15 pm Revision 0a173299 (arvados): Merge branch 'master' of git://git.curoverse.com/arvados into 5493-f...
Nancy Ouyang
09:14 pm Revision bde53a1d (arvados): 5562: keepstub sends "100 Continue" to client. Fix test_write_three...
to return a valid response body instead of None. Peter Amstutz
09:05 pm Revision 97ddb4b8 (arvados): 5493: fix yellow mouse-moves gif
Nancy Ouyang
08:52 pm Bug #5724 (In Progress): [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on ...
Tom Clegg
08:38 pm Revision db195a54 (arvados): run-command list correct directory to be uploaded when $(task.cwd) !...
no issue # Peter Amstutz
08:21 pm Revision 6083e432 (arvados): 5562: Use cStringIO module which is more efficient than StringIO.
Peter Amstutz
08:21 pm Revision 11253aff (arvados): 5562: Add comment about UPLOAD
Peter Amstutz
08:14 pm Revision 2826ad75 (arvados): 5562: Add support for "Expect: 100-Continue" flow for PUT.
This tells cURL to wait for a "go ahead" from the Keep server (in the form of a
HTTP/1.1 "100 Continue" response) ins...
Peter Amstutz
08:10 pm Feature #3145 (Resolved): [Keep] keepstore supports read-only flag for each volume, for cases lik...
Applied in changeset arvados|commit:7990a7778f70c243b50ea878787ea83689f5b07e. Peter Amstutz
07:53 pm Feature #3145: [Keep] keepstore supports read-only flag for each volume, for cases like full, dra...
commit:e94da792 lgtm, thanks.
Nice work on the HTTP status codes that are already defined to mean exactly what we ...
Tom Clegg
06:48 pm Feature #3145 (Feedback): [Keep] keepstore supports read-only flag for each volume, for cases lik...
Peter Amstutz
06:47 pm Feature #3145 (In Progress): [Keep] keepstore supports read-only flag for each volume, for cases ...
Peter Amstutz
02:25 pm Feature #3145 (Resolved): [Keep] keepstore supports read-only flag for each volume, for cases lik...
Applied in changeset arvados|commit:624c5c8d13d6c2e21a80379928387944bedae2a3. Tom Clegg
02:20 pm Feature #3145: [Keep] keepstore supports read-only flag for each volume, for cases like full, dra...
Peter Amstutz wrote:
> 3145-close-early LGTM
>
> We should use pycurl.UPLOAD in KeepClient (refs #5562)
>
> ht...
Tom Clegg
02:04 pm Feature #3145: [Keep] keepstore supports read-only flag for each volume, for cases like full, dra...
3145-close-early LGTM
We should use pycurl.UPLOAD in KeepClient (refs #5562)
http://curl.haxx.se/libcurl/c/CURL...
Peter Amstutz
08:07 pm Revision 7990a777 (arvados): Merge branch '3145-missing-content-length-error' closes #3145
Peter Amstutz
07:44 pm Task #5869 (In Progress): Review 3145-missing-content-length-error
Tom Clegg
06:48 pm Task #5869 (Resolved): Review 3145-missing-content-length-error
Peter Amstutz
07:44 pm Task #5859 (In Progress): Update default config, add to discovery doc
Tom Clegg
03:36 pm Task #5859 (Resolved): Update default config, add to discovery doc
Tom Clegg
07:43 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
On 5562-pycurl-upload at commit:589e0f3c (after merging master to deal with pycurl version problems) I get:... Tom Clegg
01:29 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
Peter Amstutz wrote:
> On the compute node, pycurl is presumably using this package:
>
> /usr/lib/pymodules/pytho...
Tom Clegg
01:13 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
On the compute node, pycurl is presumably using this package:
/usr/lib/pymodules/python2.7/pycurl-7.19.0.egg-info
Peter Amstutz
01:10 pm Bug #5562 (Feedback): [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
... Peter Amstutz
07:24 pm Bug #5834: [API] Be careful about memory usage when responding to collections#index queries
(03:06:25 PM) Me: tomclegg: Do you want any compensation for the fact that the manifest_text in the database will be ... Brett Smith
06:09 pm Bug #5834 (In Progress): [API] Be careful about memory usage when responding to collections#index...
Brett Smith
07:05 pm Task #5870 (In Progress): Test scaling performance on exome and whole genome
Peter Amstutz
07:05 pm Task #5870 (Closed): Test scaling performance on exome and whole genome
Peter Amstutz
06:46 pm Task #5864 (Resolved): Review 5856-read-exact
Peter Amstutz
05:39 pm Task #5864 (In Progress): Review 5856-read-exact
Brett Smith
04:44 pm Task #5864 (Resolved): Review 5856-read-exact
Peter Amstutz
06:45 pm Task #5868 (In Progress): Review 5562-pycurl-upload
Tom Clegg
06:44 pm Task #5868 (Resolved): Review 5562-pycurl-upload
Tom Clegg
06:39 pm Revision 589e0f3c (arvados): 5562: Use cStringIO module which is more efficient than StringIO.
Peter Amstutz
06:30 pm Revision dffb8b5e (arvados): Merge branch '5856-read-exact' closes #5856
Peter Amstutz
06:29 pm Bug #5856: gzip.open(f) sometimes throws struct.error (unpack requires a string argument of lengt...
commit:c42ccd1f is good to merge. Thanks. Brett Smith
06:22 pm Bug #5856 (Resolved): gzip.open(f) sometimes throws struct.error (unpack requires a string argume...
Brett Smith wrote:
> Reviewing commit:4570521
>
> I'm not sure it makes much sense for the tests to manipulate @s...
Peter Amstutz
05:25 pm Bug #5856: gzip.open(f) sometimes throws struct.error (unpack requires a string argument of lengt...
Reviewing commit:4570521
I'm not sure it makes much sense for the tests to manipulate @sfile.arvadosfile@ directly...
Brett Smith
05:02 pm Bug #5856 (In Progress): gzip.open(f) sometimes throws struct.error (unpack requires a string arg...
Peter Amstutz
04:45 pm Bug #5856 (Resolved): gzip.open(f) sometimes throws struct.error (unpack requires a string argume...
Applied in changeset arvados|commit:4570521e9d639806b1f25c93822d5cf0dbfe42d0. Peter Amstutz
04:42 pm Bug #5856 (In Progress): gzip.open(f) sometimes throws struct.error (unpack requires a string arg...
Peter Amstutz
03:30 pm Bug #5856 (Resolved): gzip.open(f) sometimes throws struct.error (unpack requires a string argume...
Applied in changeset arvados|commit:c807aef7059b253512ba5da5d535e89e800b9c11. Peter Amstutz
06:25 pm Bug #4458: [Workbench] Replace e-mail address in menu bar with user icon and make sure bread crum...
* Breadcrumbs are now visible in the page even when it small
** The breadcrumbs do disappears as you keep reducing t...
Radhika Chippada
03:34 pm Bug #4458 (In Progress): [Workbench] Replace e-mail address in menu bar with user icon and make s...
Radhika Chippada
06:21 pm Revision c42ccd1f (arvados): 5856: Tweak tests. Fix typo.
Peter Amstutz
06:21 pm Task #5867 (Resolved): Review branch: 4458-breadcrumbs-in-small-screens
Radhika Chippada
06:19 pm Revision 02676af9 (arvados): 4458: breadcrumbs now visible in small window sizes; also, use user ...
Radhika Chippada
06:08 pm Feature #5866 (New): Document the 'arv' tool
The command line 'arv' tool is very useful when trying to automate tasks that communicate with the Arvados API server... Abram Connelly
06:02 pm Bug #5845: Pipeline has failed but no jobs are marked as failed
The bug is not that the job failed but that workbench is not displaying the failure.
The job failed because I mis-...
Abram Connelly
05:00 pm Bug #5845: Pipeline has failed but no jobs are marked as failed
From the pipeline instance logs:
Error creating job for component RefreshReport: Repository not found: '$USER'
Jo...
Bryan Cosca
05:59 pm Revision e94da792 (arvados): Return error if Content-Length header is missing instead of panicing.
Peter Amstutz
05:55 pm Revision 94129ac4 (arvados): Use pycurl.UPLOAD instead of CUSTOMREQUEST 'PUT'. Set INFILESIZE an...
READFUNCTION. Peter Amstutz
05:41 pm Task #5857 (New): Review 3793-clean-docker-images-wip
Brett Smith
01:25 pm Task #5857 (In Progress): Review 3793-clean-docker-images-wip
Brett Smith
01:25 pm Task #5857 (Resolved): Review 3793-clean-docker-images-wip
Brett Smith
05:09 pm Story #5865 (New): [Crunch] Run a local job using a docker image directly from the shell VM (with...
The objective is to make this development cycle much quicker:
* Edit Dockerfile.
* Rebuild docker image.
* Run job...
Tom Clegg
04:41 pm Revision 4570521e (arvados): ArvadosFileReader object always tries to return the exact amount of ...
This is to avoid breaking stuff like gzip that assumes it always gets the exact
amount of data unless EOF. (From the...
Peter Amstutz
04:03 pm Feature #5863 (New): API documentation updates
The "Arvados API documentation":http://doc.arvados.org/api/methods.html is difficult to understand. Here are a two p... Abram Connelly
03:39 pm Task #5862 (New): Fill in component params from pipeline params in a-r-p-i
Tom Clegg
03:39 pm Task #5861 (New): Allow editing pipeline parameters in workbench
Tom Clegg
03:38 pm Task #5860 (New): Provide detail about expected information/presentation
Tom Clegg
03:37 pm Bug #5835: [SDK] arv-copy breaks with namespaced git repository names
I'm having trouble reproducing. Given this pipeline template:... Brett Smith
03:30 pm Revision f94d59e8 (arvados): Merge branch '5562-pycurl' refs #5562
Tom Clegg
03:30 pm Revision 3da2281b (arvados): 5562: Use static method. Fix "TypeError: _socket_open() takes exactl...
Tom Clegg
03:29 pm Revision c807aef7 (arvados): ArvadosFileReader object always tries to return the exact amount of ...
This is to avoid breaking stuff like gzip that assumes it always gets the exact
amount of data unless EOF. (From the...
Peter Amstutz
03:16 pm Revision caaa8219 (arvados): 5562: Use static method. Fixes "TypeError: _socket_open() takes exac...
Tom Clegg
03:05 pm Task #5858 (Resolved): Review branch: 5843-subproject-deletion-owner-name-constraint
Radhika Chippada
02:59 pm Revision ec359b66 (arvados): 5843: rename objects that contain xx_owner_uuid_name_unique constrai...
Radhika Chippada
02:48 pm Task #5693 (Closed): Review 5692-pysdk-signed-manifest-locator
Tom Clegg
02:45 pm Task #5693 (Resolved): Review 5692-pysdk-signed-manifest-locator
Tom Clegg
02:39 pm Task #5795 (Resolved): Review branch: 5780-sharing-popup-message
Tom Clegg
02:25 pm Revision 624c5c8d (arvados): Merge branch '3145-close-early' closes #3145
Tom Clegg
02:25 pm Bug #5836 (Resolved): [API] Remote API error messages should make it clear that they are remote.
Applied in changeset arvados|commit:a4211acb465bd42869bf2a2f9fad6ff2c5e518e0. Tom Clegg
02:24 pm Revision a4211acb (arvados): Merge branch '5836-remote-api-server-errors-made-obvious' closes #5836
Tom Clegg
02:16 pm Task #5849 (Resolved): Review 3145-close-early
Peter Amstutz
01:53 pm Revision 6c9dde5e (arvados): 5562: Use WRITEFUNCTION instead of WRITEDATA for compatibility with ...
Tom Clegg
01:34 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
3793-clean-docker-images-wip is up for review. A few notes:
* *THIS IS PYTHON 3*. I asked Ward if this was okay ...
Brett Smith
01:24 pm Revision 4dc84fdc (arvados): 3793: Add Docker image cleaner service for compute nodes.
This service monitors Docker events. When no containers are active,
it arranges to keep the most recently used image...
Brett Smith
01:47 am Support #5833: Cannot get Arvados installed
Interesting - it looks like you either already have a skydns container running, or maybe you have another dns resolve... Ward Vandewege

04/29/2015

09:53 pm Bug #5856 (Resolved): gzip.open(f) sometimes throws struct.error (unpack requires a string argume...
One of the tasks from https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-pfu68urmcrq00mo failed wi... Sarah Guthrie
09:27 pm Bug #5834: [API] Be careful about memory usage when responding to collections#index queries
That sounds like a great solution Tom. The data manager doesn't really care how many results it gets, as long as it g... Misha Zatsman
08:50 pm Bug #5766 (Resolved): [SDK] setup.py install always gets latest arvados-python-sdk from PyPi, eve...
Applied in changeset arvados-dev|commit:274c7abf3aee7dee8bfe648f485087a5a0ab59ed. Peter Amstutz
08:50 pm Feature #5412 (Resolved): [SSO] Support LDAP-only configuration
Applied in changeset sso-provider|commit:80acc50a1d23b6378682a4729726772d1d616e3d. Peter Amstutz
08:46 pm Task #5710 (Resolved): Review 5692-pysdk-manifest-text-flush
Peter Amstutz
08:46 pm Task #5786 (Resolved): Review 5766-pip-sdk-install in arvados-dev
Peter Amstutz
08:46 pm Revision 274c7abf (arvados-dev): Merge branch '5766-pip-sdk-install' closes #5766
Peter Amstutz
08:46 pm Revision 274c7abf (arvados): Merge branch '5766-pip-sdk-install' closes #5766
Peter Amstutz
08:44 pm Revision 80acc50a (sso-provider): Merge branch '5412-ldap-support' closes #5412
Peter Amstutz
08:18 pm Support #5832: [Support] how to include a bioboxes docker image as a new pipeline?
Hi Albert,
You can use `arv keep docker` to download docker images from the docker registry.
There's a little m...
Ward Vandewege
08:14 pm Bug #4458: [Workbench] Replace e-mail address in menu bar with user icon and make sure bread crum...
This will also solve the overlay problem (menu bar makes breadcrumbs bar invisible) between main and mobile view. Ward Vandewege
08:08 pm Task #5855 (New): Add Workbench support
Tom Clegg
08:08 pm Task #5854 (New): Add default display_order on server side
Tom Clegg
07:46 pm Task #5853 (New): Document pipeline parameters API
Tom Clegg
07:39 pm Task #5852 (Resolved): Write install docs
Tom Clegg
07:38 pm Task #5851 (Resolved): Write integration tests
Tom Clegg
07:36 pm Bug #5850 (Closed): All clients authenticate directly against SSO server without going through AP...
Tom Clegg
07:35 pm Task #3844 (Resolved): Agressively close PUT connections when there are no writable volumes.
Tom Clegg
07:28 pm Bug #5836 (In Progress): [API] Remote API error messages should make it clear that they are remote.
Tom Clegg
07:09 pm Task #5849 (Resolved): Review 3145-close-early
Tom Clegg
07:07 pm Task #5847 (Resolved): Review 5562-pycurl
Tom Clegg
02:06 pm Task #5847 (Resolved): Review 5562-pycurl
Tom Clegg
06:56 pm Revision 8af4c5ff (arvados): 3145: Respond to PUT without reading request body if no volumes are ...
Tom Clegg
06:10 pm Bug #5562 (Resolved): [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
Applied in changeset arvados|commit:acc7d4a40ae78e866c983624ec36b7bae3b918a9. Tom Clegg
03:55 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
(From IRC: agreed that when talking to a Keep node, the timeout should already be 20 seconds, so setting LOW_SPEED_TI... Peter Amstutz
03:40 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
http://curl.haxx.se/docs/faq.html#I_want_a_different_time_out
We should set http://curl.haxx.se/libcurl/c/CURLOPT_...
Peter Amstutz
02:54 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
* In @KeepService.get()@ it looks like a 404 response will be treated as an error and cause the connection to be rese... Peter Amstutz
02:13 pm Bug #5562: [SDKs] Fix timeout problems by switching from urllib et al. to PycURL
Test package is here, and /tmp/arvados-python-client-0.1.20150429043929.tar.gz on shell.q... Tom Clegg
06:08 pm Bug #5843 (In Progress): [Workbench] Undeleteable sub-project
Radhika Chippada
06:07 pm Bug #5843: [Workbench] Undeleteable sub-project
Collections, groups, and pipeline_templates have the owner_uuid_name_unique constraint.
Currently, when a collecti...
Radhika Chippada
02:51 pm Bug #5843: [Workbench] Undeleteable sub-project
I think there was another subproject in Home project with that same name and hence the deletion (moving into Home pro... Radhika Chippada
05:45 pm Revision acc7d4a4 (arvados): Merge branch '5562-pycurl' closes #5562
Tom Clegg
05:38 pm Revision 213ace8b (arvados): 5562: Enable TCP Keepalive for Keep requests. refs #5822
Tom Clegg
05:38 pm Revision ea7c7efb (arvados): 5562: Return UA to pool if it worked well enough to get an HTTP status.
Tom Clegg
04:31 pm Revision e2494026 (arvados): Renamed RemoteApiServerError to APIServerError and NewRemoteApiServe...
Reworked error messages to feature error details more prominently.
These changes were requested by code review at
ht...
Misha Zatsman
03:10 pm Revision 4008f2a6 (arvados): 5562: Return UA to pool if it worked well enough to get an HTTP status.
Tom Clegg
02:57 pm Revision cfcefb3d (arvados): 5562: Enable TCP Keepalive for Keep requests. refs #5822
Tom Clegg
02:05 pm Task #5789 (Resolved): Test somehow
Tom Clegg
01:28 pm Feature #5846 (New): [Workbench] [Fiddlesticks] Live job log should show recent history
Jobs can get in this state if the arv-put process that crunch-job ran to create the log fails. See, e.g., qr1hi-8i9s... Peter Amstutz
01:10 pm Bug #5826 (Resolved): [Workbench] Pipeline Instance input tab should be more verbose
Applied in changeset arvados|commit:61d399a57fd1e867cc243a0dab0fad73d9689734. Radhika Chippada
01:07 pm Revision 61d399a5 (arvados): closes #5826
Merge branch '5826-unreadable-inputs-error' Radhika Chippada
12:44 pm Revision e01762a0 (arvados): 5826: use present? instead of !empty?
Radhika Chippada
04:39 am Revision 7ab494e4 (arvados): 5562: Use pycurl library (instead of requests) for Keep transactions.
Tom Clegg
04:39 am Revision 20b988d5 (arvados): 5562: Add fake keepstore server with configurable problems.
Tom Clegg

04/28/2015

11:08 pm Revision 71ba1157 (arvados): 5562: Add fake keepstore server with configurable problems.
Tom Clegg
10:29 pm Revision 0191b582 (arvados): Added tests to confirm that error messages indicate that error is re...
Fixed punctuation. Misha Zatsman
10:29 pm Bug #5845 (Closed): Pipeline has failed but no jobs are marked as failed
... Abram Connelly
10:16 pm Revision de5f63b3 (arvados): Rewrote ArvadosApiError as RemoteApiServerError:
* Name change to indicate that it's a remote error, not a local one.
* Rewrote Error() method to explicitly state tha...
Misha Zatsman
10:16 pm Bug #5826: [Workbench] Pipeline Instance input tab should be more verbose
Peter said: as long as a non-empty string is provided for a Collection or File dataclass, we need to check readabilit... Radhika Chippada
07:48 pm Bug #5826 (In Progress): [Workbench] Pipeline Instance input tab should be more verbose
Reopening because Peter said this was actually due to a bug in the template and the Run button should be disabled. Radhika Chippada
10:03 pm Revision 48c6eca6 (arvados): 5826: revert the previous update that checked if readable only for p...
instead check as long as a collection datatype is presented with a non-empty string. Radhika Chippada
09:56 pm Bug #5843: [Workbench] Undeleteable sub-project
I renamed it to '...' and then was able to delete it. Abram Connelly
09:33 pm Bug #5843 (Resolved): [Workbench] Undeleteable sub-project
I cannot remove sub-project
@https://workbench.su92l.arvadosapi.com/projects/su92l-j7d0g-3rbmaji2ifc5gm4@
from ...
Abram Connelly
09:50 pm Revision ef677302 (arvados): Started logging memory reserved in addition to memory used.
Started using GetOrCreateMap() in loggerutil
Updated comments, cleaned up typos.
Misha Zatsman
09:10 pm Bug #5834: [API] Be careful about memory usage when responding to collections#index queries
Manifests are allowed to be over 64 MB which means a page of 100 can easily be over 6.4 GB.
API server doesn't _gu...
Tom Clegg
08:51 pm Bug #5834: [API] Be careful about memory usage when responding to collections#index queries
Server Ward Vandewege
03:35 pm Bug #5834: [API] Be careful about memory usage when responding to collections#index queries
Consistently, after reading 25,149 collections with datamanager, when I query for the next set, the SDK returns: #<No... Ward Vandewege
03:32 pm Bug #5834 (Resolved): [API] Be careful about memory usage when responding to collections#index qu...
API server logs:... Ward Vandewege
08:22 pm Bug #5842 (Resolved): [Node Manager] Too many nodes being started
Some time around 4:07 PM 4/28/2015 EDT, GATK Queue job qr1hi-8i9sb-e4ggp059unk0tjg started and queued 5 additional jo... Peter Amstutz
07:50 pm Feature #5412: [SSO] Support LDAP-only configuration
LGTM Ward Vandewege
07:50 pm Task #5616 (Resolved): Review 5412-ldap-support
Ward Vandewege
07:49 pm Task #5616 (In Progress): Review 5412-ldap-support
Ward Vandewege
07:38 pm Bug #5841 (New): [Workbench] Link to script sources on github when repository is a github url
Tom Clegg
07:33 pm Feature #5840 (New): [API] Relax repository name constraints to permit [-_.] -- ideally allow any...
Tom Clegg
07:17 pm Task #5825 (Resolved): Review branch: 5622-fix-timeout-pdh-page
Radhika Chippada
01:03 pm Task #5825 (In Progress): Review branch: 5622-fix-timeout-pdh-page
Brett Smith
07:05 pm Feature #5622 (Resolved): [Workbench] Fix timeout when generating long "list of collections with ...
Applied in changeset arvados|commit:ec0c9f0d12560296d4b678c8ad33e1b82221e626. Radhika Chippada
06:48 pm Feature #5622: [Workbench] Fix timeout when generating long "list of collections with this pdh" o...
Radhika Chippada wrote:
> New branch with the quick fix: 5622-fix-timeout-pdh-page
commit:19db486 is good to merg...
Brett Smith
06:21 pm Feature #5622: [Workbench] Fix timeout when generating long "list of collections with this pdh" o...
New branch with the quick fix: 5622-fix-timeout-pdh-page Radhika Chippada
05:18 pm Feature #5622: [Workbench] Fix timeout when generating long "list of collections with this pdh" o...
From IRC:
tomclegg
12:59 it seems like the "quick fix" here is to stick a limit=20 and an "N more not shown" wher...
Radhika Chippada
02:54 pm Feature #5622: [Workbench] Fix timeout when generating long "list of collections with this pdh" o...
Seems to me the "list of collections with this PDH" tab should be doing an infinite-scroll+filtering enabled @collect... Tom Clegg
02:02 pm Feature #5622: [Workbench] Fix timeout when generating long "list of collections with this pdh" o...
Brett:
I am not comfortable taking up the task of separating this into a new route as part of this bug fix (was init...
Radhika Chippada
01:44 pm Feature #5622: [Workbench] Fix timeout when generating long "list of collections with this pdh" o...
Reviewing commit:5b95344
I'm becoming increasingly concerned that CollectionsController#show is handling too many ...
Brett Smith
06:43 pm Revision ec0c9f0d (arvados): closes #5622
Merge branch '5622-fix-timeout-pdh-page' Radhika Chippada
06:25 pm Story #5837 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
Ward Vandewege
06:06 pm Revision 19db486c (arvados): 5622: when there are too many collections matching a pdh, show only ...
Radhika Chippada
06:04 pm Bug #5836 (Resolved): [API] Remote API error messages should make it clear that they are remote.
When the API server returns an error indicating that it is out of memory, the go sdk client code returns an error who... Misha Zatsman
05:40 pm Bug #5835 (Closed): [SDK] arv-copy breaks with namespaced git repository names
Peter Amstutz
03:38 pm Bug #5831 (Resolved): [SDKs] CollectionReader.open(filename, 'r') fails (arvados/keep.py 665 in g...
Radhika Chippada
02:08 pm Bug #5831 (In Progress): [SDKs] CollectionReader.open(filename, 'r') fails (arvados/keep.py 665 i...
Radhika Chippada
01:28 am Bug #5831: [SDKs] CollectionReader.open(filename, 'r') fails (arvados/keep.py 665 in get_from_cac...
When running on just one node, task 22 failed from the same error:
https://workbench.su92l.arvadosapi.com/pipeline_i...
Sarah Guthrie
03:16 pm Bug #4458: [Workbench] Replace e-mail address in menu bar with user icon and make sure bread crum...
* As noted by Nancy in note #3, the app switches to mobile view now and the mobile menu is displayed.
* Dashboard ...
Radhika Chippada
03:13 pm Support #5833 (Feedback): Cannot get Arvados installed
Please help me figure this out. I am very keen to use Arvados and implement many pipelines here.
$ ./arvdock start...
Darshan Singh
02:47 pm Task #5797 (Resolved): Review branch: 5796-collection-search-index
Radhika Chippada
02:27 pm Bug #3770 (Resolved): [Workbench] Fiddlesticks in Job Log tab for unreadable Log
Fixed by #5365 Radhika Chippada
01:48 pm Revision f406277f (arvados): 5562: Use pycurl library (instead of requests) for Keep transactions.
Tom Clegg
01:46 pm Revision b6c7ee61 (arvados): Check if cache slot is not None before trying to test the read flag....
Peter Amstutz
01:43 pm Task #5816 (Resolved): Review 5739-no-sqlite3
Tom Clegg
01:40 pm Revision 9c76a339 (arvados): 5622: add comments to infinite_scroll.js explaining how to add infin...
Radhika Chippada
01:40 pm Bug #5739 (Resolved): [Workbench] Remove artificial sqlite3 dependency
Applied in changeset arvados|commit:040fdf6da00318b5b8e8e83eceeec783680ecb1c. Tom Clegg
01:12 pm Support #5832 (New): [Support] how to include a bioboxes docker image as a new pipeline?
Hi,
The bioboxes project has started producing docker containters. For example:
https://github.com/bioboxes/vel...
Albert Vilella
12:18 pm Revision a6136a82 (arvados): Merge branch 'master' into 5622-pdh-collections-page-paging
Radhika Chippada
06:10 am Revision 040fdf6d (arvados): Merge branch '5739-no-sqlite3' closes #5739
Tom Clegg
06:09 am Task #5691 (Resolved): Review 3126-remote-git-url
Tom Clegg

04/27/2015

10:55 pm Bug #5827 (Resolved): Pipeline Template error: undefined method 'split'
Applied in changeset arvados|commit:8464bb48ba769c8bf0984c8b1493ca43fd902891. Radhika Chippada
10:12 pm Bug #5827 (In Progress): Pipeline Template error: undefined method 'split'
Radhika Chippada
02:33 pm Bug #5827 (Resolved): Pipeline Template error: undefined method 'split'
From qr1hi-p5p6p-yl7m33m4enxtocb:
Error encountered: #<ActionView::Template::Error: undefined method `split' for {:r...
Bryan Cosca
10:55 pm Bug #5826 (Resolved): [Workbench] Pipeline Instance input tab should be more verbose
Applied in changeset arvados|commit:8464bb48ba769c8bf0984c8b1493ca43fd902891. Radhika Chippada
09:54 pm Bug #5826: [Workbench] Pipeline Instance input tab should be more verbose
I think it is failing because of the following component value:... Radhika Chippada
09:50 pm Bug #5826 (In Progress): [Workbench] Pipeline Instance input tab should be more verbose
Radhika Chippada
07:52 pm Bug #5826: [Workbench] Pipeline Instance input tab should be more verbose
This is probably related: The "Input your outputname to allelotype" parameter should be a text box. I've fixed it and... Bryan Cosca
02:14 pm Bug #5826 (Resolved): [Workbench] Pipeline Instance input tab should be more verbose
!butwhichinput.png!
The user should be able to see which input is not readable, maybe by a red highlight of the in...
Bryan Cosca
10:48 pm Revision 8464bb48 (arvados): closes #5826
closes #5827
Merge branch '5826-unreadable-inputs-error'
Radhika Chippada
10:38 pm Bug #5831: [SDKs] CollectionReader.open(filename, 'r') fails (arvados/keep.py 665 in get_from_cac...
Same bug on different pipeline instance on different data: https://workbench.su92l.arvadosapi.com/pipeline_instances/... Sarah Guthrie
10:08 pm Bug #5831 (Resolved): [SDKs] CollectionReader.open(filename, 'r') fails (arvados/keep.py 665 in g...
This bug appeared on job: https://workbench.su92l.arvadosapi.com/jobs/su92l-8i9sb-vu3ycb8jl6hm8x3
Pipeline instance:...
Sarah Guthrie
10:30 pm Revision 5b1602a5 (arvados): 5827: check readable only attrvalue is a string
Radhika Chippada
09:55 pm Task #5784 (Resolved): Review 5490-crunch-tighten-job-reuse-wip
Applied in changeset arvados|commit:03d89302f14a4a1c448b32d62679bab14e23fa23. Brett Smith
05:00 pm Task #5784 (In Progress): Review 5490-crunch-tighten-job-reuse-wip
Radhika Chippada
09:55 pm Bug #5688 (Resolved): [API] Accept a git revision range in runtime_constraints, deprecate "min" a...
Applied in changeset arvados|commit:03d89302f14a4a1c448b32d62679bab14e23fa23. Brett Smith
09:55 pm Bug #5490 (Resolved): [Crunch] Job should not be reused when docker tag _or_ arvados sdk version ...
Applied in changeset arvados|commit:03d89302f14a4a1c448b32d62679bab14e23fa23. Brett Smith
09:43 pm Bug #5490: [Crunch] Job should not be reused when docker tag _or_ arvados sdk version now resolve...
Brett: LGTM. I could not find any issues to comment. Thanks. Radhika Chippada
09:55 pm Bug #5388 (Resolved): [Crunch] Jobs do not re-run with latest docker image if job is unchanged bu...
Applied in changeset arvados|commit:03d89302f14a4a1c448b32d62679bab14e23fa23. Brett Smith
09:53 pm Revision 03d89302 (arvados): Merge branch '5490-crunch-tighten-job-reuse-wip'
Closes #3341, #5388, #5490, #5688, #5784. Brett Smith
09:48 pm Revision 4b17e787 (arvados): 5490: Test API server handling of git hash-like branch names.
If you have a branch that looks like a commit hash, different git subcommands do different things. After extended di... Brett Smith
09:48 pm Revision 68dfd41d (arvados): 5490: Require exact matches in API server's default job reuse filters.
The previous default filters would reuse jobs that used any Docker
image with the matching name, and/or Arvados SDK v...
Brett Smith
09:48 pm Revision d054beda (arvados): 5490: Clean up API server previous job fixtures.
* Every fixture that specified an arvados_sdk_version constraint
should also specify a docker_image constraint, to ...
Brett Smith
09:48 pm Revision 9bfd0d77 (arvados): 5490: Refactor API server job_reuse_controller_test.
Teach the convenience methods to start from any fixture job as a basis
for submitting new ones and comparing.
Brett Smith
09:48 pm Revision 5b0d540a (arvados): 5490: Test API server finds Docker images with hash names.
This is in the same spirit as the previous, analogous commit for git
branches.
Brett Smith
08:58 pm Revision 11a007fd (arvados): 5826: check readable only when it is a data collection pdf or uuid.
Radhika Chippada
08:08 pm Feature #5829 (Resolved): [SSO] improve UI for ldap/local account login
When SSO provider is configured to use (exactly one of) either LDAP or local authentication:
* A user (who isn't alr...
Ward Vandewege
07:31 pm Feature #5828 (Closed): [Workbench] Create new collection with selected files copy streams as wel...
Create new collection with selected files currently creates a collection without any streams. This makes it difficult... Sarah Guthrie
04:10 pm Story #5623: [Crunch] Specify Crunch2 features and APIs
Here's my CWL wishlist / proposed clean sheet redesign of job request record for crunch v2:
* uuid, owner_uuid, mo...
Peter Amstutz
03:25 pm Task #5798 (Resolved): Review 5554-delete-job-log-rows-wip
Applied in changeset arvados|commit:97403e08475b328115373a2c6a23e82116199aad. Brett Smith
03:25 pm Story #5554 (Resolved): [API] Delete crunch job log messages from logs table after the jobs finish
Applied in changeset arvados|commit:97403e08475b328115373a2c6a23e82116199aad. Brett Smith
03:06 pm Story #5554: [API] Delete crunch job log messages from logs table after the jobs finish
Radhika Chippada wrote:
> * has_readable_logs regexp: can we use CollectionHelper for regexp matching rather than re...
Brett Smith
02:45 pm Story #5554: [API] Delete crunch job log messages from logs table after the jobs finish
Just a couple minor comments:
* has_readable_logs regexp: can we use CollectionHelper for regexp matching rather t...
Radhika Chippada
03:24 pm Revision 97403e08 (arvados): Merge branch '5554-delete-job-log-rows-wip'
Closes #5554, #5798. Brett Smith
03:23 pm Revision 81fb9f6e (arvados): 5554: Add Rake task to delete old job log records.
Brett Smith
03:23 pm Revision 123ef960 (arvados): 5554: Clean up erroneous fixture pipeline state.
Brett Smith
03:23 pm Revision 45b556d1 (arvados): 5554: Workbench links finished job logs from pipeline instance log tab.
This is an affordance to help users find logs after they're removed
from the API server's logs table. The display is...
Brett Smith
03:17 pm Revision 08378f19 (arvados): 5554: Add progress logs header.
Brett Smith
03:05 pm Revision d5d43d27 (arvados): 5554: Fixup pipeline instance model to avoid duplication.
Brett Smith
03:01 pm Story #2256: [Workbench] Users can access an Arvados shell through the Web
Design sketch:
* Run a tty.js daemon by default on each shell node. Add authentication logic that uses the API to...
Peter Amstutz
02:56 pm Story #2256: [Workbench] Users can access an Arvados shell through the Web
As a 5 minute proof of concept, I installed on one of my shell nodes that I had root on:... Abram Connelly
02:52 pm Story #2256: [Workbench] Users can access an Arvados shell through the Web
https://github.com/chjj/tty.js/ Peter Amstutz
02:25 pm Bug #5780 (Resolved): [Workbench] When sharing a project and searching/selecting users, explain t...
Applied in changeset arvados|commit:b1db376a4532ba3484929b3214e59056877d1695. Radhika Chippada
02:18 pm Bug #5780: [Workbench] When sharing a project and searching/selecting users, explain that users a...
commit:f6f6ed6 is good to merge. Thanks. Brett Smith
02:23 pm Revision b1db376a (arvados): closes #5780
Merge branch '5780-sharing-popup-message' Radhika Chippada
02:22 pm Revision 81668355 (arvados): Merge branch 'master' into 5780-sharing-popup-message
Radhika Chippada
01:54 pm Task #5795 (In Progress): Review branch: 5780-sharing-popup-message
Brett Smith
01:52 pm Bug #5766: [SDK] setup.py install always gets latest arvados-python-sdk from PyPi, even when alre...
Please merge commit:8b51595. Thanks. Brett Smith
01:35 pm Task #5825 (Resolved): Review branch: 5622-fix-timeout-pdh-page
Radhika Chippada
01:35 pm Task #5786 (In Progress): Review 5766-pip-sdk-install in arvados-dev
Brett Smith
01:34 pm Bug #5739: [Workbench] Remove artificial sqlite3 dependency
commit:0054f6b is good to merge. Thanks. Brett Smith
01:33 pm Feature #5622 (In Progress): [Workbench] Fix timeout when generating long "list of collections wi...
Radhika Chippada
01:30 pm Revision 5b953441 (arvados): 5622: one more test assertion for tab_counts for hash matches tab.
Radhika Chippada
01:16 pm Task #5816 (In Progress): Review 5739-no-sqlite3
Brett Smith

04/26/2015

10:01 pm Revision 648bcf7d (arvados): 5622: add test for infinite scrolling for hash matches page.
Radhika Chippada
08:41 pm Revision 7f430fb0 (arvados): 5622: add tab_counts to hash_matches tab
Radhika Chippada
09:38 am Revision 5d24ae66 (arvados-dev): v3.6.3
Sitaram Chamarty
01:59 am Revision 1d9bae1d (arvados): Merge branch 'master' into 5622-pdh-collections-page-paging
Radhika Chippada
01:58 am Revision 05250216 (arvados): 5622: white space
Radhika Chippada
01:54 am Revision 0260d6ee (arvados): 5622: add paging to hash matches display page.
Radhika Chippada
12:22 am Revision 276cf761 (arvados-dev): git-annex-shell: accept repo paths without '~/'
It seems that (some versions of) git-annex use repository paths that simply
start with '/' instead of '/~/', so make ...
Benoît Knecht
12:22 am Revision dd8bc172 (arvados-dev): allow limited remote use of 'git config'
gitolite tester

04/24/2015

10:15 pm Story #5554: [API] Delete crunch job log messages from logs table after the jobs finish
My earlier comment was mistaken. While it's true that this branch does not remove pipeline stderr logs, currently cr... Brett Smith
10:10 pm Revision 5374510c (arvados): 5554: Clean up erroneous fixture pipeline state.
Brett Smith
10:10 pm Revision 1aee2f37 (arvados): 5554: Fixup: Test the Rake task.
Brett Smith
10:10 pm Revision fbf2382d (arvados): 5554: Workbench links finished job logs from pipeline instance log tab.
This is an affordance to help users find logs after they're removed
from the API server's logs table. The display is...
Brett Smith
08:35 pm Story #5824 (Resolved): [Workbench] [Keep] collection browse/download server
Location
* source:services/keep-web
* deb/rpm package name: keep-web
Authentication mechanisms needed
* Accept ...
Tom Clegg
08:06 pm Story #3198 (In Progress): [FUSE] Writable streaming arv-mount
Peter Amstutz
07:51 pm Feature #5416 (Resolved): [API] Clone git repositories without using an SSH private key
Tom Clegg
07:51 pm Feature #3455 (Resolved): [Workbench] Install cgit or Gitweb or similar git frontend for browsing...
Tom Clegg
07:50 pm Task #5687 (Resolved): Review 5416-browse-repo-tree (with 5416-ssl-proxy on arvados-dev)
Tom Clegg
06:46 pm Bug #5820 (New): [Workbench] Missing link target in iframe error message
If a collection disappears while open in workbench, the tab reloads and the error message suggests browsing all colle... Tom Clegg
06:46 pm Feature #5787 (In Progress): [Crunch] Add Crunch support to GATK Queue
Ward Vandewege
06:46 pm Bug #5819: Cannot install Arvados
It happened 10 times or so. And I am stuck at this point.
Please note that following worked on command line.
apt-...
Darshan Singh
06:35 pm Bug #5819: Cannot install Arvados
Darshan Singh wrote:
> I followed intructions at
> http://doc.arvados.org/install/install-docker.html
>
> I kee...
Ward Vandewege
06:29 pm Bug #5819 (New): Cannot install Arvados
Hi,
I followed intructions at
http://doc.arvados.org/install/install-docker.html
I keep getting error at:
Ste...
Darshan Singh
04:18 pm Task #5816 (Resolved): Review 5739-no-sqlite3
Tom Clegg
02:37 pm Bug #5814: give arv a --debug option
The title of this issue should be changed, but I can't change it. Pjotr Prins
02:30 pm Bug #5814: give arv a --debug option
Oh, sorry. After editing arv to show the exception it actually says
/gnu/store/m3syi7s4idxwkqmrppinm19hrv9nhvg7-...
Pjotr Prins
02:11 pm Bug #5814 (New): give arv a --debug option
arv keep docker
Please install all required gems:
gem install activesupport andand curb google-api-client jso...
Pjotr Prins
07:13 am Revision 41068df2 (arvados): 5739: Remove unnecessary sqlite3 dependency.
Tom Clegg

04/23/2015

10:24 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Currently, Arvados isn't very smart about the "someone queued 1000 jobs" case. Because of that, and the job-warmup ti... Tom Clegg
10:10 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Here's an illustrative line from a Queue job.... Tom Clegg
06:47 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
h3. starting Arvados job_tasks from Queue
A crunch job can't do "add a job_task, and wait for it to finish" becaus...
Tom Clegg
09:52 pm Revision 749b8714 (arvados): run_test_server doesn't assume ARVADOS_API_TOKEN is set.
This makes it slightly more feasible to run this script (and by
extension tests for individual components like Workbe...
Brett Smith
09:28 pm Revision 9e0100ce (arvados): Fix typo. No issue #
Tom Clegg
07:41 pm Bug #5713: [FUSE] File access sometimes takes too long on su92l
... Abram Connelly
06:52 pm Story #5554: [API] Delete crunch job log messages from logs table after the jobs finish
Brett said:
> @stderr_log_history@ is still likely to find logs for the pipeline instance itself, which only exist...
Radhika Chippada
06:32 pm Story #5554: [API] Delete crunch job log messages from logs table after the jobs finish
Radhika Chippada wrote:
> * Can you please make the default setting value 30 in application.default.yml file?
>
> ...
Brett Smith
05:48 pm Story #5554: [API] Delete crunch job log messages from logs table after the jobs finish
Review comments:
* Can you please make the default setting value 30 in application.default.yml file?
* Would yo...
Radhika Chippada
04:42 pm Story #5554: [API] Delete crunch job log messages from logs table after the jobs finish
5554-delete-job-log-rows-wip is up for review. Suggested test: add @finished_at: <%= 14.days.ago.to_s(:db) %>@ to th... Brett Smith
03:09 pm Story #5554 (In Progress): [API] Delete crunch job log messages from logs table after the jobs fi...
Brett Smith
06:47 pm Bug #3793 (In Progress): [Crunch] Docker containers not removed consistently, filling disk
Brett Smith
06:25 pm Revision 0bef99f4 (arvados): 5554: Fixup documentation per code review.
Brett Smith
06:06 pm Revision bfee777f (arvados): Merge branch 'master' into 5720-ajax-loading-error
Radhika Chippada
06:03 pm Bug #5720: [Workbench] Search for pipeline templates breaks
Reviewing commit:e5f039f
It seems like the basic issue here is that we're taking a non-string type (a Date) and pu...
Brett Smith
05:46 pm Task #5776 (In Progress): Review branch: 5720-ajax-loading-error
Brett Smith
05:33 pm Task #5798 (In Progress): Review 5554-delete-job-log-rows-wip
Radhika Chippada
04:40 pm Task #5798 (Resolved): Review 5554-delete-job-log-rows-wip
Brett Smith
05:10 pm Bug #5796 (Resolved): [API] search index on collections fails sometimes. Make it not fail by remo...
Applied in changeset arvados|commit:f095b4447de612fd1cd7bee5f9121df76cd65434. Radhika Chippada
05:05 pm Bug #5796: [API] search index on collections fails sometimes. Make it not fail by removing file_n...
commit:559fdf1 is good to merge. Thanks. Brett Smith
05:03 pm Bug #5796: [API] search index on collections fails sometimes. Make it not fail by removing file_n...
Added down migration with file_names in it.
Not sure why the column order is being updated. Instead of manually ch...
Radhika Chippada
04:56 pm Bug #5796: [API] search index on collections fails sometimes. Make it not fail by removing file_n...
Comments on commit:2b39eaf.
Can you please write the down migration? It'll be the same as the up migration, excep...
Brett Smith
04:12 pm Bug #5796: [API] search index on collections fails sometimes. Make it not fail by removing file_n...
Added a new migration script that drops and recreates search index on collections table without the file_names column... Radhika Chippada
02:48 pm Bug #5796 (In Progress): [API] search index on collections fails sometimes. Make it not fail by r...
Radhika Chippada
02:48 pm Bug #5796 (Resolved): [API] search index on collections fails sometimes. Make it not fail by remo...
ERROR: index row size 2768 exceeds maximum 2712 for index "collections_search_index" Radhika Chippada
05:06 pm Revision f095b444 (arvados): closes #5796
Merge branch '5796-collection-search-index' Radhika Chippada
05:01 pm Revision 559fdf14 (arvados): 5796: add down migration
Radhika Chippada
04:48 pm Task #5797 (In Progress): Review branch: 5796-collection-search-index
Brett Smith
04:13 pm Task #5797 (Resolved): Review branch: 5796-collection-search-index
Radhika Chippada
04:40 pm Revision da15fc09 (arvados): 5554: Add Rake task to delete old job log records.
Brett Smith
04:10 pm Revision 2b39eafa (arvados): 5796: omit file_names column from collections search index.
Radhika Chippada
02:37 pm Revision 7538d084 (arvados): Merge branch 'master' into 5720-ajax-loading-error
Radhika Chippada
02:00 pm Revision 97ca7222 (arvados): 5416: Test with HEAD in current tree, not master: jenkins index has ...
Improve logging in test suite.
refs #5416
Tom Clegg
01:25 am Task #5795 (Resolved): Review branch: 5780-sharing-popup-message
Radhika Chippada
01:25 am Bug #5780: [Workbench] When sharing a project and searching/selecting users, explain that users a...
Implementation notes:
* Added a "message" display to chooser. Pass message to chooser when sharing popup is being ...
Radhika Chippada
01:21 am Revision f6f6ed67 (arvados): 5780: Display message in chooser popup if one is provided. Use this ...
explaining to user that only those users or groups that the user is allowed to access are displayed. Radhika Chippada
12:01 am Bug #5794 (New): Docker run shows up everytime in the beginning of a job and the task exists 1 bu...
from qr1hi-8i9sb-9wytp6ji25uxiwt
2015-04-22_23:58:59 salloc: Granted job allocation 274
2015-04-22_23:59:01 qr1hi...
Bryan Cosca

04/22/2015

09:56 pm Story #3198: [FUSE] Writable streaming arv-mount
Reviewing 3198-inode-cache at commit:2139ee84
* Any chance of getting tests for this? I know it's difficult to in...
Brett Smith
02:56 pm Story #3198: [FUSE] Writable streaming arv-mount
Additional notes on 3198-inode-cache:
File and all of its subclasses moved to fusefile.py. Mostly unmodified exce...
Peter Amstutz
07:27 pm Bug #5780 (In Progress): [Workbench] When sharing a project and searching/selecting users, explai...
Radhika Chippada
07:17 pm Bug #5780: [Workbench] When sharing a project and searching/selecting users, explain that users a...
In IRC:
tomclegg
3:12 radhika: I think it might be better to put it in the "select users" box, but wouldn't call ...
Radhika Chippada
06:28 pm Revision 1765cd32 (arvados): Merge branch '5416-browse-repo-tree' refs #5416
Tom Clegg
06:27 pm Revision 3002e7a6 (arvados): Merge branch '5416-ssl-proxy' refs #5416
Tom Clegg
06:27 pm Revision 3002e7a6 (arvados-dev): Merge branch '5416-ssl-proxy' refs #5416
Tom Clegg
06:12 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Tests in 5416-browse-repo-tree pass.
It would be nice if you could incorporate 5416-use-netrc-credentials so it wo...
Peter Amstutz
05:35 pm Feature #5416: [API] Clone git repositories without using an SSH private key
In arvados-dev 5416-ssl-proxy, if the test fails (due to a misconfiguration on my part, here) it doesn't shut down ke... Peter Amstutz
06:11 pm Task #5774 (Resolved): Review branch: 5663-doc-rake-secret
Radhika Chippada
04:53 pm Task #5774 (In Progress): Review branch: 5663-doc-rake-secret
Tom Clegg
05:42 pm Story #5793 (New): [Workbench] Add search filter to "/links" page
Radhika Chippada
05:35 pm Bug #5663 (Resolved): [Documentation] Use "...puts rand()..." instead of "rake secret" in apiserv...
Applied in changeset arvados|commit:2054cdb05d79a3c45e8346661adc81062c383b16. Radhika Chippada
04:53 pm Bug #5663: [Documentation] Use "...puts rand()..." instead of "rake secret" in apiserver/workbenc...
LGTM, thanks! Tom Clegg
05:35 pm Bug #5783 (Resolved): [Workbench] Add new ssh key modal cancels instead of submits when enter is ...
Applied in changeset arvados|commit:698b9c0ebf2f12c72718ebde13c63e904fff3332. Radhika Chippada
05:29 pm Bug #5783 (In Progress): [Workbench] Add new ssh key modal cancels instead of submits when enter ...
Radhika Chippada
05:34 pm Task #5791 (New): [Workbench] Job log memory and swap lines should use the same scale
The attached screenshot shows a job log graph for a job that's using 8GiB of memory and 20MiB of swap. The graph mak... Brett Smith
05:33 pm Bug #5523: [Crunch] crunchstat should not report errors during normal timing races
Here is an example: https://cloud.curoverse.com/collections/111de0eb53db4ff9849dc2e63178425d+85/qr1hi-8i9sb-8vyxlg0da... Bryan Cosca
05:31 pm Revision 2054cdb0 (arvados): closes #5663
Merge branch '5663-doc-rake-secret' Radhika Chippada
05:30 pm Revision d65e411a (arvados): Merge branch 'master' into 5663-doc-rake-secret
Radhika Chippada
05:29 pm Bug #5790 (Resolved): [SDKs] arv-copy does not select the correct Docker image to copy
A user just reported a bug where arv-copy was failing trying to copy a nonexistent collection UUID while copying a pi... Brett Smith
05:27 pm Revision 698b9c0e (arvados): closes #5783
5783: add type="button" for Cancel button in add ssh key popup. Radhika Chippada
04:55 pm Task #5789 (In Progress): Test somehow
Tom Clegg
04:54 pm Task #5789 (Resolved): Test somehow
Tom Clegg
04:54 pm Task #5639 (Resolved): Update test utils to mock pycurl instead of requests
Tom Clegg
04:54 pm Story #5788 (New): [SDKs] [refactor] Dry up KeepService get() and put() in arvados/keep.py
Tom Clegg
04:54 pm Task #5638 (Resolved): Update keep client library
Tom Clegg
04:22 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Pjotr Prins wrote:
> Pjotr Prins wrote:
> > https://github.com/broadgsa/gatk/blob/master/public/gatk-queue/src/main...
Pjotr Prins
03:55 pm Feature #5787: [Crunch] Add Crunch support to GATK Queue
Pjotr Prins wrote:
> https://github.com/broadgsa/gatk/blob/master/public/gatk-queue/src/main/scala/org/broadinstitut...
Pjotr Prins
03:40 pm Feature #5787 (Resolved): [Crunch] Add Crunch support to GATK Queue

https://github.com/broadgsa/gatk/blob/master/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engin...
Pjotr Prins
03:12 pm Task #5786 (Resolved): Review 5766-pip-sdk-install in arvados-dev
Peter Amstutz
03:07 pm Revision 8b51595b (arvados): 5766: Make sure it doesn't try to fetch arvados packages from PyPi, ...
we only install the local ones. Peter Amstutz
03:07 pm Revision 8b51595b (arvados-dev): 5766: Make sure it doesn't try to fetch arvados packages from Py...
we only install the local ones. Peter Amstutz
03:05 pm Bug #5766 (In Progress): [SDK] setup.py install always gets latest arvados-python-sdk from PyPi, ...
Peter Amstutz
02:36 pm Revision e5aebef9 (arvados): Merge branch 'master' into 5663-doc-rake-secret
Radhika Chippada
02:16 pm Revision 2dcda0de (arvados): 5416: Use netrc to store credentials
Peter Amstutz
02:14 pm Task #5725 (In Progress): Review 3198-inode-cache
Brett Smith
12:46 pm Task #5785 (Resolved): Documentation and code cleanup
Peter Amstutz
12:46 pm Task #5719 (Resolved): Process event bus updates
Peter Amstutz
12:46 pm Task #5719 (In Progress): Process event bus updates
Peter Amstutz
12:46 pm Task #5445 (Resolved): Update FUSE to use new SDK
Peter Amstutz
12:46 pm Task #5718 (Resolved): Inode caching does not use unlimited memory
Peter Amstutz
12:46 pm Task #5630 (In Progress): Write tests
Peter Amstutz
12:20 pm Bug #5675 (Resolved): [Workbench] Show project Subprojects tab when in anonymous view.
Applied in changeset arvados|commit:66e68045ed5b7c4ebca49d81e58ef6f821e8bb89. Radhika Chippada
12:16 pm Revision 66e68045 (arvados): closes #5675
Merge branch '5675-project-subprojects-in-anonymous-view' Radhika Chippada

04/21/2015

11:48 pm Revision a80da842 (arvados-dev): openssh 6.8 again... forgot sshkeys-lint the last time!
Sitaram Chamarty
09:12 pm Revision 296e1b20 (arvados): 3198: Support for listening for events to trigger collection updates...
Peter Amstutz
08:52 pm Bug #5490: [Crunch] Job should not be reused when docker tag _or_ arvados sdk version now resolve...
More design from IRC:
(03:36:45 PM) Me: So maybe the right thing to do is to always interpret hashes as commits ov...
Brett Smith
08:51 pm Task #5784 (Resolved): Review 5490-crunch-tighten-job-reuse-wip
Brett Smith
08:48 pm Revision 34c1b7be (arvados): 5490: Require exact matches in API server's default job reuse filters.
The previous default filters would reuse jobs that used any Docker
image with the matching name, and/or Arvados SDK v...
Brett Smith
08:48 pm Revision 9ab0e274 (arvados): 5490: Clean up API server previous job fixtures.
* Every fixture that specified an arvados_sdk_version constraint
should also specify a docker_image constraint, to ...
Brett Smith
08:48 pm Revision 53eb212f (arvados): 5490: Test API server handling of git hash-like branch names.
If you have a branch that looks like a commit hash, different git subcommands do different things. After extended di... Brett Smith
08:48 pm Revision 5f4ce1c3 (arvados): 5490: Test API server finds Docker images with hash names.
This is in the same spirit as the previous, analogous commit for git
branches.
Brett Smith
08:48 pm Revision 79a83a09 (arvados): 5490: Refactor API server job_reuse_controller_test.
Teach the convenience methods to start from any fixture job as a basis
for submitting new ones and comparing.
Brett Smith
08:40 pm Bug #5783 (Resolved): [Workbench] Add new ssh key modal cancels instead of submits when enter is ...
When adding a new ssh key in workbench, if the user fills out all the fields and hits enter, the modal exits without ... Sarah Guthrie
08:20 pm Feature #5782 (New): [Workbench] Support entering boolean script_parameters when editing a pipeli...
Tom Clegg
08:07 pm Story #5781 (In Progress): [API] [DRAFT] Provide API methods for manipulating and combining colle...
Currently workbench provides “create a new collection by combining selected collections” and “create a new collection... Radhika Chippada
07:47 pm Bug #5662: [FUSE] cd/ls sometimes takes too long on su92l
This is still occurring today, and isn't explained by "fuse gets too big and starts swapping" (it happens when FUSE i... Tom Clegg
07:06 pm Bug #5779 (Closed): Search users in sharing tab not working?
Only possible when in same group Joep de Ligt
04:40 pm Bug #5779 (Closed): Search users in sharing tab not working?
When I search for a collaborator with an account on curoverse he doesn't show up as a user to share the project with Joep de Ligt
06:59 pm Task #5639 (In Progress): Update test utils to mock pycurl instead of requests
Tom Clegg
06:59 pm Task #5637 (Resolved): Update package dependencies
Tom Clegg
06:43 pm Bug #5780 (Resolved): [Workbench] When sharing a project and searching/selecting users, explain t...
Tom Clegg
05:48 pm Revision b05e1bb4 (arvados): Merge branch 'master' into 5663-doc-rake-secret
Radhika Chippada
05:47 pm Revision 9816d2cf (arvados): Merge branch 'master' into 5675-project-subprojects-in-anonymous-view
Radhika Chippada
05:46 pm Revision e5f039f2 (arvados): Merge branch 'master' into 5720-ajax-loading-error
Radhika Chippada
05:39 pm Revision f69d2824 (arvados): Merge branch 'master' into 3198-writable-fuse
Conflicts:
sdk/python/arvados/arvfile.py
Peter Amstutz
05:36 pm Bug #5682 (Resolved): [Workbench] Can't view/download files under subdirectories in stream
Resolved by #5179 Radhika Chippada
05:30 pm Bug #5179 (Resolved): [Workbench] [SDKs] Incorrect collection display when stream has entries wit...
Applied in changeset arvados|commit:da705110826943b04151f959e059b5f4ffcc4c5e. Radhika Chippada
04:17 pm Bug #5179: [Workbench] [SDKs] Incorrect collection display when stream has entries with subdirect...
comments on 5179-dirs-in-filenames @ commit:17e59fe
Code looks good. (The "rpartition" threw me off for a bit by u...
Tom Clegg
05:27 pm Task #5773 (Resolved): Review branch: 5179-dirs-in-filenames
Radhika Chippada
04:02 pm Task #5773 (In Progress): Review branch: 5179-dirs-in-filenames
Tom Clegg
05:23 pm Revision 70517408 (arvados): refs #5179 : gem version in workbench
Radhika Chippada
05:18 pm Revision da705110 (arvados): closes #5179
Merge branch '5179-dirs-in-filenames' Radhika Chippada
05:16 pm Revision 8a42d33f (arvados): 5179: one more test with multilevel manifest text
Radhika Chippada
04:56 pm Revision 2b42046d (arvados): Merge branch 'master' into 5179-dirs-in-filenames
Radhika Chippada
03:44 pm Revision 4077a9af (arvados): 3198: Implement rename() (efficient move within/between collections).
Peter Amstutz
02:35 pm Feature #5778 (New): [FUSE] Support efficient copy at command line
Keep can perform efficient copy-on-write of files and directories, but POSIX doesn't provide an API for this. We've ... Peter Amstutz
03:59 am Revision 32131dfa (arvados): 3198: Fix test deadlock. Track inode lifetimes.
Peter Amstutz
03:53 am Task #5777 (Resolved): Resolve merge conflicts, check tests
Tom Clegg
01:04 am Revision 53f785c2 (arvados): Added logger util GetOrCreateMap() and started using it everywhere.
Moved logging of summary info into ReadCollections.Summarize().
Renamed ComputeBlockReplicationCounts(readServers *Re...
Misha Zatsman

04/20/2015

09:02 pm Task #5638 (In Progress): Update keep client library
Tom Clegg
09:02 pm Task #5777 (In Progress): Resolve merge conflicts, check tests
Tom Clegg
09:02 pm Task #5777 (Resolved): Resolve merge conflicts, check tests
Tom Clegg
08:58 pm Revision 08717a74 (arvados): 5416: Remove second trailing slash in breadcrumbs link.
Tom Clegg
08:58 pm Revision de679534 (arvados): 5416: Disable repository browsing (and skip tests) if git version is...
Tom Clegg
08:58 pm Revision 94b57902 (arvados): 5416: Use http://foo:bar@host:port/ instead of credential helper.
Tom Clegg
08:58 pm Revision 983e7c81 (arvados): 5416: Fix protected method that should have been public.
Tom Clegg
08:58 pm Revision 3c36af3d (arvados): 5416: Do not override git urls for remote hosted repos.
Tom Clegg
08:58 pm Revision 86860e7d (arvados): 5416: Run arv-git-httpd and nginx ssl proxy in test suite.
Tom Clegg
08:58 pm Revision e2412504 (arvados): 5416: Add read-only clone_urls attribute to Repository resources, de...
Tom Clegg
08:58 pm Revision 9136a1b1 (arvados): 5416: Browse git repository contents in workbench.
Tom Clegg
08:58 pm Revision 4f99b52f (arvados): 5416: Fix comment.
Tom Clegg
08:30 pm Revision c674deff (arvados): Revert errant change in f8e6cb3. refs #3126
Tom Clegg
08:11 pm Task #5716 (Resolved): Review branch: 5647-login-dropdown
Radhika Chippada
07:23 pm Revision 916a3a8b (arvados): Docker: fix the build of the sso docker container.
No issue # Ward Vandewege
06:45 pm Story #3126 (Resolved): [API] Support use of anonymous git url (like github https) as repository ...
Applied in changeset arvados|commit:86e078ae126f6651428219c726c34da3bd7f7495. Tom Clegg
06:44 pm Task #5776 (Resolved): Review branch: 5720-ajax-loading-error
Radhika Chippada
06:43 pm Bug #5720: [Workbench] Search for pipeline templates breaks
Implementation notes:
It appears that the check for new ajax request is failing. I added console.log and found tha...
Radhika Chippada
06:21 pm Bug #5720 (In Progress): [Workbench] Search for pipeline templates breaks
Radhika Chippada
06:40 pm Revision 86e078ae (arvados): Merge branch '3126-remote-git-url' closes #3126
Tom Clegg
06:33 pm Revision 37ab1709 (arvados): 5720: ajax new request check update
Radhika Chippada
06:32 pm Revision e36e6c4e (arvados): 3126: Skip some unnecessary db resets.
Tom Clegg
06:31 pm Revision 29a1b2c8 (arvados): 3126: Use localhost to simulate API failures. reset_application_conf...
nstead of setup. Remove superfluous cleanup. Tom Clegg
06:31 pm Revision 2fe2dca0 (arvados): 3126: Fix test. Avoid excess "git init" by probing with "git branch"...
Tom Clegg
06:31 pm Revision 528f9bb7 (arvados): 3126: Always act as current_user in Commit.find_commit_range.
Tom Clegg
06:31 pm Revision c5506094 (arvados): 3126: Accept remote http/https/git url as repository attr in jobs.cr...
Tom Clegg
06:31 pm Revision f8e6cb30 (arvados): 3126: Handle "no local repository" case better.
Tom Clegg
06:31 pm Revision b3a23a94 (arvados): 3126: Delete git cache dir in test teardown. Remove no-op test.
Tom Clegg
06:31 pm Revision 0f56ce4b (arvados): 3126: Do not try to do anything with job.repository in crunch-dispat...
Tom Clegg
06:31 pm Revision 430ed273 (arvados): 3126: Update API docs.
Tom Clegg
06:03 pm Task #5771 (Resolved): Review branch: 5620-collection-selections
Radhika Chippada
02:46 pm Task #5771 (In Progress): Review branch: 5620-collection-selections
Tom Clegg
04:55 pm Revision 3355f801 (arvados): closes #5573
Merge branch '5573-user-activity-page-performance' Radhika Chippada
04:44 pm Revision ae34bc2d (arvados): Merge branch 'master' into 5573-user-activity-page-performance
Radhika Chippada
04:40 pm Bug #5753 (Resolved): [Workbench] Job name column is displayed even though job only supports desc...
Applied in changeset arvados|commit:a0993e451f8a5e209df74dc9f8f0e55bdf1c73bd. Radhika Chippada
02:38 pm Bug #5753: [Workbench] Job name column is displayed even though job only supports description
commit:de0f310 LGTM, thanks. Tom Clegg
04:40 pm Bug #5620 (Resolved): [Workbench] Collection#show page search filter is neither cleared nor appli...
Applied in changeset arvados|commit:1fe347f8cf77564a791b9f98963fc73ee6802c4f. Radhika Chippada
03:01 pm Bug #5620: [Workbench] Collection#show page search filter is neither cleared nor applied when bac...
1.5 comments at commit:4ccec6c:
Glad <code class="javascript">$('input').trigger('input');</code> works, but I thi...
Tom Clegg
04:36 pm Revision a0993e45 (arvados): closes #5753
Merge branch '5753-job-name-column-in-project-page' Radhika Chippada
04:30 pm Revision 9ede4c6a (arvados): Merge branch 'master' into 5753-job-name-column-in-project-page
Radhika Chippada
04:29 pm Revision 1fe347f8 (arvados): closes #5620
Merge branch '5620-collection-selections' Radhika Chippada
04:23 pm Bug #5766: [SDK] setup.py install always gets latest arvados-python-sdk from PyPi, even when alre...
So removing --upgrade isn't the whole story. There's a pip bug, too:
http://stackoverflow.com/questions/8579879/i...
Peter Amstutz
03:42 pm Revision c5cd44ad (arvados): 5620: added comment to input trigger event
Radhika Chippada
02:43 pm Task #5758 (Resolved): Review branch: 5753-job-name-column-in-project-page
Radhika Chippada
02:38 pm Task #5758 (In Progress): Review branch: 5753-job-name-column-in-project-page
Tom Clegg
01:55 pm Task #5751 (Resolved): Review 3145-readonly-volumes
Tom Clegg
01:18 pm Bug #5426: [Workbench] Large downloads through workbench fail
Actually, it appears that the original download listed in the ticket also does not download completely. It terminates... Radhika Chippada

04/19/2015

03:19 am Task #5741 (Resolved): Review branch: 5417-not-start-pipeline-with-unreadable-inputs
Radhika Chippada
03:17 am Task #5774 (Resolved): Review branch: 5663-doc-rake-secret
Radhika Chippada
03:17 am Bug #5663: [Documentation] Use "...puts rand()..." instead of "rake secret" in apiserver/workbenc...
Notes:
* Updated API and Workbench documentation to use "puts rand" instead of "rake secret"
* Also updated SSO...
Radhika Chippada
03:13 am Bug #5663 (In Progress): [Documentation] Use "...puts rand()..." instead of "rake secret" in apis...
Radhika Chippada
03:12 am Revision 3aaf2058 (arvados): 5663: update documentation to use "puts rand" in place of "rake secret"
Radhika Chippada
02:36 am Bug #5682 (In Progress): [Workbench] Can't view/download files under subdirectories in stream
Radhika Chippada
02:33 am Task #5773 (Resolved): Review branch: 5179-dirs-in-filenames
Radhika Chippada
02:33 am Bug #5179: [Workbench] [SDKs] Incorrect collection display when stream has entries with subdirect...
Implementation notes:
* Updated Keep#files method as per Tom's note. Added test fixture and test.
* Updated wor...
Radhika Chippada
02:30 am Bug #5179 (In Progress): [Workbench] [SDKs] Incorrect collection display when stream has entries ...
Radhika Chippada
02:25 am Revision 17e59fe0 (arvados): 5179: update arvados ruby sdk gem version in workbench.
Radhika Chippada
02:22 am Revision e1eabe76 (arvados): 5179: update files method to move dir parts to streamname.
Radhika Chippada

04/18/2015

02:56 am Bug #5720: [Workbench] Search for pipeline templates breaks
This issue is purely related to the ajax reloading. A few scenarios where the issue can be experienced:
* I think ...
Radhika Chippada
02:41 am Revision 910a5f7a (arvados): 5675: include Subprojects tab in project#show for anonymous users.
Radhika Chippada
02:19 am Bug #5675 (In Progress): [Workbench] Show project Subprojects tab when in anonymous view.
Radhika Chippada
12:46 am Bug #5426 (In Progress): [Workbench] Large downloads through workbench fail
I'm re-opening this bug.
The collection mentioned above downloads fine, now that we have proxy_buffering disabled....
Ward Vandewege

04/17/2015

09:49 pm Bug #5521: [Workbench] Slow download speed from browser
Bryan - this ticket requires more information: which file, exactly, were they trying to download?
Now that qr1hi l...
Ward Vandewege
06:05 pm Bug #5521 (In Progress): [Workbench] Slow download speed from browser
Tom Clegg
09:19 pm Feature #5416: [API] Clone git repositories without using an SSH private key
After lots of testing, I've convinced myself the inconsistent failures are the fault of git (or something under it).
...
Tom Clegg
09:08 pm Task #5771 (Resolved): Review branch: 5620-collection-selections
Radhika Chippada
09:07 pm Bug #5620 (In Progress): [Workbench] Collection#show page search filter is neither cleared nor ap...
Radhika Chippada
09:07 pm Bug #5620: [Workbench] Collection#show page search filter is neither cleared nor applied when bac...
Implementation notes:
Added ready handler for input. To test, use Chrome (and probably Safari) to view a collectio...
Radhika Chippada
06:57 pm Bug #5620: [Workbench] Collection#show page search filter is neither cleared nor applied when bac...
Suggestions
* Perhaps the browser sends an event when it puts stuff in the input, like "input" or "change" or "autoc...
Tom Clegg
08:58 pm Revision 4ccec6c3 (arvados): 5620: add ready handler for input
Radhika Chippada
08:48 pm Revision d6485694 (arvados-dev): 5416: Support testargs for go bits, like "services/arv-git-httpd...
Tom Clegg
08:48 pm Revision f9bc13bd (arvados-dev): 5416: Run keepproxy, arv-git-httpd, and SSL proxy services durin...
Tom Clegg
08:48 pm Revision f9bc13bd (arvados): 5416: Run keepproxy, arv-git-httpd, and SSL proxy services during Wo...
Tom Clegg
08:48 pm Revision d6485694 (arvados): 5416: Support testargs for go bits, like "services/arv-git-httpd_tes...
Tom Clegg
08:42 pm Bug #5766: [SDK] setup.py install always gets latest arvados-python-sdk from PyPi, even when alre...
I suspect if we don't use --upgrade we'll need to manually clear the virtualenv when not using --skip-install. This m... Tom Clegg
06:26 pm Bug #5766: [SDK] setup.py install always gets latest arvados-python-sdk from PyPi, even when alre...
I'm not sure if the @--upgrade@ flag provides any provides any upside here, if our normal process is to re-create the... Peter Amstutz
06:10 pm Bug #5766 (Resolved): [SDK] setup.py install always gets latest arvados-python-sdk from PyPi, eve...
@run-tests.sh@ installs pip packages this way:... Peter Amstutz
07:06 pm Feature #5769 (New): [OPS] Routinely check for stale Gemfile.lock
Tom Clegg
07:03 pm Bug #5720: [Workbench] Search for pipeline templates breaks
Is this just happening when the search term ends with a space, or is that a coincidence?
If that's not it, it woul...
Tom Clegg
06:49 pm Bug #5179: [Workbench] [SDKs] Incorrect collection display when stream has entries with subdirect...
Looks like this is a bug in Keep#files in source:sdk/ruby/lib/arvados/keep.rb#L164 -- each_file_spec provides [stream... Tom Clegg
06:33 pm Bug #5604 (Rejected): [Workbench] Fiddlesticks when going back from collection#show to collection...
We are removing the collections page. See #5743 Radhika Chippada
06:32 pm Feature #5768 (New): [Node Manager] Add max_node_per_user config
This should make it possible for one user to queue many dozens of jobs (intentionally or not) without preventing ever... Tom Clegg
06:21 pm Bug #5481: [Workbench] Pipeline instance page does not automatically refresh when pipeline does n...
I'm guessing this is what it looks like when we haven't done #5767 yet:
# Workbench renders page with current pipeli...
Tom Clegg
06:18 pm Feature #5767 (New): [API] Websockets subscribe API should accept a start timestamp, so clients d...
Tom Clegg
05:17 pm Bug #5753 (In Progress): [Workbench] Job name column is displayed even though job only supports d...
Radhika Chippada
05:14 pm Bug #5753: [Workbench] Job name column is displayed even though job only supports description
Since we do not display description in project#show for any object types, it would be desirable that you create a sep... Radhika Chippada
05:15 pm Task #5758 (Resolved): Review branch: 5753-job-name-column-in-project-page
Radhika Chippada
02:59 pm Revision de0f310b (arvados): 5753: show name column in project#show page when the object supports...
Radhika Chippada
02:47 pm Story #3126: [API] Support use of anonymous git url (like github https) as repository in jobs.create
Tests are passing now, commit:de3e44a LGTM Peter Amstutz
01:37 pm Revision d477846a (arvados): 5416: Use http://foo:bar@host:port/ instead of credential helper.
Tom Clegg
02:15 am Revision e9be782d (arvados): 5573: The activity page retrieves too much data that it does not nee...
Radhika Chippada
01:04 am Revision 34abff57 (arvados): 5416: Disable repository browsing (and skip tests) if git version is...
Tom Clegg
01:04 am Revision d4deb059 (arvados): 5416: Remove second trailing slash in breadcrumbs link.
Tom Clegg
01:04 am Revision 0929ea35 (arvados): 5416: Add read-only clone_urls attribute to Repository resources, de...
Tom Clegg

04/16/2015

10:10 pm Bug #5417 (Resolved): [Workbench] Show error condition / refuse to start a pipeline instance if s...
Applied in changeset arvados|commit:6a8f05bbd4e8ae51464ece5ee73898d7f58edd71. Radhika Chippada
06:28 pm Bug #5417: [Workbench] Show error condition / refuse to start a pipeline instance if some inputs ...
On commit:dc96093e, just one small last thing:
Radhika Chippada wrote:
> * While testing, I noticed that the func...
Brett Smith
05:46 pm Bug #5417: [Workbench] Show error condition / refuse to start a pipeline instance if some inputs ...
Brett said:
> In pipeline_instances.js, you more or less copied the JavaScript code to highlight missing required ...
Radhika Chippada
01:56 pm Bug #5417: [Workbench] Show error condition / refuse to start a pipeline instance if some inputs ...
Reviewing commit:0b1d679
In pipeline_instances.js, you more or less copied the JavaScript code to highlight missin...
Brett Smith
10:06 pm Revision 6a8f05bb (arvados): closes #5417
Merge branch '5417-not-start-pipeline-with-unreadable-inputs' Radhika Chippada
10:06 pm Revision dcf97f13 (arvados): Merge branch 'master' into 5417-not-start-pipeline-with-unreadable-i...
Radhika Chippada
10:05 pm Revision 52a9e646 (arvados): 5417: one more test condition for dataclass=File
Radhika Chippada
09:28 pm Revision 4d078362 (arvados): Merge branch '3145-readonly-volumes' refs #3145
Tom Clegg
09:18 pm Revision b0ec9527 (arvados): 5417: in case of a File dataclass with unreadable input and uneditab...
Radhika Chippada
09:11 pm Feature #3145: [Keep] keepstore supports read-only flag for each volume, for cases like full, dra...
3145-readonly-volumes LGTM Peter Amstutz
07:33 pm Feature #3145: [Keep] keepstore supports read-only flag for each volume, for cases like full, dra...
commit:41caa50 on 3145-readonly-volumes Tom Clegg
08:42 pm Task #5751 (In Progress): Review 3145-readonly-volumes
Peter Amstutz
04:15 pm Task #5751 (Resolved): Review 3145-readonly-volumes
Tom Clegg
08:40 pm Revision 90b9ddc1 (arvados): 5416: Fix comment.
Tom Clegg
08:40 pm Revision feb6833d (arvados): 5416: Disable repository browsing (and skip tests) if git version is...
Tom Clegg
08:40 pm Revision 8634d02f (arvados): 5416: Browse git repository contents in workbench.
Tom Clegg
08:40 pm Revision 1816e68e (arvados): 5416: Do not override git urls for remote hosted repos.
Tom Clegg
08:40 pm Revision 84166880 (arvados): 5416: Run arv-git-httpd and nginx ssl proxy in test suite.
Tom Clegg
08:40 pm Revision faabe2f8 (arvados): 5416: Add read-only clone_urls attribute to Repository resources, de...
Tom Clegg
08:31 pm Revision d8626f8a (arvados): 5416: Disable repository browsing (and skip tests) if git version is...
Tom Clegg
08:26 pm Revision 5549904b (arvados): 3198: Support for mkdir, rmdir, unlink, rename. Improve exception c...
Peter Amstutz
07:52 pm Revision d88c3bf8 (arvados): 5416: Use http://foo:bar@host:port/ instead of credential helper.
Tom Clegg
07:30 pm Bug #5490: [Crunch] Job should not be reused when docker tag _or_ arvados sdk version now resolve...
This bug and #3341 have the same basic underlying issue: when you don't specify your own filters for these runtime co... Brett Smith
04:01 pm Bug #5490: [Crunch] Job should not be reused when docker tag _or_ arvados sdk version now resolve...
From IRC:
(11:54:19 AM) Me: Instead, I think it's just one of those things where the API server uses much more pre...
Brett Smith
03:45 pm Bug #5490: [Crunch] Job should not be reused when docker tag _or_ arvados sdk version now resolve...
tb05z-d1hrv-33xt7slr5xvje5a is a copy of the same pipeline instance that specifies arvados_sdk_version 18148ec24bf63e... Brett Smith
03:30 pm Bug #5490: [Crunch] Job should not be reused when docker tag _or_ arvados sdk version now resolve...
The example above stems from the way we interpret git version ranges. Here's the git rev-parse call generated by the... Brett Smith
07:20 pm Revision e1445f72 (arvados): 5416: Use http://foo:bar@host:port/ instead of credential helper.
Tom Clegg
07:14 pm Bug #5753 (Resolved): [Workbench] Job name column is displayed even though job only supports desc...
In workbench, when trying to name a job under 'Jobs and pipelines' Tab in a project, I get the error 'Name Name links... Sarah Guthrie
07:01 pm Bug #5388: [Crunch] Jobs do not re-run with latest docker image if job is unchanged but docker im...
Diagnosing this specific pipeline may be complicated by #5752. Brett Smith
06:45 pm Bug #5752 (Resolved): [SDKs] Fix unreliable image timestamp recording in arv keep docker
Docker metadata links for Docker image collections should include an @image_timestamp@ property. This helps the API ... Brett Smith
06:28 pm Revision d0375085 (arvados): 5417: revert unreadable-input check for links since no such case exi...
Radhika Chippada
06:02 pm Revision fc9a042a (arvados): 5417: update created_at time on pipeline_in_publicly_accessible_proj...
Radhika Chippada
05:47 pm Revision 7afe2c73 (arvados): Merge branch 'master' into 5417-not-start-pipeline-with-unreadable-i...
Radhika Chippada
05:35 pm Revision dc96093e (arvados): 5417: a few changes from based on review feedback. also, account for...
Radhika Chippada
04:16 pm Revision 41caa507 (arvados): 3145: Add -readonly flag. Accept multiple -volume arguments.
* Leave -volumes (and accept comma-separated dir lists) for backward
compatibility.
* Detect read-only filesystems...
Tom Clegg
04:15 pm Task #5750 (Resolved): Add tests
Tom Clegg
02:30 pm Task #5750 (Resolved): Add tests
Tom Clegg
02:30 pm Task #5747 (Resolved): Set readonly flag from mount opts in FindKeepVolumes
Tom Clegg
02:30 pm Task #5746 (Resolved): Accept readonly flag in -volumes=... argument
Tom Clegg
02:25 pm Bug #5742 (Resolved): [Workbench] the user setup page creates broken shell usernames
Applied in changeset arvados|commit:397191893819083925600a61e2f355a3b6513354. Brett Smith
02:04 pm Bug #5742 (In Progress): [Workbench] the user setup page creates broken shell usernames
Brett Smith
02:18 pm Revision 39719189 (arvados): 5742: User setup process uses username for VM login, not repo name.
Closes #5742. Brett Smith
01:06 pm Task #5741 (In Progress): Review branch: 5417-not-start-pipeline-with-unreadable-inputs
Brett Smith
08:53 am Revision 9d1daf12 (arvados): 3145: Add -readonly flag. Accept multiple -volume arguments.
* Leave -volumes (and accept comma-separated dir lists) for backward
compatibility.
* Detect read-only filesystems...
Tom Clegg
05:27 am Task #5749 (Resolved): Use activerecord-nulldb-adapter instead
Tom Clegg
05:27 am Task #5749 (Resolved): Use activerecord-nulldb-adapter instead
Tom Clegg

04/15/2015

09:39 pm Bug #5713: [FUSE] File access sometimes takes too long on su92l
Caused by #5748 Ward Vandewege
09:36 pm Bug #5748 (Resolved): [Keep] sometimes, Keep sucks up 100% cpu and becomes really slow after a while
We have some keepstore servers that have r/o disks (only). After running for a few hours, the keepstored process beco... Ward Vandewege
09:24 pm Task #5746 (In Progress): Accept readonly flag in -volumes=... argument
Tom Clegg
09:23 pm Task #5746 (Resolved): Accept readonly flag in -volumes=... argument
Tom Clegg
09:24 pm Task #5747 (Resolved): Set readonly flag from mount opts in FindKeepVolumes
Tom Clegg
09:20 pm Feature #3145 (In Progress): [Keep] keepstore supports read-only flag for each volume, for cases ...
Tom Clegg
09:19 pm Bug #5745 (Resolved): [Keep] keepstore should serialize file reads/writes, but not directory look...
h3. background
The most obvious benefit of this change is that, even when keepstore is busy, the process of probin...
Tom Clegg
09:09 pm Story #3126: [API] Support use of anonymous git url (like github https) as repository in jobs.create
I installed a new jessie system, had test failures, and fixed (now at commit:de3e44a). But my https:// test failed to... Tom Clegg
08:51 pm Revision 23a940aa (arvados): 3198: Can modify file, collection objects, changes are reflected in ...
Peter Amstutz
08:50 pm Revision de3e44ac (arvados): 3126: Delete git cache dir in test teardown. Remove no-op test.
Tom Clegg
08:24 pm Bug #5744: PermissionDenied error writing job output of pipeline_instance qr1hi-d1hrv-4zczpddlf3m...
Some notes, this has run succesfully before here: qr1hi-d1hrv-dl3bjgemakkt5aw
Here are some failed instances:
q...
Bryan Cosca
08:11 pm Bug #5744 (Closed): PermissionDenied error writing job output of pipeline_instance qr1hi-d1hrv-4z...
This pipeline instance https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-4zczpddlf3m9uh4 failed in the end w... Radhika Chippada
08:10 pm Task #5721 (Resolved): Review 5717-crunch-dynamic-max-tasks-per-node-wip
Applied in changeset arvados|commit:d2e7a97c8d24ef8ae61d860e9c972626f80cf2b4. Brett Smith
03:57 pm Task #5721 (In Progress): Review 5717-crunch-dynamic-max-tasks-per-node-wip
Tom Clegg
08:10 pm Feature #5717 (Resolved): [Crunch] Use tasks_this_level to calculate a virtual max_tasks_per_node
Applied in changeset arvados|commit:d2e7a97c8d24ef8ae61d860e9c972626f80cf2b4. Brett Smith
08:03 pm Feature #5717: [Crunch] Use tasks_this_level to calculate a virtual max_tasks_per_node
commit:55bc432 LGTM, thanks Tom Clegg
08:02 pm Feature #5717: [Crunch] Use tasks_this_level to calculate a virtual max_tasks_per_node
Tom Clegg wrote:
> I think it's worth adding a comment near ...
Brett Smith
04:39 pm Feature #5717: [Crunch] Use tasks_this_level to calculate a virtual max_tasks_per_node
Comments on commit:24b0da5
I think it's worth adding a comment near ...
Tom Clegg
08:07 pm Revision d2e7a97c (arvados): Merge branch '5717-crunch-dynamic-max-tasks-per-node-wip'
Closes #5717, #5721. Brett Smith
08:04 pm Revision dcedf346 (arvados): 5717: crunch-job uses fewer slots when few tasks at this level.
When crunch-job begins tasks at a new level, it looks at the number of
tasks scheduled for that level. If that's sma...
Brett Smith
08:00 pm Bug #5743 (New): [Workbench] Replace type-specific #index pages with generic code
ProjectsController#show has a set of routes, controllers, and views that are capable of listing/filtering/sorting/inf... Radhika Chippada
07:57 pm Revision 55bc4321 (arvados): 5717: Fixups from code review.
Brett Smith
07:45 pm Revision d062a3ce (arvados): 3126: Fix test. Avoid excess "git init" by probing with "git branch"...
Tom Clegg
07:39 pm Bug #5742 (Resolved): [Workbench] the user setup page creates broken shell usernames
The shell username links get created as user/user instead of user, because that's what is now needed for git. Ward Vandewege
07:39 pm Revision f91b1eae (arvados): 3198: Store filename/directory name in ArvadosFile/Subcollection obj...
Simplify callbacks to support a single callback, and allow callback on
Subcollection. Notify MOD event on file flush.
Peter Amstutz
07:34 pm Task #5741 (Resolved): Review branch: 5417-not-start-pipeline-with-unreadable-inputs
Radhika Chippada
07:33 pm Bug #5417: [Workbench] Show error condition / refuse to start a pipeline instance if some inputs ...
implementation notes:
* Extended the existing pipeline_instances.js
** Previously, this was showing a red (pink ...
Radhika Chippada
07:26 pm Feature #5740 (New): [OPS] Add diagnostics script for shell nodes
We should have a way to test if our shell nodes are fully functional. A diagnostics script that can be run regularly.... Ward Vandewege
07:20 pm Bug #5714 (Resolved): [Node Manager] Diagnose and fix bugs on GCE
Applied in changeset arvados|commit:0d8d66df56992a39cc032ba482e1ff88de7f22ab. Brett Smith
07:11 pm Bug #5714: [Node Manager] Diagnose and fix bugs on GCE
5714-gce-setup-bugfixes-wip LGTM Ward Vandewege
07:14 pm Revision 0d8d66df (arvados): Merge branch '5714-gce-setup-bugfixes-wip'
Closes #5714, #5715. Brett Smith
07:14 pm Revision de340890 (arvados): 5714: Avoid Node Manager race conditions around stop_if_no_cloud_node.
Checking .is_alive() seems to always lead to race conditions.
Instead, have CloudNodeSetupActor.stop_if_no_cloud_node...
Brett Smith
07:14 pm Revision ddd8d6e3 (arvados): 5714: Node Manager setup process retries Arvados errors.
This fixes a regression from 6ab7cf882cd9a268374b880b5e55b4c8946406b4. Brett Smith
07:10 pm Task #5715 (Resolved): Review 5714-gce-setup-bugfixes-wip
Ward Vandewege
07:07 pm Task #5715 (In Progress): Review 5714-gce-setup-bugfixes-wip
Ward Vandewege
06:49 pm Revision 0b1d679a (arvados): 5417: fix typo
Radhika Chippada
06:45 pm Bug #5739 (In Progress): [Workbench] Remove artificial sqlite3 dependency
Tom Clegg
06:25 pm Bug #5739 (Resolved): [Workbench] Remove artificial sqlite3 dependency
We don't use it, so we shouldn't require anyone to install it. Tom Clegg
06:26 pm Revision 0054f6b8 (arvados): 5739: Remove unnecessary sqlite3 dependency.
Tom Clegg
06:16 pm Bug #5738 (New): [API] Validate that selected columns are selectable, and return an error if not
h3. Background
Insufficient sanity checking causes an easy client error to generate an obtuse error message.
h3...
Peter Amstutz
06:11 pm Bug #5737 (Resolved): [API] [Workbench] Ruby 2.2 or 2.3 compatibility
Known issues
* eventmachine 1.0.3 is incompatible with ruby 2.2. "bundle update eventmachine" puts it at 1.0.7 which...
Tom Clegg
05:44 pm Revision bb138099 (arvados): 5417: add additional test updates to verify Run button status when i...
Radhika Chippada
05:07 pm Admin #5726 (Resolved): arv-get times out
This is now fixed, please try again.
Thanks,
Ward.
Ward Vandewege
06:27 am Admin #5726 (Resolved): arv-get times out
Following the tutorial:
pjotrprins@shell.qr1hi:~$ arv pipeline run --run-pipeline-here --template qr1hi-p5p6p-it...
Pjotr Prins
04:05 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
personally, I really hate the "popup and overlay everything when you first login" modal behavior we implemented righ... Nancy Ouyang
03:45 pm Bug #5736: [Node Manager] Reuse node records after shutting down the cloud node set up with them
If it helps, here's one daemon test I wrote for the behavior.... Brett Smith
03:44 pm Bug #5736 (New): [Node Manager] Reuse node records after shutting down the cloud node set up with...
When Node Manager uses an Arvados node record to set up a new compute node, it records the time that setup starts. I... Brett Smith
03:43 pm Task #5603 (Resolved): Review 5414-keep-service-hints
Tom Clegg
03:18 pm Feature #5735 (Resolved): [Workbench] Edit box for project description should be bigger
h3. Background
Edit box is woefully small. See picture. Ironically the rendered Description tab looks more reasona...
Bryan Cosca
02:14 pm Revision efa11924 (arvados): 5417: when input is unreadable, present visual cue even when it is n...
Radhika Chippada
01:07 pm Feature #5733 (New): Add GNU Guix to Arvados
GNU Guix is a next generation software package manager and works well with Docker. GNU Guix is supporting an increasi... Pjotr Prins
01:00 pm Feature #5732 (New): Add Docker support on the cloud shell host
On the shell host (hell.qr1hi) Docker is not installed:
pjotrprins@shell.qr1hi:~$ docker run --interactive --t...
Pjotr Prins
11:41 am Bug #5731 (New): Arvados.pm not included in ruby/python SDK install
When following these instructions: http://doc.arvados.org/user/tutorials/tutorial-firstscript.html
This results in...
Joep de Ligt
11:15 am Bug #5730: Can not clone git repo for addinc Crunch script
Aha, I got the repo name wrong (as it is listed in my profile). It should have been git@git.qr1hi.arvadosapi.com:pjot... Pjotr Prins
11:09 am Bug #5730 (Closed): Can not clone git repo for addinc Crunch script
Following the docs:
128!pjotrprins@shell.qr1hi:~$ git clone git@git.qr1hi.arvadosapi.com:$USER/$USER.git
Clon...
Pjotr Prins
10:48 am Bug #5720: [Workbench] Search for pipeline templates breaks
Maybe related to #5726 Pjotr Prins
10:46 am Feature #5729 (New): Documentation: In writing a crunch script it would be nice to show the match...
The template example shows "Tutorial align using bwa mem and SortSam", the python script example shows "compute the M... Pjotr Prins
09:35 am Feature #5728 (New): ssh port 2222 is blocked on many networks
Use standard port 22 if possible. Alternatively allow tunneling over port 443 with stunnel4 or give VPN access. Pjotr Prins
06:51 am Feature #5727 (New): arv-get complains an incomplete file exists
arv-get --progress 49bae1066f4ebce72e2587a3efa61c7d+88/ .
got me a time-out (see other issue). When I rerun the ...
Pjotr Prins

04/14/2015

09:07 pm Task #5445 (In Progress): Update FUSE to use new SDK
Peter Amstutz
03:15 pm Task #5445 (New): Update FUSE to use new SDK
Peter Amstutz
03:14 pm Task #5445 (In Progress): Update FUSE to use new SDK
Peter Amstutz
08:55 pm Bug #5490: [Crunch] Job should not be reused when docker tag _or_ arvados sdk version now resolve...
tb05z-d1hrv-zm8v47frcn1mqgn might be more illustrative: it reused jobs with arvados_sdk_version d8abf0b06cc38a1e1030e... Brett Smith
07:08 pm Bug #5490 (In Progress): [Crunch] Job should not be reused when docker tag _or_ arvados sdk versi...
Brett Smith
08:42 pm Revision 499d871d (arvados): Merge branch '3198-inode-cache' into 3198-writable-fuse
Peter Amstutz
08:41 pm Revision 4ac1cbf8 (arvados): 3198: Use new Collection/ArvadosFile API.
Peter Amstutz
08:06 pm Story #3126: [API] Support use of anonymous git url (like github https) as repository in jobs.create
I'm getting API test failures:... Peter Amstutz
03:00 pm Story #3126: [API] Support use of anonymous git url (like github https) as repository in jobs.create
Ah, sorry -- "we didn't need any changes there" was not true! Fixed, rebased on current master, now at commit:85378b8.
Tom Clegg
07:33 pm Revision 976f560a (arvados): 5417: add "unreadable inputs provided" visual cue for an editable pi...
Radhika Chippada
07:23 pm Story #3198: [FUSE] Writable streaming arv-mount
3198-inode-cache lays groundwork for writable FUSE.
* Refactors classes from one big file into fresh.py, fusefile....
Peter Amstutz
07:23 pm Revision 2139ee84 (arvados): 3198: Fix logging
Peter Amstutz
07:13 pm Feature #5035: [Documentation] Document the minimum docker image / Dockerfile that can be used to...
TODO:
* use a generic (non-Arvados) wheezy image as a base.
* also provide a from-zero version (starting with deboo...
Tom Clegg
07:11 pm Task #5725 (Resolved): Review 3198-inode-cache
Peter Amstutz
07:10 pm Revision 416a7c3a (arvados): 3198: Manage inode cache based on (approximate) object size instead ...
count. It's only a soft limit on memory usage but still a big improvement. Peter Amstutz
06:52 pm Bug #5614 (New): [Workbench] 504 error returned when trying to create a large new collection
Moving back to bug triage to encourage consideration and planning of some of the larger development efforts discussed... Brett Smith
06:43 pm Feature #5712: Smarter node allocation for small jobs
#4299 would go a long way to address this, and support other Node Manager features, without requiring the user to spe... Brett Smith
06:06 pm Bug #5714: [Node Manager] Diagnose and fix bugs on GCE
It seems very possible that the race condition is the real source of our trouble. I just caught this happening again... Brett Smith
05:36 pm Bug #5724 (Resolved): [API] Advertise BlobSignatureTTL in discovery doc. Fix name/comments on def...
The default_trash_lifetime config setting (and the defaultTrashLifetime discovery doc key) are currently unused and w... Tom Clegg
05:14 pm Task #5721 (Resolved): Review 5717-crunch-dynamic-max-tasks-per-node-wip
Brett Smith
05:13 pm Revision 24b0da55 (arvados): 5717: crunch-job uses fewer slots when few tasks at this level.
When crunch-job begins tasks at a new level, it looks at the number of
tasks scheduled for that level. If that's sma...
Brett Smith
04:27 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Peter Amstutz wrote:
> I think showing everything by default actually makes it more annoying, because if you have 10...
Tom Clegg
03:43 pm Bug #5720: [Workbench] Search for pipeline templates breaks
I was pressing run a pipeline in project: qr1hi-j7d0g-l1emsbyyx6wyjdh and the template was from project: qr1hi-j7d0g-... Bryan Cosca
03:41 pm Bug #5720 (Resolved): [Workbench] Search for pipeline templates breaks
!search_break_1.gif! Bryan Cosca
03:15 pm Task #5718 (In Progress): Inode caching does not use unlimited memory
Peter Amstutz
03:14 pm Task #5718 (Resolved): Inode caching does not use unlimited memory
Peter Amstutz
03:15 pm Task #5719 (Resolved): Process event bus updates
Peter Amstutz
03:02 pm Feature #5717 (Resolved): [Crunch] Use tasks_this_level to calculate a virtual max_tasks_per_node
Following up on #5642 and commit:6261cf90.
[From IRC. Edited for clarity.]
(10:44:23 AM) Me: What if we stuck ...
Brett Smith
03:00 pm Revision 85378b8c (arvados): 3126: Always act as current_user in Commit.find_commit_range.
Tom Clegg
03:00 pm Revision 966585bc (arvados): 3126: Do not try to do anything with job.repository in crunch-dispat...
Tom Clegg
03:00 pm Revision 99401ace (arvados): 3126: Update API docs.
Tom Clegg
03:00 pm Revision 4c209418 (arvados): 3126: Accept remote http/https/git url as repository attr in jobs.cr...
Tom Clegg
02:50 pm Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
For future, suggest making login drop-down menu show on click instead of hover, to keep consistency with other menus.... Nancy Ouyang
02:00 pm Feature #5647 (Resolved): [Workbench] Log-in on anonymous redirects to google sign-in with no war...
Applied in changeset arvados|commit:912464ad82bad38f1ce7984b6d4b19734a9816a9. Radhika Chippada
01:59 pm Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
Thanks Brett. Made the text change. And left the hover-dropdown implementation as is to use css-based solution. Since... Radhika Chippada
01:47 pm Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
One small comment on the text in commit:1f6a187: the menu item uses the verb "Log-in." Most of Workbench uses "Log i... Brett Smith
01:20 pm Feature #5647 (In Progress): [Workbench] Log-in on anonymous redirects to google sign-in with no ...
Radhika Chippada
11:37 am Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
Updated after Nancy viewed and commented back. Radhika Chippada
04:43 am Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
<a href="<%= arvados_api_client.arvados_login_url(return_to: root_url) %>"> <span class="fa fa-lg fa-... Nancy Ouyang
04:18 am Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
Radhika, possible choice
!login-ion-dropdown.png!
Nancy Ouyang
04:02 am Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
Added a hover dropdown to login link using text suggested in #5647-9 (Note #9), omitting the image after talking to N... Radhika Chippada
03:36 am Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
For future reference, I think imgur.com handles multiple log-in methods well
Sign In
!{width: 30%}imgur-signin.png!...
Nancy Ouyang
02:30 pm Revision 771ee3aa (arvados): 5642: crunch-job keeps $tasks_this_level in sync with new tasks.
We previously tried to accomplish this by reculculating the value
before every THISROUND
loop (bae652c25653d21aece17e...
Brett Smith
02:04 pm Feature #5493 (Resolved): [Workbench] Add "Getting Started" modal inside Workbench
Radhika Chippada
01:53 pm Revision 912464ad (arvados): closes #5647
Merge branch '5647-login-dropdown' Radhika Chippada
01:53 pm Revision c50acf62 (arvados): 5647: minor text update
Radhika Chippada
01:24 pm Task #5716 (In Progress): Review branch: 5647-login-dropdown
Brett Smith
04:07 am Task #5716 (Resolved): Review branch: 5647-login-dropdown
Radhika Chippada
05:03 am Revision 1f6a187a (arvados): 5647: as a team we need to learn to weigh options with their worth; ...
Radhika Chippada
04:23 am Revision 08c4f5f0 (arvados): 5647: add icon to the new login dropdown link
Radhika Chippada
03:53 am Revision 33d54abd (arvados): 5647: minor tweak to dropdown text
Radhika Chippada
03:45 am Task #5440 (Resolved): [Documentation] Revert doc-to-homepage
Applied in changeset arvados|commit:18ac672a5c9b5416e21a3d45ed268f2edb509786. Radhika Chippada
02:56 am Task #5440: [Documentation] Revert doc-to-homepage
Review comments:
* Please remove the commented code once you are through with all your doc migration as we talked....
Radhika Chippada
03:42 am Revision cdecff51 (arvados): Merge branch 'master' into 5647-login-dropdown
Radhika Chippada
03:41 am Revision 18ac672a (arvados): closes #5440
Merge branch '5440-remove-doc-getting-started' Radhika Chippada
03:40 am Revision cd8db86a (arvados): 5440: remove usused getting_started images
Radhika Chippada
03:34 am Revision 0bff4d89 (arvados): 5647: add a hover dropdown login item.
Radhika Chippada
03:12 am Revision be238c74 (arvados): 5440: reword quickstart
Nancy Ouyang
02:54 am Revision aefbec0f (arvados): 3126: Always act as current_user in Commit.find_commit_range.
Tom Clegg
02:35 am Revision a756a90a (arvados): linkfix, reword quickstart section on homepage
Nancy Ouyang
02:31 am Revision 58585938 (arvados): 3126: Do not try to do anything with job.repository in crunch-dispat...
Tom Clegg
02:31 am Revision bb38e24b (arvados): 3126: Update API docs.
Tom Clegg
02:31 am Revision 0fdc60ff (arvados): 3126: Accept remote http/https/git url as repository attr in jobs.cr...
Tom Clegg
02:21 am Revision 8e2150eb (arvados): Fix indentation. Remove errant unclosed <p> tag. refs #5493
Tom Clegg
02:04 am Revision d743a56a (arvados): 5440: remove all links to /start temporarily to avoid confusing user
Put in quickstart sections on docs homepage for both 1) public pipeline 2) pipeline developers
Revert changes made in...
Nancy Ouyang
02:00 am Revision aafef3d2 (arvados): If provided, use TMPDIR instead of /tmp. No issue #
Tom Clegg
01:47 am Revision 6261cf90 (arvados): Fix loop label that became disconnected in bae652c, causing crash on...
Tom Clegg
12:26 am Revision 1b2afc5a (arvados): Merge branch 'master' of git.curoverse.com:arvados into 5440-remove-...
Nancy Ouyang

04/13/2015

09:08 pm Revision 72cb9197 (arvados): 3198: Fixed arv-mount for refactoring.
Peter Amstutz
09:05 pm Revision 0f119f77 (arvados): Merge branch '5414-keep-service-hints' refs #5414
Tom Clegg
08:53 pm Revision 0d1d51b9 (arvados): refs #5493
Merge branch '5493-getting-started-modal' Radhika Chippada
08:51 pm Revision 3bc94fb2 (arvados): 5493: popup size
Radhika Chippada
08:50 pm Bug #5714: [Node Manager] Diagnose and fix bugs on GCE
5714-gce-setup-bugfixes-wip is up for review. It fixes a clear error retry problem, and avoids a potential race cond... Brett Smith
07:19 pm Bug #5714 (Resolved): [Node Manager] Diagnose and fix bugs on GCE
Right now Node Manager keeps getting into a state where a ComputeNodeSetupActor dies, and then things go south from t... Brett Smith
08:49 pm Task #5715 (Resolved): Review 5714-gce-setup-bugfixes-wip
Brett Smith
08:48 pm Revision 0c166be2 (arvados): 5714: Avoid Node Manager race conditions around stop_if_no_cloud_node.
Checking .is_alive() seems to always lead to race conditions.
Instead, have CloudNodeSetupActor.stop_if_no_cloud_node...
Brett Smith
08:47 pm Revision 58e91ef7 (arvados): 5493: popup size and a typo
Radhika Chippada
08:42 pm Revision d8d82841 (arvados): 3198: Implement cache management for directory objects.
Peter Amstutz
08:34 pm Revision e5b35f15 (arvados): 5493: make popup size fixed
Radhika Chippada
08:25 pm Revision 986e124a (arvados): 5493: public pipeline wiki page link added in page 3
Radhika Chippada
08:24 pm Revision 3280e2dc (arvados): 5414: Merge branch 'master' into 5414-keep-service-hints
Tom Clegg
08:18 pm Feature #4223: [SDKs] arv keep docker --download to get image from Arvados
h3. Docs and interface
Not sure of the background wrt prioritizing this with thin requirements/expectations, but f...
Tom Clegg
03:56 pm Feature #4223 (In Progress): [SDKs] arv keep docker --download to get image from Arvados
Peter Amstutz
08:11 pm Revision 3f59bec0 (arvados): 1 2 3 ul>ol 3rd page
Nancy Ouyang
08:09 pm Revision a632845c (arvados): 5493: that did not sit well
Radhika Chippada
07:53 pm Revision 84f85c50 (arvados): 5493: remove confusing btn class on explanation button spans to not ...
Radhika Chippada
07:50 pm Revision dbdd9451 (arvados): Merge branch 'master' of git.curoverse.com:arvados into 5440-remove-...
Nancy Ouyang
07:47 pm Revision 3e271eb8 (arvados): Merge branch 'master' into 5493-getting-started-modal
Radhika Chippada
07:39 pm Revision fe923555 (arvados): typo
Nancy Ouyang
07:37 pm Revision 8c51527d (arvados): 5714: Node Manager setup process retries Arvados errors.
This fixes a regression from 6ab7cf882cd9a268374b880b5e55b4c8946406b4. Brett Smith
07:35 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Radhika is reviewing the code and will manage merge to master. Nancy Ouyang
03:07 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Work in progress. Nancy Ouyang
07:31 pm Revision 01dae203 (arvados): dashed line
Nancy Ouyang
07:16 pm Revision 6c4d59cb (arvados): format pg 3, 4
Nancy Ouyang
07:02 pm Feature #5414: [Keep] Use data stored remotely (not in local keepstore)
Tom, LGTM. And thank you for explaining initializer loading and renaming.
Radhika Chippada
06:01 pm Feature #5414: [Keep] Use data stored remotely (not in local keepstore)
Radhika Chippada wrote:
> Tom:
> Just a few minor observation about the updates.
>
> * formatting is off for kee...
Tom Clegg
01:46 am Feature #5414: [Keep] Use data stored remotely (not in local keepstore)
Tom:
Just a few minor observation about the updates.
* formatting is off for keepclient.rb (may be you need to re...
Radhika Chippada
06:57 pm Bug #5713 (New): [FUSE] File access sometimes takes too long on su92l
Every once in a while, accessing files or data from the keep mount becomes unusably slow from the shell nodes.
Som...
Abram Connelly
06:20 pm Revision 93f6a595 (arvados): minor format changes
Nancy Ouyang
06:16 pm Revision 92b3f3ed (arvados): formatted first 2 pages
Nancy Ouyang
05:51 pm Revision 9fb28073 (arvados): 5414: Rename zz_preload* to preload*; alphabetical names are not nee...
Tom Clegg
05:51 pm Revision 3f016eae (arvados): 5414: Rename zz_load* to load*; alphabetical names are not needed an...
Tom Clegg
05:47 pm Feature #5712 (New): Smarter node allocation for small jobs
Background:
Currently, nodes will spin up if the job is ready to be run, or in queue. In template talk, a job will...
Bryan Cosca
05:47 pm Revision d72f3039 (arvados): 5414: Control initializer load order using require_relative instead ...
Tom Clegg
05:30 pm Revision 249e9001 (arvados): 3198: Fixed imports. Tests pass again.
Peter Amstutz
05:28 pm Revision cc133acd (arvados): 5414: Add test case for unrecognized/future hints.
Tom Clegg
05:25 pm Task #5686 (Resolved): Review 5614-workbench-optimize-combine-collections-wip
Applied in changeset arvados|commit:43aa02f5af636f874bac5ffe96cff0061bcd6a44. Brett Smith
12:35 am Task #5686 (In Progress): Review 5614-workbench-optimize-combine-collections-wip
Radhika Chippada
05:22 pm Revision a8ef8be8 (arvados): 5614: Update Workbench Gemfile for new Ruby SDK.
Refs #5614. Brett Smith
05:22 pm Revision 320c333f (arvados): 5414: Fix up formatting.
Tom Clegg
05:21 pm Revision 43aa02f5 (arvados): Merge branch '5614-workbench-optimize-combine-collections-wip'
Refs #5614, #4943. Closes #5686. Brett Smith
05:20 pm Revision ee60fe9a (arvados): 5614: Improve Workbench combine collections performance.
* Get links with API list calls, instead of fetching each one
individually.
* Get a list mapping portable data has...
Brett Smith
05:17 pm Revision 8893e8cf (arvados): 5614: Add Collection#each_file to Ruby SDK.
Brett Smith
05:17 pm Revision ef257288 (arvados): 5614: Workbench renders error flash separately from others.
Brett Smith
05:17 pm Revision 0acda438 (arvados): 5614: Ruby SDK cp_r method creates streams as needed.
Brett Smith
05:17 pm Revision 95298001 (arvados): 5614: Use assert_includes more in Workbench tests for better diagnos...
Brett Smith
05:17 pm Revision c17712a6 (arvados): 5614: Add Collection#exist? to Ruby SDK.
Brett Smith
05:15 pm Bug #5692 (Resolved): [SDK] Can't get signed manifest locator from new Collection API.
Applied in changeset arvados|commit:ec8879aa56810dfc6475ad8cdc56770ff91f84f2. Peter Amstutz
05:08 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
commit:ee0411e is good to merge, thanks. Brett Smith
04:52 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
Brett Smith wrote:
> At commit:679eef4, @test_diff_apply_with_token@ is calling the private @_get_manifest_text()@ m...
Peter Amstutz
04:20 pm Bug #5692 (New): [SDK] Can't get signed manifest locator from new Collection API.
At commit:679eef4, @test_diff_apply_with_token@ is calling the private @_get_manifest_text()@ method. This test suit... Brett Smith
03:56 pm Bug #5692 (In Progress): [SDK] Can't get signed manifest locator from new Collection API.
Peter Amstutz
03:23 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
Brett Smith wrote:
> Reviewing commit:c162a42
>
> Is it necessary to add another behavior-controlling boolean kno...
Peter Amstutz
03:01 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
Reviewing commit:c162a42
Is it necessary to add another behavior-controlling boolean knob to the list of @manifest...
Brett Smith
02:21 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
Brett Smith wrote:
> Reviewing commit:88f5731
>
> * Giving ArvadosFile.flush() a default @num_retries=None@ is a ...
Peter Amstutz
05:11 pm Bug #5614: [Workbench] 504 error returned when trying to create a large new collection
Radhika Chippada wrote:
> * As for provenance graph related concerns: In the event that something went wrong after t...
Brett Smith
02:42 pm Bug #5614: [Workbench] 504 error returned when trying to create a large new collection
* Yes, unfortunately distinct does not help in this case. Please ignore that comment.
* As for provenance graph re...
Radhika Chippada
02:19 pm Bug #5614: [Workbench] 504 error returned when trying to create a large new collection
Radhika Chippada wrote:
> Review comments:
>
> * Is this update sufficient enough to address all the performance i...
Brett Smith
12:47 am Bug #5614: [Workbench] 504 error returned when trying to create a large new collection
Review comments:
* Is this update sufficient enough to address all the performance issues around combining large c...
Radhika Chippada
05:10 pm Revision ec8879aa (arvados): Merge branch '5692-pysdk-manifest-text-flush' closes #5692
Peter Amstutz
05:09 pm Revision 100d8d1b (arvados): 3198: Start by refactoring.
Peter Amstutz
04:51 pm Revision ee0411ef (arvados): 5692: Don't call _get_manifest_text from test if we don't need to.
Peter Amstutz
04:43 pm Revision 2dc43b83 (arvados): 3126: Do not try to do anything with job.repository in crunch-dispat...
Tom Clegg
04:39 pm Revision bd4fd500 (arvados): dropped a header
Nancy Ouyang
04:37 pm Revision 87322631 (arvados): text content done; formatting needed
Nancy Ouyang
04:02 pm Revision 77b9859a (arvados): refs #5365
Merge branch '5365-not-link-unreadables' Radhika Chippada
04:01 pm Revision 93ba131c (arvados): 5365: when the attrvalue is not a uuid, link_to_if_arvados_object
Radhika Chippada
04:00 pm Revision 5ef491be (arvados): 5614: Workbench shows error flash if combining collections fails to ...
Brett Smith
03:59 pm Revision dec39dc8 (arvados): 5614: Workbench renders error flash separately from others.
Brett Smith
03:59 pm Story #3126: [API] Support use of anonymous git url (like github https) as repository in jobs.create
commit:78be33b... Peter Amstutz
03:56 pm Story #4685 (In Progress): [Crunch] CWL prototype workflow runner in Arvados
Peter Amstutz
03:56 pm Story #5623 (In Progress): [Crunch] Specify Crunch2 features and APIs
Peter Amstutz
03:49 pm Task #5689 (In Progress): Review 4223-arv-keepdocker-download
Tom Clegg
03:23 pm Revision 679eef49 (arvados): 5692: Move implementation to internal _get_manifest_text(). Fix typos.
Peter Amstutz
02:51 pm Task #5691 (In Progress): Review 3126-remote-git-url
Peter Amstutz
02:30 pm Task #5711 (Resolved): Requirements / API for Crunch v2
Peter Amstutz
02:21 pm Feature #5416: [API] Clone git repositories without using an SSH private key
> Any objection to changing this to gitUrl or gitUrlBase to match the other similar discovery doc fields (baseUrl, ro... Peter Amstutz
02:19 pm Task #5678 (Feedback): Review 4685-crunch-cwl-support
Peter Amstutz
02:18 pm Revision c162a425 (arvados): 5692: Add flush flag to manifest_text() which calls commit_all(). A...
portable_manifest_text() which returns the stripped, normalized manifest text
free of side effects. Fixed tests.
Peter Amstutz
02:16 pm Revision b1aa4281 (arvados): 5614: Fixup Ruby SDK cp_r test.
Brett Smith
01:57 pm Revision 4bbb24c0 (arvados): 5614: Use assert_includes very consistently in combine collections t...
Brett Smith

04/12/2015

10:26 pm Task #5671 (Resolved): Review branch: 5365-not-link-unreadables
Radhika Chippada
10:26 pm Bug #5365: [Workbench] Do not link to objects that are not readable by current user
Thanks Brett. I incorporated all these suggestions and merged into master. I think the comment "link_to_arvados_objec... Radhika Chippada
09:35 pm Bug #5365 (Resolved): [Workbench] Do not link to objects that are not readable by current user
Applied in changeset arvados|commit:6564944612790934531a3c30e6ab2cab6f329461. Radhika Chippada
09:32 pm Revision 65649446 (arvados): closes #5365
Merge branch '5365-not-link-unreadables' Radhika Chippada
09:29 pm Revision e5658eca (arvados): 5365: add back data-toggle along with link disabled for Log tab.
Radhika Chippada
01:06 pm Revision 6529d3fb (arvados): 5365: missed one updated signature update
Radhika Chippada
03:06 am Revision a12cd27d (arvados): 5365: updated signature for link_to_arvados_object_if_readable
Radhika Chippada

04/11/2015

01:04 am Feature #4823 (In Progress): [SDKs] Good Collection API for Python SDK
Reopening because some APIs aren't implemented yet, e.g., @portable_manifest_text()@, @walk()@, @listdir()@. Tom Clegg

04/10/2015

09:58 pm Bug #5499 (New): [SDKs] arv-copy fails to create collection after copying many blocks
I was unable to reproduce the problem with this test script:... Brett Smith
08:44 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
Reviewing commit:88f5731
* Giving ArvadosFile.flush() a default @num_retries=None@ is a little dicey. Since it is...
Brett Smith
06:16 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
For the sake of completeness there are two ways to tell crunch-job your task output:
* @current_task().set_output(lo...
Tom Clegg
06:01 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
The use case we're trying to fix is to be able to use the new Collection API the same way as CollectionWriter to prod... Peter Amstutz
05:43 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
The current way to end a task using the arvados SDK is to use current_task().set_output() which requires the signed m... Sarah Guthrie
04:39 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
What's the use case for this?
A manifest without block signatures (like the one we've been storing, and commit:dba...
Tom Clegg
03:41 pm Bug #5692: [SDK] Can't get signed manifest locator from new Collection API.
Reviewing commit:dbafbd69, and just one comment: please add tests for the return values in different cases. If users... Brett Smith
03:23 pm Bug #5692 (Resolved): [SDK] Can't get signed manifest locator from new Collection API.
Peter Amstutz
08:24 pm Revision 88f57312 (arvados): 5692: Backed out commit_all() from Collection.manifest_text().
Collection.save() and Collection.save_new() now return unstripped manifest
text.
Peter Amstutz
07:53 pm Bug #5663: [Documentation] Use "...puts rand()..." instead of "rake secret" in apiserver/workbenc...
Putting "foobar" in the default config is not acceptable because it allows the application to start up with secret se... Tom Clegg
07:40 pm Task #5710 (In Progress): Review 5692-pysdk-manifest-text-flush
Brett Smith
07:28 pm Task #5710 (Resolved): Review 5692-pysdk-manifest-text-flush
Peter Amstutz
07:27 pm Revision de7c71aa (arvados): 5692: Collection.manifest_text(strip=False) will flush open files an...
all blocks to be committed in order to return a manifest text with valid
authorization tokens. Fix tests affected by...
Peter Amstutz
07:07 pm Bug #5365: [Workbench] Do not link to objects that are not readable by current user
Reviewing commit:02840ce9
The story says, "The Log tab should be greyed out / disabled / un-clickable" when the lo...
Brett Smith
05:53 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Peter Amstutz wrote:
> workbench/app/models/repository.rb#http_fetch_url doesn't use 'gitHttpBase' which is advertis...
Tom Clegg
05:33 pm Feature #5416: [API] Clone git repositories without using an SSH private key
workbench/app/models/repository.rb#http_fetch_url doesn't use 'gitHttpBase' which is advertised in the discovery docu... Peter Amstutz
03:17 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Tom Clegg wrote:
> These failures seem to say "git exited 128 without saying anything on stdout or stderr" (sort of ...
Brett Smith
05:42 pm Task #5693 (Feedback): Review 5692-pysdk-signed-manifest-locator
Peter Amstutz
03:42 pm Task #5693 (In Progress): Review 5692-pysdk-signed-manifest-locator
Brett Smith
03:31 pm Task #5693 (Closed): Review 5692-pysdk-signed-manifest-locator
Peter Amstutz
05:33 pm Revision 645b161d (arvados): Merge branch '5493-getting-started-modal' of git.curoverse.com:arvad...
Conflicts:
apps/workbench/app/views/getting_started/_getting_started_popup.html.erb
Nancy Ouyang
05:32 pm Revision 6dffa00d (arvados): fix merge conflicts
Nancy Ouyang
05:21 pm Feature #5694 (Resolved): [Workbench] Log tab of running job should include logs from before you ...
If I have a current running job and I noticed that one task failed, I would like to see what failed about it while th... Bryan Cosca
04:57 pm Revision dcd96ef8 (arvados): first page prototype
Nancy Ouyang
03:30 pm Revision dbafbd69 (arvados): 5692: Return signed manifest locator from Collection.save() and Coll...
Peter Amstutz
02:45 pm Task #5687 (In Progress): Review 5416-browse-repo-tree (with 5416-ssl-proxy on arvados-dev)
Peter Amstutz
01:27 pm Story #5585 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
Ward Vandewege
08:25 am Story #3126: [API] Support use of anonymous git url (like github https) as repository in jobs.create
Notes about 3126-remote-git-url:
* The commit+tree needed for a job is now copied into the internal repository dur...
Tom Clegg
07:56 am Revision 19e42582 (arvados): 3126: Accept remote http/https/git url as repository attr in jobs.cr...
Tom Clegg
07:56 am Revision 78be33b1 (arvados): 3126: Update API docs.
Tom Clegg
07:40 am Revision fb2299c6 (arvados): 3126: Update API docs.
Tom Clegg
07:40 am Task #5691 (Resolved): Review 3126-remote-git-url
Tom Clegg
07:40 am Task #5690 (Resolved): Update docs
Tom Clegg
01:23 am Task #5690 (Resolved): Update docs
Tom Clegg
01:18 am Revision 9218a7e9 (arvados-dev): 5416: Run keepproxy, arv-git-httpd, and SSL proxy services durin...
Tom Clegg
01:18 am Revision ad6d063c (arvados-dev): 5416: Support testargs for go bits, like "services/arv-git-httpd...
Tom Clegg
01:18 am Revision decff518 (arvados-dev): 5416: Terminate connections on the configured test database (not...
Tom Clegg
01:18 am Revision decff518 (arvados): 5416: Terminate connections on the configured test database (not nec...
Tom Clegg
01:17 am Task #5636 (Resolved): Fetch remote repo to internal.git if needed during job#save
Tom Clegg
01:17 am Task #5635 (Resolved): Validate repository name as name, url, or uuid during job#save
Tom Clegg

04/09/2015

10:09 pm Revision daafe9a3 (arvados): 3126: Accept remote http/https/git url as repository attr in jobs.cr...
Tom Clegg
09:46 pm Revision c7092d77 (arvados): 3126: Accept remote http/https/git url as repository attr in jobs.cr...
Tom Clegg
07:41 pm Task #5636 (In Progress): Fetch remote repo to internal.git if needed during job#save
Tom Clegg
04:56 pm Bug #5417 (In Progress): [Workbench] Show error condition / refuse to start a pipeline instance i...
Radhika Chippada
04:28 pm Story #4685: [Crunch] CWL prototype workflow runner in Arvados
Peter Amstutz wrote:
> Ok. I will write the initial cwl_runner to submit jobs which use run-command.
Please, noo...
Tom Clegg
02:03 pm Story #4685: [Crunch] CWL prototype workflow runner in Arvados
Tom Clegg wrote:
> Peter Amstutz wrote:
> > cwl_job should really be named "crunch v2". It doesn't actually do any...
Peter Amstutz
02:31 am Story #4685: [Crunch] CWL prototype workflow runner in Arvados
(aside: #5416 already has good support for running arv-git-httpd in run_test_servers...) Tom Clegg
02:23 am Story #4685: [Crunch] CWL prototype workflow runner in Arvados
Peter Amstutz wrote:
> cwl_job should really be named "crunch v2". It doesn't actually do anything specific to CWL,...
Tom Clegg
03:54 pm Revision 02840ce9 (arvados): 5365: do not link to docker_image_locator if not readable; also prel...
Radhika Chippada
03:11 pm Story #5623: [Crunch] Specify Crunch2 features and APIs
Peter Amstutz wrote:
> In order to completely support CWL workflows out of the box, Crunch will need to provide the ...
Tom Clegg
01:59 pm Story #5623: [Crunch] Specify Crunch2 features and APIs
In order to completely support CWL workflows out of the box, Crunch will need to provide the following features:
#...
Peter Amstutz
03:05 pm Feature #5493: [Workbench] Add "Getting Started" modal inside Workbench
Update: mockup now in Workbench.
!Screenshot from 2015-04-09 11_04_32.png!
Nancy Ouyang
02:33 pm Bug #5365: [Workbench] Do not link to objects that are not readable by current user
Addressed the comments above. A few notes:
* Workbench did not offer @distinct before, which made it not possible ...
Radhika Chippada
02:15 pm Feature #4223: [SDKs] arv keep docker --download to get image from Arvados
Add --download option to arv-keepdocker to fetch a Docker image from Keep and load it locally. Refactor keepdocker t... Peter Amstutz
02:15 pm Revision 743f59e5 (arvados): 4223: Add --download option to arv-keepdocker to fetch a Docker imag...
and load it locally. Refactor keepdocker to enable SDK users to better access
upload/download functionality. Fix AP...
Peter Amstutz
02:14 pm Task #5689 (In Progress): Review 4223-arv-keepdocker-download
Peter Amstutz
02:13 pm Revision 41bd04e7 (arvados): Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada
02:08 pm Revision 2af59ce3 (arvados): 5365: add controller tests for preload_for_pdhs and collection_for_p...
Radhika Chippada
01:37 pm Revision 23c44c89 (arvados): 5365: preload editable component inputs
Radhika Chippada
05:00 am Bug #5688 (Resolved): [API] Accept a git revision range in runtime_constraints, deprecate "min" a...
The current set of miscellaneous git revision filters makes it possible to select versions, but it is hard to underst... Tom Clegg
01:45 am Task #5687 (Resolved): Review 5416-browse-repo-tree (with 5416-ssl-proxy on arvados-dev)
Tom Clegg
01:42 am Task #5486 (Resolved): Add arv-git-httpd to run_test_servers
Tom Clegg
01:42 am Task #5487 (Resolved): Click job script_name to see source code (plain)
Tom Clegg
01:25 am Revision d16fcbb4 (arvados): 5416: Do not override git urls for remote hosted repos.
Tom Clegg
01:25 am Revision 41b9c964 (arvados): 5416: Browse git repository contents in workbench.
Tom Clegg
01:25 am Revision 574281ca (arvados): 5416: Run arv-git-httpd and nginx ssl proxy in test suite.
Tom Clegg
01:25 am Revision 6696741b (arvados): 5416: Fix comment.
Tom Clegg
12:50 am Bug #4458: [Workbench] Replace e-mail address in menu bar with user icon and make sure bread crum...
Here's a screenshot with menu minimized to make the issue super-clear.
!lack-of-dashboard2.png!
Nancy Ouyang

04/08/2015

11:48 pm Revision 9daf42fb (arvados): 5365: add @distinct handling to workbench select queries and use thi...
Radhika Chippada
09:03 pm Bug #3793: [Crunch] Docker containers not removed consistently, filling disk
https://forums.docker.com/t/command-to-remove-all-unused-images/20/5
Suggestion: cron job
* Check `df`, do nothin...
Tom Clegg
09:03 pm Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
Click for drop-down menu, solution mockup below:
!login-dropdown.png!
Nancy Ouyang
08:38 pm Feature #5647: [Workbench] Log-in on anonymous redirects to google sign-in with no warning; feels...
Suggestion:
* Hover-dropdown the login button, with a "Sign up / log in with Google" item.
(Minimize extra clicks...
Tom Clegg
08:41 pm Task #5686 (Resolved): Review 5614-workbench-optimize-combine-collections-wip
Brett Smith
08:39 pm Revision a89ca478 (arvados): 5614: Ruby SDK cp_r method creates streams as needed.
Brett Smith
08:39 pm Revision 79f2985e (arvados): 5614: Improve Workbench combine collections performance.
* Get links with API list calls, instead of fetching each one
individually.
* Get a list mapping portable data has...
Brett Smith
08:39 pm Revision 2b9671a7 (arvados): 5614: Add Collection#each_file to Ruby SDK.
Brett Smith
08:39 pm Revision fceecc54 (arvados): 5614: Use assert_includes more in Workbench tests for better diagnos...
Brett Smith
08:39 pm Revision 552e26d7 (arvados): 5614: Add Collection#exist? to Ruby SDK.
Brett Smith
06:40 pm Revision ff4b9540 (arvados): Merge branch '5416-git-config' refs #5416
Tom Clegg
06:14 pm Bug #5685 (Resolved): [SDKs] In Go SDK keepclient, use defaultCollectionReplication as default Wa...
Tom Clegg
05:29 pm Feature #5414: [Keep] Use data stored remotely (not in local keepstore)
Now at commit:37b57a0 Tom Clegg
05:29 pm Feature #5414: [Keep] Use data stored remotely (not in local keepstore)
Radhika Chippada wrote:
> Review comments:
>
> * Mostly looks good and I was able to follow the updates towards t...
Tom Clegg
05:20 pm Bug #5365: [Workbench] Do not link to objects that are not readable by current user
Radhika Chippada wrote:
> * Just an observation about preloading data: When the user cannot read the objects, the pr...
Brett Smith
02:34 pm Bug #5365: [Workbench] Do not link to objects that are not readable by current user
Brett said:
> * When a logged in user views a pipeline instance page, job UUIDs are not rendered.
There were mult...
Radhika Chippada
05:12 pm Bug #5417: [Workbench] Show error condition / refuse to start a pipeline instance if some inputs ...
(IRC) bcosc
11:24 qr1hi-p5p6p-8584ylktoumirn0 is a good template for testing, its the one we specifically want this ...
Radhika Chippada
04:53 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Brett Smith wrote:
> The failures change on each run, and I did get a passing run, so I figured this was likely a se...
Tom Clegg
04:04 pm Feature #5416: [API] Clone git repositories without using an SSH private key
Ward Vandewege wrote:
> The jenkins tests fail consistently (see run 1448-1452) with this error:
>
> [...]
>
>...
Tom Clegg
04:41 pm Revision f9382ce9 (arvados): 5416: Improve logging.
Tom Clegg
04:06 pm Story #4685: [Crunch] CWL prototype workflow runner in Arvados
Tom Clegg wrote:
> Crunch-dispatch/crunch-job (or their replacements), not the cwl runner, is in charge of dispatc...
Peter Amstutz
03:18 pm Story #4685: [Crunch] CWL prototype workflow runner in Arvados
You are conflating two different components here, which is partly my fault because the naming is confusing.
cwl_jo...
Peter Amstutz
02:50 pm Story #4685: [Crunch] CWL prototype workflow runner in Arvados
Peter Amstutz wrote:
> Notes on 4685-crunch-cwl-support at commit:42008041173b0f7dcc4e90023517767396c64f78
>
> sd...
Tom Clegg
03:13 am Story #4685: [Crunch] CWL prototype workflow runner in Arvados
Notes on 4685-crunch-cwl-support at commit:42008041173b0f7dcc4e90023517767396c64f78
sdk/python/arvados/commands/cw...
Peter Amstutz
04:03 pm Revision 6ab9f329 (arvados): 5416: Do not blow up tests when git global config is uninitialized.
Tom Clegg
03:46 pm Revision 37b57a09 (arvados): 5414: Do not blow up if local config file is empty.
Tom Clegg
03:46 pm Revision 58bd86e6 (arvados): 5414: Use reflect.DeepEqual instead of comparing serialized maps.
Tom Clegg
03:45 pm Revision 9ae180ec (arvados): 5414: Add client support for Keep service hints.
Also, some incidental improvements in nearby code:
* Consistent logging in keepproxy, with one reusable logging stat...
Tom Clegg
03:45 pm Revision 6b00d3b8 (arvados): 5414: Add TestGetWithLocalServiceHint.
Tom Clegg
03:45 pm Revision 9e60acc6 (arvados): 5414: Clean up Locator / MakeLocator() API.
Tom Clegg
03:35 pm Revision 0efa7d7a (arvados): 5416: Do not override git urls for remote hosted repos.
Tom Clegg
02:37 pm Revision 8e4ed0ed (arvados): Merge branch 'master' into 5493-getting-started-modal
Radhika Chippada
02:24 pm Revision 15fef381 (arvados): 5365: Additional test verifications for Log tab display.
Radhika Chippada
02:22 pm Revision 6a99c212 (arvados): 5416: Run arv-git-httpd and nginx ssl proxy in test suite.
Tom Clegg
02:21 pm Bug #5682 (Resolved): [Workbench] Can't view/download files under subdirectories in stream
collection qr1hi-4zz18-tw19sdspe9ljqgk
!view_download_files_from_sub.gif!
Bryan Cosca
02:18 pm Revision 0a81dc07 (arvados): 5416: Browse git repository contents in workbench.
Tom Clegg
02:18 pm Revision 293e691d (arvados): 5416: Fix comment.
Tom Clegg
02:17 pm Revision b4ec5ebe (arvados-dev): 5416: Run keepproxy, arv-git-httpd, and SSL proxy services durin...
Tom Clegg
01:50 pm Bug #5642 (Resolved): [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on c...
Applied in changeset arvados|commit:e009f03d9f3a620f375cf187291bd12c2bf1d74c. Brett Smith
01:38 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
LGTM Peter Amstutz
01:47 pm Revision e009f03d (arvados): Merge branch '5642-crunch-job-swap-limits-wip'
Closes #5642, #5664. Brett Smith
01:46 pm Revision bae652c2 (arvados): 5642: crunch-job uses higher memory limit when running few tasks.
This gives a task all of the node's RAM when it's the only task
running this round, which is more in line with user e...
Brett Smith
01:46 pm Revision e1456a12 (arvados): 5642: Explicitly make all swap available under Docker in crunch-job.
Without this, Docker 1.2 through 1.5 send subprocesses SIGKILL if they
exceed the memory limit. Refer to #5642 for a...
Brett Smith
01:43 pm Revision ae2787c9 (arvados): 5365: trailing white space
Radhika Chippada
01:38 pm Task #5664 (Resolved): Review 5642-crunch-job-swap-limits-wip
Peter Amstutz
01:37 pm Revision 78e0599b (arvados): Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada
01:35 pm Revision 8dcbc531 (arvados): 5365: preload output collection uuids and jobs to help improve perfo...
Radhika Chippada

04/07/2015

09:43 pm Revision 83759d40 (arvados): Include arvados/collection in the Ruby SDK gem.
No issue #. Brett Smith
07:04 pm Bug #5614 (In Progress): [Workbench] 504 error returned when trying to create a large new collection
Brett Smith
06:50 pm Task #5680 (In Progress): Async dispatch hooks from CWL engine
Peter Amstutz
06:49 pm Task #5680 (Resolved): Async dispatch hooks from CWL engine
Peter Amstutz
06:50 pm Task #5679 (In Progress): CWL job runner framework
Peter Amstutz
06:48 pm Task #5679 (Resolved): CWL job runner framework
Peter Amstutz
06:49 pm Task #5681 (Closed): Task dispatch from CWL job runner
Peter Amstutz
06:47 pm Task #5678 (Feedback): Review 4685-crunch-cwl-support
Peter Amstutz
06:33 pm Revision 42008041 (arvados): 4685: Can now run tasks!
Peter Amstutz
06:05 pm Revision f01af635 (arvados): 5365: preload jobs during pipeline display to improve performance.
Radhika Chippada
06:05 pm Bug #5499 (In Progress): [SDKs] arv-copy fails to create collection after copying many blocks
Brett Smith
05:29 pm Bug #5499: [SDKs] arv-copy fails to create collection after copying many blocks
Digging a little more, I found where the arv-copy process tried to find the collection on the destination cluster. T... Brett Smith
01:48 pm Bug #5499: [SDKs] arv-copy fails to create collection after copying many blocks
The create request apparently did not make it to the API server at all. In the logs, the nearest collection-related ... Brett Smith
03:21 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
Peter Amstutz wrote:
> Brett Smith wrote:
> > Peter Amstutz wrote:
> > > Debian Jessie has Docker 1.3.3, which doe...
Brett Smith
02:19 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
Brett Smith wrote:
> Peter Amstutz wrote:
> > Debian Jessie has Docker 1.3.3, which does not have the --memory-swap...
Peter Amstutz
01:53 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
Peter Amstutz wrote:
> Debian Jessie has Docker 1.3.3, which does not have the --memory-swap flag. I'm not sure whe...
Brett Smith
01:38 pm Bug #5642: [Crunch] subprocesses get SIGKILL when they exceed Docker memory limit on compute nodes
Debian Jessie has Docker 1.3.3, which does not have the --memory-swap flag. I'm not sure when it was introduced, but... Peter Amstutz
03:19 pm Revision 71cbc637 (arvados): 5642: Only use Docker memory limits when it supports --memory-swap.
--memory-swap is pretty new (newer than 1.3.3), so we don't want to
require it. At the same time, we don't want to i...
Brett Smith
03:08 pm Revision 957a251e (arvados): 5642: Fixup spacing.
The previous version is functional but this can help prevent an
accident in future development.
Brett Smith
02:46 pm Revision cd1f6c0f (arvados): Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada
02:46 pm Revision add9525f (arvados): 5365: refactor link to object if readable logic
Radhika Chippada
02:40 pm Bug #5653 (Resolved): [SDKs] arv-copy of Pipeline Template did not copy all branches required to ...
Applied in changeset arvados|commit:407ac18e99051a67d4a615bfe2189d5562334f12. Brett Smith
02:09 pm Bug #5653: [SDKs] arv-copy of Pipeline Template did not copy all branches required to remote Repo...
commit:9b0ace3 LGTM.
Repository creating feature request filed separately at #5676.
Peter Amstutz
02:00 pm Bug #5653: [SDKs] arv-copy of Pipeline Template did not copy all branches required to remote Repo...
Peter Amstutz wrote:
> This probably qualifies as bikeshedding, but would this be a good opportunity to take advanta...
Brett Smith
01:50 pm Bug #5653: [SDKs] arv-copy of Pipeline Template did not copy all branches required to remote Repo...
This probably qualifies as bikeshedding, but would this be a good opportunity to take advantage of the new capability... Peter Amstutz
02:34 pm Revision 407ac18e (arvados): Merge branch '5653-arv-copy-multiple-branches-wip'
Closes #5653, #5673. Brett Smith
02:34 pm Revision bfb34761 (arvados): 5653: arv-copy copies multiple commits from the same repository+pipe...
arv-copy previously used the repository name alone to determine which
job scripts it had already copied to the destin...
Brett Smith
02:22 pm Bug #5677 (Resolved): [API] Silence harmless message "ERROR: must be owner of extension plpgsql"
... Peter Amstutz
02:10 pm Task #5673 (Resolved): Review 5653-arv-copy-multiple-branches-wip
Peter Amstutz
02:05 pm Bug #5352 (Resolved): [Crunch] Dispatcher not handling node allocation failures
Applied in changeset arvados|commit:92052dc0b2f80a16420483a756fcebedc6c6ec3c. Brett Smith
01:43 pm Bug #5352: [Crunch] Dispatcher not handling node allocation failures
That's convenient that SLURM has a feature to help with exactly this situation.
commit:a9c5882 LGTM
Peter Amstutz
01:57 pm Revision 92052dc0 (arvados): Merge branch '5352-crunch-dispatch-salloc-tempfail-wip'
Closes #5352, #5670. Brett Smith
01:57 pm Revision 6520efd1 (arvados): 5352: crunch-dispatch treats node allocation failure as temporary.
Imagine a scenario where multiple crunch-dispatch processes are
sitting idle, then suddenly a new job appears in the ...
Brett Smith
01:55 pm Feature #5676 (New): [SDK] arv-copy automatically creates new repository(ies) on the destination ...
arv-copy currently checks out a destination repository and pushes branches to it. Now that Arvados lets users create... Peter Amstutz
01:44 pm Task #5670 (Resolved): Review 5352-crunch-dispatch-salloc-tempfail-wip
Peter Amstutz
01:39 pm Task #5670 (In Progress): Review 5352-crunch-dispatch-salloc-tempfail-wip
Peter Amstutz
01:39 pm Task #5628 (Resolved): Meeting about crunch strategy
Peter Amstutz
01:14 pm Task #5664 (In Progress): Review 5642-crunch-job-swap-limits-wip
Peter Amstutz
02:50 am Revision 87e7d085 (arvados): 4685: One task test
Peter Amstutz

04/06/2015

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

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