Activity

From 07/27/2015 to 08/25/2015

08/25/2015

10:16 pm Bug #6940: [Documentation] Document running Workbench under Software Collections
Downloading just worked when I followed the instructions, so yay! and LGTM. Thanks.
Filed #7129 with some unrelate...
Tom Clegg
10:01 pm Bug #7129 (New): [Documentation] RVM and passenger recipes are missing details
While reviewing #6940 I ran into a couple of hiccups:
# I have to @yum install curl which tar@ in order to get the R...
Tom Clegg
08:54 pm Revision 10e69ac6 (arvados): 6600: Unit tests for single ApiErrors work
Bryan Cosca
07:49 pm Feature #7128 (New): [Documentation] Include description of arv-edit in the User Guide
arv-edit is incredibly helpful when working with pipeline templates and instances. Including it in the User Guide, wh... Sarah Guthrie
07:48 pm Feature #7024: [Keep] keepstore status.json should report runtime environment
Some debug information will require us to start hiding (at least some of) the status report behind an admin token, or... Tom Clegg
06:13 pm Feature #7024: [Keep] keepstore status.json should report runtime environment
Clearing the story points with the expectation that there are going to be many requests added in the next couple of d... Brett Smith
07:10 pm Revision ee1801fe (arvados): 6781: Clarify "logins" vs. "get_all_logins" APIs by moving common co...
Tom Clegg
07:05 pm Bug #6993 (Duplicate): [Workbench] Job log tab crashes when the job's log is the empty collection
We are going to fix this by implementing #5846. Brett Smith
07:01 pm Revision d78a9000 (arvados): 6859: add test that creates and salvages a collection with invalid m...
Radhika Chippada
06:56 pm Feature #7127 (New): [API] Job log cleaner should not clean logs when the job's log is the empty ...
Ward Vandewege
06:51 pm Bug #7113: [Deployment] [Spike] Investigate the RPM equivalent of debconf
Refer to "this ops page":https://arvados.org/projects/ops/wiki/Parameters_of_Arvados_components for a sample of the k... Brett Smith
06:01 pm Revision 54819dd7 (arvados): Merge branch 'master' into 6859-fix-invalid-manifests
Radhika Chippada
06:00 pm Revision 2656de63 (arvados): 6859: script does not catch expections during salvaging; instead the...
Radhika Chippada
05:52 pm Bug #6759: [Deployment] Distro packages for Ruby gems are broken
I removed the code from build-packages that builds the packages for the gems. Ward Vandewege
05:51 pm Revision 638a0c4d (arvados): 6781: Do not try /get_all_logins (the new /logins route is now 2 yea...
Tom Clegg
05:31 pm Bug #6918: [Documentation] keepproxy CORS headers get doubled, don't work
Tom Clegg wrote:
> Peter Amstutz wrote:
> > Tom Clegg wrote:
> > > @keep.example.com@ should be changed to @keep.u...
Peter Amstutz
03:57 pm Bug #6918 (In Progress): [Documentation] keepproxy CORS headers get doubled, don't work
Peter Amstutz wrote:
> Tom Clegg wrote:
> > @keep.example.com@ should be changed to @keep.uuid_prefix.your.domain@ ...
Tom Clegg
01:55 pm Bug #6918 (Resolved): [Documentation] keepproxy CORS headers get doubled, don't work
Applied in changeset arvados|commit:b5a7183d43ca4607fdc259267087e7f795d14de2. Peter Amstutz
05:07 pm Revision 2c9b40bd (arvados): Fix up additional places in keepproxy install docs to use example
"keep$uuid_prefix.your.domain" consistently. refs #6918 Peter Amstutz
05:02 pm Revision 19a2e9a9 (arvados): 6507: Remove unused imports, move _init_ssh_key() into base, set hos...
Peter Amstutz
05:00 pm Story #6781: [Documentation] Document user shell account creation script
Tom Clegg wrote:
> Ward Vandewege wrote:
> > * arvados: the scope in the doc was wrong (missing /logins at the end)...
Ward Vandewege
04:42 pm Revision e513251f (arvados): Merge branch 'master' into 6859-fix-invalid-manifests
Radhika Chippada
04:40 pm Revision 81b8e05d (arvados): Merge branch 'master' into 6260-test-datamanager
Radhika Chippada
04:39 pm Revision 5b5fd04b (arvados): 6260: datamanager integration testing - WIP
Radhika Chippada
04:38 pm Bug #6263: [Git] Can't push via arv-git-httpd
commit:6feefc5 splits the git cgi stuff out of auth_handler.go into git_handler.go, and adds tests for the new env va... Tom Clegg
04:38 pm Revision fd45d425 (arvados-dev): 6260: add datamanager to run-tests.sh
Radhika Chippada
04:38 pm Revision fd45d425 (arvados): 6260: add datamanager to run-tests.sh
Radhika Chippada
04:35 pm Task #7061 (Resolved): Set REMOTE_PORT in arv-git-httpd
Tom Clegg
04:35 pm Task #7062 (Resolved): Test env var behavior with stub
Tom Clegg
04:33 pm Revision 6feefc59 (arvados): 6263: Split git-specific stuff into git_handler.go, add tests for ne...
Tom Clegg
04:11 pm Bug #5923: Fiddlesticks when trying to view a log file
This is probably an effective duplicate of #7008. Workbench's log viewer code assumes it gets back a collection with... Brett Smith
03:57 pm Bug #7123 (Resolved): [Crunch] Should not save any log record when log writing fails
We've seen a few instances recently where crunch-job can't save the job's log because writing to Keep fails. At leas... Brett Smith
03:44 pm Task #7053 (In Progress): Review 6940-workbench-centos-install-wip
Tom Clegg
03:27 pm Bug #7119 (Duplicate): Pipeline instance failed and log collection is empty
I'm going to close this as a multi-duplicate.
Basically, everything failed because of #6997. This includes the or...
Brett Smith
02:24 pm Task #7040 (Resolved): Review 6918-remove-nginx-cors-headers
Peter Amstutz
02:17 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
Ward Vandewege wrote:
> Okay so the kernel issue has been ruled out (keep11 and keep12 died again).
>
> Tom Clegg...
Ward Vandewege
12:53 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
From https://groups.google.com/forum/#!topic/golang-nuts/0WSOKnHGBZE/discussion (re. "not releasing memory")
> We ...
Tom Clegg
12:18 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load

Okay so the kernel issue has been ruled out (keep11 and keep12 died again).
Tom Clegg wrote:
> Tom Clegg wrote:...
Ward Vandewege
04:38 am Bug #6997: [Keep] keepstore reboots GCE host under heavy load
Tom Clegg wrote:
> Can we try with non-zero swap, _and_ max-buffers set to not exceed total RAM? It looks like we've...
Tom Clegg
01:54 pm Revision b5a7183d (arvados): Merge branch '6918-remove-nginx-cors-headers' closes #6918
Peter Amstutz
01:51 pm Revision 9f277b55 (arvados): 6918: Further clean up recommended nginx proxy configuration.
Peter Amstutz
01:18 pm Task #6898 (Resolved): Review 6640-projects-menu-incomplete
Tom Clegg
12:09 pm Introducing the Arvados Web shell
Arvados includes a full suite of command-line tools to create and query objects, upload and download collections, and... Brett Smith

08/24/2015

11:02 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
Can we try with non-zero swap, _and_ max-buffers set to not exceed total RAM? It looks like we've tried both of these... Tom Clegg
10:57 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
https://github.com/golang/go/issues/8832 suggests
* linux kernel bug prevents memory from being freed as expected
*...
Tom Clegg
10:20 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
vmstat 1 on keep11.s just before rebooting.... Tom Clegg
09:31 pm Bug #6997 (In Progress): [Keep] keepstore reboots GCE host under heavy load
Tom Clegg
06:20 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
For the curious, main.func·003 is newBufferPool(), so it makes sense that it would be responsible for the vast majori... Peter Amstutz
06:17 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
After running a little longer:... Peter Amstutz
06:14 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
I found something!... Peter Amstutz
02:56 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
Nico Cesar wrote:
> about overcommit:
>
> here are the 3 modes:
>
> https://www.kernel.org/doc/Documentation/v...
Tom Clegg
12:15 pm Bug #6997 (New): [Keep] keepstore reboots GCE host under heavy load
about overcommit:
here are the 3 modes:
https://www.kernel.org/doc/Documentation/vm/overcommit-accounting
ba...
Nico César
09:35 pm Revision fc1a358d (arvados): 7041: pyvcf was missing from backports in trusty
refs #7041 Nico César
09:35 pm Revision fc1a358d (arvados-dev): 7041: pyvcf was missing from backports in trusty
refs #7041 Nico César
08:51 pm Revision 28bdfc61 (arvados): flailing 8.24 4.51
Bryan Cosca
06:09 pm Bug #7121 (Resolved): [Keep] keepstore should use only one buffer for each PUT (and should not de...
PUT uses 2x 64 MiB buffers if the block already exists on disk. One buffer is used to read the request body, the othe... Tom Clegg
04:23 pm Bug #7120 (New): [Keep] keepproxy should log real IP address
Currently, if keepproxy sees an X-Real-IP header, it logs that value (and the X-Forwarded-For value if provided) inst... Tom Clegg
03:43 pm Bug #6918: [Documentation] keepproxy CORS headers get doubled, don't work
Peter Amstutz wrote:
> Tom Clegg wrote:
> > AFAIK all of these are useless for keepproxy. "proxy_redirect off" is e...
Tom Clegg
02:42 pm Bug #6918: [Documentation] keepproxy CORS headers get doubled, don't work
Tom Clegg wrote:
> AFAIK all of these are useless for keepproxy. "proxy_redirect off" is especially worth removing s...
Peter Amstutz
01:23 am Bug #6918: [Documentation] keepproxy CORS headers get doubled, don't work
AFAIK all of these are useless for keepproxy. "proxy_redirect off" is especially worth removing since the only thing ... Tom Clegg
03:17 pm Revision 73bfa624 (arvados): added test_init_temp for a shorter version of test_init without pseu...
Bryan Cosca
02:49 pm Revision a99c7bb0 (arvados): 6918: Fix server_name in example nginx config. Remove client_body_b...
Peter Amstutz
02:43 pm Task #7106 (Resolved): Review 6941-docs-fix-www-data
Peter Amstutz
02:43 pm Task #7105 (Resolved): Fix docs
Peter Amstutz
02:39 pm Bug #7119 (Duplicate): Pipeline instance failed and log collection is empty
Pipeline instance: https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-8noje7tynl2vdis
I am unab...
Sarah Guthrie
02:05 pm Bug #6941 (Resolved): [Documentation] Fix www-data references in git server install guide
Applied in changeset arvados|commit:9494d7df964f24d7d8d53a09233d696d4ffcc234. Peter Amstutz
02:01 pm Bug #6941: [Documentation] Fix www-data references in git server install guide
Ward Vandewege wrote:
> 6941-docs-fix-www-data up for review LGTM.
>
> There is one more occurrence of www-data i...
Peter Amstutz
02:03 pm Revision 9494d7df (arvados): Merge branch '6941-docs-fix-www-data' closes #6941
Peter Amstutz
12:28 am Task #7062 (In Progress): Test env var behavior with stub
Tom Clegg
12:28 am Task #7061 (Closed): Set REMOTE_PORT in arv-git-httpd
Tom Clegg
12:28 am Task #7061 (In Progress): Set REMOTE_PORT in arv-git-httpd
Tom Clegg
12:23 am Task #6952 (Resolved): Review 5824-go-sdk
Tom Clegg
12:21 am Story #6781: [Documentation] Document user shell account creation script
Ward Vandewege wrote:
> * arvados: the scope in the doc was wrong (missing /logins at the end)
(By "wrong" you me...
Tom Clegg
12:05 am Revision 7c4d45b9 (arvados): 6997: Avoid unnecessarily inefficient dirent sorting (and a mismatch...
Tom Clegg
12:02 am Revision 687d7572 (arvados): 6997: In Go 1.5, "all iface, any port" must be written ":0", not ":".
Tom Clegg

08/23/2015

03:32 am Bug #6868: [SSO] Template calls undefined method after fresh local accounts installation
This problem seems to go away after setting
allow_account_registration: true
in application.yml.
ming fang

08/22/2015

07:17 am Bug #6997: [Keep] keepstore reboots GCE host under heavy load
100x 64MiB buffers + 10% GOGC means we expect _at least_ 7381975040 bytes (7208960 KiB) rss. We've seen the OOM-kille... Tom Clegg
02:05 am Bug #6997: [Keep] keepstore reboots GCE host under heavy load
Ward Vandewege wrote:
> Nico Cesar wrote:
> > My recommendation is to take swap off and lower the slot from 100 to ...
Ward Vandewege

08/21/2015

09:48 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
Nico Cesar wrote:
> My recommendation is to take swap off and lower the slot from 100 to 60
Done for all the su92...
Ward Vandewege
09:47 pm Bug #6997 (In Progress): [Keep] keepstore reboots GCE host under heavy load
Ward Vandewege
09:37 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
we got "compute.instances.hostError an instance" on all the failing nodes and GCE rebooted the machines. ... Nico César
08:07 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
check the references here: http://golang.org/pkg/runtime/#MemStats Nico César
02:40 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
Nico Cesar wrote:
> memory keeps being allocated.
>
> I wish we could graph this easily ...
>
> [...]
>
>...
Nico César
02:19 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
memory keeps being allocated.
I wish we could graph this easily ... ...
Nico César
09:47 pm Bug #6941 (In Progress): [Documentation] Fix www-data references in git server install guide
Ward Vandewege
08:42 pm Bug #6941: [Documentation] Fix www-data references in git server install guide
6941-docs-fix-www-data up for review LGTM.
There is one more occurrence of www-data in our install guide, in the A...
Ward Vandewege
08:52 pm Bug #7114: [Deployment] Add a configuration template to the keepproxy package
Currently the template is expected to include information to be able to run Nginx in front of Keepproxy to provide SS... Brett Smith
08:42 pm Bug #7114 (New): [Deployment] Add a configuration template to the keepproxy package
[Nico has assembled the list of what information needs to be configured. Add it here.] Brett Smith
08:44 pm Bug #7115 (New): [Deployment] Add an nginx site configuration to the keepproxy package
Functional requirements:
* The configuration should use a server name, internal and public port numbers, and SSL c...
Brett Smith
08:38 pm Bug #7113 (New): [Deployment] [Spike] Investigate the RPM equivalent of debconf
We're currently planning to add debconf templates to our packages to make them easier to deploy. People installing b... Brett Smith
08:34 pm Feature #6034: [Deployment] Add sysvinit script to the keepproxy package
I'm reverting Tom's change, in the spirit of having one issue be about one thing. I'll file a separate story about d... Brett Smith
08:33 pm Revision a53d5ecd (arvados): 6941: Add note about needing to fill in correct web server user in p...
www-data was used before. Peter Amstutz
08:31 pm Story #6884: [Deployment] Plan addition of init scripts to Arvados daemon packages
We had some discussion about this in a planning meeting.
There's broad support for having packages install a servi...
Brett Smith
08:31 pm Task #7106 (In Progress): Review 6941-docs-fix-www-data
Peter Amstutz
07:36 pm Task #7106 (Resolved): Review 6941-docs-fix-www-data
Peter Amstutz
08:22 pm Bug #7111 (New): [SDKs] Test arv-copy
arv-copy is currently completely untested. This is especially unfortunate because it's a real workhorse Arvados tool... Brett Smith
08:20 pm Feature #3223: [Documentation] Tutorial for adding a crunch script wrapper for an existing tool t...
Is this still needed now that we support external repositories? Brett Smith
08:19 pm Bug #7099: [SDKs] CLI SDK tools use Ruby SDK
Or maybe we don't want to do this, maybe we'd rather rewrite it all in Python (#5468). Brett Smith
01:43 pm Bug #7099 (New): [SDKs] CLI SDK tools use Ruby SDK
The CLI SDK includes the commands @arv@, @arv-tag@, and @arv-run-pipeline-instance@. All of these tools are duplicat... Brett Smith
07:51 pm Revision 9f88440d (arvados): arv-tag respects more valid ARVADOS_API_HOST_INSECURE values.
This makes it more consistent with other tools, including `arv`
itself. No issue #.
Brett Smith
07:43 pm Task #7105 (In Progress): Fix docs
Peter Amstutz
07:36 pm Task #7105 (Resolved): Fix docs
Peter Amstutz
03:36 pm Revision 22e1fd1a (arvados): 6600: Added pseudocode as test infrastructure
Bryan Cosca
03:28 pm Bug #6640 (Resolved): [Workbench] Ensure projects menu consistently shows all "my projects"
Manoj Malipeddu
03:27 pm Bug #6640 (In Progress): [Workbench] Ensure projects menu consistently shows all "my projects"
#7100 is created to address the issue with ArvadosResourceList. Manoj Malipeddu
03:25 pm Bug #6640 (Resolved): [Workbench] Ensure projects menu consistently shows all "my projects"
Applied in changeset arvados|commit:1cecdfb6fabf47c921e7f422063368621619dcfb. Manoj Malipeddu
03:23 pm Revision 1cecdfb6 (arvados): closes #6640
Merge branch '6640-all-projects-dup' Manoj Malipeddu
03:03 pm Bug #7100 (New): [Workbench] Reusing ArvadosResourceList results in inconsistent results
See #6640 for a historical perspective of this issue. In that issue, it was observed that the results of all_projects... Radhika Chippada
02:57 pm Revision f92e43f8 (arvados): Merge branch 'master' into 6640-all-projects-dup
Manoj Malipeddu
02:22 pm Task #6979 (Resolved): Do not offer "Add a new repository" and "Add a new SSH key" buttons when a...
Radhika Chippada
02:22 pm Task #6990 (Resolved): Review 6652-test-system-menu
Radhika Chippada
02:21 pm Story #6781: [Documentation] Document user shell account creation script
Moving to sprint 2015-09-02 so that Tom can readdress it when he is back from his break. Leaving the story point assi... Radhika Chippada
02:13 pm Task #7060 (Resolved): Review 6942-improve-compute-node-setup-script
Ward Vandewege
02:09 pm Bug #6942: [Documentation] Improve compute node setup script
Excellent, thank you. I applied both changes and merged. Ward Vandewege
12:57 pm Bug #6942: [Documentation] Improve compute node setup script
Reviewing commit:21f2d53
* The curl command at the very end of the script also needs its URL changed to use @$ARVA...
Brett Smith
02:09 pm Revision ba0bc2f7 (arvados): Merge branch '6942-improve-compute-node-setup-script'
closes #6942 Ward Vandewege
02:08 pm Revision 77c7b991 (arvados): Merge branch 'master' into 6942-improve-compute-node-setup-script
Ward Vandewege
02:08 pm Revision c62a4ff1 (arvados): Some more improvements based on review feedback.
closes #6942 Ward Vandewege
01:35 pm Revision 6a79f929 (arvados): arv-tag authenticates to the API server with OAuth2.
No issue #. Brett Smith

08/20/2015

09:53 pm Bug #6997: [Keep] keepstore reboots GCE host under heavy load
Added swap on all the su92l keep nodes. I had to fight to keep keep9-13 in the air; 9 and 11 actually went down (OOM)... Ward Vandewege
08:41 pm Revision a6e5b740 (arvados): flailing and added more comments
Bryan Cosca
08:15 pm Bug #7010 (Resolved): [Documentation] Document API/Git server's Git 1.7.10 requirement
Applied in changeset arvados|commit:80d3540193e78a2dfee8373490a0f9e67f9d804a. Radhika Chippada
06:23 pm Bug #7010: [Documentation] Document API/Git server's Git 1.7.10 requirement
... Peter Amstutz
02:52 pm Bug #7010 (In Progress): [Documentation] Document API/Git server's Git 1.7.10 requirement
Radhika Chippada
02:48 pm Bug #7010: [Documentation] Document API/Git server's Git 1.7.10 requirement
There was a little discussion in the office about recommending that CentOS 6 users get Git 1.7.10 a particular way. ... Brett Smith
08:11 pm Task #7036 (Resolved): Document git version
Radhika Chippada
02:48 pm Task #7036 (In Progress): Document git version
Radhika Chippada
08:10 pm Task #7037 (Resolved): Review branch 7010-git-version
Peter Amstutz
06:27 pm Task #7037 (In Progress): Review branch 7010-git-version
Peter Amstutz
08:10 pm Bug #7012 (Resolved): [Documentation] Remove Docker-based install from the installation guide
Applied in changeset arvados|commit:64b5df6b8c744a6a5d7dae5ef57966c9d0cc57f3. Peter Amstutz
08:07 pm Revision 64b5df6b (arvados): Merge branch '7012-no-docker-install-doc' closes #7012
Peter Amstutz
08:04 pm Revision 6e515829 (arvados): 6918: Update documentation to remove CORS headers from sample nginx
configuration. Add sample ssl_, proxy_ and client_ settings as well. Peter Amstutz
08:03 pm Task #7040 (In Progress): Review 6918-remove-nginx-cors-headers
Peter Amstutz
08:03 pm Task #7039 (Resolved): Fix docs
Peter Amstutz
06:37 pm Task #7039 (In Progress): Fix docs
Peter Amstutz
08:03 pm Revision 80d35401 (arvados): closes #7010
Merge branch '7010-git-version' Radhika Chippada
08:03 pm Revision 53ee080a (arvados): Merge branch 'master' into 7010-git-version
Radhika Chippada
07:39 pm Bug #6918: [Documentation] keepproxy CORS headers get doubled, don't work
Also for completeness http://wiki.nginx.org/HttpHeadersMoreModule provides "more_set_header" which actually replaces ... Peter Amstutz
07:27 pm Bug #6918: [Documentation] keepproxy CORS headers get doubled, don't work
Another option is to teach keepproxy to look for a proxy header and suppress the CORS headers when a request comes th... Peter Amstutz
06:45 pm Task #7035 (Resolved): Review 7012-no-docker-install-doc
Bryan Cosca
06:36 pm Task #7035 (In Progress): Review 7012-no-docker-install-doc
Peter Amstutz
06:44 pm Revision 748680bc (arvados): 7010: trimmed version git version note.
Radhika Chippada
06:41 pm Revision e09bff41 (arvados): still flailing
Bryan Cosca
06:36 pm Revision 59015445 (arvados): 7012: Remove Docker install from _config.yml as well.
Peter Amstutz
06:34 pm Revision 03a84f92 (arvados): 7012: Rewrite introduction page to remove links to Docker install an...
description of the manual installation method. Peter Amstutz
06:33 pm Task #7034 (Resolved): Remove links
Peter Amstutz
06:05 pm Revision b9551860 (arvados): 6507: Fix test
Peter Amstutz
06:04 pm Revision 44494089 (arvados): 6507: Use get_image() instead of list_images() for image lookup.
Peter Amstutz
06:02 pm Revision a8ed4672 (arvados): flailing disregard commit
Bryan Cosca
06:01 pm Task #7060 (In Progress): Review 6942-improve-compute-node-setup-script
Brett Smith
05:13 pm Bug #6940: [Documentation] Document running Workbench under Software Collections
I should add that I tested everything by starting from a new centos:6 Docker container and following the install guid... Brett Smith
05:09 pm Bug #6940: [Documentation] Document running Workbench under Software Collections
6940-workbench-centos-install-wip is up for review.
The Nginx setup instructions had to move up to keep the instal...
Brett Smith
04:08 pm Bug #6940: [Documentation] Document running Workbench under Software Collections
Setting in .bashrc doesn't work because the nginx user's shell is not bash, which causes Passenger to invoke the chil... Brett Smith
02:51 pm Bug #6940 (In Progress): [Documentation] Document running Workbench under Software Collections
Brett Smith
04:59 pm Revision 5b43c0e8 (arvados): 6940: Workbench install guide describes using Nginx with Software Co...
Because Workbench invokes arv-get, it needs this configuration to find
arv-get in the Software Collection root.
Brett Smith
03:40 pm Bug #6942 (Resolved): [Documentation] Improve compute node setup script
Applied in changeset arvados|commit:21f2d53a70dbf6ae04db07e163f4485e3af47478. Ward Vandewege
03:34 pm Revision 21f2d53a (arvados): Improve compute node setup script.
closes #6942 Ward Vandewege
03:20 pm Revision 06dd898f (arvados): 6940: Use nginx as WWW_OWNER on Red Hat distributions.
We recommend deploying with Nginx, and this script interacts with
Nginx. The default Nginx configuration that Phusio...
Brett Smith
03:20 pm Revision 06dd898f (arvados-dev): 6940: Use nginx as WWW_OWNER on Red Hat distributions.
We recommend deploying with Nginx, and this script interacts with
Nginx. The default Nginx configuration that Phusio...
Brett Smith
03:13 pm Revision 9c9defdd (arvados): 6940: Move arvados-workbench-upgrade.sh down in install guide.
The script tries to restart Nginx, so Nginx should be set up first.
No issue #.
Brett Smith
02:55 pm Story #6260 (In Progress): [Keep] Integration test between data manager, API and keepstore.
Radhika Chippada
02:47 pm Revision 74ea7122 (arvados): 7010: add note in install guides that we need git version 1.7.10 or ...
Radhika Chippada
06:26 am Task #7062 (Resolved): Test env var behavior with stub
Tom Clegg
06:26 am Task #7061 (Resolved): Set REMOTE_PORT in arv-git-httpd
Tom Clegg
06:25 am Task #7054 (Resolved): Replicate, confirm which versions and run scripts are in play
Tom Clegg
06:25 am Bug #6263 (In Progress): [Git] Can't push via arv-git-httpd
Tom Clegg
06:25 am Bug #6263: [Git] Can't push via arv-git-httpd
Gitolite needs... Tom Clegg
06:18 am Revision 1de4f2fb (arvados): 6263: Set flag to skip gitolite permission checks, and set SERVER_AD...
Tom Clegg
06:18 am Revision b20aa99b (arvados): 6263: Pass through environment variables needed by gitolite-shell.
Tom Clegg
06:11 am Revision 9b9528c5 (arvados): 6263: Set flag to skip gitolite permission checks, and set SERVER_AD...
Tom Clegg
05:56 am Revision 88a9005a (arvados): 6263: Set flag in run script to skip gitolite permission checks.
Tom Clegg
05:51 am Revision 7f8f29de (arvados): 6263: Pass through environment variables needed by gitolite-shell.
Tom Clegg
03:59 am Revision 6791c56b (arvados): 6640: Fix whitespace, remove excess end tag.
Tom Clegg
03:56 am Revision 9a4c7cb6 (arvados): 6640: Replace paging test with all_projects bugfix test.
Tom Clegg

08/19/2015

11:18 pm Revision 647c3bac (arvados): 6859: Always raise an exception on errors during salvaging. Catch an...
Radhika Chippada
10:01 pm Revision 39f461e6 (arvados): more flailing, I think I figured out how to mock the methods in job_...
Bryan Cosca
09:41 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
OK! This (commit:60aa782) is an excellent demonstration. I see now how @limit was infecting the all_projects list.
...
Tom Clegg
07:16 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
In commit:60aa782479f0f97d880bddec1bb35a397f06707e:
In branch: 6640-projects-menu-incomplete-bugfix
Added tests i...
Manoj Malipeddu
03:22 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
Radhika Chippada wrote:
> ** When the dashboard is shown, projects#index is loaded which invokes all_projects method...
Tom Clegg
03:02 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
In commit:2c630802a9bf570c3ced2f7d42c2346ef814b578:
Reverted bugfix.
Manoj Malipeddu
09:34 pm Revision 15696397 (arvados): 6640: dup all_projects when reusing it for find_objects_for_index, to
avoid infecting the projects dropdown menu with this request's filter
params.
Tom Clegg
09:11 pm Story #6781: [Documentation] Document user shell account creation script
I reviewed both branches and pushed a commit to each of them:
* arvados: the scope in the doc was wrong (missing /...
Ward Vandewege
09:04 pm Revision b051b44d (arvados): 6781: Fix scope for user-sync script in documentation.
Ward Vandewege
08:11 pm Task #7060 (Resolved): Review 6942-improve-compute-node-setup-script
Brett Smith
08:08 pm Task #7057 (Resolved): review 6939-package-sso-server branch on both the arvados-dev repository a...
Ward Vandewege
08:04 pm Task #7054 (Resolved): Replicate, confirm which versions and run scripts are in play
Tom Clegg
08:03 pm Task #7053 (Resolved): Review 6940-workbench-centos-install-wip
Brett Smith
08:01 pm Task #7052 (Resolved): Review 6638-python-backport-dependencies-wip
Brett Smith
08:01 pm Task #7051 (Resolved): Review 6260-test-datamanager branches in arvados and arvados-dev repositor...
Radhika Chippada
08:01 pm Task #6912 (New): Determine dependencies for various distros
Brett Smith
06:55 pm Task #6912 (In Progress): Determine dependencies for various distros
Tom Clegg
01:28 pm Task #6912 (Resolved): Determine dependencies for various distros
Tom Clegg
08:01 pm Task #6949 (Resolved): Review 6638-backport-deps (arvados + arvados-dev)
Brett Smith
06:37 pm Task #6949 (In Progress): Review 6638-backport-deps (arvados + arvados-dev)
Peter Amstutz
08:00 pm Task #7049 (Resolved): Review 6263-arv-gitolite
Tom Clegg
08:00 pm Task #7046 (Resolved): Review 6953-docker-image-cleaner
Tom Clegg
07:48 pm Task #7040 (Resolved): Review 6918-remove-nginx-cors-headers
Peter Amstutz
07:48 pm Task #7039 (Resolved): Fix docs
Peter Amstutz
07:44 pm Task #7037 (Resolved): Review branch 7010-git-version
Peter Amstutz
07:44 pm Task #7036 (Resolved): Document git version
Peter Amstutz
07:44 pm Task #7035 (Resolved): Review 7012-no-docker-install-doc
Peter Amstutz
07:44 pm Task #7034 (Resolved): Remove links
Peter Amstutz
07:13 pm Revision 60aa7824 (arvados): 6640: Added tests to reproduce bug on dashboard.
Manoj Malipeddu
06:57 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
Tom Clegg wrote:
> Another bug: the deps and build-deps can't just say "openssl | gnutls" because the runtime depend...
Brett Smith
06:41 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
Another bug: the deps and build-deps can't just say "openssl | gnutls" because the runtime dependency depends on whic... Tom Clegg
06:49 pm Revision 1c4f6b59 (arvados-dev): Stop building broken debs for our gems. We don't use them and th...
never worked. We can reintroduce a working version later.
refs #6781
Ward Vandewege
06:32 pm Task #6897 (In Progress): Review 6781-arvados-login-sync (on arvados-dev and arvados)
Ward Vandewege
06:22 pm Revision 96b2b2fe (arvados): Merge branch 'master' into 6859-fix-invalid-manifests
Radhika Chippada
04:39 pm Revision 36b7f52b (arvados): refs #6640
Merge branch '6640-projects-menu' Manoj Malipeddu
04:15 pm Bug #6994: [Deployment] our rails packages need to install certain files/directories as owned by ...
Ward signed off on the idea. Brett Smith
03:55 pm Bug #7026: [Node Manager] Mishandles stop signals
One possibility: the "docs for stop_all":https://www.pykka.org/en/latest/api/#pykka.ActorRegistry.stop_all say actors... Brett Smith
03:43 pm Bug #7026 (New): [Node Manager] Mishandles stop signals
There are two issues here. They might have the same root cause, so for now, I'm filing one issue. If it turns out t... Brett Smith
03:52 pm Revision 58f1ae16 (arvados): 6640: Show only My Projects in dropdowns: use search modal for share...
Manoj Malipeddu
03:38 pm Revision 67b5f18f (arvados): Merge branch '6640-projects-menu-incomplete' of git.curoverse.com:ar...
Manoj Malipeddu
03:37 pm Revision 5cf141d8 (arvados): 6640: Reverted bugfix.
Manoj Malipeddu
03:29 pm Revision e1b3e2d2 (arvados): 6640: Show only My Projects in dropdowns: use search modal for share...
Manoj Malipeddu
03:24 pm Revision 22a1738a (arvados): 6640: UI updates.
Manoj Malipeddu
03:22 pm Revision 5467329d (arvados): 6507: Fix tests
Peter Amstutz
03:19 pm Revision 0600e457 (arvados): 6507: Set hostname tag in arvados_create_kwargs instead of sync_node.
Peter Amstutz
03:13 pm Revision 8552d320 (arvados): 6507: Paste in command line for creating service principals instead ...
referencing generic documentation. Peter Amstutz
03:07 pm Revision 0fde046a (arvados): 6507: Added notes to sample azure configuration file
Peter Amstutz
02:57 pm Revision 2c630802 (arvados): 6640: Reverted bugfix.
Manoj Malipeddu
02:36 pm Revision 45a172b5 (arvados): 6507: Add basic azure driver tests.
Peter Amstutz
02:25 pm Bug #6753: [API] Asset pipeline does not work unless config/environments/production.rb is present...
To confirm that this is truly a problem for API server (Rails3) the same way it was in Workbench (Rails4):
* Delet...
Tom Clegg
01:59 pm Feature #7024 (New): [Keep] keepstore status.json should report runtime environment
Some useful/easy things to report in @/status.json@ that can be useful for troubleshooting:
* GOGC env (or 100 if no...
Tom Clegg
01:40 pm Bug #6862 (Resolved): [Documentation] What do you need to know about using Git with Arvados
Applied in changeset arvados|commit:8dccf76ea830057d433b07c40bc2c1294891ea39. Bryan Cosca
01:35 pm Revision 8dccf76e (arvados): closes #6862
Merge branch '6862-git-doc-guide-new' Bryan Cosca
01:30 pm Bug #6652 (Resolved): [API] Error "Owner uuid must refer to a user with a username" when creating...
Applied in changeset arvados|commit:c1ceb0f74d5547c56cf6cdde56044adba171efaf. Manoj Malipeddu
01:21 pm Bug #6652: [API] Error "Owner uuid must refer to a user with a username" when creating a new repo...
In commit:3bfb9c5cbf5dd56b84fd17f9e1dcdd6a219fe5fe:
Added else statement and changed assertion to use assert_text ...
Manoj Malipeddu
01:25 pm Revision 0d7ba600 (arvados): Merge branch 'master' into 6640-projects-menu-incomplete
Manoj Malipeddu
01:24 pm Story #6260: [Keep] Integration test between data manager, API and keepstore.
Radhika is working on this, but started late, so we knew we wouldn't finish it this sprint. Moving it to the next, w... Brett Smith
01:24 pm Revision c1ceb0f7 (arvados): closes #6652
Merge branch '6652-test-system-menu' Manoj Malipeddu
01:19 pm Task #6889 (Resolved): Review 6862-git-doc-guide-new
Radhika Chippada
01:19 pm Revision 3bfb9c5c (arvados): 6652: Added assertion and changed assertion to use assert_text instead
of page.has_text?. Manoj Malipeddu
01:17 pm Bug #7002: [Workbench] workbench move and copy is incomplete
Radhika Chippada wrote:
> This is actually two separate issues. (1) workbench move is incomplete, and (2) workbench ...
Brett Smith
12:16 pm Bug #7002: [Workbench] workbench move and copy is incomplete
This is actually two separate issues. (1) workbench move is incomplete, and (2) workbench copy is incomplete. In case... Radhika Chippada
01:15 pm Revision 7ba5211a (arvados): Merge branch 'master' into 6652-test-system-menu
Manoj Malipeddu

08/18/2015

09:23 pm Revision c46ab7c6 (arvados): Create, destroy, tag nodes.
Peter Amstutz
08:44 pm Revision bdeee3f4 (arvados): 6862: Fixed typos and syntax in git-arvados-guide
Bryan Cosca
08:22 pm Bug #6862: [Documentation] What do you need to know about using Git with Arvados
Radhika Chippada wrote:
> * Please add a sentence along the lines “Create a git a repository named *tutuorial-branch...
Bryan Cosca
08:13 pm Bug #6862: [Documentation] What do you need to know about using Git with Arvados
* Please add a sentence along the lines “Create a git a repository named *tutuorial-branch* in the *tutorial* Arvados... Radhika Chippada
07:33 pm Bug #6862: [Documentation] What do you need to know about using Git with Arvados
On Commit 406b3de5426bf0d63564410cf6caf2834ba2b7bb
Radhika Chippada wrote:
> * Working with an Arvados git reposi...
Bryan Cosca
06:00 pm Bug #6862: [Documentation] What do you need to know about using Git with Arvados
* Working with an Arvados git repository is analogous to working with other public repositories. If you are already f... Radhika Chippada
03:26 pm Bug #6862: [Documentation] What do you need to know about using Git with Arvados
Branch 6862-git-doc-guide-new commit 39c9193f03471aa7826769b34d6b55890a2c98a3
Radhika Chippada wrote:
> Also, ini...
Bryan Cosca
02:43 am Bug #6862: [Documentation] What do you need to know about using Git with Arvados
Also, initial review comments for the newly added "Working with Arvados git repository" page.
* Title: please repl...
Radhika Chippada
01:52 am Bug #6862: [Documentation] What do you need to know about using Git with Arvados
Looking at branch 6862-git-doc-guide, at commit commit:ba85c6f5e9454e7fe3c40dc744345cb399d45f0c
Bryan: It appears ...
Radhika Chippada
07:36 pm Revision 406b3de5 (arvados): 6862: Moved clone arvados repository from tutorial-submit-job to git...
Bryan Cosca
07:01 pm Bug #7008: [Workbench] Crashes with Fiddlesticks when trying to view a pipeline instance graph co...
General agreement on the proposed fix in discussion. Brett Smith
06:53 pm Bug #7004: [Deployment] Remove dependency on third-party keyservers
Ward to publish our key over HTTPS, and maybe third-party keys we rely on for installation like RVM's.
1 story poi...
Brett Smith
06:49 pm Revision 9cfdca66 (arvados): 6600: quick changes, rebase this commit
Bryan Cosca
06:42 pm Bug #6885: [Deployment] Add meaningful package versions to distro packages
Empty commits don't work to trigger new package builds for our own packages, since they look for commits that affect ... Brett Smith
01:24 pm Bug #6885: [Deployment] Add meaningful package versions to distro packages
The fpm-info.sh mechanism recently added to arvados-dev gives us another channel to do this. For packages with sourc... Brett Smith
06:37 pm Bug #6967: [API] [Workbench] application.default.yml should not call git, at least in production
Plan:
* Update API server and Workbench packages to include a file with the version.
* The production section of ...
Brett Smith
06:17 pm Bug #7015 (Resolved): [Documentation] Refresh user guide
For the entire Arvados user guide, look for documentation that is out-of-date, and prepare a branch that brings those... Brett Smith
06:09 pm Bug #6263: [Git] Can't push via arv-git-httpd
This is expected to be address in our Gitolite deployment—either the way we set it up, or in the Gitolite code itself... Brett Smith
06:06 pm Bug #7012: [Documentation] Remove Docker-based install from the installation guide
Brett to specify where on the wiki the build-from-source documentation should go. Brett Smith
04:12 pm Bug #7012 (Resolved): [Documentation] Remove Docker-based install from the installation guide
Our install guide currently documents installing Arvados from Docker images, either our pre-built versions or from so... Brett Smith
05:02 pm Bug #6770: incomplete recursive copying of pipeline templates with arv-copy
Update: you'll probably need commit:dac77d5d53bb56054b91ba2ed223a49da08848f8. Brett Smith
03:25 pm Revision 39c9193f (arvados): 6862: Added a quick guide to git, from git clone to git push.
Bryan Cosca
03:14 pm Feature #5676: [SDK] arv-copy automatically creates new repository(ies) on the destination cluster
The "copy over HTTPS" story exists separately as #6605. Dedicating this story to the other half, "create new destina... Brett Smith
01:39 pm Bug #6754: [Workbench] Report HTTP error instead of sending 0-byte file when error fetching from ...
Updating description based on Tom's note. Brett Smith
01:29 pm Bug #7001: [SDKs] Recursive pipeline instance arv-copy doesn't copy job objects, losing metadata
Sarah Guthrie wrote:
> I would also like to point out that I will predict the empty source information, provenance g...
Brett Smith
01:12 pm Bug #6922: [API] [Maybe] Update API server to support Git 1.7.2
Updating to reflect that this ticket is controversial and lower priority. Split off the "document 1.7.10 requirement... Brett Smith
01:05 pm Bug #7010 (Resolved): [Documentation] Document API/Git server's Git 1.7.10 requirement
The API server and Git server require Git 1.7.10. Add a note about this requirement:
* in the API server install ...
Brett Smith
12:50 pm Bug #7009 (Duplicate): When using git clone "https" instead of "git@", user is unable to push to ...
Duplicates #6263. Brett Smith
12:44 pm Revision dac77d5d (arvados): 6095: Brown paper bag fix the last commit.
I swear I tried to test before I pushed, but I used --no-recursive,
which meant we never got to this code. That also...
Brett Smith
04:29 am Revision 38195163 (arvados): 6859: mocking Kernel system method had the undersirable side effect ...
Radhika Chippada
04:06 am Revision 65f76d01 (arvados): Merge branch 'master' into 6859-fix-invalid-manifests
Radhika Chippada
03:13 am Bug #6652: [API] Error "Owner uuid must refer to a user with a username" when creating a new repo...
Review comments:
* Please add an else block for "if add_button_text" in the test...
Radhika Chippada

08/17/2015

11:39 pm Bug #6862: [Documentation] What do you need to know about using Git with Arvados
Branch 6862-git-doc-guide is up for review.
I tried to keep it very simple. This is for bioinformaticians who have...
Bryan Cosca
11:38 pm Revision ba85c6f5 (arvados): 6862: Added git commands clone, checkout, add, commit, push
Bryan Cosca
10:58 pm Bug #7009 (Duplicate): When using git clone "https" instead of "git@", user is unable to push to ...
... Bryan Cosca
10:37 pm Revision 66787390 (arvados): 6600: still trying to make a spy
Bryan Cosca
10:07 pm Bug #7001: [SDKs] Recursive pipeline instance arv-copy doesn't copy job objects, losing metadata
I would also like to point out that I will predict the empty source information, provenance graphs, used-by graphs, a... Sarah Guthrie
09:41 pm Bug #7001: [SDKs] Recursive pipeline instance arv-copy doesn't copy job objects, losing metadata
Sarah Guthrie wrote:
> I would guess these problems are caused by the fact that the jobs are not copied with the pip...
Brett Smith
06:47 pm Bug #7001 (New): [SDKs] Recursive pipeline instance arv-copy doesn't copy job objects, losing met...
The instance in question is https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-38ewfna4842vrnr, wh... Sarah Guthrie
09:39 pm Bug #7008 (New): [Workbench] Crashes with Fiddlesticks when trying to view a pipeline instance gr...
See #7001 for original bug report and details. This happens because Workbench tries to look up jobs from other clust... Brett Smith
09:34 pm Revision 45fcd8ae (arvados): 6095: Stop demoting OrderedDicts to dicts in arv-copy.
History: first there was 79564b0ac7d03327cc351bbd6df544ab1f776380.
This preserved the order of copied pipeline templa...
Brett Smith
09:20 pm Bug #7002: [Workbench] workbench move and copy is incomplete
This might be a duplicate of #6606. That's really a call for Tom to make. The question is: do we want to fix this b... Brett Smith
06:53 pm Bug #7002 (New): [Workbench] workbench move and copy is incomplete
When copying/moving a pipeline instance, I expect inputs, outputs, logs, docker images, and jobs to be copied/moved w... Sarah Guthrie
08:54 pm Bug #7006: [Docker] Fix SSO configuration in published images
As a short-term fix, I updated SSO_CLIENT_NAME in Jenkins' build configuration to match what auth.curoverse.com. Tha... Brett Smith
07:25 pm Bug #7006 (Closed): [Docker] Fix SSO configuration in published images
You can't log in to the API server running in our published Docker image. It's configured to use auth.curoverse.com ... Brett Smith
08:52 pm Bug #6998: [Docker] Workbench image doesn't serve HTTPS
I pushed the simple fix, which makes this less pressing. I'll leave this ticket open if we want to consider more tho... Brett Smith
03:55 pm Bug #6998 (Closed): [Docker] Workbench image doesn't serve HTTPS
Steps to reproduce:... Brett Smith
08:50 pm Revision d929be45 (arvados): 6998: Set force_ssl: false in Workbench Docker image.
This better matches the existing Docker image configuration, which
currently does not serve HTTPS at all. Refs #6998.
Brett Smith
08:12 pm Bug #7000: [Docker] API server starts before PostgreSQL is ready
Adding a test for postgres availability to passenger.sh would probably solve this. Here's an example of such a test:
...
Ward Vandewege
06:40 pm Bug #7000 (Closed): [Docker] API server starts before PostgreSQL is ready
The API server Docker image runs both the Passenger server and PostgreSQL under supervisord. No relation is declared... Brett Smith
07:50 pm Bug #7007 (Closed): [Docker] Bootstrap font fails to load in Workbench Docker image
Brett Smith
07:34 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
In commit:041fb50eb0b55d37bd165bec25a2285183326cce:
Cursor is now a pointer when hovering over add and search butt...
Manoj Malipeddu
07:26 pm Revision 041fb50e (arvados): 6640: Changed menu items names and assertions.
Manoj Malipeddu
07:15 pm Bug #7005 (Closed): [Docker] API server uses omniauth.rb for SSO configuration, not application.yml
Update it to use the modern configuration. Brett Smith
06:56 pm Bug #7004 (New): [Deployment] Remove dependency on third-party keyservers
There are several places where our documentation or build tools instruct people to get a GPG key from pool.sks-keyser... Brett Smith
06:55 pm Bug #7003 (New): [Workbench] warn user when navigation will cause input text to be lost
This bug has bitten me mostly when editing project descriptions - I accidentally navigate to a different tab: Descrip... Sarah Guthrie
06:31 pm Bug #5794: Docker run shows up everytime in the beginning of a job and the task exists 1 but the ...
Note that this output doesn't show up in the final job log. You have to watch the live stderr logs.
I note that t...
Brett Smith
06:20 pm Bug #6994: [Deployment] our rails packages need to install certain files/directories as owned by ...
How do you feel about making the upgrade script a proper postinst script as a way to fix this?
Doing it right in t...
Brett Smith
05:50 pm Revision 50756843 (arvados): 6600: Created retry loop for task_set_output to work for HTTP_succes...
Bryan Cosca
05:34 pm Revision 77d89dee (arvados): Merge branch 'master' into 6640-projects-menu-incomplete
Manoj Malipeddu
04:21 pm Revision 21f6342d (arvados): 6859: reset ARVADOS_API_HOST and ARVADOS_API_TOKEN in teardown metho...
Radhika Chippada
04:03 pm Revision aabab05b (arvados): 6640: Changed assertion and fixed bug causing different amount
of projects to show up. Manoj Malipeddu
03:28 pm Revision 3c068341 (arvados): 6859: observed that an exit from test running is captured and misint...
Radhika Chippada
02:59 pm Revision a25971ca (arvados): Merge branch 'master' into 6859-fix-invalid-manifests
Radhika Chippada
02:58 pm Revision 44686828 (arvados): 6859: add one more test with error during arv-put
Radhika Chippada
02:42 pm Revision ee15a556 (arvados): 6640: No limit on all projects and added assertions in application l...
Manoj Malipeddu
02:32 pm Revision 32e495e4 (arvados): Merge branch '6600-pysdk-api-retries' of git.curoverse.com:arvados i...
Bryan Cosca
02:25 pm Bug #6996: [Node Manager] a node filled up its /tmp which killed slurm and docker, node unusable....
Remember that in the initial development of Node Manager, we decided it was best to take the conservative approach of... Brett Smith
02:22 pm Revision 94a99632 (arvados): 6640: Removed integration test and added controller test, fixed bug
causing different projects to be seen. Manoj Malipeddu
02:20 pm Revision b1faa1ee (arvados): recovering from corrupt files
Bryan Cosca
01:57 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
A few notes on what's been merged so far:
Right now the Python SDK depends on a couple of -dev packages. There ar...
Brett Smith
04:08 am Story #6781 (In Progress): [Documentation] Document user shell account creation script
Tom Clegg

08/16/2015

07:18 am Bug #6997 (In Progress): [Keep] keepstore reboots GCE host under heavy load
h2. Steps to reproduce
# Start keepstore[1].
# Write 3K small files[2] (so the index isn't trivially small).
# H...
Tom Clegg
04:16 am Revision ba094b97 (arvados): 5824: Fix up error checking and early-close behavior inCollectionFil...
Tom Clegg
03:15 am Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
* Finally, after much digging, identified the root cause of the issue that resulted in the two different Project drop... Radhika Chippada
01:37 am Revision 1ee305e5 (arvados): 5824: Enable blob signing in integration tests, and send keepstore l...
For some reason, sending keepstore logs to stdout seems to make
keepstore crash silently when invoked from a Go integ...
Tom Clegg
01:37 am Revision e7f7945d (arvados): 5824: Add doc.go
Tom Clegg
01:37 am Revision 5be8366e (arvados): 5824: add (*KeepClient)CollectionFileReader()
Tom Clegg
01:37 am Revision 59976e55 (arvados): 5824: Add keepdl.
Tom Clegg
01:37 am Revision dbebb56b (arvados): 5824: Use vhosts in curl integration tests. Add large file test.
Tom Clegg
01:37 am Revision 310ccee9 (arvados): 5824: Support vhost-based collection lookups.
Tom Clegg
01:37 am Revision cdecbc7f (arvados): 5824: Add Content-Length header.
Tom Clegg
01:37 am Revision 374ce34b (arvados): 5824: Assign MIME type by file extension. closes #6327
Tom Clegg
01:37 am Revision 26ffcd38 (arvados): 5824: Add install doc
Tom Clegg
01:01 am Revision 73aca60f (arvados): Accept libcurl4-openssl-dev as an alternative to libcurl4-gnutls-dev...
Tom Clegg

08/15/2015

11:55 pm Bug #6996 (New): [Node Manager] a node filled up its /tmp which killed slurm and docker, node unu...
A job on (then) compute0 filled up all of /tmp by writing .sam files (in the wrong place?):... Ward Vandewege
11:32 pm Revision 9d9cb633 (arvados): 6600: Can throw HttpError and ApiError in unit tests
Bryan Cosca
02:25 am Revision 75bbb895 (arvados): Use relative data_files paths so package is installable in a virtual...
Unfortunately this also means /usr/pam-configs/arvados moves to
/usr/local/pam-configs/arvados, where pam-auth-update...
Tom Clegg

08/14/2015

09:55 pm Task #6901 (Resolved): Add tests
Tom Clegg
09:55 pm Task #6985 (Resolved): Add to "shell server" install doc page
Tom Clegg
04:06 am Task #6985 (Resolved): Add to "shell server" install doc page
Tom Clegg
09:53 pm Revision 63e0133d (arvados): 6781: Add arvados-login-sync section to shell server install page.
Tom Clegg
09:45 pm Bug #6994 (New): [Deployment] our rails packages need to install certain files/directories as own...
h2. Bug
Right now those ownerships are ensured in the scripts
/usr/local/bin/arvados-api-server-upgrade.sh
...
Ward Vandewege
09:41 pm Revision 366da75f (arvados-dev): 6781: Add arvados-login-sync.
Tom Clegg
09:38 pm Revision 68c70c54 (arvados): 6781: Add arvados-login-sync section to shell server install page.
Tom Clegg
09:38 pm Revision eda3946f (arvados): 6781: Add test cases and packaging support.
Tom Clegg
09:37 pm Revision 39a62064 (arvados): 6781: Add arvados-login-sync (was update-shell-accounts.rb)
Ward Vandewege
09:37 pm Revision dbc73778 (arvados): 6781: Use env vars instead of yaml config file.
Tom Clegg
09:34 pm Bug #6993 (Duplicate): [Workbench] Job log tab crashes when the job's log is the empty collection
Brett Smith
09:34 pm Revision 1f0466a3 (arvados): Merge branch '6638-backport-deps' refs #6638
Tom Clegg
09:32 pm Revision 81b4b709 (arvados-dev): Merge branch '6638-backport-deps' refs #6638
Tom Clegg
09:32 pm Revision 81b4b709 (arvados): Merge branch '6638-backport-deps' refs #6638
Tom Clegg
09:26 pm Bug #6762: [FUSE][Performance] Job to md5sum 1TiB of 1MiB files in parallel is very slow
Brett Smith wrote:
> It's also possible that the discovery document isn't being cached between these commands. If t...
Brett Smith
08:34 pm Bug #6762: [FUSE][Performance] Job to md5sum 1TiB of 1MiB files in parallel is very slow
This is a very noisy experiment, enough so that I wonder how much it tells us about any one component.
The job is ...
Brett Smith
08:11 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
centos6:... Peter Amstutz
07:03 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
libattr-dev is needed for xattr.h which is needed by libfuse-dev which is needed to build the native code portion of ... Peter Amstutz
02:37 am Bug #6638: [Deployment] Python package backports should declare their C dependencies
Tom Clegg wrote:
> I didn't run into libattr troubles so it didn't get listed as a dependency. It seems to be includ...
Brett Smith
07:54 pm Bug #6992 (New): [API] Support numeric filter comparisons for numeric fields
I expected this to work:... Brett Smith
07:22 pm Revision 7701a7ad (arvados): Make sure to also deploy switchyard.
No issue # Ward Vandewege
07:22 pm Revision 7701a7ad (arvados-dev): Make sure to also deploy switchyard.
No issue # Ward Vandewege
07:18 pm Bug #6991: [Keep] multiple response.Writeheader calls
This message
http: multiple response.WriteHeader calls
is just telling us that the 500 in the log won't mat...
Tom Clegg
06:42 pm Bug #6991 (New): [Keep] multiple response.Writeheader calls
I'm seeing a lot of this in the logs of production keep servers:... Ward Vandewege
07:10 pm Task #6960 (Resolved): Review 6950-install-guide-job-test-wip
Applied in changeset arvados|commit:3401991df49ba927ac4b1fe47c6e3b7ad1d26883. Brett Smith
03:54 pm Task #6960 (In Progress): Review 6950-install-guide-job-test-wip
Tom Clegg
07:10 pm Bug #6950 (Resolved): [Documentation] Reconsider job creation test in Crunch dispatcher install g...
Applied in changeset arvados|commit:3401991df49ba927ac4b1fe47c6e3b7ad1d26883. Brett Smith
04:26 pm Bug #6950: [Documentation] Reconsider job creation test in Crunch dispatcher install guide
LGTM -- just two nits:
"your collection's content address" seems a bit mysterious -- afaics we haven't created a c...
Tom Clegg
07:04 pm Revision 3401991d (arvados): Merge branch '6950-install-guide-job-test-wip'
Closes #6950, #6960. Brett Smith
06:57 pm Bug #4507 (Duplicate): [SDKs] arv ws should exit on ctrl-c
Duplicate of #5016, where this was fixed. Brett Smith
06:46 pm Revision 050be075 (arvados): 6950: Improve "make a job" check in Crunch dispatch install guide.
* This check ensures that Crunch has something to dispatch. It
doesn't test anything about the disptacher itself. ...
Brett Smith
06:43 pm Revision 3987bcc3 (arvados): 6859: add test for salvage_collection
Radhika Chippada
06:37 pm Revision b0dd0080 (arvados-dev): 6638: Use (git clone; git checkout) -- git clone --branch doesn'...
Tom Clegg
06:37 pm Revision b0dd0080 (arvados): 6638: Use (git clone; git checkout) -- git clone --branch doesn't wo...
Tom Clegg
06:36 pm Revision 8d09d23a (arvados-dev): 6638: Use (git clone; git checkout) -- git checkout --branch doe...
Tom Clegg
06:13 pm Task #6990 (Resolved): Review 6652-test-system-menu
Manoj Malipeddu
06:12 pm Bug #6652: [API] Error "Owner uuid must refer to a user with a username" when creating a new repo...
In commit:84d14d659b8c31c266a3b08e688171f90fe46cad:
Add a new repository and add a new authorized key buttons no l...
Manoj Malipeddu
06:06 pm Revision 84d14d65 (arvados): 6652: Add a new repository and add a new authorized key buttons no l...
appear in the admin pages and tests have been updated. Manoj Malipeddu
05:48 pm Revision d5341150 (arvados): 6507: Initial commit
Peter Amstutz
03:20 pm Revision 850807f8 (arvados): 6640: Removed unecessary code from body, change cursor pointer for s...
added a test for search all projects and changed assertion. Manoj Malipeddu
03:01 pm Revision c0aa6085 (arvados): add test_init.py
Bryan Cosca
02:56 pm Revision 40ba58c7 (arvados): flailing at 10:55am 8.14.15
Bryan Cosca
12:40 pm Bug #6987 (New): [Documentation] Document base docker image for Arvados
Using bcosc/arv-base and its Dockerfile, describe the necessary packages needed to include in a base Debian image in ... Bryan Cosca
12:38 pm Story #6986 (New): Create a base arvados docker image for CentOS
Transform existing bcosc/arv-base image from Debian to CentOS. This includes finding equivalent packages from the exi... Bryan Cosca
12:04 pm Revision 24171564 (arvados-dev): minor typo in pattern...
note that this does not affect anything, since the 6 extra characters that
would be matched are not part of the base6...
Sitaram Chamarty
05:41 am Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
h3. New menu
Looks good. Two small requests:
I get a "text cursor" pointer when my mouse is on "Search" and "Cr...
Tom Clegg
04:06 am Task #6898 (In Progress): Review 6640-projects-menu-incomplete
Tom Clegg
04:05 am Task #6900 (Resolved): Build and publish gem
Tom Clegg
04:05 am Task #6902 (Resolved): Build and publish deb and rpm
Tom Clegg
04:05 am Task #6899 (Resolved): Modify sync script to use env vars instead of yaml
Tom Clegg
04:04 am Bug #6934 (Resolved): [Authentication] Write tests for pam module and shellinabox config
Tom Clegg
04:04 am Task #6963 (Resolved): Review 6934-pam
Tom Clegg
01:06 am Revision 42e27f90 (arvados): 6859: Add check for ENV[ARVADOS_API_TOKEN] and handle any other issu...
Radhika Chippada
12:38 am Revision fcc0a767 (arvados): Performance optimization for the run_upload_packages.py script: only
rebuild the freight cache for the distribution that is being updated.
No issue #
Ward Vandewege
12:38 am Revision fcc0a767 (arvados-dev): Performance optimization for the run_upload_packages.py script: ...
rebuild the freight cache for the distribution that is being updated.
No issue #
Ward Vandewege

08/13/2015

09:41 pm Revision 749b3082 (arvados): 6859: use --as-stream and improved arg parsing.
Radhika Chippada
09:06 pm Revision bdffa02f (arvados): 6934: Add sdk/pam to run_upload_packages.py refs #6934
Tom Clegg
09:06 pm Revision bdffa02f (arvados-dev): 6934: Add sdk/pam to run_upload_packages.py refs #6934
Tom Clegg
09:06 pm Revision 5e854410 (arvados): 6600: Added support for mock_api in task_set_output and began task_s...
Bryan Cosca
08:34 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
I didn't run into libattr troubles so it didn't get listed as a dependency. It seems to be included in the docker ima... Tom Clegg
08:13 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
Branches:
* arvados-dev 6638-backport-deps, commit:arvados-dev|3f03b72
* arvados 6638-backport-deps, commit:80213c8...
Tom Clegg
02:40 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
debian7 has a bit of a hiccup:... Tom Clegg
08:06 pm Revision 59c684f9 (arvados-dev): 6638: Add postgres libraries to build containers, so bundler can...
Tom Clegg
08:06 pm Revision 59c684f9 (arvados): 6638: Add postgres libraries to build containers, so bundler can bui...
Tom Clegg
08:06 pm Revision bf4baab1 (arvados): 6638: Build current version of arvados-src, not github master.
Tom Clegg
08:06 pm Revision bf4baab1 (arvados-dev): 6638: Build current version of arvados-src, not github master.
Tom Clegg
08:06 pm Revision 3f03b72f (arvados): 6638: Fix rvm usage error. Straighten out "need new gem" and "need t...
Tom Clegg
08:06 pm Revision 3f03b72f (arvados-dev): 6638: Fix rvm usage error. Straighten out "need new gem" and "ne...
Tom Clegg
08:05 pm Revision dfc5f784 (arvados): 6638: Read package dependencies from fpm-info.sh in source tree.
Tom Clegg
08:05 pm Revision dfc5f784 (arvados-dev): 6638: Read package dependencies from fpm-info.sh in source tree.
Tom Clegg
08:03 pm Revision 80213c81 (arvados): 6638: 6934: Fix up shellinabox example and add to package.
Tom Clegg
08:03 pm Revision 73dcc984 (arvados): 6638: Add package deps for llfuse and pycurl backports
Tom Clegg
06:39 pm Revision 636d833e (arvados): Merge branch 'master' into 6859-fix-invalid-manifests
Radhika Chippada
06:25 pm Bug #6652: [API] Error "Owner uuid must refer to a user with a username" when creating a new repo...
Reopening to address the last comment added by Tom in note #12.
So, what needs to be done: When accessed from admi...
Radhika Chippada
06:22 pm Bug #6652 (In Progress): [API] Error "Owner uuid must refer to a user with a username" when creat...
Radhika Chippada
06:23 pm Task #6979 (Resolved): Do not offer "Add a new repository" and "Add a new SSH key" buttons when a...
Radhika Chippada
05:44 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
In commit:2af4936125781b0e60ce66f47f45ed6f856bcda0:
Project menu has been updated to have three new menu items and...
Manoj Malipeddu
05:33 pm Task #6945 (Resolved): Review UI design mocks
Manoj Malipeddu
05:33 pm Task #6944 (Resolved): Mock up specified UI
Manoj Malipeddu
05:30 pm Revision 2af49361 (arvados): 6640: Project menu now shows more than 200 projects, test checks for
300 projects instead of 200. Manoj Malipeddu
04:38 pm Revision fe42be0d (arvados): Merge branch 'master' into 6640-projects-menu-incomplete
Manoj Malipeddu
04:37 pm Revision e0330818 (arvados): 6640: Fixed syntax error.
Manoj Malipeddu
03:45 pm Bug #6968 (New): [SDKs] arv-copy continues copying when a collection's content address is wrong, ...
Currently when arv-copy copies a collection by content address (e.g., from a pipeline), it assumes that the content a... Brett Smith
03:43 pm Revision 3599db93 (arvados): 6640: Added test to test project menu, checked link for browse publi...
Manoj Malipeddu
03:15 pm Story #6572 (Resolved): [Documentation] Install guide demonstrates how to copy a pipeline from Cu...
Applied in changeset arvados|commit:209ae8068a9952ecf8ae20311719b25f05a3e4cb. Radhika Chippada
03:06 pm Story #6572: [Documentation] Install guide demonstrates how to copy a pipeline from Curoverse Cloud
"Configure source and destination while using anonymous access token for source" -> "Configuring source and destinati... Bryan Cosca
03:13 pm Task #6910 (Resolved): Review branch: 6572-doc-copy-pipeline
Radhika Chippada
03:13 pm Revision 209ae806 (arvados): closes #6572
Merge branch '6572-doc-copy-pipeline' Radhika Chippada
03:12 pm Revision e9ce5eb4 (arvados): 6572: minor section title updates
Radhika Chippada
03:09 pm Revision a70f39f3 (arvados): Merge branch 'master' into 6572-doc-copy-pipeline
Radhika Chippada
02:42 pm Revision f369f469 (arvados): 6640: Modified tests and added fixture for 201 projects.
Manoj Malipeddu
02:21 pm Task #6901 (In Progress): Add tests
Tom Clegg
02:21 pm Task #6900 (In Progress): Build and publish gem
Tom Clegg
02:21 pm Task #6911 (Resolved): Update build scripts to add distro-specific dependencies for backported pa...
Tom Clegg
01:29 pm Revision 08a10afd (arvados): 6859: fix issue with tempfile not actually being written and also up...
Radhika Chippada
12:50 pm Revision a0daf49f (arvados): Merge branch 'master' into 6859-fix-invalid-manifests
Radhika Chippada
12:14 pm Bug #6967 (Resolved): [API] [Workbench] application.default.yml should not call git, at least in ...
Both API server and Workbench call git a couple of times in @application.default.yml@:... Brett Smith
04:32 am Revision d1131e5f (arvados): 6638: Add python sdk package dependencies.
Tom Clegg
04:15 am Revision 988b1304 (arvados): 6638: Dry up debug printfs.
Tom Clegg
04:15 am Revision 988b1304 (arvados-dev): 6638: Dry up debug printfs.
Tom Clegg
03:06 am Revision 4e76299b (arvados): Merge branch '6934-pam' refs #6934
Tom Clegg
03:06 am Revision 4e76299b (arvados-dev): Merge branch '6934-pam' refs #6934
Tom Clegg
03:04 am Revision f96550cc (arvados): Merge branch '6934-pam' refs #6934
Tom Clegg
02:37 am Revision 586ea290 (arvados): 6934: Recommend system-log-daemon metapackage, not rsyslog specifica...
Tom Clegg
02:36 am Revision 3d595c9b (arvados): 6934: Build libpam-arvados only for targets that have libpam-python.
Tom Clegg
02:36 am Revision 3d595c9b (arvados-dev): 6934: Build libpam-arvados only for targets that have libpam-pyt...
Tom Clegg

08/12/2015

09:17 pm Bug #6934: [Authentication] Write tests for pam module and shellinabox config
Tom Clegg wrote:
> Brett Smith wrote:
> > @sdk/python/fpm-info.sh@ is still in the branch. Though it's functionall...
Brett Smith
08:37 pm Bug #6934: [Authentication] Write tests for pam module and shellinabox config
Tom Clegg wrote:
> ** integration/test_pam.py → setup.py test --test-suite=integration crashes "ImportError: No...
Tom Clegg
08:20 pm Bug #6934: [Authentication] Write tests for pam module and shellinabox config
Brett Smith wrote:
> @sdk/python/fpm-info.sh@ is still in the branch. Though it's functionally a noop for now, it m...
Tom Clegg
06:55 pm Bug #6934: [Authentication] Write tests for pam module and shellinabox config
Tom Clegg wrote:
> Removed the package dependency stuff from this branch, except sdk/pam/fpm-info.sh, which will jus...
Brett Smith
04:21 pm Bug #6934: [Authentication] Write tests for pam module and shellinabox config
Removed the package dependency stuff from this branch, except sdk/pam/fpm-info.sh, which will just be ignored until #... Tom Clegg
01:28 pm Bug #6934: [Authentication] Write tests for pam module and shellinabox config
*(Edit: ignore this, see note-5)*
The sdk/python/fpm-info.sh I added here isn't really right -- libcurl should be ...
Tom Clegg
09:13 pm Revision ca35c58c (arvados): Merge branch 'master' into 6859-fix-invalid-manifests
Radhika Chippada
08:41 pm Revision 3dc08cb9 (arvados): 6934: Move integration tests into separate dir.
Now, "python setup.py --test-suite integration_tests" will run
integration tests, and "python setup.py" won't -- rega...
Tom Clegg
08:26 pm Story #6884: [Deployment] Plan addition of init scripts to Arvados daemon packages
Joshua Randall wrote:
> I think the binary packages should only install init support that works with the system that...
Brett Smith
08:19 pm Revision 69e7600c (arvados-dev): 6934: Add libpam-python dependency on all targets.
Tom Clegg
08:19 pm Revision 69e7600c (arvados): 6934: Add libpam-python dependency on all targets.
Tom Clegg
07:59 pm Revision 7671ee34 (arvados): 6934: Fix Dockerfile instructions. Use default test port. Use arvado...
Tom Clegg
07:53 pm Revision 07f2ff36 (arvados): 6859: updated script to append all locators to newly created manifes...
Radhika Chippada
06:57 pm Task #6963 (In Progress): Review 6934-pam
Brett Smith
03:48 pm Task #6963 (Resolved): Review 6934-pam
Tom Clegg
05:57 pm Revision ebaa21aa (arvados-dev): 6934: Merge branch 'master' into 6934-pam
Tom Clegg
05:57 pm Revision ebaa21aa (arvados): 6934: Merge branch 'master' into 6934-pam
Tom Clegg
05:55 pm Revision 98d6a7c2 (arvados): Merge branch '5824-go-sdk' refs #5824
Tom Clegg
05:45 pm Revision c0f9c128 (arvados): 5824: Merge branch 'master' into 5824-go-sdk
Tom Clegg
05:44 pm Story #5824: [Workbench] [Keep] collection browse/download server
Branch 5824-go-sdk lgtm. Radhika Chippada
04:09 pm Revision c249e926 (arvados): 6934: Add pam_sm tests.
Tom Clegg
04:09 pm Revision bf23a991 (arvados): 6934: Split module
Tom Clegg
04:09 pm Revision 4c3860e6 (arvados): 6934: Put wrapper in /lib/security/ instead of writing dist-packages...
Tom Clegg
04:09 pm Revision f8daac93 (arvados): 6934: Add packaging instructions
Tom Clegg
04:07 pm Revision c18ab400 (arvados-dev): 6934: Package libpam-arvados using Python recipe. Add sdk/pam to...
Tom Clegg
04:07 pm Revision c18ab400 (arvados): 6934: Package libpam-arvados using Python recipe. Add sdk/pam to run...
Tom Clegg
04:05 pm Revision 8da21217 (arvados): Merge branch 'master' into 6640-projects-menu-incomplete
Manoj Malipeddu
03:55 pm Revision 48f294f5 (arvados): 6934: Fixup packaging
Tom Clegg
03:55 pm Revision 3d8b5718 (arvados): 6934: Split module
Tom Clegg
03:55 pm Revision b12d869f (arvados): 6934: Add pam_sm tests.
Tom Clegg
03:55 pm Revision aa0ead51 (arvados): 6934: Put wrapper in /lib/security/ instead of writing dist-packages...
Tom Clegg
03:54 pm Revision f95a7131 (arvados): 6934: Add packaging instructions
Tom Clegg
03:06 pm Revision 687a5246 (arvados): 6859: added salvage_collection.rb script.
Radhika Chippada
03:05 pm Revision d07162cf (arvados): Merge branch 'master' into 6572-doc-copy-pipeline
Radhika Chippada
02:14 pm Revision af8e8532 (arvados): 6640: Search button now only shows projects.
Manoj Malipeddu

08/11/2015

11:04 pm Bug #6652 (Resolved): [API] Error "Owner uuid must refer to a user with a username" when creating...
This bug was fixed and merged with #6663. Now this succeeds:... Tom Clegg
02:09 pm Bug #6652: [API] Error "Owner uuid must refer to a user with a username" when creating a new repo...
I played with Tom's suggestion "moving self.owner_uuid ||= current_user.uuid into a before_validation method" and thi... Radhika Chippada
09:39 pm Task #6960 (Resolved): Review 6950-install-guide-job-test-wip
Brett Smith
09:39 pm Bug #6950 (In Progress): [Documentation] Reconsider job creation test in Crunch dispatcher instal...
I've done the above in 6950-install-guide-job-test-wip. Brett Smith
09:10 pm Bug #6950: [Documentation] Reconsider job creation test in Crunch dispatcher install guide
Brett Smith wrote:
> As the guide is currently written, it's not runnable there, because no repositories exist in th...
Tom Clegg
08:05 pm Bug #6950: [Documentation] Reconsider job creation test in Crunch dispatcher install guide
Tom Clegg wrote:
> I agree this is a non sequitur in its current place, and it would make more sense at the end of g...
Brett Smith
08:03 pm Bug #6950 (New): [Documentation] Reconsider job creation test in Crunch dispatcher install guide
Brett Smith
07:07 pm Bug #6950 (In Progress): [Documentation] Reconsider job creation test in Crunch dispatcher instal...
Taking this on because I already half-wrote the patch so I might as well finish the job. Brett Smith
09:38 pm Revision c25d075d (arvados): 6950: Improve "make a job" check in Crunch dispatch install guide.
* This check ensures that Crunch has something to dispatch. It
doesn't test anything about the disptacher itself. ...
Brett Smith
09:28 pm Story #5824: [Workbench] [Keep] collection browse/download server
Radhika Chippada wrote:
> It seems like this is a good method that we could be using more in future though? If I am ...
Tom Clegg
03:27 am Story #5824: [Workbench] [Keep] collection browse/download server
* Tom said:
> I agree it's not httpserver-specific, but I don't like "util" any better (the package name "util" is...
Radhika Chippada
01:06 am Story #5824: [Workbench] [Keep] collection browse/download server
Radhika Chippada wrote:
> Can you call "resource" as type or resource_type? It is not clear to me that “resource” he...
Tom Clegg
09:27 pm Revision 493e39c8 (arvados): 5824: Test invalid argument vs. 404.
Tom Clegg
08:39 pm Bug #6844: [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB collection
FWIW I was able to use the latest version to copy the original collection. Thanks. Brett Smith
08:19 pm Bug #6959 (New): [SDKs] arv-copy raises an unexpected backtrace on ^C
I sent ^C to an arv-copy process while it was in the middle of uploading data to Keep. That wrote this traceback:
...
Brett Smith
08:05 pm Bug #6938 (Resolved): [Documentation] Install guide needs to set up git server before creating st...
Applied in changeset arvados|commit:2825758b45ca273e7bcf176b636ff36487d25857. Brett Smith
07:59 pm Revision 2825758b (arvados): 6938: Install guide covers git server before standard objects.
The standard objects page covers creating the arvados git repository,
which requires Git hosting to be set up already...
Brett Smith
07:40 pm Revision 094d247c (arvados): 5824: Add tests for UUIDMatch and PDHMatch.
Tom Clegg
07:40 pm Revision 2566020d (arvados): 5824: Return InvalidArgument (not 404) for poor argument choices tha...
Tom Clegg
07:03 pm Bug #6885: [Deployment] Add meaningful package versions to distro packages
Current expected solution: arvados-dev includes a configuration file that includes triples of (source package name, s... Brett Smith
06:38 pm Bug #6918: [Documentation] keepproxy CORS headers get doubled, don't work
Discussion:
* It's probably better to just remove the lines from the configuration.
* The docs can also tell you ...
Brett Smith
06:32 pm Bug #6922: [API] [Maybe] Update API server to support Git 1.7.2
Kicking this off for lack of engineering consensus. Possible solutions:
* Change the code as anticipated in the c...
Brett Smith
06:29 pm Story #6958 (Resolved): [Deployment] Arrange to run tests on CentOS 6
Brett Smith
06:24 pm Story #6957 (New): [SSO] Move sso-provider into arvados tree
Unless there's some (licensing?) reason not to, we should put sso-provider in services/sso so our packaging and testi... Tom Clegg
06:11 pm Story #6884: [Deployment] Plan addition of init scripts to Arvados daemon packages
Nico notes that pleaserun is good for generating skeleton scripts, but it's not sharp enough to include the output ve... Brett Smith
05:51 pm Revision 5dd20e4a (arvados): Merge branch '6260-work-queue-status' refs #6260
Tom Clegg
05:11 pm Bug #6943 (Duplicate): [Git hosting] arvados-git-httpd should return 4xx, not 5xx, for authentica...
Duplicates #6780. I'll merge the descriptions. Brett Smith
04:13 pm Revision 2a779600 (arvados): 6572: update to make it clear that the user can access anonymous tok...
Radhika Chippada
04:09 pm Bug #6886: [Documentation] A user with an older install may land in a page that requires the "lat...
The only prerequisite listed on the prerequisites page that actually needs to be installed ahead of time is the packa... Brett Smith
03:41 pm Bug #6937 (Duplicate): Only admin accounts can share their own repositories with arbitrary people
Duplicates #5297. Brett Smith
03:29 pm Bug #6954 (New): [Deployment] Rails app packages should declare their dependencies
For each of the API server, Workbench, and SSO server (if we have it):
* Extend @fpm-info.sh@ for the component so...
Brett Smith
03:17 pm Feature #5297: [Workbench] Enable users to share with any other user
History, for anyone interested:
* We originally had this feature as part of #2044.
* As Tom mentioned, we intenti...
Brett Smith
03:16 pm Bug #6835 (Duplicate): [Workbench] Make it possible to share project with other users I can't see
Closing as duplicate of #5297. Brett Smith
03:13 pm Revision c52b7c3f (arvados): 6260: Add explanatory comment about testing /status.json.
Tom Clegg
03:07 pm Revision aae24688 (arvados): 6260: Rename ReportDone to DoneItem.
Tom Clegg
03:07 pm Revision 318d446a (arvados): 6260: Improve Gate explanation.
Tom Clegg
03:00 pm Revision 1f20939e (arvados): 6640: UI updates.
Manoj Malipeddu
02:55 pm Bug #6834: How to add users to a newly created group?
Nancy, given this discussion, what would you say are the outstanding issue(s) from this? At this point, it's a littl... Brett Smith
02:47 pm Revision 68287acb (arvados): Merge branch 'master' into 6572-doc-copy-pipeline
Radhika Chippada
02:46 pm Revision 110f0377 (arvados): 6934: Split module
Tom Clegg
02:46 pm Revision 35a26ea6 (arvados): 6934: Add pam_sm tests.
Tom Clegg
02:45 pm Story #6260: [Keep] Integration test between data manager, API and keepstore.
Reviewed branch 6260-work-queue-status at commit:d89b7ae1f6fa35dd3627ead14c855751f1de2193
* Given the amount of ch...
Radhika Chippada
02:35 pm Bug #6953 (Resolved): [Documentation] Document installation of the Docker image cleaner on comput...
Extend the compute node install guide so it tells users:
* To install the @arvados-docker-cleaner@ package.
* To ...
Brett Smith
02:30 pm Bug #6571: [Workbench] Project description styled differently based on whether or not the user ca...
I'm guessing this happens because a markup difference that lets users edit the description causes different CSS style... Brett Smith
02:23 pm Bug #6358: [SDKs] Python Keep client uses wrong probe order for put()
Updating the subject to reflect what sounds like the more likely issue here. I'm doing that understanding, like Tom ... Brett Smith
02:08 pm Bug #5426: [Workbench] Large downloads through workbench fail
I think we're very likely to deal with this via #5824. Brett Smith
02:07 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
Looks great, thanks! (Assuming the separator and the shared projects listed at the bottom go away of course -- I assu... Tom Clegg
01:50 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
Updated project menu. Manoj Malipeddu
01:46 pm Bug #6934: [Authentication] Write tests for pam module and shellinabox config
Refactored as a python module with a tiny wrapper that goes in /lib/security. Made logging better. Added tests. Updat... Tom Clegg
06:26 am Revision 982a80e5 (arvados): 6934: Put wrapper in /lib/security/ instead of writing dist-packages...
Tom Clegg
01:07 am Task #6952 (Resolved): Review 5824-go-sdk
Tom Clegg
12:45 am Revision 98feead9 (arvados): 5824: Add test for nonexistent resource type.
Tom Clegg
12:39 am Revision 8e671a54 (arvados): 5824: Document ClientPool.
Tom Clegg
12:39 am Revision bd583d21 (arvados): 5824: Doc/comment fixes, add test for "Get empty UUID"
Tom Clegg
12:26 am Revision fbe23d04 (arvados): 5824: Use fmt "%+q" instead of custom escaping.
Tom Clegg
12:26 am Revision 6423d36f (arvados): 5824: Do not JSON-encode string params. Fixup comments for godoc.
Tom Clegg
12:26 am Revision e736def3 (arvados): 5824: Add UUID and PDH matchers.
Tom Clegg
12:26 am Revision 1e5f8ef2 (arvados): 5824: Fix up comments for godoc.
Tom Clegg
12:26 am Revision fe4f75a4 (arvados): 5824: Add Get() method to arvadosclient.
Tom Clegg
12:26 am Revision e14e011f (arvados): 5824: Move quoted-logging function to SDK.
Tom Clegg
12:26 am Revision 9f45d7dd (arvados): 5824: Move client pool to SDK.
Tom Clegg
12:26 am Revision c2f71880 (arvados): Shut down API server after suite (noticed during 5824, otherwise no ...
Tom Clegg
12:26 am Revision 173ebc11 (arvados): 5824: Move spying ResponseWriter to SDK.
Tom Clegg
12:26 am Revision 2dfb886e (arvados): 5824: gofmt
Tom Clegg
12:25 am Revision e889ec14 (arvados): 5824: Move HTTP server code to SDK.
Tom Clegg
12:25 am Revision d2e54674 (arvados): 5824: Move request auth code into an SDK package. Support more ways ...
Tom Clegg

08/10/2015

11:27 pm Bug #6950: [Documentation] Reconsider job creation test in Crunch dispatcher install guide
I agree this is a non sequitur in its current place, and it would make more sense at the end of git setup page, at th... Tom Clegg
06:40 pm Bug #6950 (Resolved): [Documentation] Reconsider job creation test in Crunch dispatcher install g...
As of this writing, the Crunch dispatch install guide includes a "Git Repositories" section that includes a sample jo... Brett Smith
10:08 pm Story #5824: [Workbench] [Keep] collection browse/download server
Review comments for 5824-go-sdk branch at commit:be4e5f225cf1615504ee2c1feb0f200d6904716c
* func (c ArvadosClient...
Radhika Chippada
09:01 pm Task #6945 (In Progress): Review UI design mocks
Tom Clegg
06:00 pm Task #6945 (Resolved): Review UI design mocks
Manoj Malipeddu
08:59 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
Looking good. Couple of requests:
* "alternate_project_menu.png" is better in every way. (The story description aske...
Tom Clegg
07:28 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
A different option for the project menu. Manoj Malipeddu
06:43 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
Snapshot of new project menu. Manoj Malipeddu
05:59 pm Bug #6640 (In Progress): [Workbench] Ensure projects menu consistently shows all "my projects"
Manoj Malipeddu
08:50 pm Task #6912 (In Progress): Determine dependencies for various distros
Tom Clegg
08:11 pm Revision 522404b2 (arvados): closes #6858
Merge branch '6858-job-re-run-documentation' Bryan Cosca
06:35 pm Revision 86284313 (arvados): refs #6827
Merge branch '6827-short-token' Radhika Chippada
06:33 pm Revision f618b651 (arvados): Improve crunch-dispatch runit script in install guide.
* Modernize crunch-dispatch's prerequisites.
* Document what this script is.
* Consolidate environment variables for ...
Brett Smith
06:32 pm Revision 2d9cae58 (arvados): Include example service script for keepproxy.
Conveniently you just need this one line, which should work equally
well in all kinds of supervisors. No issue #.
Brett Smith
06:32 pm Revision 7c89127a (arvados): 6827: fix error in setting valid token.
Radhika Chippada
06:32 pm Task #6949 (Resolved): Review 6638-backport-deps (arvados + arvados-dev)
Tom Clegg
06:26 pm Bug #6638 (In Progress): [Deployment] Python package backports should declare their C dependencies
Tom Clegg
06:26 pm Task #6911 (In Progress): Update build scripts to add distro-specific dependencies for backported...
Tom Clegg
06:20 pm Revision 70ddebda (arvados): 6827: set validApiToken flag after ensuring that getting list of rep...
Radhika Chippada
06:19 pm Revision a6edcb02 (arvados): Merge branch 'master' into 6827-short-token
Radhika Chippada
06:13 pm Revision be4e5f22 (arvados): Merge branch 'master' into 5824-go-sdk
Conflicts:
services/arv-git-httpd/auth_handler.go
Tom Clegg
05:59 pm Task #6944 (Resolved): Mock up specified UI
Manoj Malipeddu
05:54 pm Story #6572: [Documentation] Install guide demonstrates how to copy a pipeline from Curoverse Cloud
"Let's access one such public pipeline and copy to your cluster so" ==> "Let's access a public pipeline and copy it t... Bryan Cosca
03:28 pm Story #6572: [Documentation] Install guide demonstrates how to copy a pipeline from Curoverse Cloud
Tested arv-copy with anonymous token from qr1hi and verified that it works. Radhika Chippada
03:26 pm Story #6572 (In Progress): [Documentation] Install guide demonstrates how to copy a pipeline from...
Radhika Chippada
05:50 pm Story #6260: [Keep] Integration test between data manager, API and keepstore.
6260-work-queue-status refactors WorkQueue a bit so current pull and trash queue status can be retrieved
* by client...
Tom Clegg
05:46 pm Bug #6943 (Duplicate): [Git hosting] arvados-git-httpd should return 4xx, not 5xx, for authentica...
Currently, as verified by tests, arvados-git-httpd returns 500 when the servers are all working perfectly but the cli... Tom Clegg
05:37 pm Feature #6769: arv-git-httpd manages repository creation instead of gitolite.
I agree arvados-git-httpd should stick to providing an authenticated HTTP channel to hosted git repos.
By design, ...
Tom Clegg
05:07 pm Revision ae2478d6 (arvados): 6827: Test logging handler with short token.
Tom Clegg
05:07 pm Revision a7c537fe (arvados): 6827: Test logging handler with short token.
Tom Clegg
04:45 pm Revision d89b7ae1 (arvados): 6260: Pull entire status object out of WorkQueue atomically.
Tom Clegg
04:44 pm Revision 4de0af80 (arvados): 6260: Fix races in keepstore tests. Expose WorkQueue in-progress/que...
Tom Clegg
04:44 pm Revision ab689cf0 (arvados): 6260: gofmt
Tom Clegg
04:44 pm Revision 5562d6d5 (arvados): 6260: Expose queue sizes in /status.json. Fix sleep/race in trash_wo...
Tom Clegg
03:45 pm Bug #6827 (Resolved): arvados-git-httpd prints plaintext user passwords to its output
Applied in changeset arvados|commit:e0213cbec6a151e077b8cca00700815c3c3d18e7. Radhika Chippada
03:42 pm Bug #6827: arvados-git-httpd prints plaintext user passwords to its output
Thanks Nico. Added a comment in auth_handler.go as suggested. Radhika Chippada
01:42 pm Bug #6827: arvados-git-httpd prints plaintext user passwords to its output
I'm reviewing 3959d7afff8bb3c3b8da9eb7d178919275180f2a
After reading the issue. It's unclear to me from the code t...
Nico César
03:44 pm Bug #6942 (Resolved): [Documentation] Improve compute node setup script
Near the bottom of the compute node install guide, there's a shell script that includes a Python script to create the... Brett Smith
03:41 pm Revision 9a3fd168 (arvados): 6934: Fixup packaging
Tom Clegg
03:41 pm Task #6895 (Resolved): Review branch: 6827-no-passwords-in-logs
Radhika Chippada
03:41 pm Revision e0213cbe (arvados): closes #6827
Merge branch '6827-no-passwords-in-logs' Radhika Chippada
03:40 pm Revision 2553fde5 (arvados): 6827: add a comment that only the first 10 characters of a valid tok...
Radhika Chippada
03:38 pm Bug #6941 (Resolved): [Documentation] Fix www-data references in git server install guide
The git server install guide references the www-data user and group in a couple of places. This user is Debian-speci... Brett Smith
03:38 pm Revision 88a6b112 (arvados): 6862: Added git-arvados-guide first draft documentation
Bryan Cosca
03:37 pm Bug #6940: [Documentation] Document running Workbench under Software Collections
Investigated so far:
* The Software Collection includes a shell script at @/opt/rh/python27/enable@ that makes the...
Brett Smith
03:33 pm Bug #6940 (Resolved): [Documentation] Document running Workbench under Software Collections
Our Python SDK RPM is currently built to work with Red Hat's Python 2.7 Software Collection. This means that in orde... Brett Smith
03:33 pm Revision 63b82f43 (arvados): Merge branch 'master' into 6827-no-passwords-in-logs
Radhika Chippada
03:32 pm Task #6917 (Resolved): Review branch 6880-remove-user-delete-button
Radhika Chippada
03:29 pm Bug #6939 (Resolved): [Deployment] Package the SSO server
Functional requirements:
* Create SSO server packages for all of our supported distributions. Its structure shoul...
Brett Smith
03:26 pm Bug #6938 (Resolved): [Documentation] Install guide needs to set up git server before creating st...
The "Creating standard objects" page assumes the git server is already set up, but the current install guide ordering... Brett Smith
03:25 pm Revision c009ae5d (arvados): 6572: add a new page in install guide to "copy a pipeline template f...
Radhika Chippada
02:42 pm Revision df53e3b0 (arvados): 6934: Add packaging instructions
Tom Clegg
02:41 pm Revision 83c4da9b (arvados-dev): 6934: Package libpam-arvados using Python recipe. Read additiona...
Tom Clegg

08/09/2015

05:05 am Revision 132bbb69 (arvados): 6934: Load config from pam conf instead of yaml. Add docker/integrat...
Tom Clegg

08/08/2015

08:42 pm Bug #6862 (In Progress): [Documentation] What do you need to know about using Git with Arvados
Bryan Cosca
03:32 pm Revision 507110dc (arvados): 6934: Improve and test logging
Tom Clegg
03:17 pm Revision 17023357 (arvados): 6934: Replace custom config with yaml. Simplify code path.
Tom Clegg
02:50 am Revision 4fc61379 (arvados): 6934: Add arvados_pam package.
Tom Clegg

08/07/2015

10:38 pm Bug #6600: [SDKs] All PySDK functions that make API calls must support a num_retries argument
In 84cc9874760687a061dc489f5a19db66cb06108e:
Comments:
Do we want a backoff_growth? Maybe we want a quick retry...
Bryan Cosca
06:23 pm Bug #6600: [SDKs] All PySDK functions that make API calls must support a num_retries argument
The "retry_method" decorator is really just another way to set a default num_retries: it doesn't actually retry anyth... Tom Clegg
03:39 pm Bug #6600: [SDKs] All PySDK functions that make API calls must support a num_retries argument
Just checking if my logic is correct:
For task_set_output, current_task, current_job, it should be like this:
<pr...
Bryan Cosca
01:18 am Bug #6600 (In Progress): [SDKs] All PySDK functions that make API calls must support a num_retrie...
Bryan Cosca
10:36 pm Revision 84cc9874 (arvados): Added RetryLoop to current_task, current_job, and task_set_output wi...
Bryan Cosca
10:25 pm Bug #6937 (Duplicate): Only admin accounts can share their own repositories with arbitrary people
Sally can't share her sguthrie repository (with the Tiling project code) with an arbitrary user, because she is not a... Nancy Ouyang
10:22 pm Revision ca9cbfd8 (arvados): Add docs to Node Manager's base compute node driver.
This adds a docstring or comment description to every method in the class. Brett Smith
09:05 pm Story #6572: [Documentation] Install guide demonstrates how to copy a pipeline from Curoverse Cloud
I noticed an issue as I was writing this document. It is:
From IRC:
radhika
4:44 The user needs current_token ...
Radhika Chippada
07:04 pm Bug #6934 (Resolved): [Authentication] Write tests for pam module and shellinabox config
Tom Clegg
06:28 pm Revision 7d04c898 (arvados): Merge branch '6844-py-mem-leak' of git.curoverse.com:arvados into 66...
Get memory-leak fix Bryan Cosca
06:05 pm Bug #6844 (Resolved): [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB collec...
Applied in changeset arvados|commit:2a96c097e5a176018d078a5d6985403072e8672e. Tom Clegg
05:52 pm Bug #6844: [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB collection
LGTM Radhika Chippada
03:07 pm Bug #6844: [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB collection
I'd still like to see about making a memory-leak test case for this, but I don't think it should block merging the fi... Tom Clegg
06:07 am Bug #6844 (In Progress): [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB col...
Tom Clegg
06:05 am Bug #6844: [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB collection
6844-py-mem-leak @ commit:f809883
The fix is in commit:0988acb
Bad news: lost a feature.
* The memory leak was...
Tom Clegg
05:57 pm Revision 2a96c097 (arvados): Merge branch '6844-py-mem-leak' closes #6844
Tom Clegg
05:55 pm Revision 970907f2 (arvados): 6844: Clean up websocket tests, fix possible deadlock, reduce unnece...
* Use onevent=q.put_nowait, so "too many events" raises Queue.Full
instead of blocking the websocket thread.
* Sim...
Tom Clegg
05:52 pm Task #6903 (Resolved): Review 6844-py-mem-leak
Radhika Chippada
05:52 pm Task #6903 (In Progress): Review 6844-py-mem-leak
Radhika Chippada
05:42 pm Bug #6933 (New): [Documentation] Use the same example/demo users and domain names throughout
Currently we have screenshots with developers' usernames and email addresses, and the reader is left to wonder whethe... Tom Clegg
03:40 pm Revision 4b096c9a (arvados): 6600: Added _add_task function with default num_retries=5 for one_ta...
Bryan Cosca
03:31 pm Bug #6827: arvados-git-httpd prints plaintext user passwords to its output
commit:3959d7afff8bb3c3b8da9eb7d178919275180f2a
Per Joshua Randall's and Tom's comments above:
* Log only when i...
Radhika Chippada
03:25 pm Revision 3959d7af (arvados): 6827: log only valid token and only the first 10 characters.
Radhika Chippada
02:56 pm Revision 61974cf1 (arvados-dev): Make sure that we build arvados-src package with the correct ver...
the git tree, not latest.
No issue #
Ward Vandewege
02:56 pm Revision 61974cf1 (arvados): Make sure that we build arvados-src package with the correct version of
the git tree, not latest.
No issue #
Ward Vandewege
02:39 pm Revision f8098830 (arvados): 6844: Clean up websocket tests, fix possible deadlock, reduce unnece...
* Use onevent=q.put_nowait, so "too many events" raises Queue.Full
instead of blocking the websocket thread.
* Sim...
Tom Clegg
12:59 pm Revision bdb85052 (arvados): Make rvm-exec version in crunch-dispatch run script less specific.
Any Ruby 2.1 is fine; we don't specifically need 2.1.1. We use
`default` elsewhere throughout our documentation, so ...
Brett Smith
12:54 pm Revision 50ff63e9 (arvados): Add Gitolite UMASK setting to install guide.
No issue #. Brett Smith
12:50 pm Revision 06f774bc (arvados): Add client_max_body_size to Nginx install configurations.
Nginx's default value for this setting is 1m, so adjusting it is all
but required to do useful work. No issue #.
Brett Smith
12:44 pm Revision 4357a60b (arvados): Highlight dynamic fields in Keep service registration instructions.
No issue #. Brett Smith
12:42 pm Revision c24168b7 (arvados): Install Git in shell server install guide.
I don't think we expressly use curl for anything, but reusing the
install template seemed easy enough. In the future...
Brett Smith
12:39 pm Revision 6cfe8a2a (arvados): Remove redundant console line from Workbench install guide.
No issue #. Brett Smith
06:05 am Task #6906 (Closed): Reproduce leakage in a test case
Tom Clegg
06:05 am Task #6905 (Resolved): Investigate
Tom Clegg
06:05 am Task #6908 (Resolved): Plug leak
Tom Clegg
05:45 am Revision 9209660a (arvados): 6844: Clear inserted data/logs after websocket tests.
Tom Clegg
05:40 am Revision f46b05c0 (arvados): 6844: Always write a valid \n-terminated manifest. Confine exception...
Tom Clegg
05:40 am Revision d2d7138c (arvados): 6844: Return valid locator (hash+size) if 0 copies requested.
Tom Clegg
05:40 am Revision fc851b24 (arvados): 6844: Skip uselessly writing unsigned manifest to Keep.
Tom Clegg
05:40 am Revision 0988acb4 (arvados): 6844: Do not use inspect.getcallargs: it leaks memory. Passing num_r...
Tom Clegg
03:02 am Revision 34a84410 (arvados): #6600: Added num_retries to task_set_output, current_task, current_j...
Bryan Cosca

08/06/2015

09:47 pm Revision 8fe01fcc (arvados): API server install guide suggests a more likely websocket_address.
/websocket is hardcoded as the websocket endpoint in our own code, so
that's where it'll be when people use the provi...
Brett Smith
09:31 pm Bug #6600: [SDKs] All PySDK functions that make API calls must support a num_retries argument
Tom Clegg wrote:
> I think it would be ideal to get the num_retries logic into the execute() method.
At least for...
Brett Smith
09:22 pm Bug #6600: [SDKs] All PySDK functions that make API calls must support a num_retries argument
We have some @@retry_method@ stuff already in the python sdk, probably better to continue using that rather than use ... Tom Clegg
09:07 pm Bug #6600: [SDKs] All PySDK functions that make API calls must support a num_retries argument
So first idea on how to approach this is to install this package: https://pypi.python.org/pypi/retrying.
Then in a...
Bryan Cosca
08:30 pm Feature #6858 (Resolved): [Documentation] Document the necessary steps to re-run jobs without com...
Applied in changeset arvados|commit:8089b2f5c97b1db9bd826a1b6488f1b060830def. Bryan Cosca
07:12 pm Feature #6858: [Documentation] Document the necessary steps to re-run jobs without computing again
There is an extra space character after "This section shows which version control parameters should be tuned to make ... Radhika Chippada
07:07 pm Feature #6858: [Documentation] Document the necessary steps to re-run jobs without computing again
Radhika Chippada wrote:
> * Can you please remove the extra “and” from description then?
>
> * “This section show...
Bryan Cosca
06:50 pm Feature #6858: [Documentation] Document the necessary steps to re-run jobs without computing again
* Can you please remove the extra “and” from description then?
* “This section shows what parameters you need to v...
Radhika Chippada
06:22 pm Feature #6858: [Documentation] Document the necessary steps to re-run jobs without computing again
Radhika Chippada wrote:
> * Is there an extra “and” in the description of the ticket (... arvados_sdk_version, docke...
Bryan Cosca
05:38 pm Feature #6858: [Documentation] Document the necessary steps to re-run jobs without computing again
* Is there an extra “and” in the description of the ticket (... arvados_sdk_version, docker_image hash -and- in your ... Radhika Chippada
03:58 pm Feature #6858: [Documentation] Document the necessary steps to re-run jobs without computing again
Radhika,
I added a note on the bottom of doc/user/tutorials/running-external-program.html about job reproducibilit...
Bryan Cosca
08:27 pm Revision 8089b2f5 (arvados): Merge branch '6858-job-re-run-documentation'
closes #6858 Bryan Cosca
08:10 pm Revision 97f16e9b (arvados): 6858: Fixed syntax and added notes to re-use the same hashes from pr...
Bryan Cosca
08:10 pm Revision 43338e77 (arvados): 6858: Added new section 'Re-using your pipeline run' and moved all v...
Bryan Cosca
08:08 pm Revision bbf7272a (arvados): 6858: Added note about job reproducibility and version control with ...
Bryan Cosca
08:08 pm Revision 03d5c4df (arvados): 6851: reorder install guide pages; right after api server, install w...
Radhika Chippada
07:48 pm Revision 261fe4c6 (arvados): Haha, no seriously, don't deploy Workbench with snakeoil certs.
No issue #. Brett Smith
07:45 pm Revision 664ca8ac (arvados): Merge branch 'master' of https://github.com/curoverse/arvados
closes #6858 Bryan Cosca
07:40 pm Bug #6916 (Resolved): [Workbench] 'Home' column and links are shown in all pages under the admin ...
Applied in changeset arvados|commit:427d9052d59ca7819acba9fb2e5f381d3e44a53e. Radhika Chippada
04:10 pm Bug #6916 (In Progress): [Workbench] 'Home' column and links are shown in all pages under the adm...
Radhika Chippada
02:03 pm Bug #6916 (Resolved): [Workbench] 'Home' column and links are shown in all pages under the admin ...
The Home column and the links to Home projects should only be shown in the /users page. Radhika Chippada
07:40 pm Bug #6880 (Resolved): [Workbench] Remove delete functionality from Users table
Applied in changeset arvados|commit:427d9052d59ca7819acba9fb2e5f381d3e44a53e. Radhika Chippada
07:19 pm Bug #6880: [Workbench] Remove delete functionality from Users table
I think this
if object.editable? and object.deletable?
should just be
if object.deletable?
(if a ...
Tom Clegg
04:08 pm Bug #6880: [Workbench] Remove delete functionality from Users table
Branch 6880-remove-user-delete-button at 467b636f7d1b34f7695f55af972ae90132fc8063
* Contains fix for this issue a...
Radhika Chippada
03:29 pm Bug #6880: [Workbench] Remove delete functionality from Users table
Tom said in IRC:
11:14 radhika: we really need to kick the "writing logic and local variables in views" habit. Thi...
Radhika Chippada
02:06 pm Bug #6880: [Workbench] Remove delete functionality from Users table
While testing this very simple "remove Delete button" implementation, I noticed that the "Home" link is shown on "all... Radhika Chippada
12:53 pm Bug #6880 (In Progress): [Workbench] Remove delete functionality from Users table
Radhika Chippada
07:35 pm Revision b923dd32 (arvados): Merge branch '6858-job-re-run-documentation'
Bryan Cosca
07:33 pm Revision 427d9052 (arvados): closes #6880
closes #6916
Merge branch '6880-remove-user-delete-button'
Radhika Chippada
07:31 pm Revision c8bea0c6 (arvados): 6880: improved deletable? check
Radhika Chippada
07:21 pm Revision 2ba7fad4 (arvados): closes #6858 Merge branch 6858-job-re-run-documentation
Bryan Cosca
07:21 pm Revision 93e0931e (arvados): Merge branch 'master' into 6880-remove-user-delete-button
Radhika Chippada
07:19 pm Bug #6846: [Workbench] Top nav login link loses user's place in Workbench
Radhika Chippada wrote:
> I am also wondering if it would be feasible to use the same login link generation logic (a...
Brett Smith
05:51 pm Bug #6846: [Workbench] Top nav login link loses user's place in Workbench
Thanks for clarifying Nancy.
I am also wondering if it would be feasible to use the same login link generation log...
Radhika Chippada
05:43 pm Bug #6846: [Workbench] Top nav login link loses user's place in Workbench
If I got to
https://workbench.su92l.arvadosapi.com/projects/su92l-j7d0g-swtofxa2rct8495
I get ...
Nancy Ouyang
07:16 pm Bug #6926 (New): Node Manager did not spin up enough nodes
I tried spinning up 82 nodes today and only 68 spun up and it waited an hour and a half. I have a couple ideas.
If...
Bryan Cosca
07:15 pm Task #6890 (Resolved): Review 6858-job-re-run-documentation
Radhika Chippada
04:23 pm Task #6890 (In Progress): Review 6858-job-re-run-documentation
Radhika Chippada
07:06 pm Revision 4f4d8ae4 (arvados): Fixed syntax and added notes to re-use the same hashes from previous...
Bryan Cosca
07:06 pm Bug #6920: [Workbench] Remove Keep disks link?
We don't use Keep disks, but we expect to start using them at some point in the future. Removing the pages from workb... Ward Vandewege
04:36 pm Bug #6920 (New): [Workbench] Remove Keep disks link?
Workbench's admin menu still has a link for Keep disks. This is surprising and unintuitive in modern installs that t... Brett Smith
06:38 pm Task #6917 (In Progress): Review branch 6880-remove-user-delete-button
Tom Clegg
04:06 pm Task #6917 (Resolved): Review branch 6880-remove-user-delete-button
Radhika Chippada
06:22 pm Revision f56323e1 (arvados): Added new section 'Re-using your pipeline run' and moved all version...
Bryan Cosca
05:53 pm Bug #6827 (In Progress): arvados-git-httpd prints plaintext user passwords to its output
Radhika Chippada
05:21 pm Revision db717120 (arvados): crunch-dispatch preserves LD_LIBRARY_PATH environment variable.
This helps it run better in environments using Software Collections to
satisfy dependencies. No issue #.
Brett Smith
05:14 pm Bug #6923 (Resolved): [Crunch] crunch-job install script calls `dpkg-query` - needs a cross-distr...
Because @dpkg-query@ usually isn't installed on Red Hat-based systems. This creates a spurious error in the logs. Brett Smith
05:13 pm Bug #6922 (New): [API] [Maybe] Update API server to support Git 1.7.2
As a matter of practice, we require at least git 1.7.10. CentOS 6 ships with git 1.7.2. There are at least two git-... Brett Smith
04:52 pm Revision b7c99efa (arvados): Install guide notes that snakeoil certs break browser uploads.
You know, with all the usual caveats that users theoretically control
what certs their browser does and doesn't trust...
Brett Smith
04:39 pm Bug #6921 (New): [SDKs] `arv create` creates an object from an empty file
When you run @arv create@, you start with a file that has @{}@ in it. You're expected to fill in the necessary JSON.... Brett Smith
04:32 pm Bug #6919 (New): [Documentation] Make keepproxy install guide follow nginx conventions
The keepproxy install guide follows a common pattern: get the service running under runit; install nginx; configure n... Brett Smith
04:27 pm Bug #6918 (Resolved): [Documentation] keepproxy CORS headers get doubled, don't work
Our current install guide for keepproxy suggests that you use a few @add_header@ lines to add CORS headers to error r... Brett Smith
04:18 pm Revision 54ad7986 (arvados): Quote `git_repo_ssh_base` value in git install guide.
Without this, the YAML gem complains that you're trying to do some
unallowed variable interpolation. No issue #.
Brett Smith
04:18 pm Revision 5f642789 (arvados): Add perl-Crypt-SSLeay as a Perl SDK dependency on Red Hat.
No issue #. Brett Smith
04:18 pm Revision 092e1b42 (arvados): Fix `websocket_address` typo throughout API install guide.
No issue #. Brett Smith
04:18 pm Revision 5916ac79 (arvados): Add `bundle exec` needed to run script in keepproxy install guide.
No issue #. Brett Smith
04:00 pm Revision 29a54ec4 (arvados): Do not split partition config across lines. No issue #
slurm.conf(5) from slurm 2.3.4: "Each line of partition configuration
information should represent a different partit...
Tom Clegg
04:00 pm Revision 467b636f (arvados): 6880: added deletable? method and used to determine whether or not t...
6916: created and moved logic into show_home_button partial rather than determine whether or not to show the button i... Radhika Chippada
03:54 pm Revision 2f719adb (arvados): Added note about job reproducibility and version control with arvado...
Bryan Cosca
02:57 pm Revision 75eaaaa7 (arvados): 6880: Omit delete button from users index table; add controller tests.
6916: Show Home link in users page only and not in all other pages accessed via admin settings menu such as /reposito... Radhika Chippada
12:55 pm Story #6851 (Resolved): [Documentation] Fix circular dependencies around installing the shell server
Applied in changeset arvados|commit:d6b2ead0824fe6810917e5281b4feb969528eb46. Radhika Chippada
12:39 pm Story #6851 (In Progress): [Documentation] Fix circular dependencies around installing the shell ...
Radhika Chippada
12:50 pm Revision d6b2ead0 (arvados): closes #6851
Merge branch '6851-install-guide-flow' Radhika Chippada
12:50 pm Task #6904 (Resolved): Review
Radhika Chippada
12:48 pm Revision 15ac44ec (arvados): 6851: reorder install guide pages; right after api server, install w...
Radhika Chippada
12:16 pm Story #6884: [Deployment] Plan addition of init scripts to Arvados daemon packages
I think the binary packages should only install init support that works with the system that the package supports, bu... Joshua Randall
05:06 am Revision 69573d5d (arvados): 6260: gofmt
Tom Clegg
05:06 am Revision 0b96908a (arvados): 6260: Fix races in keepstore tests. Expose WorkQueue in-progress/que...
Tom Clegg
05:06 am Revision b48ad532 (arvados): 6260: Expose queue sizes in /status.json. Fix sleep/race in trash_wo...
Tom Clegg

08/05/2015

10:05 pm Story #6277 (Resolved): [API] Make manifest format validation more strict, to make "munge" method...
Applied in changeset arvados|commit:7e112cd7504e7e379604e2b1fd46b53054a24050. Radhika Chippada
09:55 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
Tom wrote:
> "nil manifest_text" tests don't belong in the "create/update collection with invalid manifest ...
...
Radhika Chippada
08:16 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
Couple of minor things
The "nil manifest_text" tests don't belong in the "create/update collection with invalid ma...
Tom Clegg
06:52 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
commit:27daf08f38eec505c224e7776678b32d50241e13
Addressed all your comments. I also added "default_empty_manifest"...
Radhika Chippada
04:08 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
We need a unit test, too: the model should prevent invalid manifests from getting into the database _ever_, not just ... Tom Clegg
10:00 pm Revision 7e112cd7 (arvados): closes #6277
Merge branch '6277-check_manifest_validity' Radhika Chippada
09:56 pm Task #6789 (Resolved): Remove manage account button
Radhika Chippada
09:56 pm Task #6488 (Resolved): Fail collection.create/update calls with invalid manifests.
Radhika Chippada
09:55 pm Task #6882 (Resolved): Review branch: 6277-check_manifest_validity
Radhika Chippada
02:49 pm Task #6882 (In Progress): Review branch: 6277-check_manifest_validity
Tom Clegg
09:51 pm Revision 5641c4b1 (arvados): 6277: slightly improved tests
Radhika Chippada
08:40 pm Task #6745 (Resolved): Review 6598-crunch-progress-stats
Tom Clegg
08:01 pm Bug #6663 (Resolved): [Documentation] Document git repository setup
Tom Clegg
04:58 pm Bug #6663: [Documentation] Document git repository setup
Tom Clegg wrote:
> Brett Smith wrote:
> > Sorry, I was not specific enough. I only meant to refer to the extra hea...
Brett Smith
04:26 pm Bug #6663: [Documentation] Document git repository setup
Brett Smith wrote:
> Sorry, I was not specific enough. I only meant to refer to the extra headers set with @proxy_s...
Tom Clegg
12:28 pm Bug #6663: [Documentation] Document git repository setup
Brett Smith wrote:
> Figuring out the right way to deal with runit and other related infrastructure will take a litt...
Brett Smith
11:52 am Bug #6663: [Documentation] Document git repository setup
Tom Clegg wrote:
> Brett Smith wrote:
> > * I'm skeptical about the suggested proxy headers. I know for sure X-Ext...
Brett Smith
07:56 pm Task #6912 (Resolved): Determine dependencies for various distros
Tom Clegg
07:55 pm Task #6911 (Resolved): Update build scripts to add distro-specific dependencies for backported pa...
Tom Clegg
07:53 pm Task #6910 (Resolved): Review branch: 6572-doc-copy-pipeline
Radhika Chippada
07:51 pm Feature #6860 (Duplicate): [Documentation] Copying a public pipeline from qr1hi to an Arvados pri...
Definitely duplicates #6572 (but I'm glad we're on the same page about it :) ). Brett Smith
07:50 pm Bug #6873: [Documentation] Copying/Editing a public pipeline to your project
I think there's a lot of overlap between this and #6572. We should probably figure out the right way to merge them. Brett Smith
07:49 pm Task #6908 (Resolved): Plug leak
Tom Clegg
07:49 pm Task #6906 (Closed): Reproduce leakage in a test case
Tom Clegg
07:48 pm Task #6905 (Resolved): Investigate
Tom Clegg
07:48 pm Task #6904 (Resolved): Review
Radhika Chippada
07:48 pm Task #6903 (Resolved): Review 6844-py-mem-leak
Tom Clegg
07:48 pm Task #6902 (Resolved): Build and publish deb and rpm
Tom Clegg
07:48 pm Task #6901 (Resolved): Add tests
Tom Clegg
07:47 pm Task #6900 (Resolved): Build and publish gem
Tom Clegg
07:47 pm Task #6899 (Resolved): Modify sync script to use env vars instead of yaml
Tom Clegg
07:47 pm Task #6898 (Resolved): Review 6640-projects-menu-incomplete
Manoj Malipeddu
07:47 pm Task #6897 (Resolved): Review 6781-arvados-login-sync (on arvados-dev and arvados)
Tom Clegg
07:46 pm Task #6895 (Resolved): Review branch: 6827-no-passwords-in-logs
Radhika Chippada
07:15 pm Task #6891 (Resolved): Review branch 6600-pysdk-execute-retries
Bryan Cosca
07:14 pm Task #6890 (Resolved): Review 6858-job-re-run-documentation
Bryan Cosca
07:14 pm Task #6889 (Resolved): Review 6862-git-doc-guide-new
Bryan Cosca
07:13 pm Bug #6862: [Documentation] What do you need to know about using Git with Arvados
Since we already have "Working with Arvados repositories" section, I will add this as another page after "Adding a ne... Bryan Cosca
06:45 pm Revision 27daf08f (arvados): 6277: add default_empty_manifest before_validation filter and update...
Radhika Chippada
06:29 pm Revision 29d73c8a (arvados): Merge branch 'master' into 6277-check_manifest_validity
Radhika Chippada
06:28 pm Revision 559acee1 (arvados): 6277: more tests with error checking
Radhika Chippada
05:45 pm Story #6588 (Resolved): [Workbench] UX - webshell login button placement
Applied in changeset arvados|commit:9036e4876fa3710b12a1dfb465652c04b9a73901. Manoj Malipeddu
05:35 pm Story #6588: [Workbench] UX - webshell login button placement
Just a few minor.
* Thanks for noticing the icon for the virtual machines menu item and fixing it :)
* In test ...
Radhika Chippada
04:26 pm Story #6588: [Workbench] UX - webshell login button placement
In commit:bdabb9aa520b598107e319e51638f899f136aff5:
Used phrase "user setting menu" and checks for full link.
Manoj Malipeddu
02:54 pm Story #6588: [Workbench] UX - webshell login button placement
Review comments:
* Can you please use the phrase "user setting menu" in apps/workbench/test/integration/user_setti...
Radhika Chippada
02:32 pm Story #6588: [Workbench] UX - webshell login button placement
In commit:44d4d43331979c87cee5df9ff952fd80a6e9c5f8:
Removed last use of manage account page and reworded tests to ...
Manoj Malipeddu
05:42 pm Revision 9036e487 (arvados): closes #6588
Merge branch '6588-split-manage-account' Manoj Malipeddu
05:42 pm Revision e76165d4 (arvados): Merge branch 'master' into 6588-split-manage-account
Manoj Malipeddu
05:41 pm Revision 48dd2558 (arvados): 6588: Removed unused objects in user_settings_menu_test.
Manoj Malipeddu
05:35 pm Revision 595d517e (arvados): Merge branch 'master' into 6277-check_manifest_validity
Radhika Chippada
05:30 pm Revision 3bd89a0d (arvados): Update bundle. No issue #
Tom Clegg
04:28 pm Revision baccfce6 (arvados): Merge branch 'master' into 6588-split-manage-account
Manoj Malipeddu
04:27 pm Task #6524 (Resolved): Review 6157-worker-hostnames
Tom Clegg
04:27 pm Task #6725 (Resolved): Review 6663-git-server
Tom Clegg
04:25 pm Revision f097af1e (arvados): Merge branch '6663-git-server' refs #6663
Tom Clegg
04:24 pm Revision bdabb9aa (arvados): 6588: Changed settings menu to user settings menu and changed text i...
Manoj Malipeddu
04:21 pm Revision 62f471c5 (arvados): 6663: Add back nginx configs to match tested values.
Tom Clegg
04:12 pm Revision 5cff00f1 (arvados): Merge branch 'master' into 6277-check_manifest_validity
Radhika Chippada
02:30 pm Revision 44d4d433 (arvados): 6588: Removed last reference to manage account page and reworded tests
to not use manage account. Manoj Malipeddu
02:08 pm Bug #6886 (New): [Documentation] A user with an older install may land in a page that requires th...
We might want to address this situation as part of our "make it easy to install arvados" effort.
My arvados instal...
Radhika Chippada
12:39 pm Bug #6885 (Resolved): [Deployment] Add meaningful package versions to distro packages
As we improve our deployment infrastructure, it's happening more and more that we make improvements to our packages t... Brett Smith
12:23 pm Story #6884 (Resolved): [Deployment] Plan addition of init scripts to Arvados daemon packages
This is a planning story. The expected outcome is more well-specified stories.
Background: Right now our install ...
Brett Smith
12:12 pm Bug #6883 (New): [Deployment] arvados-api-server-upgrade.sh should set up git_repositories_dir
See the discussion about @git_repositories_dir@ in "#6663 note 28":https://arvados.org/issues/6663#note-28 for backgr... Brett Smith
12:06 pm Revision 5f3ac75b (arvados): 6157: Copyedits to compute node name docs.
Mostly for wording and typographic consistency within the page.
Refs #6157.
Brett Smith
02:00 am Revision b8048416 (arvados-dev): Fix logic bug in run-deploy: deploy api server first before gath...
the git revision from it to make sure the correct arvados/jobs docker
image is installed.
No issue #
Ward Vandewege
02:00 am Revision b8048416 (arvados): Fix logic bug in run-deploy: deploy api server first before gathering
the git revision from it to make sure the correct arvados/jobs docker
image is installed.
No issue #
Ward Vandewege
01:25 am Bug #6157 (Resolved): [Documentation] Explain extra steps needed when compute hostnames are not fooN
Applied in changeset arvados|commit:e0a1fc70f919741a8ad840dc40cfcc87f2751722. Tom Clegg
01:23 am Revision e0a1fc70 (arvados): Merge branch '6157-worker-hostnames' closes #6157
Tom Clegg

08/04/2015

11:57 pm Story #6588: [Workbench] UX - webshell login button placement
Review comments for "delete manage account button" at commit:89fccf123374c67e738381ea840e3535b2d1074f
* arvados/se...
Radhika Chippada
08:45 pm Story #6588: [Workbench] UX - webshell login button placement
In commit:89fccf123374c67e738381ea840e3535b2d1074f:
Got rid of manage account button and updated tests.
Manoj Malipeddu
07:57 pm Story #6588: [Workbench] UX - webshell login button placement
LGTM, thanks! Running tests now after merging master, but assuming you've already done that, please merge. Tom Clegg
05:04 pm Story #6588: [Workbench] UX - webshell login button placement
In commit:cca0d86de72487988b1a7d657e67143121461a0f:
Go directly to pages instead of going through home page and lo...
Manoj Malipeddu
03:02 pm Story #6588: [Workbench] UX - webshell login button placement
Could you change "/users/zzzzz-tpzed-l1s2piq4t4mps8r/virtual_machines" to "/users/#{users(:spectator).uuid}/virtual_m... Tom Clegg
02:35 pm Story #6588: [Workbench] UX - webshell login button placement
In commit:8f93d1332a25d29aa96211920e1b399a1e94482c:
Made the changes you recommended to the tests.
Manoj Malipeddu
11:29 pm Revision e9bee65d (arvados): refs #6588
Merge branch '6588-documentation' Radhika Chippada
11:28 pm Revision 68481a07 (arvados): 6588: replace manage_account page references with the new SSH keys a...
Radhika Chippada
10:27 pm Task #6744 (Resolved): Explain this decision at install-crunch-dispatch.html
Tom Clegg
10:24 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
commit:004243ab59e3a2fc36a708b66373297dd83e0b91 in branch 6277-check_manifest_validity
* Updated before_validation...
Radhika Chippada
10:21 pm Task #6882 (Resolved): Review branch: 6277-check_manifest_validity
Radhika Chippada
10:19 pm Revision 004243ab (arvados): 6277: enforce manifest validation
Radhika Chippada
09:30 pm Revision b369dfc8 (arvados): 6157: Explain how choice of hostnames relates to slurm and arvados.
Tom Clegg
08:46 pm Task #6697 (Resolved): Code UI after design review
Manoj Malipeddu
08:46 pm Task #6698 (Resolved): Review 6588-split-manage-account
Manoj Malipeddu
08:44 pm Task #6699 (Resolved): Update documentation
Radhika Chippada
08:44 pm Task #6791 (Resolved): Review documentation updates: branch 6588-documentation
r Radhika Chippada
08:37 pm Task #6791: Review documentation updates: branch 6588-documentation
In user/getting_started/vm-login-with-webshell
Please change "Clinking on this button will open up" to "Clicking o...
Bryan Cosca
08:43 pm Revision 6e65fde6 (arvados): refs #6588
Merge branch '6588-documentation' Radhika Chippada
08:42 pm Revision 3ba1af7f (arvados): 6588: fix typo
Radhika Chippada
08:41 pm Revision 89fccf12 (arvados): 6588: Removed manage account button, modified tests and deleted views.
Manoj Malipeddu
08:20 pm Revision f2f4727c (arvados): Merge branch 'master' into 6588-documentation
Radhika Chippada
08:02 pm Task #6488 (In Progress): Fail collection.create/update calls with invalid manifests.
Radhika Chippada
08:01 pm Task #6747 (Resolved): Review summarization data (note #22)
Radhika Chippada
08:01 pm Revision 44184f3b (arvados): refs #6588
Merge branch '6588-split-manage-account' Manoj Malipeddu
07:59 pm Bug #6834: How to add users to a newly created group?
Complete documentation for how to make a new group and add users to it:
# Login to shell (potentially as admin?).
#...
Nancy Ouyang
07:32 pm Bug #6834: How to add users to a newly created group?
Thanks -- Creating a group via the commandline worked, via Workbench did not (show ability to add users), which was w... Nancy Ouyang
07:47 pm Bug #6663: [Documentation] Document git repository setup
Brett Smith wrote:
> To continue the philosophical discussion: I'm all for providing our own installation instructio...
Tom Clegg
03:34 pm Bug #6663: [Documentation] Document git repository setup
As an end user, I find myself somewhat annoyed with the repeated suggestions to use runit to supervise processes. I t... Joshua Randall
02:09 pm Bug #6663: [Documentation] Document git repository setup
Tom Clegg wrote:
> Brett Smith wrote:
> > * The story says, "Link to the gitolite installation documentation for de...
Brett Smith
06:46 am Bug #6663: [Documentation] Document git repository setup
Brett Smith wrote:
> * The story says, "Link to the gitolite installation documentation for details." In general, I...
Tom Clegg
07:17 pm Bug #6881 (New): np.savez and np.savez_compressed exit normally but do not create files in collec...
Pipeline instance using np.savez_compressed: https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-4s... Sarah Guthrie
07:06 pm Bug #6827: arvados-git-httpd prints plaintext user passwords to its output
Joshua Randall wrote:
> Perhaps you could check the provided API token to verify that it appears to be in the shape ...
Tom Clegg
06:53 pm Bug #6640: [Workbench] Ensure projects menu consistently shows all "my projects"
Discussed writing a separate infinite scrolling, filterable list page. Tom to write a spec. Story pointing based on... Brett Smith
06:49 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
Suggest we get the list of dependencies to add from the existing packages in Debian and CentOS. For most of our pytho... Ward Vandewege
06:38 pm Bug #6638: [Deployment] Python package backports should declare their C dependencies
fpm has a lot of options, and we're starting to use more and more.
we should have a arvados/services/:service:/fp...
Nico César
06:18 pm Bug #6862: [Documentation] What do you need to know about using Git with Arvados
> However, if we're going to talk about integration with pipeline templates, it might make sense to have a page title... Bryan Cosca
05:58 pm Bug #6862: [Documentation] What do you need to know about using Git with Arvados
Bryan Cosca wrote:
> * Create new arvados Git repository.
This page already exists as "Adding a new arvados repos...
Brett Smith
05:58 pm Feature #6858: [Documentation] Document the necessary steps to re-run jobs without computing again
Suggest adding this to "Writing a pipeline template." Brett Smith
05:46 pm Bug #6880: [Workbench] Remove delete functionality from Users table
Adjusting per Radhika's comment. Brett Smith
05:42 pm Bug #6880: [Workbench] Remove delete functionality from Users table
When I originally identified this issue #3628, Tom suggested that we should not provide the delete button in the user... Radhika Chippada
04:07 pm Bug #6880: [Workbench] Remove delete functionality from Users table
So what do you want?
* The Workbench delete interface gets removed
* The Workbench delete interface reports the e...
Brett Smith
03:39 pm Bug #6880 (Resolved): [Workbench] Remove delete functionality from Users table
h2. Story
Removing users from Arvados is impractical. Workbench currently offers a delete ("trash") button in the...
Ward Vandewege
05:41 pm Bug #3628 (Duplicate): [Workbench] The "delete" button in users page is not working
Radhika Chippada
05:39 pm Revision 10556d8e (arvados): 6663: Fix config/application.yml -> application.yml.
Tom Clegg
05:39 pm Revision 6f883592 (arvados): 6663: Add non-runit-dependent daemon startup script.
Tom Clegg
05:39 pm Revision 6fad718e (arvados): 6663: Finish editing sentence.
Tom Clegg
05:28 pm Task #6871 (Resolved): Review branch: 6476-actions-show-not-need-token
Radhika Chippada
05:19 pm Revision f7e00eb5 (arvados): 6663: Remove unneeded nginx config, clarify where config should be a...
Tom Clegg
05:03 pm Bug #6157 (In Progress): [Documentation] Explain extra steps needed when compute hostnames are no...
Tom Clegg
05:02 pm Revision cca0d86d (arvados): 6588: Go directly to pages instead of going through home page and se...
for more specific details on pages. Manoj Malipeddu
03:01 pm Bug #6844: [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB collection
I spent an hour digging into this and didn't immediately find the source. I spent some time scrutinizing our PyCurl ... Brett Smith
02:45 pm Story #6476 (Resolved): [Workbench] actions#show should be implemented without requiring an API t...
Applied in changeset arvados|commit:5b2e3d9c92b34603912872c2e10e13da91268a29. Radhika Chippada
02:31 pm Story #6476: [Workbench] actions#show should be implemented without requiring an API token
Thanks for explaining. I think explaining that in code comments or a commit message as well would be helpful (I thin... Brett Smith
01:48 pm Story #6476: [Workbench] actions#show should be implemented without requiring an API token
There is going to be subtle difference in UX.
If a user goes to, let's say, qr1hi/projects/<project_uuid> or qr1hi...
Radhika Chippada
02:19 am Story #6476: [Workbench] actions#show should be implemented without requiring an API token
Radhika Chippada wrote:
> Brett asked:
>
> > why do we only skip the filter for certain classes of API objects
>...
Brett Smith
02:42 pm Revision 5b2e3d9c (arvados): closes #6476
Merge branch '6476-actions-show-not-need-token' Radhika Chippada
02:41 pm Revision e3289097 (arvados): 6476: add comment
Radhika Chippada
02:34 pm Revision 9fcd7e96 (arvados): Merge branch 'master' into 6476-actions-show-not-need-token
Radhika Chippada
02:33 pm Revision 8f93d133 (arvados): 6588: Formatted tests and changed others to be more efficient.
Manoj Malipeddu
02:17 pm Bug #6873 (New): [Documentation] Copying/Editing a public pipeline to your project
Everyone has their own GATK "snowflake". Being able to exactly show how to use the public gatk pipeline as a base and... Bryan Cosca
01:55 pm Story #6872 (New): Add an arvados PPA to launchpad
In order for users to do a simple ... Nico César
01:00 pm Feature #6838 (Resolved): Configurable docker binary location
Applied in changeset arvados|commit:b958c247cba0cc0a9b13dfd4fbc10c1a807b5074. Tom Clegg
10:41 am Feature #6838: Configurable docker binary location
Tom Clegg wrote:
> OK, stripped off the docker.io->docker commits, now back at commit:e8ba9a04. We can merge the "ca...
Brett Smith
09:11 am Feature #6838: Configurable docker binary location
FWIW, I believe docker.io is the default binary name on all debian-derived distros (as far as I know, the official do... Joshua Randall
06:52 am Feature #6838: Configurable docker binary location
OK, stripped off the docker.io->docker commits, now back at commit:e8ba9a04. We can merge the "can override" patch no... Tom Clegg
02:57 am Feature #6838: Configurable docker binary location
Okay, so, I swear I'm not tormenting you with this, I'm just working with the best information I have at the time. B... Brett Smith
12:57 pm Revision b958c247 (arvados): Merge branch '6838-docker-path' closes #6838
Tom Clegg
06:36 am Revision 01a76d36 (arvados): 6663: More explicit gitolite version advice, and link to home page.
Tom Clegg
05:58 am Revision 30d1623c (arvados): 6663: Split "install runit" into debian and red hat variants.
Tom Clegg
05:49 am Revision c94bc0d5 (arvados): 6663: Add "restart nginx" instructions.
Tom Clegg
05:41 am Revision 89dcdd01 (arvados): 6663: Update nginx config to look more like API server's.
Tom Clegg
05:30 am Revision 70a9d868 (arvados): 6663: Formatting fixes.
Tom Clegg
05:28 am Revision 4c5925a0 (arvados): 6663: Fix API config example for HTTPS, add corresponding SSH example.
Tom Clegg
05:21 am Revision b9a61af3 (arvados): 6663: gitolite, not arvados-git-sync.rb, creates empty repos.
Tom Clegg
05:08 am Revision 821cb42d (arvados): 6663: Clarify "gitolite installed in X" vs. "hosted repos stored in ...
Tom Clegg
04:59 am Revision cec08599 (arvados): 6663: Clarify port 22 goes to sshd.
Tom Clegg
04:47 am Revision ed2e9fec (arvados): 6663: Clarify default vs. example git_repositories_dir.
Tom Clegg
04:46 am Revision 0c96fc85 (arvados): 6663: Fix wrong bash prompt in example transcript.
Tom Clegg
04:45 am Revision 2e927624 (arvados): 6663: Update default git_repositories_dir to match install guide.
Tom Clegg
01:36 am Revision 5f708f62 (arvados): 6476: simpler conditional check
Radhika Chippada

08/03/2015

11:52 pm Bug #6827: arvados-git-httpd prints plaintext user passwords to its output
Ok, so mostly this is me being stupid because I hadn't realised that I was supposed to send my arvados username and a... Joshua Randall
10:53 pm Story #6476: [Workbench] actions#show should be implemented without requiring an API token
Brett asked:
> why do we only skip the filter for certain classes of API objects
Please look at projects_contro...
Radhika Chippada
10:00 pm Story #6476: [Workbench] actions#show should be implemented without requiring an API token
Reviewing commit:80abb8a, and I just have a question: why do we only skip the filter for certain classes of API objec... Brett Smith
10:17 pm Bug #6663: [Documentation] Document git repository setup
I think you should leave the specific instructions on how to install gitolite (but also link to the gitolite docs). G... Joshua Randall
09:30 pm Bug #6663: [Documentation] Document git repository setup
Comments on commit:7e77373. I have not had the opportunity to test your instructions yet; but I wanted to provide so... Brett Smith
08:08 pm Bug #6663: [Documentation] Document git repository setup
There is a typo: "The git user needs its own SSH key. (It must be able to run ssh gitlocalhost@ from scripts.)"
Sh...
Joshua Randall
07:53 pm Bug #6663: [Documentation] Document git repository setup
On `install-arv-git-httpd.html`, "DNS and network configuration should be set up so port 443 reaches your HTTPS proxy... Joshua Randall
07:20 pm Bug #6663: [Documentation] Document git repository setup
Preview updated to commit:97fa1e2, notably
* http://6663.tom.shell.9tee4.arvadosapi.com/install/install-arv-git-http...
Tom Clegg
04:54 pm Bug #6663: [Documentation] Document git repository setup
Peter Amstutz wrote:
> Related to instructions for the user to test things out: the user needs to create at least on...
Tom Clegg
04:49 pm Bug #6663: [Documentation] Document git repository setup
Peter Amstutz wrote:
> So, this is awesome, all our documentation should be like this.
Thanks! Funny, while writi...
Tom Clegg
10:02 pm Story #6588: [Workbench] UX - webshell login button placement
Looks great, thanks!
Couple of minor requests:
Fix indentation in the new test cases in @apps/workbench/test/in...
Tom Clegg
05:52 pm Story #6588: [Workbench] UX - webshell login button placement
In commit:a789f895a5cdbc2a548787f99197f9861521106b
Changed routes to be under /users, used @object, removed render...
Manoj Malipeddu
10:00 pm Task #6871 (In Progress): Review branch: 6476-actions-show-not-need-token
Brett Smith
09:33 pm Task #6871 (Resolved): Review branch: 6476-actions-show-not-need-token
Radhika Chippada
09:31 pm Revision 80abb8a0 (arvados): Merge branch 'master' into 6476-actions-show-not-need-token
Radhika Chippada
09:31 pm Revision b3a25028 (arvados): 6476: skip require_thread_api_token filter when anonymous browsing i...
Radhika Chippada
07:50 pm Revision 7e773735 (arvados): Merge branch 'master' into 6663-git-server
Conflicts:
doc/install/install-api-server.html.textile.liquid
Tom Clegg
06:56 pm Revision 15c86f88 (arvados): closes #6414
Merge branch '6414-anonymous-public-projects-link' Manoj Malipeddu
06:52 pm Revision 95135f30 (arvados): 6414: Added an assertion to test if objects are equal.
Manoj Malipeddu
06:50 pm Bug #6864: [Documentation] Update arv-keep-docker Documentation to pull from the Arvados repository
Realized this was done already with: http://doc.arvados.org/user/topics/arv-docker.html
But changed the descriptio...
Bryan Cosca
05:58 pm Bug #6864 (New): [Documentation] Update arv-keep-docker Documentation to pull from the Arvados re...
-Things to note:-
-Arv keep docker will show you all the images on the Arvados registry.-
-How to pull them and w...
Bryan Cosca
06:48 pm Bug #6868 (New): [SSO] Template calls undefined method after fresh local accounts installation
Steps to reproduce: follow the SSO installation documentation at commit:434be0f. Configure local accounts, and creat... Brett Smith
06:32 pm Bug #6867 (New): [Documentation] Have a running wiki/doc on all the Bioinformatic tools and Refer...
We have BWA/samtools/other stuff already, so we should have users just point to that in their pipeline templates/crun... Bryan Cosca
06:30 pm Task #6487 (Resolved): Summarize invalid manifests present in production servers' databases
Radhika Chippada
06:28 pm Task #6486 (Resolved): Review production logs to confirm no real clients are submitting any inval...
Radhika Chippada
06:10 pm Task #6739 (Resolved): Review 6591-6674-6676-nginx-docs-wip
Applied in changeset arvados|commit:434be0f7e6420fee1b99e78466ee4a4d734734c1. Brett Smith
05:17 pm Task #6739 (In Progress): Review 6591-6674-6676-nginx-docs-wip
Nico César
06:10 pm Bug #6676 (Resolved): [Documentation] Fully document the SSO installation process
Applied in changeset arvados|commit:434be0f7e6420fee1b99e78466ee4a4d734734c1. Brett Smith
06:10 pm Bug #6674 (Resolved): [Documentation] Don't recommend nginx16 Software Collection
Applied in changeset arvados|commit:434be0f7e6420fee1b99e78466ee4a4d734734c1. Brett Smith
05:25 pm Bug #6674: [Documentation] Don't recommend nginx16 Software Collection
review 028c4d1b6732121f32addf6fd601367ce0ff2f27
I review the docs, and the change seems ok to me
Nico César
06:10 pm Bug #6591 (Resolved): [Documentation] Improve suggested nginx configuration
Applied in changeset arvados|commit:434be0f7e6420fee1b99e78466ee4a4d734734c1. Brett Smith
06:05 pm Revision 434be0f7 (arvados): Merge branch '6591-6674-6676-nginx-docs-wip'
Closes #6591, #6674, #6676, #6739 (woo!). Brett Smith
06:04 pm Bug #6866 (New): [Documentation] General reference guide on how to do simple tasks
Something like https://arvados.org/projects/arvados/wiki/pipeline_template_template, but with actual documentation.
...
Bryan Cosca
06:03 pm Revision b5b88cda (arvados): 6676: Install docs recommend running SSO server behind Nginx.
This provides a straightforward way to get the server running as a
daemon, and matches our suggestions for other Web ...
Brett Smith
06:03 pm Revision b6f800ae (arvados): 6591: Add ssl_certificate lines to sample install nginx configs.
Brett Smith
06:03 pm Feature #6865 (New): [Documentation] Higher Level Python SDK Reference Page
I think this would be super important for those trying to use the python sdk for the first time.
Notes to make sur...
Bryan Cosca
05:57 pm Revision d44692de (arvados): 6674: Install docs use Phusion's install instructions exclusively.
Don't suggest installing nginx packages from a distribution or
backports collection, because that conflicts with the ...
Brett Smith
05:57 pm Revision 93655055 (arvados): 6591: Improve install docs around $external_client variable.
Our Nginx configuration uses this variable to automatically set
X-External-Client: 1 in API request headers when clie...
Brett Smith
05:57 pm Revision a812a13a (arvados): 6591: Suggest proxy timeouts in install doc Nginx configs.
These settings match what we use in production. The defaults are more
aggressive and can cause 503 responses for lar...
Brett Smith
05:49 pm Revision a789f895 (arvados): 6588: Changed routes to be under /users, used @object and updated
tests. Manoj Malipeddu
05:36 pm Bug #6863 (New): [Documentation] Clarify the different ways to input your tools to Arvados
A quick version from the port-a-pipeline wiki.
* Install on Docker...
Bryan Cosca
05:15 pm Bug #6862 (Resolved): [Documentation] What do you need to know about using Git with Arvados
Provide a rough guide on how git works and how to work with your own repository.
* Create new arvados Git reposito...
Bryan Cosca
04:38 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
Moved the summary output files into #6859 Radhika Chippada
04:19 pm Revision 97fa1e26 (arvados): 6663: Use a more obviously fake token.
Tom Clegg
04:15 pm Task #6673 (Resolved): merge 6221-write-trash-list only once keepstore is deployed with -no-delet...
Applied in changeset arvados|commit:4d6e05c25c6a5d72afee37f8165b006267b4183d. Brett Smith
04:15 pm Bug #6221 (Resolved): [Data Manager] implement Delete
Applied in changeset arvados|commit:4d6e05c25c6a5d72afee37f8165b006267b4183d. Brett Smith
04:10 pm Revision 4d6e05c2 (arvados): Merge branch '6221-write-trash-list'
Closes #6221, #6673. Brett Smith
03:59 pm Task #6740 (Closed): Review 6591-6674-6676-nginx-docs-wip
Nico will review this is #6739. Brett Smith
03:45 pm Feature #6860 (Duplicate): [Documentation] Copying a public pipeline from qr1hi to an Arvados pri...
Users who have a new cluster set up would like to test their cluster to make sure it works properly. Documentation is... Bryan Cosca
03:31 pm Feature #6858 (Resolved): [Documentation] Document the necessary steps to re-run jobs without com...
Write that you need to explicitly state the git commit hash (script_version), arvados_sdk_version, docker_image hash ... Bryan Cosca
02:02 pm Revision 41bb13b7 (arvados): Merge branch 'master' into 6588-split-manage-account
Manoj Malipeddu
03:16 am Revision 5ce4ffe6 (arvados): 6838: Prefer invoking docker rather than docker.io in docs.
Tom Clegg
03:15 am Bug #6598 (Resolved): [Crunch] Fix crunch-job's update_progress_stats post-5717
Applied in changeset arvados|commit:6988f4d44d2f8f7fc4aa2c381334c44d3133cf31. Tom Clegg
03:10 am Revision 6988f4d4 (arvados): Merge branch '6598-crunch-progress-stats' closes #6598
Tom Clegg
12:20 am Bug #6847 (Resolved): [Crunch] Move Docker DNS configuration to Docker daemon
Applied in changeset arvados|commit:bb58564d632498a394ee75b07d17f41b724ef824. Brett Smith
12:10 am Revision bb58564d (arvados): Merge branch '6847-docker-dns-wip'
Closes #6847, #6853. Brett Smith

08/02/2015

10:27 pm Bug #6676: [Documentation] Fully document the SSO installation process
Brett Smith wrote:
> If these suggestions just lead to expected changes, go ahead and merge the branch, then assign ...
Brett Smith
10:23 pm Bug #6139 (Duplicate): [OPS] Jenkis Job arvados-api-server should create unique databases so it c...
I'm marking this as a duplicate of #6273 since that has more discussion. Brett Smith
04:08 pm Task #6853 (Resolved): Review 6847-docker-dns-wip
Ward Vandewege
04:08 pm Task #6853 (In Progress): Review 6847-docker-dns-wip
Ward Vandewege
02:07 pm Task #6853 (Resolved): Review 6847-docker-dns-wip
Brett Smith
04:08 pm Bug #6847: [Crunch] Move Docker DNS configuration to Docker daemon
6847-docker-dns-wip LGTM Ward Vandewege
01:53 pm Bug #6847 (In Progress): [Crunch] Move Docker DNS configuration to Docker daemon
Brett Smith
03:42 pm Bug #6846: [Workbench] Top nav login link loses user's place in Workbench
Nancy, please confirm:
Clicking the log in link within in the body of the Page not found error page (I notice you ...
Radhika Chippada
03:12 pm Story #6851: [Documentation] Fix circular dependencies around installing the shell server
I recommend option 1, installing workbench before shell server.
First of, this would be quicker and would require ...
Radhika Chippada
02:07 pm Revision 71e1b1d6 (arvados): 6847: Handle Docker DNS in Docker daemon configuration.
crunch-job currently uses the host's public IP address as a DNS
resolver for containers. This requires all compute n...
Brett Smith

08/01/2015

08:34 pm Bug #6598: [Crunch] Fix crunch-job's update_progress_stats post-5717
commit:a76d715 is good to merge. Thank you. Brett Smith
08:30 pm Task #6721 (Resolved): Review 6590-api-config-docs
Applied in changeset arvados|commit:f3504dc2b40eaa4235092b671ce0bece43732904. Brett Smith
08:30 pm Bug #6590 (Resolved): [Documentation] Improve documentation of API server configuration variables
Applied in changeset arvados|commit:f3504dc2b40eaa4235092b671ce0bece43732904. Brett Smith
08:28 pm Task #6745 (In Progress): Review 6598-crunch-progress-stats
Brett Smith
08:27 pm Task #6725: Review 6663-git-server
Tom, please assign future review work to me. Brett Smith
08:25 pm Revision f3504dc2 (arvados): Merge branch '6590-api-config-docs'
I am breaking our own rules here, since this merge includes a
non-trivial commit from me that hasn't been reviewed. ...
Brett Smith
08:19 pm Revision 5ef15a74 (arvados): 6590: Aesthetic improvements to the API install guide.
This implements the flow and grammar fixes requested in
<https://arvados.org/issues/6590#note-7>. It also separates ...
Brett Smith
07:43 pm Bug #6591 (In Progress): [Documentation] Improve suggested nginx configuration
Brett Smith
06:12 pm Bug #6591: [Documentation] Improve suggested nginx configuration
$external_client has never been an nginx variable. We define it ourselves. Describing a better solution. Brett Smith
07:43 pm Bug #6674 (In Progress): [Documentation] Don't recommend nginx16 Software Collection
Brett Smith
07:28 pm Story #6851 (Resolved): [Documentation] Fix circular dependencies around installing the shell server
In the install docs, the ordering of installing a shell server has a few problems:
* The documentation tells you t...
Brett Smith
07:14 pm Task #6739: Review 6591-6674-6676-nginx-docs-wip
Because I was making many small nginx changes at the same time, I did them in a single branch to reduce the likelihoo... Brett Smith
07:13 pm Task #6740: Review 6591-6674-6676-nginx-docs-wip
Because I was making many small nginx changes at the same time, I did them in a single branch to reduce the likelihoo... Brett Smith
07:07 pm Task #6832 (Resolved): Add nginx instructions and sample configuration
Brett Smith
07:07 pm Revision 028c4d1b (arvados): 6676: Install docs recommend running SSO server behind Nginx.
This provides a straightforward way to get the server running as a
daemon, and matches our suggestions for other Web ...
Brett Smith
07:05 pm Revision 8f6b342c (arvados): 6591: Suggest proxy timeouts in install doc Nginx configs.
These settings match what we use in production. The defaults are more
aggressive and can cause 503 responses for lar...
Brett Smith
07:03 pm Revision 502c9790 (arvados): 6591: Improve install docs around $external_client variable.
Our Nginx configuration uses this variable to automatically set
X-External-Client: 1 in API request headers when clie...
Brett Smith
06:59 pm Revision bd9bcaf0 (arvados): 6674: Install docs use Phusion's install instructions exclusively.
Don't suggest installing nginx packages from a distribution or
backports collection, because that conflicts with the ...
Brett Smith

07/31/2015

08:41 pm Bug #6663: [Documentation] Document git repository setup
Related to instructions for the user to test things out: the user needs to create at least one repository first, othe... Peter Amstutz
08:36 pm Bug #6663: [Documentation] Document git repository setup
Peter Amstutz wrote:
> Also
>
> [...]
I think maybe I ran the script as root and so FETCH_HEAD was owned by ro...
Peter Amstutz
08:28 pm Bug #6663: [Documentation] Document git repository setup
Also... Peter Amstutz
08:27 pm Bug #6663: [Documentation] Document git repository setup
So, this is awesome, all our documentation should be like this.
* Example secret keys should be obviously bogus ("...
Peter Amstutz
02:36 pm Bug #6663: [Documentation] Document git repository setup
6663-git-server preview at http://6663.tom.shell.9tee4.arvadosapi.com/install/install-arv-git-httpd.html Tom Clegg
06:10 am Bug #6663: [Documentation] Document git repository setup
Came across a confusing bug/limitation that should probably be documented, and logged better by arv-git-httpd when it... Tom Clegg
08:33 pm Bug #6850 (New): Unclear how to clone shared repo
I shared read-access to a repo through my "manage_account" settings. However, under the other account, if I run git c... Nancy Ouyang
08:28 pm Bug #6849 (New): Git repo browser feature only accessible to admins
Our shiny new in-browser git repo browsing feature is only accessible to the owner of a project and admin users, rega... Nancy Ouyang
08:02 pm Bug #6847 (Resolved): [Crunch] Move Docker DNS configuration to Docker daemon
crunch-job has this code to build its @docker run@ command:... Brett Smith
07:45 pm Bug #6846 (Resolved): [Workbench] Top nav login link loses user's place in Workbench
If I'm not logged in and open a link to a project I can access, I get access denied. However, after I log-in, I get r... Nancy Ouyang
07:21 pm Bug #6844: [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB collection
Peter Amstutz wrote:
> Check the keepproxy logs. This is a case where the real error is hidden from view.
Everyt...
Brett Smith
07:08 pm Bug #6844: [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB collection
Check the keepproxy logs. This is a case where the real error is hidden from view. Peter Amstutz
07:02 pm Bug #6844 (Resolved): [SDKs] arv-copy consistently gets MemoryError trying to copy an 8GiB collec...
qr1hi-4zz18-c1t7uidtqs5sg82 is public reference data for the Tuxedo pipeline. It's 8GiB.
I am trying to copy this...
Brett Smith
07:10 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
Adding *invalid_manifests_db_lookup_output.txt files for all our environments.
These collection uuids are obtained...
Radhika Chippada
04:13 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
Ran the validation check script against 9tee4 db dump. There are 21 manifests not terminating with \n character and n... Radhika Chippada
12:37 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
Reworked on my script to use collection api instead of db lookup and tested in 9tee4, su92l, and qr1hi. Here are the ... Radhika Chippada
07:06 pm Bug #6845 (New): crunch job log doesn't print the commands it is running in a usable format (at l...
The crunch log contains entries of the form "Running [%s]" which is great because you can tell what is going on and i... Joshua Randall
06:11 pm Story #6840 (New): [SDKs] Teach arv-copy to copy whole projects
Currently, trying to copy a project aborts with the error:... Brett Smith
06:04 pm Bug #6770 (In Progress): incomplete recursive copying of pipeline templates with arv-copy
This was hopefully fixed in commit:1b8caff3ad598744e4a0379b01fc95ca4838caa0. If you get a chance to test with that, ... Brett Smith
05:18 pm Task #6746 (Resolved): Fix summary calculation
Tom Clegg
05:17 pm Bug #6598: [Crunch] Fix crunch-job's update_progress_stats post-5717
Tested commit:a76d715 on 4xphq.
Before:
https://workbench.4xphq.arvadosapi.com/collections/58f9d7718475a24e87f7...
Tom Clegg
04:17 pm Bug #6598 (In Progress): [Crunch] Fix crunch-job's update_progress_stats post-5717
Tom Clegg
05:10 pm Revision a76d7155 (arvados): 6598: Fix misreported "running tasks" stat.
Tom Clegg
04:08 pm Task #6791: Review documentation updates: branch 6588-documentation
Branch ready for review now. Thanks. Radhika Chippada
04:07 pm Revision 147d27f6 (arvados): 6838: Change default docker executable from docker.io to docker.
Tom Clegg
04:03 pm Revision 3e428f95 (arvados): 6838: Change default docker executable from docker.io to docker.
Tom Clegg
04:02 pm Revision e8ba9a04 (arvados): 6838: If env var override is not set, let crunch-job use its default.
Tom Clegg
03:43 pm Revision fe7f9a43 (arvados): 6588: User settings menu item name updates.
Radhika Chippada
03:36 pm Revision 6870192a (arvados): Merge branch 'master' into 6588-documentation
Radhika Chippada
03:33 pm Revision 8c65288a (arvados): 6598: Fix misreported "running tasks" stat.
Tom Clegg
02:47 pm Feature #6838: Configurable docker binary location
Brett Smith wrote:
> Actually, I had a belated thought: in the spirit of DRY, would it be better if crunch-dispatch ...
Tom Clegg
01:59 pm Feature #6838: Configurable docker binary location
Actually, I had a belated thought: in the spirit of DRY, would it be better if crunch-dispatch only added @--docker-b... Brett Smith
01:55 pm Feature #6838: Configurable docker binary location
The code change looks good to me, and +1 for updating the documentation.
Part of me wonders if we would've gotten ...
Brett Smith
01:41 pm Feature #6838: Configurable docker binary location
I'm looking at this. Brett Smith
04:24 am Feature #6838 (Resolved): Configurable docker binary location
From https://github.com/curoverse/arvados/pull/20
This is useful because it allows one to start the crunch dispatc...
Tom Clegg
02:39 pm Task #6725 (In Progress): Review 6663-git-server
Peter Amstutz
02:39 pm Bug #6676 (In Progress): [Documentation] Fully document the SSO installation process
Peter Amstutz
02:27 pm Bug #6676: [Documentation] Fully document the SSO installation process
Brett Smith wrote:
> Reviewing commit:8e74a5f. Most of this is just little grammar stuff, and I know you're not res...
Peter Amstutz
02:35 pm Task #6744 (In Progress): Explain this decision at install-crunch-dispatch.html
Tom Clegg
02:34 pm Task #6728 (Resolved): Document how to install a full arv-git-httpd repo hosting system (that wor...
Tom Clegg
02:32 pm Task #6715 (Resolved): Review 6676-document-sso
Peter Amstutz
02:32 pm Revision 620fb9e0 (arvados): Merge branch '6676-document-sso' refs #6676
Peter Amstutz
02:31 pm Revision 43a95731 (arvados): Merge branch 'master' into 6676-document-sso
Peter Amstutz
02:28 pm Revision 31a61e32 (arvados): 6676: Grammar fixes.
Peter Amstutz
02:28 pm Task #6698 (In Progress): Review 6588-split-manage-account
Tom Clegg
02:26 pm Revision 1b8caff3 (arvados): Fix type checks in arv-copy recursive collection copying.
This is necessary follow-up from
79564b0ac7d03327cc351bbd6df544ab1f776380. API objects are now
OrderedDicts instead ...
Brett Smith
02:26 pm Story #6588: [Workbench] UX - webshell login button placement
At commit:cda68ba...
I think the word "manage" is unnecessary in these routes. And if we are putting these routes ...
Tom Clegg
02:12 pm Revision 61da6612 (arvados): arv-copy git check doesn't catch system exceptions.
No issue #. Brett Smith
01:37 pm Revision e51a22dc (arvados): 6663: Document git setup.
Tom Clegg
05:02 am Revision 1000275d (arvados): Whitespace
No issue # Tom Clegg
05:02 am Revision 465cb922 (arvados): Merge branch 'git-commit-debug' of https://github.com/wtsi-hgi/arvados
No issue # Tom Clegg
04:32 am Revision d2cbbe5a (arvados): 6838: Document CRUNCH_JOB_DOCKER_BIN in example run script. Sync up ...
Tom Clegg
04:25 am Revision 8d2aebfd (arvados): Merge branch 'crunch-dispatch-docker-bin-env' of https://github.com/...
Tom Clegg
01:55 am Bug #6834: How to add users to a newly created group?
There is only an admin interface for this right now. (Users can create groups on the command line but it's even less ... Tom Clegg
01:21 am Revision 60f3ef78 (arvados): Makes it possible to set docker_bin in crunch-job
Adds a new environment variable (CRUNCH_JOB_DOCKER_BIN) that
crunch-dispatch.rb passes along to crunch-job (or if uns...
Joshua C. Randall
01:00 am Revision 800e8ba4 (arvados): Adds useful log warnings re: repo failures
Instruments the find_commit_range function such that it logs an
explanatory warning in any case when it fails to find...
Joshua C. Randall

07/30/2015

10:14 pm Bug #6835 (Duplicate): [Workbench] Make it possible to share project with other users I can't see
I would like to share a project containing private data with another person.
Potential solutions?
1) Private shar...
Nancy Ouyang
10:10 pm Bug #6834 (Closed): How to add users to a newly created group?
As admin, I can create groups, however I cannot figure out how to add users to those groups. Maybe a workbench GUI wo... Nancy Ouyang
09:43 pm Revision 70ce2cc8 (arvados): Fix stale "Install Ruby and Bundler" links.
Now that these instructions are an include, include them everywhere
they're referenced. No issue #.
Brett Smith
09:39 pm Bug #6833 (Resolved): [FUSE] arv-mount caches manifests too long, ends up using expired Keep sign...
Caught a VM getting 401 like this:... Tom Clegg
09:34 pm Revision 449c9871 (arvados): RVM setup instructions tell you to install Bundler after activation.
On hosts that do not have any Ruby installed, the previous
instructions won't work, because the `gem` tool is only av...
Brett Smith
09:29 pm Bug #6590: [Documentation] Improve documentation of API server configuration variables
Reviewing commit:415ecc4.
* Can you explain to me what's going on with @hardcoded_api_tokens.rb.example@?
* Pleas...
Brett Smith
07:31 pm Bug #6590 (In Progress): [Documentation] Improve documentation of API server configuration variables
Peter Amstutz
08:31 pm Task #6832 (Resolved): Add nginx instructions and sample configuration
Brett Smith
08:31 pm Bug #6676 (New): [Documentation] Fully document the SSO installation process
Reviewing commit:8e74a5f. Most of this is just little grammar stuff, and I know you're not responsible for some of i... Brett Smith
07:05 pm Bug #6676 (In Progress): [Documentation] Fully document the SSO installation process
Peter Amstutz
07:05 pm Bug #6676: [Documentation] Fully document the SSO installation process
Brett Smith wrote:
> Comments on commit:5ac198c8. I started a Docker container from debian:jessie and followed inst...
Peter Amstutz
02:53 pm Bug #6676: [Documentation] Fully document the SSO installation process
Comments on commit:5ac198c8. I started a Docker container from debian:jessie and followed instructions from there. ... Brett Smith
08:16 pm Revision 8a4463cb (arvados): 6663: Document git setup.
Tom Clegg
08:15 pm Bug #6592 (Resolved): [Crunch] crunch-job should handle cleanup step failures like install step f...
Applied in changeset arvados|commit:6dff0705fd3b4e0acde7bdf5821ef115ba74099b. Tom Clegg
07:34 pm Bug #6592: [Crunch] crunch-job should handle cleanup step failures like install step failures
CLI tests using Perl pass for me now (yes!), the rest of it looks good to me. Peter Amstutz
07:32 pm Bug #6592 (In Progress): [Crunch] crunch-job should handle cleanup step failures like install ste...
Peter Amstutz
04:01 pm Bug #6592: [Crunch] crunch-job should handle cleanup step failures like install step failures
Updated to install the Perl SDK and check its dependencies in run-tests.sh, instead of loading Arvados.pm from the so... Tom Clegg
07:38 pm Story #6476: [Workbench] actions#show should be implemented without requiring an API token
From IRC:
tom
3:20 I think the test would be
3:20 1. enable anonymous config
3:20 2. take uuid of a publicly ac...
Radhika Chippada
07:36 pm Story #6476 (In Progress): [Workbench] actions#show should be implemented without requiring an AP...
Manoj Malipeddu
07:38 pm Revision 7034b1b4 (arvados-dev): Merge branch '6592-test-perl' refs #6592
Tom Clegg
07:38 pm Revision 7034b1b4 (arvados): Merge branch '6592-test-perl' refs #6592
Tom Clegg
07:37 pm Revision 6dff0705 (arvados): Merge branch '6592-retry-if-cleanupfail' closes #6592
Tom Clegg
07:33 pm Task #6733 (Resolved): Review 6592-retry-if-cleanupfail
Peter Amstutz
07:32 pm Bug #6663 (In Progress): [Documentation] Document git repository setup
Peter Amstutz
02:05 pm Bug #6663: [Documentation] Document git repository setup
Indeed. Updated with explanatory comments, and fixed a few vague/misleading variable names (which were already my fau... Tom Clegg
07:17 pm Task #6726 (Resolved): Put update-gitolite script in a more appropriate place
Tom Clegg
07:16 pm Revision 39fe0413 (arvados): Merge branch '6663-bugfixes' refs #6663
Tom Clegg
07:15 pm Task #6785 (Resolved): Review 6663-bugfixes
Peter Amstutz
07:10 pm Revision 415ecc43 (arvados): 6590: Rename database.yml.sample to database.yml.example so be consi...
between application.yml.example and database.yml.example Peter Amstutz
07:09 pm Story #6830 (Resolved): [API] [keep-balance] Option to return unsigned manifests from collections...
In certain use cases (notably keep-balance) it is necessary to retrieve a collection's manifest_text, but not necessa... Radhika Chippada
07:02 pm Revision 8e74a5f2 (arvados): 6676: Reorganize instructions a bit more. Fix createdb instructions...
rendering. Fix typo in Google+ authentication setup. Peter Amstutz
06:59 pm Revision 68879028 (sso-provider): Improve documentation of configuration defaults and examples. r...
Peter Amstutz
06:58 pm Bug #6827 (Resolved): arvados-git-httpd prints plaintext user passwords to its output
sudo -u git arvados-git-httpd -address=:9001 -git-command="$(which git)" -repo-root=/opt/arvados_git/repositories
20...
Joshua Randall
06:51 pm Revision 9b3223e5 (arvados): 6414: When viewing a public project, the text "Public Projects" now
links to the main public projects page. Added a test to verify link
is there.
Manoj Malipeddu
06:30 pm Revision f871d579 (arvados): 6414: Anonymous users can click the text Public Projects to browse
all public projects. Added a test to verify if the link exists. Manoj Malipeddu
05:23 pm Revision 157a1746 (arvados): 6590: Reorganize application.default.yml. Improve documentation for...
API server configuration. Remove obsolete hardcoded api tokens setting. Peter Amstutz
05:23 pm Task #6721 (In Progress): Review 6590-api-config-docs
Peter Amstutz
05:23 pm Task #6720 (Resolved): Write
Peter Amstutz
04:11 pm Task #6720 (In Progress): Write
Peter Amstutz
03:56 pm Revision 52c8fd37 (arvados): Do not mess with PERLLIB in crunch-job tests; let run-tests.sh do that.
Replace this with mocking crunch-refresh-trigger, so crunchenv still
has a reason to live.
Tom Clegg
03:55 pm Revision 8797ab13 (arvados): 6592: List runtime dependencies for Perl SDK.
Tom Clegg
03:44 pm Revision eafd0331 (arvados): 6592: Build and install the Perl SDK so sdk/cli tests can use it.
Tom Clegg
03:44 pm Revision eafd0331 (arvados-dev): 6592: Build and install the Perl SDK so sdk/cli tests can use it.
Tom Clegg
02:04 pm Revision 8699ba0b (arvados): 6663: Admins and repository owners can_manage, not just can_write
(even though that might not translate to any additional functions with
the current gitolite config).
Tom Clegg
02:03 pm Story #6794 (Duplicate): users git repository should not be empty.
Duplicates #6027. Brett Smith
02:02 pm Story #6794 (Duplicate): users git repository should not be empty.
when I started my first pipeline I clone my nico/nico repository but it came up empty
it took me 30 minutes to ...
Nico César
01:51 am Task #6487 (In Progress): Summarize invalid manifests present in production servers' databases
Radhika Chippada
01:50 am Task #6486 (In Progress): Review production logs to confirm no real clients are submitting any in...
Radhika Chippada

07/29/2015

09:35 pm Revision 747e22c9 (arvados): 6663: Add explanatory comments and fix some unhelpful variable names.
Tom Clegg
09:10 pm Revision 00f6df4a (arvados): 6588: Removed manage account button and updated tests and links.
Manoj Malipeddu
08:54 pm Story #6277: [API] Make manifest format validation more strict, to make "munge" methods simpler a...
I did a:... Nico César
08:43 pm Revision ee4cd856 (arvados): 6157: Explain how choice of hostnames relates to slurm and arvados.
Tom Clegg
08:31 pm Task #6733 (In Progress): Review 6592-retry-if-cleanupfail
Peter Amstutz
08:14 pm Bug #6663: [Documentation] Document git repository setup
Comments on 6663-bugfixes:
* In @RepositoriesController#get_all_permissions@ it looks like if a user is a member o...
Peter Amstutz
07:29 pm Bug #6663: [Documentation] Document git repository setup
Peter Amstutz wrote:
> I'm getting API server test failures?
>
> [...]
Went away after cleaning up my applicat...
Peter Amstutz
06:26 pm Bug #6663: [Documentation] Document git repository setup
I'm getting API server test failures?... Peter Amstutz
02:32 pm Bug #6663: [Documentation] Document git repository setup
6663-bugfixes (commit:7019bc98) has a few bugfixes that are needed to make the "set up arvados.git" part work sensibly. Tom Clegg
07:27 pm Task #6738 (Resolved): Test case
Tom Clegg
05:49 pm Task #6738 (In Progress): Test case
Tom Clegg
07:27 pm Bug #6592: [Crunch] crunch-job should handle cleanup step failures like install step failures
Additional changes in 6592-retry-if-cleanupfail besides the obvious thing:
* Use @set -o pipefail@ for the @mount | ...
Tom Clegg
07:12 pm Revision a3d4fc92 (arvados): 6592: Add crunch-job integration tests.
Tom Clegg
06:48 pm Revision eba475a9 (arvados): 6592: Exit RETRY_UNLOCKED if clean-work-dirs phase fails.
Also use "bash -o pipefail" so cleanup fails if mount or awk fails. Tom Clegg
06:46 pm Revision ec752f92 (arvados): 6592: Do not overload $Job temporarily.
Fixes failure during croak/cleanup, which assumes Job is either undef
or a real Job.
Tom Clegg
06:44 pm Revision db66ff7c (arvados): 6592: 4534: Re-enable integration tests, now that run-tests.sh bring...
Tom Clegg
06:38 pm Task #6791 (Resolved): Review documentation updates: branch 6588-documentation
Radhika Chippada
06:37 pm Task #6696 (Resolved): Review UI design mocks
Manoj Malipeddu
06:37 pm Task #6697 (In Progress): Code UI after design review
Manoj Malipeddu
06:36 pm Task #6695 (Resolved): Mock up specified UI
Manoj Malipeddu
06:34 pm Task #6732 (Resolved): Review branch 6657-no-git-in-arv-copy
Radhika Chippada
06:34 pm Task #6680 (Resolved): Document the requirement to install git in the arv-copy user guide
Radhika Chippada
06:33 pm Task #6727 (Resolved): Review branch: 6602-job-runtime-display
Radhika Chippada
06:25 pm Revision cda68ba8 (arvados): 6588: Added templates for new routes.
Manoj Malipeddu
06:24 pm Bug #6790 (New): Missing collections.
the collections:
https://workbench.su92l.arvadosapi.com/collections/d5f8f1d3491fe73c734b55a2659d7370+83
https://w...
Nico César
06:13 pm Revision 017d19d3 (arvados): Merge branch 'master' into 6588-split-manage-account
Manoj Malipeddu
06:12 pm Task #6789 (In Progress): Remove manage account button
Manoj Malipeddu
06:11 pm Task #6789 (Resolved): Remove manage account button
Manoj Malipeddu
06:10 pm Bug #6657 (Resolved): [SDKs] arv-copy has an unhelpful error message when `git` command is not av...
Applied in changeset arvados|commit:ccf30f40f46ea450d7ab3766f0923b486a7450d3. Radhika Chippada
06:05 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
Looks good to me. Peter Amstutz
06:10 pm Bug #6602 (Resolved): [Workbench] Pipeline components tab preloads all tasks; times out for jobs ...
Applied in changeset arvados|commit:7d5d40c55d2a38b12e810f3b9d3e168ee434cbd2. Radhika Chippada
06:02 pm Bug #6602: [Workbench] Pipeline components tab preloads all tasks; times out for jobs with many t...
Thank you, I appreciate the change.
The rest of it looks good to me.
Peter Amstutz
05:58 pm Bug #6602: [Workbench] Pipeline components tab preloads all tasks; times out for jobs with many t...
commit:5058d1cbdbde801a2cf7e303d83e1a626015afdd
* Removed the render_runtime_compact method
* Used render_runti...
Radhika Chippada
05:24 pm Bug #6602: [Workbench] Pipeline components tab preloads all tasks; times out for jobs with many t...
Regarding:
> Based on IRC conversation, render_runtime() should be tweaked to round off to two significant places....
Radhika Chippada
03:43 pm Bug #6602: [Workbench] Pipeline components tab preloads all tasks; times out for jobs with many t...
Instead of using @render_runtime_compact@ please use @render_runtime(duration, false)@, the second parameter of @rend... Peter Amstutz
06:06 pm Revision ccf30f40 (arvados): closes #6657
Merge branch '6657-no-git-in-arv-copy' Radhika Chippada
06:05 pm Revision 21f8e365 (arvados): Merge branch 'master' into 6657-no-git-in-arv-copy
Radhika Chippada
06:05 pm Revision 7d5d40c5 (arvados): closes #6602
Merge branch '6602-job-runtime-display' Radhika Chippada
06:02 pm Story #6588: [Workbench] UX - webshell login button placement
I did not want to edit the admin menu routes as part of this story so i just created 4 new routes. Manoj Malipeddu
05:46 pm Story #6588: [Workbench] UX - webshell login button placement
In commit:cda68ba838b2595c631231a08a8e3b3ea03d2c7f
Changed links to use new routes, modified text in notification ...
Manoj Malipeddu
03:43 pm Story #6588: [Workbench] UX - webshell login button placement
The admin-only "list all authorized_keys" page and the new "manage my keys" page should each have its own route.
I...
Tom Clegg
05:49 pm Task #6748 (Resolved): Exit RETRY_UNLOCKED if cleanup fails
Tom Clegg
03:51 pm Task #6748 (In Progress): Exit RETRY_UNLOCKED if cleanup fails
Tom Clegg
05:47 pm Revision 5058d1cb (arvados): 6602: enhance render_runtime method to display seconds when days, ho...
Radhika Chippada
05:44 pm Revision a94ec93d (arvados): 6588: Changed links to use routes and changed tests to match the
routes. Manoj Malipeddu
05:41 pm Task #6785 (In Progress): Review 6663-bugfixes
Peter Amstutz
02:33 pm Task #6785 (Resolved): Review 6663-bugfixes
Tom Clegg
05:33 pm Revision 06d6b29b (arvados): 6602: remove render_runtime_compact; instead use render_runtime with...
Radhika Chippada
04:55 pm Revision 1e613457 (arvados): 6588: update user guide to refer to the updated user settings menu i...
Radhika Chippada
03:04 pm Task #6699 (In Progress): Update documentation
Radhika Chippada
02:29 pm Revision a53880a2 (arvados): 6663: Document git setup.
Tom Clegg
02:29 pm Revision 7019bc98 (arvados): 6663: Fix repository permissions.
Users with is_active==false (except anonymous_user) are not listed by
get_all_permissions.
A repository that is shar...
Tom Clegg
02:29 pm Revision 67813302 (arvados): 6663: Fix "duplicate public_key" test: OK if the key being updated h...
Tom Clegg
02:24 pm Revision 42b24c29 (arvados): 6663: Document git setup.
Tom Clegg
02:24 pm Revision 52cf70df (arvados): 6663: Fix repository permissions.
Users with is_active==false (except anonymous_user) are not listed by
get_all_permissions.
A repository that is shar...
Tom Clegg
02:24 pm Revision 9fd9565e (arvados): 6663: Fix using default owner_uuid in repositories#create. refs #6652
Tom Clegg
02:24 pm Revision bf8ec1dd (arvados): 6663: Fix "duplicate public_key" test: OK if the key being updated h...
Tom Clegg
12:06 pm Revision 3be96c96 (arvados): 6657: refactor git check and reuse.
Radhika Chippada

07/28/2015

10:13 pm Revision b5e687f6 (arvados): 6663: Fix using default owner_uuid in repositories#create. refs #6652
Tom Clegg
10:13 pm Revision 7bb74b61 (arvados): 6663: Fix "duplicate public_key" test: OK if the key being updated h...
Tom Clegg
10:13 pm Revision 7af49bec (arvados): 6663: Document git setup.
Tom Clegg
10:13 pm Revision 3f2ceb31 (arvados): 6663: Fix repository permissions.
Users with is_active==false (except anonymous_user) are not listed by
get_all_permissions.
A repository that is shar...
Tom Clegg
10:08 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
Brett said:
> migrate_jobspec only gets called from copy_git_repos, which only gets called from copy_pipeline_insta...
Radhika Chippada
08:59 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
Radhika Chippada wrote:
> Peter said:
>
> > The check for git needs to happen in copy_pipeline_instance
>
> I ...
Brett Smith
08:54 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
Peter said:
> The check for git needs to happen in copy_pipeline_instance
I implemented this suggestion (update...
Radhika Chippada
08:18 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
Updated both copy_pipeline_instance and copy_pipeline_template methods. Radhika Chippada
08:08 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
Peter Amstutz wrote:
> * The check for git needs to happen in @copy_pipeline_instance()@ before it does anything els...
Brett Smith
07:23 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
Updated accordingly. Thanks. Radhika Chippada
05:46 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
* The check for git needs to happen in @copy_pipeline_instance()@ before it does anything else. It should go before ... Peter Amstutz
04:23 pm Bug #6657 (In Progress): [SDKs] arv-copy has an unhelpful error message when `git` command is not...
Radhika Chippada
04:07 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
commit:3282d76febc482aab302a44bf594bcf9591ff868
arv-copy command and documentation are updated.
Radhika Chippada
09:44 pm Revision 2b7d9f3f (arvados): Merge branch 'master' into 6657-no-git-in-arv-copy
Radhika Chippada
08:43 pm Revision d22b2efd (arvados): Hotfix for test, transform "/dev/stdin" to "-" in arv-put refs #6681
Peter Amstutz
08:03 pm Task #6727 (In Progress): Review branch: 6602-job-runtime-display
Peter Amstutz
08:03 pm Task #6710 (Resolved): Review 6681-arv-put-pipe
Peter Amstutz
08:03 pm Task #6105 (Resolved): Review 5990-arv-run-default-runtime
Peter Amstutz
07:56 pm Revision 6152230e (arvados): Hotfix, inode cache find() returns list instead of single item now. ...
Peter Amstutz
07:55 pm Story #6588: [Workbench] UX - webshell login button placement
In commit:fc8a283968b08b152d57a24d2c5711c876a3b379:
Added tests to user_manage_account_test and modified tests in ...
Manoj Malipeddu
03:20 pm Story #6588: [Workbench] UX - webshell login button placement
In commit:da56d26d09a6b315bdb93aed4473310b939e1bd7:
Added new pages in notifications menu, and added a test for th...
Manoj Malipeddu
07:51 pm Revision fc8a2839 (arvados): 6588: Added tests for new pages and modified existing tests to not use
manage account page. Manoj Malipeddu
07:36 pm Revision ec640346 (arvados): 6657: copy_pipeline_template method also updated to check git exist...
Radhika Chippada
07:28 pm Revision 23d0c610 (arvados): Merge branch 'master' into 6657-no-git-in-arv-copy
Radhika Chippada
07:25 pm Bug #6681 (Resolved): [SDK] arv-put fails with invalid seek when input is piped in
Applied in changeset arvados|commit:ff24bb94fdfc9dad61821aef56898e2c196c0aea. Peter Amstutz
07:18 pm Bug #6681: [SDK] arv-put fails with invalid seek when input is piped in
Peter Amstutz wrote:
> Nico Cesar wrote:
> > reviewing 229773c2aa3ddc798ae4eb1eff62f8f77db85391
> >
> > there is...
Peter Amstutz
05:35 pm Bug #6681: [SDK] arv-put fails with invalid seek when input is piped in
Nico Cesar wrote:
> reviewing 229773c2aa3ddc798ae4eb1eff62f8f77db85391
>
> there is a easy way to mess this aroun...
Peter Amstutz
07:21 pm Revision ff24bb94 (arvados): Merge branch '6681-arv-put-pipe' closes #6681
Peter Amstutz
07:15 pm Bug #6643 (Resolved): [FUSE] Crash on del self._by_uuid[obj.cache_uuid]
Applied in changeset arvados|commit:ed5230f0e823445f56e7d6940b6fb178e328718b. Peter Amstutz
07:10 pm Bug #6643: [FUSE] Crash on del self._by_uuid[obj.cache_uuid]
ok .. my tests pass... but I was not able to really test it on my machine.
we should merge and deploy and test it ...
Nico César
05:53 pm Bug #6643: [FUSE] Crash on del self._by_uuid[obj.cache_uuid]
Nico Cesar wrote:
> reviewing 119d87107846d77274fdaa52dc8cdadd2a7b9765
>
>
> [...]
>
> can be changed to
...
Peter Amstutz
07:13 pm Task #6718 (Resolved): Review 6643-fuse-del-crash
Nico César
07:09 pm Revision ed5230f0 (arvados): Merge branch '6643-fuse-del-crash' closes #6643
Peter Amstutz
06:56 pm Story #6784 (New): [Keep] Write performance tests
Brett Smith
06:56 pm Story #6783 (New): [Performance] Compare Collection performance benchmarks across components
We now have performance numbers for common collection operations in the following components:
* API server
* Pyth...
Brett Smith
06:28 pm Story #6260: [Keep] Integration test between data manager, API and keepstore.
Two points per discussion. Brett Smith
06:00 pm Revision 0c447acb (arvados): 6657: check git availability only when recursive copy is being used.
Radhika Chippada
05:48 pm Revision e39e11d5 (arvados): Merge branch 'master' into 6657-no-git-in-arv-copy
Radhika Chippada
05:41 pm Task #6732 (In Progress): Review branch 6657-no-git-in-arv-copy
Peter Amstutz
05:34 pm Revision 20462439 (arvados): 6681: Disallow additional files on command line when uploading data ...
Peter Amstutz
05:34 pm Revision 199e8843 (arvados): 6681: Disallow additional files on command line when uploading from ...
Peter Amstutz
05:33 pm Feature #6782 (New): [API] [Workbench] Generate debconf template from config yaml
This is part of enabling "apt-get install arvados-api-server" to prompt the sysadmin (or automated process) for value... Tom Clegg
05:17 pm Bug #6702: [Node Manager] Retries forever when a node creation request times out, even though the...
We just saw this again, except the original error was different: Google responded, "The zone 'projects/projname/zones... Brett Smith
05:15 pm Revision 5ac198c8 (arvados): Merge branch 'master' into 6676-document-sso
Conflicts:
doc/install/install-sso.html.textile.liquid
Peter Amstutz
05:14 pm Task #6715 (In Progress): Review 6676-document-sso
Peter Amstutz
05:14 pm Task #6716 (Resolved): Write
Peter Amstutz
05:05 pm Story #6781 (Resolved): [Documentation] Document user shell account creation script
Our shell servers run a regular cron job to add Unix user accounts for users who have permission to log in to the cor... Brett Smith
04:29 pm Revision 004bafda (arvados): Fix duplicated id in SSO install documentation.
No issue #. Brett Smith
04:28 pm Revision c2147347 (arvados): 6691: Add reference to Ubuntu trusty in Ruby install instructions.
I confirmed that these packages are all installable on Ubuntu 14.04.
Refs #6691.
Brett Smith
04:25 pm Task #6724 (Resolved): Review 6705-fix-websockets-replay
Radhika Chippada
04:20 pm Bug #6780 (New): [git] "git clone https://..." with a bogus token should respond 4xx, not 5xx
Currently, as verified by tests, arvados-git-httpd returns 500 when the servers are all working perfectly but the cli... Tom Clegg
04:06 pm Task #6680 (In Progress): Document the requirement to install git in the arv-copy user guide
Radhika Chippada
04:05 pm Revision 56d94b28 (arvados): Merge branch 'master' into 6657-no-git-in-arv-copy
Radhika Chippada
04:05 pm Revision 3282d76f (arvados): 6657: check git is installed in arv-copy
Radhika Chippada
03:16 pm Revision da56d26d (arvados): 6588: Added new pages in notifications menu for repositories, virtua...
current token and ssh keys. Added a test for these new pages. Manoj Malipeddu
02:07 pm Bug #6663: [Documentation] Document git repository setup
Work in progress makes some changes to the recommended/default config:
* Install gitolite in @~git == /var/lib/arvad...
Tom Clegg

07/27/2015

09:45 pm Task #6694 (Resolved): Document our trusty packages in the manual installation guide
Applied in changeset arvados|commit:c8f0866051391c9932a8d39bbd3cacb83e60c20e. Brett Smith
09:24 pm Task #6694 (In Progress): Document our trusty packages in the manual installation guide
Brett Smith
09:45 pm Story #6691 (Resolved): [Deployment] Build packages for Ubuntu 14.04 ("trusty")
Applied in changeset arvados|commit:c8f0866051391c9932a8d39bbd3cacb83e60c20e. Brett Smith
02:42 am Story #6691: [Deployment] Build packages for Ubuntu 14.04 ("trusty")
Brett Smith wrote:
> Tom Clegg wrote:
> > For @test -d x || mkdir x@ why not just @mkdir -p x@?
>
> Because @mkd...
Tom Clegg
09:38 pm Revision c8f08660 (arvados): 6691: Add Ubuntu trusty packages to our install guide.
Closes #6691, #6694. Brett Smith
09:24 pm Task #6763 (Resolved): Add any necessary trusty configuration to freight
Brett Smith
08:57 pm Revision 607c3ded (arvados): 6676: Add note about git and curl. Describe how to run passenger st...
Peter Amstutz
08:26 pm Story #6774: [Documentation] Better presentation/separation of install prerequisites
Related idea, when we have instructions for several different linux distributions, we could use a tabbed view to swit... Peter Amstutz
04:08 pm Story #6774 (New): [Documentation] Better presentation/separation of install prerequisites
The install documentation now includes sections on how to install prerequisites such as Ruby and PostgreSQL. These s... Peter Amstutz
08:21 pm Revision c0893f60 (arvados): 6676: Working through polishing SSO install documentation.
Peter Amstutz
08:13 pm Revision 849987da (sso-provider): Fix encoding error by using template0 explicitly. refs #6676
"PG::InvalidParameterValue: ERROR: new encoding (UTF8) is incompatible with the encoding of the template database (S... Peter Amstutz
07:44 pm Bug #6602: [Workbench] Pipeline components tab preloads all tasks; times out for jobs with many t...
From IRC:
tom: OK. How about: This pipeline took 10.8 hours to run and used 4.52 days of ...
tom: I think "node...
Radhika Chippada
07:34 pm Revision 92c6e09d (sso-provider): Put sqlite3 back in a conditional group. refs #6676
Peter Amstutz
07:20 pm Revision fd1c8009 (arvados): Merge branch 'master' into 6602-job-runtime-display
Radhika Chippada
07:19 pm Revision 6d2811a2 (arvados): 6602: update test assertion to match new format
Radhika Chippada
06:50 pm Bug #6776 (Duplicate): arv-put failed at uploading log file
This is the same root issue as #6775. Brett Smith
05:11 pm Bug #6776 (Duplicate): arv-put failed at uploading log file
From https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-pyuiujxx8dm33x2
Looks like logging timed out but ...
Bryan Cosca
06:49 pm Bug #6775 (Closed): Lost blocks on qr1hi?
Brett Smith
06:49 pm Bug #6775: Lost blocks on qr1hi?
This morning we built Python Debian packages that had a bug: their #! line referred to a Python interpreter that only... Brett Smith
05:10 pm Bug #6775 (Closed): Lost blocks on qr1hi?
From https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-huj6xpq3d27mndn#Log
2015-07-27_15:09:55 qr1hi-8i9s...
Bryan Cosca
06:42 pm Revision 00d0e607 (sso-provider): Install passenger gem refs #6676
Peter Amstutz
06:31 pm Revision c86a3350 (arvados): 6602: display runtime using the formula (min_nodes * (finished_at - ...
Radhika Chippada
06:00 pm Task #6728 (In Progress): Document how to install a full arv-git-httpd repo hosting system (that ...
Tom Clegg
05:48 pm Story #6588: [Workbench] UX - webshell login button placement
A few minor tweaks, and a realization I asked for something I shouldn't have asked for:
On "current_token_updated"...
Tom Clegg
05:44 pm Revision 3d6dba95 (sso-provider): Don't install sqlite3 gem, only support postgres. refs #6676
Peter Amstutz
05:40 pm Bug #6778 (Resolved): [Documentation] Install docs sneak 'git' install as part of PostgreSQL inst...
Applied in changeset arvados|commit:76c38b6bf63fa7329abb135a40710cbdbea18d44. Brett Smith
05:30 pm Bug #6778 (Resolved): [Documentation] Install docs sneak 'git' install as part of PostgreSQL inst...
Peter Amstutz
05:38 pm Revision 76c38b6b (arvados): 6778: Remove git install from PostgreSQL install instructions.
Closes #6778. Brett Smith
05:12 pm Story #6777 (Rejected): [Documentation] recommend ruby2.1 package on debian 8
Debian 8 (Jessie) ships with Ruby 2.1.5. The install documentation should recommend the Ruby package instead of buil... Peter Amstutz
05:07 pm Revision 0f0108a6 (arvados): Merge branch '6451-websockets-invalid-input' closes #6451
Peter Amstutz
04:59 pm Revision aa924bec (arvados): Merge branch 'master' into 6602-job-runtime-display
Radhika Chippada
04:15 pm Bug #5990 (Resolved): [SDKs] arv-run defaults to using arvados/jobs, without checking that it exi...
Applied in changeset arvados|commit:e69333d856baabf8bbbc27602850dcfe86309d23. Peter Amstutz
02:44 pm Bug #5990: [SDKs] arv-run defaults to using arvados/jobs, without checking that it exists or is r...
LGTM Nico César
02:28 pm Bug #5990: [SDKs] arv-run defaults to using arvados/jobs, without checking that it exists or is r...
Nico Cesar wrote:
> I see no unittest for this. Is because they are too hard to reproduce? I did a bunch of greps...
Peter Amstutz
04:12 pm Revision e69333d8 (arvados): Merge branch '5990-arv-run-default-runtime' closes #5990
Peter Amstutz
03:31 pm Bug #6643: [FUSE] Crash on del self._by_uuid[obj.cache_uuid]
reviewing 119d87107846d77274fdaa52dc8cdadd2a7b9765 ... Nico César
03:15 pm Bug #6681: [SDK] arv-put fails with invalid seek when input is piped in
also sdk/cli/test/test_arv-put.rb should be updated ... writing a simple "hello" from stdin and then checking the... Nico César
03:01 pm Bug #6681: [SDK] arv-put fails with invalid seek when input is piped in
reviewing 229773c2aa3ddc798ae4eb1eff62f8f77db85391
there is a easy way to mess this around.
having a stdin fil...
Nico César
02:50 pm Revision 82780d42 (arvados): 5824: fixup keepdl docs.
Tom Clegg
02:50 pm Revision d44585be (arvados-dev): Rebuild Python packages before building their distro packages.
Without this, built scripts lay around between builds, with shebang
lines for the first distro they were built for. ...
Brett Smith
02:50 pm Revision d44585be (arvados): Rebuild Python packages before building their distro packages.
Without this, built scripts lay around between builds, with shebang
lines for the first distro they were built for. ...
Brett Smith
02:50 pm Revision 9a02abe8 (arvados): 5824: fixup sdk
Tom Clegg
02:40 pm Bug #6593 (Resolved): [SDKs] arv-get should use the stdout FD directly, rather than opening /dev/...
Applied in changeset arvados|commit:66af20886def83f6a20cc1e6587de00cbf2f8b59. Peter Amstutz
02:15 pm Bug #6593: [SDKs] arv-get should use the stdout FD directly, rather than opening /dev/stdout
Peter Amstutz wrote:
> Brett Smith wrote:
> > * This bug predates your branch, but I noticed it while reading: this...
Brett Smith
01:44 pm Bug #6593: [SDKs] arv-get should use the stdout FD directly, rather than opening /dev/stdout
Brett Smith wrote:
> Reviewing commit:ce12890
>
> * Please update where the command line option help strings refe...
Peter Amstutz
02:38 pm Task #6712 (Resolved): Review 6593-arv-get-stdout
Peter Amstutz
02:38 pm Revision 66af2088 (arvados): Merge branch '6593-arv-get-stdout' closes #6593
Peter Amstutz
02:37 pm Revision 4a5adfa0 (arvados): 6593: Typo fix in KeyboardInterrupt handling.
Peter Amstutz
02:25 pm Revision a71c0bc8 (arvados): 5990: Update arv-run subcommand cli doc.
Peter Amstutz
02:06 pm Revision f4180d15 (arvados): 6451: Refactor tests slightly to call subscribe_test() in two places.
Peter Amstutz
01:51 pm Revision 171ac077 (arvados): 6451: Validate that 500 error is returned to client. Tweak code com...
Peter Amstutz
01:45 pm Revision 753c1446 (arvados): 6593: Change docstring references from /dev/stdout to just "stdout"....
to clean up open files on KeyboardInterrupt. Peter Amstutz
01:28 pm Task #6718 (In Progress): Review 6643-fuse-del-crash
Peter Amstutz
01:27 pm Task #6731 (Resolved): Review 6706-fuse-forget-crash
Peter Amstutz
01:20 pm Revision 310b5254 (arvados): Fix parameter ordering for minor change in cwltool command line sema...
Peter Amstutz
01:20 pm Revision 310b5254 (arvados-dev): Fix parameter ordering for minor change in cwltool command line ...
Peter Amstutz
01:15 pm Bug #6706 (Resolved): [FUSE] Crash in forget()
Applied in changeset arvados|commit:3e6ba5fa5f225c8aa431ce9a2796369c1e1dda2d. Peter Amstutz
01:13 pm Revision 3e6ba5fa (arvados): Merge branch '6706-fuse-forget-crash' closes #6706
Peter Amstutz
01:13 pm Revision aeb481ad (arvados): 6706: Add docstrings to close()
Peter Amstutz
01:11 pm Revision 130cbc5c (arvados): 6643: Support associating uuid with multiple inodes to fix double-re...
Peter Amstutz
01:00 pm Task #6742 (Resolved): Review arvados-dev branch 6691-trusty-packages-wip
Applied in changeset arvados-dev|commit:cc2a6672fef9bb825b2fa4b8482f4306cae491a1. Brett Smith
12:55 pm Revision cc2a6672 (arvados-dev): Merge branch '6691-trusty-packages-wip'
Refs #6691. Closes #6742. Brett Smith
12:55 pm Revision cc2a6672 (arvados): Merge branch '6691-trusty-packages-wip'
Refs #6691. Closes #6742. Brett Smith
12:54 pm Revision ae548f25 (arvados-dev): 6691: Build and ship packages for Ubuntu 14.04.
Brett Smith
12:54 pm Revision ae548f25 (arvados): 6691: Build and ship packages for Ubuntu 14.04.
Brett Smith
11:22 am Revision 18277495 (arvados): 5824: more keepdl vhost.
Tom Clegg
11:21 am Revision cddb2c4a (arvados): 5824: SDK fixup
Tom Clegg
 

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