Activity

From 07/18/2017 to 08/16/2017

08/16/2017

10:18 pm Revision 3a356c4d (arvados): 12081: Retry "update" API when called via ResourceProxy->save.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
09:57 pm Bug #12134 (Resolved): [arv-mount] Fix test deadlock by using new llfuse in test suite
Peter's patch for the thread-cancel bug has been merged upstream, but there is no new release yet.
Instead of wait...
Tom Clegg
09:19 pm Revision fdec93eb (arvados): 12123: Don't expect properties.new_attributes.components in events.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
08:17 pm Revision 294b9ea0 (arvados): 12033: arvbox: make sure to run rake npm:install
refs #12033
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege
08:15 pm Bug #12122 (Resolved): workbench shouldn't error out when config files are missing if RAILS_GROUP...
Applied in changeset arvados|commit:6f2ce945ee9ad422c3b28fb6433e22d816dddfe1. Anonymous
07:39 pm Bug #12122: workbench shouldn't error out when config files are missing if RAILS_GROUP includes '...
The patch works but.... that entire rake task doesn't exist:... Ward Vandewege
05:06 pm Bug #12122 (Resolved): workbench shouldn't error out when config files are missing if RAILS_GROUP...
Ward Vandewege
08:13 pm Revision 6f2ce945 (arvados): Merge branch '12122-rails-groups-assets-fix'
closes #12122
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege
08:10 pm Revision 4097662d (arvados): For now remove the call to rake npm:install from arvbox, it depends on
the multisite search branch (12033-multisite-search) and will be
included when that is merged.
refs #12122
Arvados-...
Ward Vandewege
07:58 pm Task #10379 (Closed): Review 10359-crunchstat-summary-serial
Tom Clegg
07:56 pm Task #12131 (Resolved): Review 12032-project-trash
Peter Amstutz
07:55 pm Task #12128 (Resolved): Review 12107-faster-git
Lucas Di Pentima
07:38 pm Task #12126 (Resolved): API server support for trash
Peter Amstutz
07:36 pm Story #12125 (In Progress): Client support for deleting projects
Peter Amstutz
07:09 pm Bug #6651: "This website is under heavy load" error makes a parsing error
this is a duplicate Nico César
05:07 pm Revision 9a26fa41 (arvados): Workbench shouldn't error out when config files are missing if
RAILS_GROUP is set and includes 'assets'.
refs #12122
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@ver...
Ward Vandewege
05:06 pm Revision 0c356edf (arvados): Merge branch '11898-no-distinct'
refs #11898
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
05:05 pm Revision 9deb1c89 (arvados): 11898: Remove superfluous uniq(&:id) call
Avoids adding DISTINCT to SQL query, which causes Postgres to do
expensive things.
Arvados-DCO-1.1-Signed-off-by: To...
Tom Clegg
05:04 pm Task #12066 (In Progress): Review 12055-nodemanager-ec2-tags
Peter Amstutz
04:35 pm Story #8937 (Resolved): [SDKs] Write integration test for when arv-put resumes from a cache with ...
Applied in changeset arvados|commit:51fe3482a5253d054e838fb1dcf3982f79650cee. Anonymous
03:10 pm Story #8937: [SDKs] Write integration test for when arv-put resumes from a cache with expired acc...
LGTM Peter Amstutz
04:31 pm Task #11894 (In Progress): Review 11309-crunchstat-summary-containers
Lucas Di Pentima
04:29 pm Revision 51fe3482 (arvados): Merge branch '8937-arvput-cached-tokens'
Closes #8937
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima
04:27 pm Bug #12055: [node manager] ec2 set tags on create
Updated libcloud code at commit 79ec53df - branch @apache-libcloud-0.20.2.dev4@
Updated nodemanager at commit:f2019e...
Lucas Di Pentima
03:53 pm Bug #12055: [node manager] ec2 set tags on create
I think you can do this in a one liner:... Peter Amstutz
03:42 pm Bug #12055: [node manager] ec2 set tags on create
Aha, here's an example raw request:... Peter Amstutz
03:27 pm Bug #12055: [node manager] ec2 set tags on create
I'm not sure this is correct:... Peter Amstutz
04:01 am Bug #12055: [node manager] ec2 set tags on create
Updates at commit:f5f91a293
Test run: https://ci.curoverse.com/job/developer-run-tests/416/
* Updated our @libclo...
Lucas Di Pentima
04:22 pm Revision f2019e70 (arvados): 12055: Code simplification.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com> Lucas Di Pentima
03:26 pm Revision 09e62332 (arvados): Make it a little more obvious which arvbox docker images are being b...
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege
03:20 pm Revision 74e03b21 (arvados): 12055: Merge branch 'master' into 12055-nodemanager-ec2-tags
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com> Lucas Di Pentima
03:09 pm Task #12006 (Resolved): Review 8937-arvput-cached-tokens
Peter Amstutz
02:54 pm Bug #11850: [CWL] arv:RunInSingleContainer should take max() of ResourceRequirements of substeps
Also need to add... Jiayong Li
02:45 pm Story #11309: [Crunch2] crunchstat-summary --container UUID should summarize container logs
11309-crunchstat-summary-containers @ commit:f04ff34e47cc5ff1e625e9a5c1b1b0cbeb810d8c
Child containers are now sor...
Tom Clegg
02:40 pm Revision f04ff34e (arvados): 11309: Sort containers by request time.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
02:32 pm Revision 6dd863d5 (arvados): 11309: Fix runtime_constraints suggestions for containers.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
03:52 am Revision f5f91a29 (arvados): 12055: Updated fake driver to make integration tests work again.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com> Lucas Di Pentima
01:58 am Revision c3896b7f (arvados): 12055: On EC2 driver, pass the tag list to the node_create call
instead of assigning them after creation.
Updated tests.
Bumped libcloud fork dependency to 0.20.2.dev4, which has th...
Lucas Di Pentima

08/15/2017

10:56 pm Story #11309: [Crunch2] crunchstat-summary --container UUID should summarize container logs
11309-crunchstat-summary-containers @ commit:dc140f2c277a7571669f5bdf492bac6448a0fba0
I added "--container UUID" a...
Tom Clegg
10:50 pm Revision dc140f2c (arvados): 11309: Drop parent container name from labels.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
09:53 pm Story #11167: [Workbench] Remove arv-get file download fallback
"workbench should refuse start if keep-web is not configured" <- that's a bad idea. we have all sort of restarts and... Nico César
08:29 pm Revision cd42a476 (arvados): 11309: Prefix errors with "notice:" or "warning:" to aid parsing.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
08:28 pm Revision 68fee3af (arvados): 11309: Fix parsing and labels. Add --threads option.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
03:26 pm Bug #12087: [arvados-ws] Memory leak
changes have been made in puppet for qr1hi su92l d8kp5 also e51c5 but puppet is disabled, until we have a downtime ... Nico César
03:21 pm Revision 6699c983 (arvados): 11309: 9001: Fix catch-all-exceptions antipattern.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
02:44 pm Story #8937: [SDKs] Write integration test for when arv-put resumes from a cache with expired acc...
Updates at commit:81352ba32
Test run: https://ci.curoverse.com/job/developer-run-tests/414/
Realized that as part...
Lucas Di Pentima
02:37 pm Revision 81352ba3 (arvados): 8937: Token expiration is already being checked, removed cache
validation method and updated integration test.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasg...
Lucas Di Pentima

08/14/2017

08:40 pm Revision 0a4e2d29 (arvados): 11309: Accommodate crunch2 crunchstat log format.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
07:31 pm Revision 67616c47 (arvados): 12033: Fix site status indicators.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
07:23 pm Revision 9f070591 (arvados): 12033: Move classes to global namespace.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:20 pm Revision 78f9bd9e (arvados): arvbox installs nodejs and sets up workbench js assets. refs #12033
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:05 pm Bug #12113: mandatory keep_web configuration missing from workbench install instructions
I see now that it is mentioned much much later in the install guide under http://doc.arvados.org/install/install-keep... Joshua Randall
05:02 pm Bug #12113 (New): mandatory keep_web configuration missing from workbench install instructions
It seems that one of keep_web_url or keep_web_download_url are now mandatory in order for workbench to start, but the... Joshua Randall
01:36 pm Bug #10349: [DOC] add cookbook section with code snippets
I started writing out some code snippits for operating on container requests based on the scripts at https://github.c... Peter Amstutz
01:33 pm Revision efd0ed5f (arvados): 10349: Working on Python code snippits for manipulating container re...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz

08/13/2017

07:32 pm Revision 35568d22 (arvados): 12033: Generalize MultisiteLoader to MergingLoader.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
07:31 pm Revision 06ff9abc (arvados): 12033: MultipageLoader and MultisiteLoader offer the same interface.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:53 pm Revision fb5ecab9 (arvados): 12033: MultipageLoader and MultisiteLoader offer the same interface.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:53 am Revision 77a65bed (arvados): 12033: Fix typo in selector.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:52 am Revision 5b246542 (arvados): 12033: Restore search term and scroll position after navigation.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg

08/11/2017

09:56 pm Revision cf065634 (arvados): 11309: Recognize containers and container requests by UUID infix.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
08:58 pm Story #11309 (In Progress): [Crunch2] crunchstat-summary --container UUID should summarize contai...
Tom Clegg
08:38 pm Story #9668 (Resolved): [Crunch2] [Workbench] Select a Javascript client framework for future dev...
Tom Clegg
08:31 pm Revision 60a39c8b (arvados): Bump cwltool for python-requests dependency fix refs #12100
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
08:02 pm Revision 1d807531 (arvados): 12100: Bump cwltool for python-requests dependency fix
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
07:30 pm Revision 888e08c4 (arvados): 12033: Add top nav link to multisite search.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
06:46 pm Revision c2943635 (arvados): Fix typo.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege
06:05 pm Story #11545 (Resolved): Create a CWL stress test for node manager
Applied in changeset arvados|commit:10402f74ccdae453ae353c389a02c0415adcf1e7. Peter Amstutz
05:58 pm Revision 10402f74 (arvados): Merge branch '11545-stress-test' closes #11545
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:57 pm Task #11757 (Resolved): Review 11545-stress-test
Peter Amstutz
05:46 pm Bug #12107 (Resolved): [API] jobs.create should not do slow git operations
It's typical for jobs.create to take ~6 seconds, with the database only accounting for about 75ms.
Our "copy commi...
Tom Clegg
05:45 pm Revision 3394f8aa (arvados): Update test to reflect slight change in cwltool packing behavior. r...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:43 pm Revision 14edbf1a (arvados): 12033: Fix double slash in href.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
03:40 pm Revision a20ea2d9 (arvados): 12033: Log out and back in to a site without forgetting it.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
03:30 pm Story #8937: [SDKs] Write integration test for when arv-put resumes from a cache with expired acc...
Lucas Di Pentima wrote:
> Updates at commit:7049888ba
> Test run: https://ci.curoverse.com/job/developer-run-tests/...
Peter Amstutz
03:19 pm Bug #10035 (Resolved): [FUSE] Determine why bcl2fastq doesn't work with writable keep mount
This works now & is used in production. Peter Amstutz
03:15 pm Bug #12100 (Resolved): Update cwltool for secondaryFile handling changes
Applied in changeset arvados|commit:33f91bb5a4ed93e9cadf21920526daa53351dbea. Peter Amstutz
03:10 pm Revision 33f91bb5 (arvados): Merge branch '12100-cwltool-update' closes #12100
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:08 pm Revision 6e2df2d9 (arvados): 12100: Bump cwltool for v1.0.2 secondaryFile handling.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
02:05 pm Revision c97e090a (arvados): 12033: Fix logging in from location with non-empty query string.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
02:03 pm Revision 6e1eda9f (arvados): 12033: Ensure current Rails login is always in sessions list.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:23 am Revision 16231ef0 (arvados): 12033: Fix auto scroll after search; acknowledge end of results.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
03:35 am Revision ea9b417b (arvados): 12033: Load more results automatically on scroll.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg

08/10/2017

09:31 pm Story #8937: [SDKs] Write integration test for when arv-put resumes from a cache with expired acc...
Updates at commit:7049888ba
Test run: https://ci.curoverse.com/job/developer-run-tests/413/
Made suggested change...
Lucas Di Pentima
08:01 pm Story #8937: [SDKs] Write integration test for when arv-put resumes from a cache with expired acc...
Looking at _cache_is_valid
* Instead of splitting the manifest into lines, could you use re.MULTILINE to find the ...
Peter Amstutz
09:26 pm Revision 7049888b (arvados): 8937: Refactored _cache_is_valid() to catch specific exceptions. Fixed
related test.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima
08:03 pm Revision 2bef371e (arvados): 8937: Merge branch 'master' into 8937-arvput-cached-tokens
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
07:55 pm Task #12006 (In Progress): Review 8937-arvput-cached-tokens
Peter Amstutz
07:38 pm Revision 7d5ae076 (arvados): 12100: Bump cwltool for v1.0.2 secondaryFile handling.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
07:03 pm Revision a6607cd8 (arvados): 11167: Fixed workbench package building scripts.
Refs #11167
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima
07:01 pm Revision 9ff99b73 (arvados): 12033: Style uuid column.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
06:20 pm Revision 2220f7f5 (arvados): 12033: Extract multisite loader to its own class.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:48 pm Revision 20147574 (arvados): 12033: Add "load more" button.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
02:11 pm Bug #12055 (In Progress): [node manager] ec2 set tags on create
Lucas Di Pentima
01:35 pm Story #11167 (Resolved): [Workbench] Remove arv-get file download fallback
Applied in changeset arvados|commit:d0a4adabafa4d132ab2333338c941acc57ca82fb. Lucas Di Pentima
11:58 am Story #11167: [Workbench] Remove arv-get file download fallback
I've tried removing it (commit:3224524c1a2d6790322448565cb5a16ea0bcb874) and some tests started to fail: https://ci.c... Lucas Di Pentima
01:32 pm Task #11937 (Resolved): Review 11167-wb-remove-arvget
Lucas Di Pentima
01:27 pm Revision d0a4adab (arvados): Merge branch '11167-wb-remove-arvget'
Closes #11167
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima
11:51 am Revision 36b43559 (arvados): 11167: Revert removing ActionController::Live from collections contr...
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima

08/09/2017

11:52 pm Revision 3224524c (arvados): 11167: Removing unnecessary ActionController::Live from collections ...
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
11:49 pm Revision 4c0dadce (arvados): 11167: Merge branch 'master' into 11167-wb-remove-arvget
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
11:47 pm Story #8937: [SDKs] Write integration test for when arv-put resumes from a cache with expired acc...
Updates at commit:7b93dc26e
Test run: https://ci.curoverse.com/job/developer-run-tests/409/
* Updated @arv-put@ c...
Lucas Di Pentima
02:19 pm Story #8937 (In Progress): [SDKs] Write integration test for when arv-put resumes from a cache wi...
Lucas Di Pentima
11:14 pm Revision 7b93dc26 (arvados): 8937: Added cache validation method to arv-put. For now it only
checks that the first signed block's locator is valid.
Added integration test.
Arvados-DCO-1.1-Signed-off-by: Lucas ...
Lucas Di Pentima
10:35 pm Revision 473c95be (arvados): 12033: Merge results from all sites into one table.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
08:37 pm Task #12001 (Resolved): Review 11925-nodemanager-watchdog-test
Peter Amstutz
07:51 pm Bug #12100 (Resolved): Update cwltool for secondaryFile handling changes
Peter Amstutz
07:11 pm Revision 0413abf9 (arvados): Merge branch '11925-nodemanager-watchdog-test' refs #11925
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
06:58 pm Task #12094 (Resolved): Review 12093-cwl-project-uuid
Peter Amstutz
06:21 pm Task #12094 (In Progress): Review 12093-cwl-project-uuid
Tom Clegg
06:12 pm Task #12094 (Resolved): Review 12093-cwl-project-uuid
Peter Amstutz
06:55 pm Bug #12093 (Resolved): arvados-cwl-runner doesn't propogate --project-uuid to submitting container
Applied in changeset arvados|commit:651e87d8d97edebd8d3cd0325dbd15d6dac0cd1c. Peter Amstutz
06:52 pm Bug #12093: arvados-cwl-runner doesn't propogate --project-uuid to submitting container
Tom Clegg wrote:
> LGTM.
>
> A more general comment: The test suite seems heavy on the copy-paste. Why do all the...
Peter Amstutz
06:30 pm Bug #12093: arvados-cwl-runner doesn't propogate --project-uuid to submitting container
LGTM.
A more general comment: The test suite seems heavy on the copy-paste. Why do all these test cases have "exce...
Tom Clegg
05:21 pm Bug #12093 (In Progress): arvados-cwl-runner doesn't propogate --project-uuid to submitting conta...
Peter Amstutz
06:53 pm Revision 651e87d8 (arvados): Merge branch '12093-cwl-project-uuid' closes #12093
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
06:38 pm Bug #12078 (Resolved): [crunch1] [crunch-job] Perl error "API method ... failed: hash- or arrayre...
Tom Clegg
06:09 pm Revision 47643ae4 (arvados): 12093: Propagate --project-uuid to runner job inside container.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
05:43 pm Revision c3af5da0 (arvados): 12033: Use browser locale to render collection timestamps.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:10 pm Story #11167: [Workbench] Remove arv-get file download fallback
IIRC this change means "include ActionController::Live" isn't needed any more in CollectionsController.
LGTM, than...
Tom Clegg
01:45 pm Bug #12087 (Resolved): [arvados-ws] Memory leak
Applied in changeset arvados|commit:e4a35f3914481226a2a4ff57618bc486839aa2ea. Tom Clegg
01:39 pm Bug #12087: [arvados-ws] Memory leak
LGTM. Peter Amstutz
01:43 pm Task #12088 (Resolved): Review 12087-ws-busy-loop
Tom Clegg
01:37 pm Task #12088 (In Progress): Review 12087-ws-busy-loop
Peter Amstutz
01:40 pm Revision e4a35f39 (arvados): Merge branch '12087-ws-busy-loop'
closes #12087
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
01:30 pm Revision c6b30895 (arvados): 11167: Added visual studio code control dir to gitignore
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
01:51 am Revision babd40cc (arvados): 12033: Link collections to remote workbench sites.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
01:51 am Revision 2289f184 (arvados): 12033: Fade out stale results.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
01:34 am Revision 6ba14712 (arvados): 12033: Add /collections/multisite search page.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg

08/08/2017

08:31 pm Story #11167: [Workbench] Remove arv-get file download fallback
Updates at commit:02a0ac50b
Test run: https://ci.curoverse.com/job/developer-run-tests/408/
Using @curl@ from the...
Lucas Di Pentima
08:26 pm Revision 02a0ac50 (arvados): 11167: Removed unnecessary conditional
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
07:53 pm Revision 82d2cce6 (arvados): 11167: Fixed integration test by replacing the use of PhantomJS with
Selenium, as the former wasn't returning all the expected response
headers.
Also, fixed the Range header used when as...
Lucas Di Pentima
07:22 pm Bug #12093 (Resolved): arvados-cwl-runner doesn't propogate --project-uuid to submitting container
Bryan Cosca
06:54 pm Task #12092 (New): [arv-mount] Add support Trashed event for projects
Tom Morris
06:52 pm Task #12091 (Resolved): [Workbench] Add Projects tab to trash page
- Can the user navigate the project hierarchy for the projects which are in the trash? Tom Morris
06:35 pm Feature #12090 (New): Collections/data access API
Support operations like
* list files/dirs in collection
* add file/dir to collection
* write/truncate an existing ...
Tom Clegg
06:29 pm Story #12089 (New): Javascript SDK
Desired facilities:
* Upload a local file ("File":https://developer.mozilla.org/en-US/docs/Web/API/File or "FileRead...
Tom Morris
05:09 pm Task #12088 (Resolved): Review 12087-ws-busy-loop
Tom Clegg
05:09 pm Bug #12087 (In Progress): [arvados-ws] Memory leak
12087-ws-busy-loop @ commit:b61a80b93308582b91e89561dc373a1ea33658a9
Tom Clegg
04:57 pm Bug #12087: [arvados-ws] Memory leak
SIGQUIT revealed many (thousands?) of goroutines like this... Tom Clegg
04:06 pm Bug #12087: [arvados-ws] Memory leak
One way for a goroutine to get stuck in a busy loop is to read from a closed channel (which returns immediately) and ... Tom Clegg
04:01 pm Bug #12087 (Resolved): [arvados-ws] Memory leak
arvados-ws process caught using 40GB rss, 48GB virt, ~75% cpu.
debug.json:...
Tom Clegg
05:07 pm Revision 5b54a802 (arvados): 12087: Remove useless continue statement.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:07 pm Revision b61a80b9 (arvados): 12087: Exit "wait for low water mark" loop if session terminates.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:07 pm Revision e19efd04 (arvados): 12087: Don't report read/write errors on terminated sessions.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
04:26 pm Revision 366381df (arvados): 12087: Fixup some problems found by go vet.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
04:25 pm Revision 61bde67a (arvados): 12087: Fix up context cancel usage.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
03:43 pm Revision 69487544 (arvados): 12033: Add session-manager page.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
02:02 pm Story #12085 (New): Add monitoring/alarm for failed/slow job dispatch & excess idle nodes
We need some additional monitoring and alarms to catch situations like yesterday's crunch-dispatch.rb file descriptor... Tom Morris
01:09 pm Revision 50c0afeb (arvados): 12033: Add mithril via npm.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg

08/07/2017

10:11 pm Story #11167: [Workbench] Remove arv-get file download fallback
Updates at commit:57647945b08a74bab02fed6adf947eb9adb8321f
Test run: https://ci.curoverse.com/job/developer-run-test...
Lucas Di Pentima
09:57 pm Revision 57647945 (arvados): 11167: Merge branch 'master' into 11167-wb-remove-arvget
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
09:52 pm Revision 5f215fab (arvados): 11167: Refactored tests to use new helper function.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
09:44 pm Revision cd94cea6 (arvados): 11167: Added response header whitelisting needed when using CORS
request to fetch partial content.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima
09:36 pm Revision 323a439a (arvados): 11167: Documented default keep_web_url setting on workbench config f...
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
09:34 pm Revision f007b09f (arvados): 11167: Added helper function to be used on collection access tests v...
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
09:02 pm Revision 3149e7de (arvados): 11167: Removed conditional code
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
05:47 pm Revision f12b4e89 (arvados): Merge branch '12027-slurm-error-text'
refs #12027
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
04:05 pm Feature #3829 (Duplicate): [Crunch] Email notification when pipeline finishes, depending on user ...
Tom Morris
03:49 pm Bug #12078 (In Progress): [crunch1] [crunch-job] Perl error "API method ... failed: hash- or arra...
Tom Clegg
02:46 pm Bug #12082 (New): [SDKs] Improve wording of Keep error messages in Python SDK
This is what we have:
arvados.errors.KeepReadError: failed to read 33b13624f658eef3a4e5da5bcae81487+67108864+A8d00...
Tom Clegg
01:58 pm Revision 9c6540b9 (arvados): 12027: Recognize a new "node failed" error message.
"srun: error: Cannot communicate with node 0. Aborting job."
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curovers...
Tom Clegg

08/05/2017

04:07 pm Bug #11136: Nginx config should speak JSON when returning its own response for unproxyable API re...
The linked #6651 contains one recipe for fixing this. Tom Morris

08/04/2017

09:16 pm Revision 9ed67680 (arvados): 12033: Add mithril via npm.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
06:42 pm Revision b3884a22 (arvados): Merge branch '12078-perl-bool-params'
refs #12078
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
06:41 pm Bug #12078: [crunch1] [crunch-job] Perl error "API method ... failed: hash- or arrayref expected"
... Tom Clegg
06:32 pm Bug #12078: [crunch1] [crunch-job] Perl error "API method ... failed: hash- or arrayref expected"
12078-perl-bool-params @ commit:64b837f87103a59efb6d4dac2b8dfa3c7c40c09a
Tom Clegg
06:19 pm Bug #12078: [crunch1] [crunch-job] Perl error "API method ... failed: hash- or arrayref expected"
debian:8 perl v5.20.2 libjson-perl 2.61-1... Tom Clegg
02:22 pm Bug #12078: [crunch1] [crunch-job] Perl error "API method ... failed: hash- or arrayref expected"
There were successful API calls:... Tom Clegg
01:16 pm Bug #12078 (Resolved): [crunch1] [crunch-job] Perl error "API method ... failed: hash- or arrayre...
Test pipeline fails on first job. Pipeline log ends with... Tom Clegg
06:30 pm Revision 64b837f8 (arvados): 12078: Fix crash encoding booleans with libjson-perl 2.90.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
01:52 pm Bug #11925: [Nodemanager] Fix unit tests
Updates @ commit:597b742a6 LGTM.
Some tests at @test_daemon.py@ are failing once in a while, the rest seem to be r...
Lucas Di Pentima

08/03/2017

09:01 pm Revision 597b742a (arvados): 11925: Two more tests wait for expected number of paired nodes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
08:45 pm Revision e6cc2310 (arvados): 11925: More tests wait for expected number of paired nodes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
08:29 pm Revision ca4049e7 (arvados): 11925: Add check for paired nodes, not just monitored nodes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
07:54 pm Revision a4ce464e (arvados): 12024: Update help message.
refs #12024
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
07:37 pm Bug #12077 (New): [Workbench] Description column doesn't contain descriptions
The Description column for a number of workbench screens contains information which is not the contents of the "descr... Tom Morris
07:07 pm Revision 70ec5fc0 (arvados): 12024: Use vendor bundle when building Go packages.
refs #12024
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
06:57 pm Revision 6706c6d4 (arvados): 11925: Explicitly join actor thread after stopping.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
05:24 pm Revision 23546c22 (arvados): 11925: Tweak test_node_pairing
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
05:02 pm Revision b02fc7b2 (arvados): 11925: Make unit tests more reliable.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
03:00 pm Revision 581cd882 (arvados): Merge branch '12024-vendor-bundle-version'
refs #12024
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
02:57 pm Revision 106c66fb (arvados): 12024: Fix checksums in vendor.json.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
01:19 pm Bug #11925: [Nodemanager] Fix unit tests
Another systemic issue:
Python mocks seem to be unreliable when shadowing builtin functions (like time.time()) wit...
Peter Amstutz

08/02/2017

08:07 pm Bug #12073 (Resolved): [Node manager] Clean up stale arvados node records
If a node goes away without node manager doing clean_arvados_node(), it will remain in the nodes table tying up a slo... Peter Amstutz
07:48 pm Task #12069 (Closed): Review
Lucas Di Pentima
07:45 pm Bug #12057 (Resolved): [node manager] boot nodes for jobs marked (Priority)
Applied in changeset arvados|commit:962a6b5be87305054a87b665dcc85d144840bb98. Peter Amstutz
05:30 am Bug #12057: [node manager] boot nodes for jobs marked (Priority)
Does this mean that #11545 is in progress? Tom Morris
05:28 am Bug #12057 (In Progress): [node manager] boot nodes for jobs marked (Priority)
Tom Morris
07:40 pm Task #12067 (New): Instrumentation
Peter Amstutz
07:40 pm Task #12066 (Resolved): Review 12055-nodemanager-ec2-tags
Peter Amstutz
07:38 pm Revision 962a6b5b (arvados): Merge branch '12057-nodemanager-priority' closes #12057
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
07:33 pm Task #12065 (New): Review
Peter Amstutz
07:18 pm Bug #11925: [Nodemanager] Fix unit tests
... Peter Amstutz
07:03 pm Bug #11925 (In Progress): [Nodemanager] Fix unit tests
Peter Amstutz
04:50 pm Bug #11925: [Nodemanager] Fix unit tests
11925-nodemanager-watchdog-test @ commit:0ac98ea67157ab1a6d92b02e59b8491d90dd1f79
Fixes flaky tests in test_compu...
Peter Amstutz
03:47 pm Bug #11925: [Nodemanager] Fix unit tests
Some structural reasons for failing node manager tests:
# Tests were written with the assumption that certain comm...
Peter Amstutz
06:55 pm Bug #10584: [FUSE] high memory consumption (possible leak) in long-running arv-mount
* Look at user interaction history with keep
* Track metrics
* Instrumentation to report memory usage / ownership
Peter Amstutz
06:48 pm Task #11827 (Resolved): Review
Tom Clegg
06:46 pm Bug #12010 (Closed): [keep-web] tests hang
Tom Clegg
03:48 pm Bug #12010: [keep-web] tests hang
Tried & failed to reproduce this locally using --repeat 32 and high system load. Haven't seen it on Jenkins again.
Tom Clegg
06:37 pm Story #11997 (Resolved): [Spike] Investigate CI packaging improvements
Tom Clegg
06:26 pm Revision 9bcdc4d7 (arvados): 11925: Update dependency on arvados-python-client to fix
test_unsatisfiable_jobs test.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>
Peter Amstutz
04:54 pm Revision acd3d380 (arvados): 11925: Fix flaky tests in test_computenode_dispatch_slurm.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
04:54 pm Revision 7a78b672 (arvados): 11925: Make watchdog test more reliable.
Add wait so that it doesn't try to shut down the threads before they have had a
chance to start. Also added services...
Peter Amstutz
04:49 pm Revision 0ac98ea6 (arvados): 11925: Fix flaky tests in test_computenode_dispatch_slurm.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
01:58 pm Bug #12058: [node manager] failing test
Yesterday I run the unit tests on my local environment, and didn't got the test @test_unsatisfiable_jobs@ to fail.
O...
Lucas Di Pentima
01:43 pm Bug #12061 (New): [Node manager] Fix flaky integration tests
test_probe_quota failed - https://ci.curoverse.com/job/run-tests-services-nodemanager/515/consoleText
test_single_no...
Tom Clegg
01:34 pm Story #11545 (In Progress): Create a CWL stress test for node manager
Peter Amstutz
01:06 pm Revision a736ea9a (arvados): 12024: Fix syntax error.
refs #12024
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
05:40 am Bug #12055: [node manager] ec2 set tags on create
I'm pretty sure that this is a duplicate and that someone (Lucas?) was already working on fixing it, but I'll add it ... Tom Morris

08/01/2017

09:51 pm Revision e474fe9c (arvados): Merge branch '12024-vendor-bundle-version'
refs #12024
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
07:31 pm Revision 560ecc87 (arvados): 12024: Build new Go packages when the vendor bundle changes.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
07:02 pm Story #12060 (New): [CWL] Run directly from git
Goal: have arvados-cwl-runner execute CWL files from a git branch as written, avoiding the "packing" step.
Executi...
Peter Amstutz
05:46 pm Bug #11925: [Nodemanager] Fix unit tests
I don't know if it's related, but I'm seeing this test fail almost every run:... Lucas Di Pentima
01:31 pm Bug #11925: [Nodemanager] Fix unit tests
11925-nodemanager-watchdog-test @ commit:f313294f95e55f595ace70e2a614557c0428f2da
The fix (adding an extra wait to...
Peter Amstutz
05:45 pm Bug #12058 (New): [node manager] failing test
... Peter Amstutz
05:33 pm Bug #12057: [node manager] boot nodes for jobs marked (Priority)
Peter Amstutz wrote:
> 12057-nodemanager-priority @ commit:43afe5cf4364c64b5022f912eaba2240c7cb0999
LGTM
Tom Clegg
05:33 pm Bug #12057: [node manager] boot nodes for jobs marked (Priority)
12057-nodemanager-priority @ commit:43afe5cf4364c64b5022f912eaba2240c7cb0999 Peter Amstutz
04:54 pm Bug #12057 (Resolved): [node manager] boot nodes for jobs marked (Priority)
While running the node manager stress test, I noticed the following behavior from slurm:... Peter Amstutz
05:31 pm Revision 43afe5cf (arvados): 12057: Add "Priority" to list of reasons to boot a new node.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
05:27 pm Revision f60671ae (arvados): 11545: CWL stress test for crunch / node manager
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
01:44 pm Task #11759 (Resolved): Review 7475-nodemgr-unsatisfiable-job-comms
Peter Amstutz
01:42 pm Revision 08235876 (arvados): 11167: Expose Content-Range response header for cross-origin reqs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
01:42 pm Bug #12055 (Resolved): [node manager] ec2 set tags on create
https://issues.apache.org/jira/browse/LIBCLOUD-930
ec2 node_create(ex_metadata) uses TagSpecification.N &rarr; htt...
Peter Amstutz

07/31/2017

07:14 pm Revision f313294f (arvados): 11925: Make watchdog test more reliable.
Add wait so that it doesn't try to shut down the threads before they have had a
chance to start. Also added services...
Peter Amstutz
06:29 pm Bug #11158 (Resolved): [FUSE] Hang on simple FUSE operation and when logging in again later
Peter Amstutz
02:55 pm Story #7475 (Resolved): [Node manager] Better communication when job is unsatisfiable
Applied in changeset arvados|commit:c0e203e7f3e9e40736eac63cbe440d5e46e379c0. Lucas Di Pentima
02:52 pm Revision c0e203e7 (arvados): Merge branch '7475-nodemgr-unsatisfiable-job-comms'
Closes #7475
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima

07/29/2017

03:05 pm Story #7475: [Node manager] Better communication when job is unsatisfiable
Sorry, I thought I tested it before pushing.
Updated at commit:3e46aaf64
Test run: https://ci.curoverse.com/job/d...
Lucas Di Pentima
03:03 pm Revision 3e46aaf6 (arvados): 7475: Fixed integration test
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
02:15 pm Story #12037 (Resolved): [CWL] Pass conformance for v1.0.1
Applied in changeset arvados|commit:386e1eefaac2021805f73732b10e9f543c221593. Peter Amstutz
02:12 pm Revision 386e1eef (arvados): Merge branch '12037-cwl-v1.0.1' closes #12037
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
02:11 pm Revision afb71039 (arvados): 7475: Merge branch 'master' into 7475-nodemgr-unsatisfiable-job-comms
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
01:40 pm Task #12040 (Resolved): Review 12037-cwl-v1.0.1
Lucas Di Pentima

07/28/2017

09:14 pm Story #12037: [CWL] Pass conformance for v1.0.1
All conformance tests now worked for me.
LGTM, thanks!
Lucas Di Pentima
07:54 pm Story #12037: [CWL] Pass conformance for v1.0.1
So the issue is that it is missing a Docker image tagged arvados/jobs:latest, compounded by the a logging bug that ob... Peter Amstutz
03:32 pm Story #12037: [CWL] Pass conformance for v1.0.1
Adding environment information.
@pip freeze@ returns:...
Lucas Di Pentima
02:11 pm Story #12037: [CWL] Pass conformance for v1.0.1
Attaching log files from a failed conformance test run on my arvbox setup Lucas Di Pentima
01:07 pm Story #12037: [CWL] Pass conformance for v1.0.1
You need to cd in to the "v1.0" directory before you paste the command line.
Peter Amstutz
08:01 pm Task #11191 (Resolved): Review 11158-fuse-projects
Peter Amstutz
07:59 pm Revision 3ad999b1 (arvados): Merge branch '11158-fuse-projects' refs #11158
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
07:51 pm Revision d69024a6 (arvados): 12037: Pull default arvados/jobs:latest image as needed.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
06:19 pm Task #12001 (In Progress): Review 11925-nodemanager-watchdog-test
Lucas Di Pentima
05:49 pm Bug #11925: [Nodemanager] Fix unit tests
The WatchdogActorTest still fails for me in my dev env, as before (this is the only nodemanager test that always fail... Radhika Chippada
01:53 pm Bug #11925: [Nodemanager] Fix unit tests
11925-nodemanager-watchdog-test @ commit:97bb15198ff6071d656d461b27e1055d84826d36 Peter Amstutz
05:25 pm Bug #12051 (New): lost job log
for https://workbench.e51c5.arvadosapi.com/pipeline_instances/e51c5-d1hrv-prpopnuyn8u43ej 55001604176962 interpretati... Bryan Cosca
04:33 pm Bug #11158: [FUSE] Hang on simple FUSE operation and when logging in again later
LGTM
-Happened to notice "if new_name" should probably also be changed to "if new_name is not None" here in fusedi...
Tom Clegg
03:30 pm Feature #11906 (Resolved): Basic authenticated http health check ("ping") for each system service
Applied in changeset arvados|commit:dfc4c2c74dc7a31ff0c0d307846b7e9525fdcf0e. Radhika Chippada
03:26 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
Reviewed updates at commit:8ae04f9f4d252a99985d7ac047413318d2f1068b for @nodemanager@. Looks good to me, thanks! Lucas Di Pentima
03:26 pm Task #12049 (Resolved): Review branch 11906-nodemanager-ping
Lucas Di Pentima
01:07 pm Task #12049 (In Progress): Review branch 11906-nodemanager-ping
Lucas Di Pentima
03:25 pm Revision dfc4c2c7 (arvados): closes #11906
Merge branch '11906-nodemanager-ping'
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>
Radhika Chippada
02:53 pm Revision b459e0fc (arvados): 11898: Remove superfluous uniq(&:id) call
Avoids adding DISTINCT to SQL query, which causes Postgres to do
expensive things.
Arvados-DCO-1.1-Signed-off-by: To...
Tom Clegg
02:50 pm Revision 8ae04f9f (arvados): 11906: use the same name "ManagementToken" to enable healthcheck in ...
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
01:51 pm Revision 97bb1519 (arvados): 11925: Make watchdog test reliable.
Use proxy to stop it instead of stopping actor object directly (which is racy).
Also added services/nodemanage_suite ...
Peter Amstutz

07/27/2017

11:05 pm Task #12049 (Resolved): Review branch 11906-nodemanager-ping
Radhika Chippada
10:53 pm Revision 286cb3b9 (arvados): 11906: add /_health/ping to nodemanager
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
09:27 pm Story #12037: [CWL] Pass conformance for v1.0.1
Reviewing updates at commit:0c817f2f9
Followed guide on https://dev.arvados.org/issues/11948#note-4 to run conform...
Lucas Di Pentima
05:38 pm Bug #12047: CWL should check yml to make sure pdh's exist
samir had the chr2vcf missing a b
"inputvcf": {
"class": "File",
"location": "keep:b7c09923c1aad2fe0e4...
Bryan Cosca
05:36 pm Bug #12047 (New): CWL should check yml to make sure pdh's exist
Changing the name because this pipeline shouldn't have run in the first place if one letter was off in the pdh. Bryan Cosca
05:34 pm Bug #12047 (Closed): CWL should check yml to make sure pdh's exist
samir said he missed one letter in the pdh. Bryan Cosca
05:27 pm Bug #12047 (New): CWL should check yml to make sure pdh's exist
https://workbench.e51c5.arvadosapi.com/jobs/e51c5-8i9sb-tll53ooc5fb8bn8
a script parameter is "keep:7c09923c1aad2f...
Bryan Cosca
05:33 pm Task #12040 (In Progress): Review 12037-cwl-v1.0.1
Lucas Di Pentima
04:39 pm Story #11167: [Workbench] Remove arv-get file download fallback
Lucas, a couple more comments in the meantime:
* application.default.yml => can you add “.com” to the test config ...
Radhika Chippada
03:29 pm Story #7475: [Node manager] Better communication when job is unsatisfiable
... Peter Amstutz
02:53 pm Story #11997 (In Progress): [Spike] Investigate CI packaging improvements
Tom Clegg
02:51 pm Task #11998 (Resolved): Review branch 11995-collecion-filetypes
Radhika Chippada
02:51 pm Task #12041 (Resolved): Review branch 11906-keep-web-ping
Radhika Chippada
01:21 pm Task #12041 (In Progress): Review branch 11906-keep-web-ping
Tom Clegg
02:40 pm Revision 8d24a822 (arvados): Merge branch '12024-zero-content-length'
refs #12024
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
02:24 pm Bug #11158: [FUSE] Hang on simple FUSE operation and when logging in again later
11158-fuse-projects commit:26e095318c7c368089ea368e6e4854b62a6c7830
Based on findings in note 16:
* Reverted ch...
Peter Amstutz
02:15 pm Revision 42c06689 (arvados): refs #11906
Merge branch '11906-arv-git-httpd-ping'
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>
Radhika Chippada
02:12 pm Revision 153ffc85 (arvados): refs #11906
Merge branch '11906-keep-web-ping'
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>
Radhika Chippada
02:06 pm Revision 26e09531 (arvados): 11158: Handle trash/untrash events for collections in projects.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
01:58 pm Revision bd96be71 (arvados): 12024: Use goamz fork to fix Go1.8-vs.-AWS transfer encoding bug.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
01:54 pm Task #12043 (Resolved): Review branch 11906-arv-git-httpd-ping
Lucas Di Pentima
01:28 pm Task #12043 (In Progress): Review branch 11906-arv-git-httpd-ping
Lucas Di Pentima
01:54 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
Updates at commit:dc929c778 - branch @11906-arv-git-httpd-ping@ LGTM, please merge. Lucas Di Pentima
01:26 pm Revision 408cbfd4 (arvados): 11158: Support incremental update of project contents based on webso...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
01:26 pm Revision 007d5447 (arvados): 11158: Improve arvados.util.list_all() implementation to avoid relyi...
items_available.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>
Peter Amstutz
01:26 pm Revision d0379cea (arvados): 11158: Restore paging to get full list of collections and projects (...
don't load other object types). Defer full listing load until first call to
items() to support efficient access of i...
Peter Amstutz
01:26 pm Revision bffd1e4e (arvados): 11158: Fixes & test updates for ProjectDirectory.
* list_all() orders by uuid and uses it for paging.
* Move dynamic item lookup from __contains__ to __getitem__ to f...
Peter Amstutz
01:26 pm Revision e2ec2f6f (arvados): 11158: New behavior for project directories. Allow 'cd' into any co...
subproject that exists on the server, even if it isn't returned in the listing.
Now applies listing limit, ordered by...
Peter Amstutz
01:26 pm Revision 5d0cd36a (arvados): Revert python sdk changes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
01:26 pm Revision 14032da4 (arvados): 11158: Fix order="modified_at".
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
11:34 am Revision 0c817f2f (arvados): 12037: Fix tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz

07/26/2017

09:19 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
I pushed a commit removing the func and servemux, and calling the health handler's ServeHTTP() directly instead.
T...
Tom Clegg
05:51 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
Branch 11906-keep-web-ping @ commit:1af8267a0d11ad9f986aec5ec7853299f3cfeb0e implements /_health/ping for keep-web.
...
Radhika Chippada
09:14 pm Revision 2d16a410 (arvados): 11906: Remove intermediary servemux and handler func.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
08:49 pm Revision 0d9d3bb3 (arvados): 12024: Use goamz fork to fix Go1.8-vs.-AWS transfer encoding bug.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
08:34 pm Revision 08b59c7e (arvados): 11167: Re-added jobs integration test, adjusted to work with keep-web.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
08:32 pm Task #12043 (Resolved): Review branch 11906-arv-git-httpd-ping
Radhika Chippada
08:30 pm Revision dc929c77 (arvados): 11906: add /_health/ping to arv-git-httpd
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
08:09 pm Story #11167: [Workbench] Remove arv-get file download fallback
Updates at commit:2918ed81152a1fe8607f433e36dceddc1cb78f74
Test run: https://ci.curoverse.com/job/developer-run-test...
Lucas Di Pentima
06:13 pm Bug #11850: [CWL] arv:RunInSingleContainer should take max() of ResourceRequirements of substeps
Suggested behavior:
* The toplevel workflow may have a resource requirement which may be an expression or a consta...
Peter Amstutz
05:49 pm Task #12041 (Resolved): Review branch 11906-keep-web-ping
Radhika Chippada
05:26 pm Revision 1188ff31 (arvados-dev): Merge branch 'master' of git.curoverse.com:arvados-dev
Git sync user
05:24 pm Revision 1b8f8926 (arvados-dev): Add regexp to recognize new error text.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
05:20 pm Revision 41b8eead (arvados-dev): Merge branch 'master' of git.curoverse.com:arvados-dev
Git sync user
05:19 pm Revision 04e107ff (arvados-dev): Propagate stderr from child process.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
05:13 pm Task #12040 (Resolved): Review 12037-cwl-v1.0.1
Peter Amstutz
04:26 pm Revision 1af8267a (arvados): 11906: add /_health/ping to keep-web
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
03:11 pm Revision 6164f448 (arvados): 12037: Support CWL v1.0.1 spec.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com> Peter Amstutz
02:46 pm Story #12037 (In Progress): [CWL] Pass conformance for v1.0.1
Peter Amstutz
02:46 pm Story #12037 (Resolved): [CWL] Pass conformance for v1.0.1
Peter Amstutz
02:44 pm Revision 8cbabbbe (arvados): Merge branch '12027-slurmfail-during-setup'
refs #12027
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg

07/25/2017

07:49 pm Story #4442 (Resolved): [API] [Workbench] Site-wide regex searching
Full text search meets the bulk of this need. Tom Morris
07:14 pm Revision a7a07723 (arvados): Merge branch '12025-perm-cache-version'
refs #12025
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
07:06 pm Revision c55c3953 (arvados): 12027: Exit "retry unlocked" if slurm fails during setup phases.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
06:51 pm Story #12032: [API] Allow projects to be deleted (ie placed in the trash can)
Implementation thoughts:
* Add is_trashed flag to groups (projects)
* Permission graph (recursive view) needs an is...
Tom Clegg
06:39 pm Story #12032 (Resolved): [API] Allow projects to be deleted (ie placed in the trash can)
As a user, I would like deleted projects to be placed in the Trash rather than cluttering my Home project and when th... Tom Morris
05:55 pm Revision b40d8d04 (arvados): 12027: Exit "retry unlocked" if slurm fails during setup phases.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
02:39 pm Revision 86b16fe1 (arvados): 12025: Change permission cache key to avoid upgrade bugs.
Also, set TTL on permission cache entries.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
02:22 pm Feature #12028 (New): Be able to create a new collection based on a subdirectory in workbench
Right now you can only click on files to create a new collection, users should also be able to click on directories. Bryan Cosca

07/24/2017

10:09 pm Revision 2918ed81 (arvados): 11167: Re-added another removed integration test, adjusted to work
with keep-web.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima
09:24 pm Bug #12026 (New): crunchstat-summary gives invalid min_cores recommendation
This recommendation doesn't make sense from a couple of points of view:
### Summary for cwl-runner (su92l-8i9sb-ll...
Tom Morris
09:02 pm Bug #11850: [CWL] arv:RunInSingleContainer should take max() of ResourceRequirements of substeps
Taking into account https://dev.arvados.org/issues/11850#note-10, I think the rule should be rephrased as follows.
...
Jiayong Li
08:53 pm Revision 12319740 (arvados): 11167: Reverted deletion of integration test. Modified it so it
can work with keep-web instead of arv-get.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima
08:52 pm Revision 1dd3f0e1 (arvados): 11167: Removed conditional that check is keep_web is configured
because workbench already do this at start.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima
07:02 pm Revision f49e418e (arvados): refs #11906
Merge branch '11906-keepproxy-ping'
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>
Radhika Chippada
06:58 pm Task #12021 (Resolved): Review branch 11906-keepproxy-ping
Lucas Di Pentima
06:16 pm Task #12021 (Resolved): Review branch 11906-keepproxy-ping
Radhika Chippada
06:57 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
Updates at commit:91f976b99d4e7f00d2c1fbfee75812c3b1b780c6 - branch @11906-keepproxy-ping@ LGTM, thanks! Lucas Di Pentima
06:33 pm Revision 741450ac (arvados): Fix unclosed P tag.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
06:32 pm Revision 5ad5450b (arvados): Update workbench dependencies.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
06:14 pm Revision 91f976b9 (arvados): 11906: add /_health/ping to keepproxy
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
02:53 pm Bug #12020 (Closed): [Tests] Flaky test in Python SDK tests.test_events.WebsocketTest.test_subscr...
... Tom Clegg
02:33 pm Revision e2807c62 (arvados): Update api server dependencies.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
02:11 pm Story #11167: [Workbench] Remove arv-get file download fallback
I didn't spend much time looking at the updates, but here are a couple initial comments.
* collections_controller ...
Radhika Chippada
02:10 pm Task #11937 (In Progress): Review 11167-wb-remove-arvget
Radhika Chippada
01:15 pm Revision 9997ada6 (arvados): 11167: Merge branch 'master' into 11167-wb-remove-arvget
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima

07/21/2017

10:13 pm Bug #4409 (New): [Workbench] Want to remove projects from Home
Re-opening. The current behavior is just plain silly. Tom Morris
09:09 pm Feature #12018 (In Progress): Synchronize group membership with external data source
As a user in a corporate environment, I want to be able to synchronize the users in my Arvados groups with my corpora... Tom Morris
08:56 pm Feature #12017 (New): Windows file system driver for Keep (arv-mount equiv)
As a user who wants to be able to run mass spectrometry software on data stored in Keep, I'd like to have a Windows f... Tom Morris
08:45 pm Story #9264 (Rejected): [Keep] Cross-compile Keepstore for Windows
Since we've already got an Azure blob storage solution, I don't see the need for this. Tom Morris
08:12 pm Revision 2354f19a (arvados): Add missing dependencies to vendor.json.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
08:06 pm Revision 2aaf62d7 (arvados): Update Go dependencies.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
07:14 pm Task #12000 (Resolved): Review 11906-health-check-lib
Tom Clegg
01:31 pm Task #12000 (In Progress): Review 11906-health-check-lib
Radhika Chippada
07:14 pm Task #11963 (Resolved): Review 11948-cwl-conformance-fix
Tom Clegg
06:17 pm Story #11167: [Workbench] Remove arv-get file download fallback
Fixed a failing integration test at commit:8f3070e16
Test run: https://ci.curoverse.com/job/developer-run-tests/393/
Lucas Di Pentima
04:57 pm Story #11167: [Workbench] Remove arv-get file download fallback
Some new updates at commit:c7187ec72
Test run: https://ci.curoverse.com/job/developer-run-tests/392/
* Removed ou...
Lucas Di Pentima
03:20 pm Story #11167: [Workbench] Remove arv-get file download fallback
Updates at commit:cd698336f - branch @11167-wb-remove-arvget@
Test run: https://ci.curoverse.com/job/developer-run-t...
Lucas Di Pentima
06:15 pm Revision 8f3070e1 (arvados): 11167: Fixed integration test about collection's sharing link.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
06:01 pm Revision 3574793a (arvados): Merge branch '11906-health-check-lib'
refs #11906
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
06:01 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
11906-health-check-lib LGTM. Thanks. Radhika Chippada
05:54 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
Radhika Chippada wrote:
> * In sdk handler.go, can we can call “type Func” as “type HealthFunc” or something to help...
Tom Clegg
05:17 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
Branch 11906-health-check-lib:
* In sdk handler.go, can we can call “type Func” as “type HealthFunc” or something ...
Radhika Chippada
01:00 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
11906-health-check-lib @ commit:0e0dc3c8ebf442a35c41816fed42fdddb53aed53
Tom Clegg
05:53 pm Revision da037c13 (arvados): 11906: Clarify "zero value" test.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:51 pm Revision fc2705f7 (arvados): 11906: Test 404 cases.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
05:49 pm Revision c834c346 (arvados): 1906: Fix up doc comment.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
04:54 pm Revision c7187ec7 (arvados): 11167: Test adjusted.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
03:25 pm Revision 058e06eb (arvados): 11167: Removed outdated comment.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
03:15 pm Revision cd698336 (arvados): 11167: Refuse to start when keep-web isn't configured.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com> Lucas Di Pentima
01:01 pm Task #11996 (Resolved): Refactor health check handlers into an SDK library
Tom Clegg

07/20/2017

09:25 pm Revision a2fc189f (arvados): 11906: Add tests for sdk/go/health.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
09:25 pm Revision 0e0dc3c8 (arvados): 11906: Remove keepstore's health-check unit tests.
Now that the health check handler has its own unit tests, keepstore
only needs to check that it's wired up correctly....
Tom Clegg
09:25 pm Revision 2835665e (arvados): 11906: Use sdk/go/health for keepstore health checks.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
09:25 pm Revision 34c4b300 (arvados): 11906: Refactor health-check handler into SDK.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
08:23 pm Revision 4feae207 (arvados): Style fixes.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
08:20 pm Revision 49b9c5f4 (arvados): 10805: Bump debian version in fuse install doc.
refs #10805
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
06:04 pm Bug #12010 (Closed): [keep-web] tests hang
From https://ci.curoverse.com/job/run-tests-remainder/1152/console... Tom Clegg
05:16 pm Feature #12009 (New): Find arvados-cwl-runner version easier in a container request
I found the arvados/jobs image commit in the api_response of a job and then i ran some shell script to find all the a... Bryan Cosca
05:10 pm Story #11995 (Resolved): [Workbench] Support more filetypes for in-browser display
Applied in changeset arvados|commit:0b51ce6bfc3c50155de18eb4440021688462fb6a. Radhika Chippada
03:34 pm Story #11995: [Workbench] Support more filetypes for in-browser display
Including ... Tom Clegg
02:20 pm Story #11995: [Workbench] Support more filetypes for in-browser display
Just one comment:
* For the @.cwl@ extension, it only works when it’s in lower case. I tried renaming a @*.bed@ to...
Lucas Di Pentima
01:32 pm Story #11995: [Workbench] Support more filetypes for in-browser display
Branch 11995-collecion-filetypes @ commit:be0830dcdc10ff352d89a20fa2a24000a5ca8984
* The file types .yaml, .csv, ....
Radhika Chippada
12:36 pm Story #11995 (In Progress): [Workbench] Support more filetypes for in-browser display
Radhika Chippada
05:04 pm Revision 0b51ce6b (arvados): closes #11995
Merge branch '11995-collecion-filetypes'
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>
Radhika Chippada
05:04 pm Revision 236a6679 (arvados): 1195: add .bed and .cwl to file types that can previewed
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
03:58 pm Revision 894c4a57 (arvados): 11995: check for cwl file type
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
03:42 pm Revision e7e1e4ff (arvados): 11898: Remove superfluous uniq(&:id) call
Avoids adding DISTINCT to SQL query, which causes Postgres to do
expensive things.
Arvados-DCO-1.1-Signed-off-by: To...
Tom Clegg
02:52 pm Revision 6cc4c2ed (arvados): 10805: Build llfuse-1.2 for ubuntu1604.
refs #10805
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
02:30 pm Revision 40e2b5df (arvados): 1195: case insensitive cwl file extension check
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
01:50 pm Bug #10805 (Resolved): [FUSE] Upgrade llfuse to 1.2, fix deadlock in test suite
Applied in changeset arvados|commit:5e5bc2b2153a0af624d75a3c348b996ddf458ef2. Tom Clegg
01:45 pm Revision 5e5bc2b2 (arvados): Merge branch '10805-avoid-llfuse-deadlock'
closes #10805
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
01:36 pm Task #11998 (In Progress): Review branch 11995-collecion-filetypes
Lucas Di Pentima
01:20 pm Revision be0830dc (arvados): 1195: add .bed and .cwl to file types that can previewed
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
12:30 pm Revision 07cd679b (arvados): 10805: Skip llfuse.close() to avoid llfuse deadlocks in test suite.
See https://bitbucket.org/nikratio/python-llfuse/issues/108
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse....
Tom Clegg

07/19/2017

09:21 pm Revision f291a43f (arvados): 11167: Removed arv-get calling code from show_file.
Adjusted/deleted related tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima
08:53 pm Revision ec20efc4 (arvados): Merge branch '10805-llfuse-1.2'
refs #10805
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
08:50 pm Revision 7e7ada63 (arvados): 10805: Fix crash during shutdown when running with llfuse 1.x.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
08:16 pm Bug #10805: [FUSE] Upgrade llfuse to 1.2, fix deadlock in test suite
10805-llfuse-1.2 @ commit:7e7ada63bca240416584871398076c1bafc90f76
* Without this change, I see stack traces all ove...
Tom Clegg
08:15 pm Revision 861786a8 (arvados): 10805: Fix crash during shutdown when running with llfuse 1.x.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
07:52 pm Task #12006 (Resolved): Review 8937-arvput-cached-tokens
Lucas Di Pentima
07:52 pm Task #12005 (New): Review
Tom Morris
07:51 pm Task #12003 (New): Review
Tom Morris
07:50 pm Task #12001 (Resolved): Review 11925-nodemanager-watchdog-test
Tom Morris
07:50 pm Bug #11850: [CWL] arv:RunInSingleContainer should take max() of ResourceRequirements of substeps
After much deliberation, I think https://dev.arvados.org/issues/11850#note-6 needs to be reconsidered. I think it's r... Jiayong Li
07:42 pm Bug #11850: [CWL] arv:RunInSingleContainer should take max() of ResourceRequirements of substeps
(4:06:18 PM) tom: jiayong: the cwl code base has a few instances of this test: "$(" in sf or "${" in sf
(4:06:38 PM)...
Jiayong Li
07:50 pm Task #12000 (Resolved): Review 11906-health-check-lib
Tom Clegg
07:44 pm Bug #11948 (Resolved): Fix failing CWL conformance tests
Tom Clegg
07:42 pm Task #11998 (Resolved): Review branch 11995-collecion-filetypes
Radhika Chippada
07:40 pm Story #11997 (Resolved): [Spike] Investigate CI packaging improvements
Tom Morris
07:32 pm Task #11996 (Resolved): Refactor health check handlers into an SDK library
Tom Clegg
07:30 pm Story #9502 (Resolved): [API] Update permissions cache as needed after select writes
Obsolete/unnecessary now that we use a recursive query for permission checks. Tom Clegg
07:03 pm Story #11857 (Rejected): [CWL] arvados-cwl-runner defaults to crunch2 if available
Radhika Chippada
07:00 pm Story #11807 (Resolved): [API] Migrate old serialized database content from YAML to JSON
Tom Clegg
06:58 pm Story #11908: Migrate Collections.properties to JSONB
Merge is blocked on PostgreSQL 9.4 dependency. Tom Clegg
06:58 pm Story #11995 (Resolved): [Workbench] Support more filetypes for in-browser display
We should offer the option for in-browser display for more filetypes including: .cwl, .yaml, .csv, .tsv, .vcf, and .b... Tom Morris
06:57 pm Bug #11994 (New): [arv-mount] Do not crash if /sys/fs/fuse/connections is empty
In debian 9 (stretch), due to a systemd-blames-kernel bug, /sys/fs/fuse/connections/ might be empty.
* https://git...
Tom Clegg
06:45 pm Bug #11519 (New): arv-get should abort on ctrl/C
Lucas Di Pentima
04:52 pm Revision ff56222d (arvados): Merge branch '11842-crunchstat-summary-dygraphs'
refs #11842
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg
02:10 pm Revision 3f7bde60 (arvados): refs #11906
Merge branch '11906-wb-ping'
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>
Radhika Chippada
02:10 pm Revision ed27ef88 (arvados): 11906: healthcheck ping for workbench
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
02:09 pm Revision a1767317 (arvados): 11906: indentation
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
01:43 pm Revision b210f531 (arvados): 11842: Remove chartjs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
01:07 pm Task #11987 (Resolved): Review branch 11906-wb-ping
Lucas Di Pentima
12:41 pm Task #11987 (In Progress): Review branch 11906-wb-ping
Lucas Di Pentima
01:07 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
Updates at commit:ffc117651144b197c9d650039a5403e972d54b7c LGTM, just one tiny detail:
Line 20 at file @apps/workb...
Lucas Di Pentima
02:39 am Revision 10138c15 (arvados): 11842: Split generic webchart code from ChartJS to WebChart.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
02:39 am Revision 85d5f916 (arvados): 11842: Generate charts with dygraphs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
02:39 am Revision a143375d (arvados): 11842: Use CDNJS for dygraphs js and css.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg

07/18/2017

10:02 pm Task #11987 (Resolved): Review branch 11906-wb-ping
Radhika Chippada
10:02 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
Branch 11906-wb-ping @ commit:ffc117651144b197c9d650039a5403e972d54b7c
Adds _health/ping to workbench.
I also m...
Radhika Chippada
06:00 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
All @services/api@ tests pass now, this LGTM. Thanks! Lucas Di Pentima
05:51 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
> File services/api/app/controllers/arvados/v1/healthcheck_controller.rb Lines 25-29
Updated
> There’s a test ...
Radhika Chippada
05:16 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
* File @services/api/app/controllers/arvados/v1/healthcheck_controller.rb@
** Lines 25-29: We could save one level o...
Lucas Di Pentima
03:26 pm Feature #11906: Basic authenticated http health check ("ping") for each system service
11906-api-ping @ commit:943b3e807126ba5dc936ceeeddbee9801dab7308
* Implemented /_health/ping for API server and ad...
Radhika Chippada
09:40 pm Revision ffc11765 (arvados): 11906: healthcheck ping for workbench
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
08:48 pm Bug #11986 (New): [OPs] Jenkins test run ordering issue
The jenkins test run https://ci.curoverse.com/job/run-tests/1142/ failed due to some issue @ commit:e65fffb60a5697ce1... Radhika Chippada
07:27 pm Revision 818daa27 (arvados): refs #11906
Merge branch '11906-api-ping'
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>
Radhika Chippada
07:18 pm Revision da94fc33 (arvados): 11906: healthcheck ping json updated
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
07:08 pm Revision 2397c4a4 (arvados): Merge branch '11980-debian9'
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
06:34 pm Revision 4442b72c (arvados): 11980: debian9 packaging plus llfuse >= 1.2
Debian Stretch is not stable so we'll be packaging for it,
llfuse >= 1.2 is required for this distro but also we nee...
Nico César
06:29 pm Story #11740: Support display & reseting of expiration dates for collections
The x-editable library we use has a "datetime" picker option: https://vitalets.github.io/x-editable/docs.html Tom Clegg
06:28 pm Story #11983 (New): On the collections page indicate expiring collections
Include a visual indication that collections are expiring and allow the user to click through to find out when the ex... Tom Morris
06:07 pm Story #11884 (Duplicate): Convert Collection properties column type to JSONB
Tom Morris
06:00 pm Task #11981 (Resolved): Review branch 11906-api-ping
Lucas Di Pentima
04:51 pm Task #11981 (In Progress): Review branch 11906-api-ping
Lucas Di Pentima
03:22 pm Task #11981 (Resolved): Review branch 11906-api-ping
Radhika Chippada
05:48 pm Revision e65fffb6 (arvados): refs #11906
Merge branch '11906-api-ping'
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>
Radhika Chippada
05:36 pm Revision 87ccfac0 (arvados-dev): Merge branch 'master' of git.curoverse.com:arvados-dev
Git sync user
05:34 pm Revision 83026883 (arvados-dev): 11980: debian9 is part of the suite
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curoverse.com>
Nico César
05:30 pm Revision b9411e85 (arvados): 11906: add _health/.* to errors_test routes
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
05:30 pm Revision 4d8e3950 (arvados-dev): Merge branch 'master' of git.curoverse.com:arvados-dev
Git sync user
05:29 pm Revision 1cff8f41 (arvados-dev): Merge branch '11332-arv-cwl-integration-testing'
refs #11332
Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curoverse.com>
Nico César
05:26 pm Revision f9f4786c (arvados-dev): Merge branch 'master' of git.curoverse.com:arvados-dev
Git sync user
05:24 pm Revision c8f73733 (arvados-dev): 11980: debian9 as a new target
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curoverse.com>
Nico César
05:11 pm Revision 5eb51309 (arvados): 11980: solving python-llfuse >1.2 dependency update
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
04:52 pm Revision add4fc98 (arvados): 11980: solving python-llfuse (< 0.41.2) but 1.2+dfsg-1 is to be inst...
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
04:14 pm Revision 5bcff13d (arvados): 11980:test-package-debian9.sh added
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
03:45 pm Revision 3622d1d6 (arvados): 11980: in debian9 procps is not there by default
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
03:27 pm Revision a70e4626 (arvados): 11980: in debian9 gpg requires a dirmgr running to import keys from ...
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
03:21 pm Revision 943b3e80 (arvados): 11906: added api ping tests
Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com> Radhika Chippada
02:59 pm Revision 869335ec (arvados): 11980: gpg doesn't come by default anymore
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
02:54 pm Revision 32a733b2 (arvados): 11980: typo
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
02:51 pm Revision faea1310 (arvados): 11980: debian stretch and libperl license change
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
02:05 pm Task #11978 (Resolved): Review branch 11906-keepstore-ping
Radhika Chippada
01:22 pm Revision 5b4d924c (arvados): 11980: initial commit to test out debian9 packaging
refs #11980
Arvados-DCO-1.1-Signed-off-by: Nicolas Cesar <nico@curoverse.com>
Nico César
 

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