Activity

From 08/22/2017 to 09/20/2017

Today

08:52 pm Bug #12246: Better crunch-run error when command not found
Using a docker image with "#!/bin/durrgh" in /bin/fail, the message is more obscure:... Tom Clegg
08:41 pm Bug #12246: Better crunch-run error when command not found
When the command doesn't exist, the error message isn't bad:... Tom Clegg
06:31 pm Bug #12246 (In Progress): Better crunch-run error when command not found
Tom Clegg
08:32 pm Bug #12298 (New): [Crunch2] Invalid container output_path causes infinite loop of futile dispatch...
Submitting a container request with no mounts and {"output_path":"/out"} results in the container being attempted rep... Tom Clegg
08:12 pm Bug #12297 (Resolved): [Workbench] dashboard fiddlesticks with minimal container request
fixed in commit:c2a861d06b51978847a02369e673eb1288ada1ee (oops, wrong issue # in commit message) Tom Clegg
07:54 pm Bug #12297 (Resolved): [Workbench] dashboard fiddlesticks with minimal container request
I created a container request... Tom Clegg
08:05 pm Revision 73b52efc (arvados): 12292: Find crunchrunner vars even when mixed into a partial line
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
08:03 pm Revision c2a861d0 (arvados): Fix dashboard crash on uncommitted container request.
refs #12246
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
08:01 pm Revision 2e185453 (arvados): 12195: Catch the special case when a RateLimitReachedError exception...
as it doesn't have a header attribute like its parent class.
Updated integration test to add a retry with this kind o...
Lucas Di Pentima
07:24 pm Revision 1176895e (arvados): 12292: Set defaults for tmpdir, outdir, keepdir
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:54 pm Bug #12073: [Node manager] Clean up stale arvados node records
So to clarify:
* A node record should get cleaned by @NodeManagerDaemonActor.update_arvados_nodes@ when @modified_...
Peter Amstutz
02:56 pm Bug #12073: [Node manager] Clean up stale arvados node records
... Peter Amstutz
12:39 pm Bug #12073: [Node manager] Clean up stale arvados node records
Re-ran tests to see if they still failed, but they finished ok: https://ci.curoverse.com/job/developer-run-tests/464/ Lucas Di Pentima
02:58 am Bug #12073: [Node manager] Clean up stale arvados node records
Updates at commit:0f1bac0cc - branch @12073-nodemanager-stale-nodes-recs@
Test run: https://ci.curoverse.com/job/dev...
Lucas Di Pentima
03:35 pm Task #12128 (Resolved): Review 12107-faster-git
Tom Clegg
03:35 pm Task #12263 (Resolved): Review 12247-no-failed-checksum
Tom Clegg
03:35 pm Bug #12247 (Resolved): [keepproxy] Fix misleading log message when GET response is interrupted
Applied in changeset arvados|commit:fb79ddbedcc8c459daccaa6eec05b07206865bae. Anonymous
01:37 am Bug #12247: [keepproxy] Fix misleading log message when GET response is interrupted
Ran @sdk/go/keepclient@ tests successfully. This LGTM, thanks. Lucas Di Pentima
03:33 pm Revision fb79ddbe (arvados): Merge branch '12247-no-failed-checksum'
closes #12247
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
02:46 pm Bug #12296: [API] [Node Manager] [Docs] Fix recommendations and explanations for various max-node...
It is necessary to have
{nodemanager_max_nodes} ≤ {apiserver_max_slots} ≤ {slurm_conf_nodes} ≤ {slurm_conf_tree_wi...
Tom Clegg
02:45 pm Bug #12296 (New): [API] [Node Manager] [Docs] Fix recommendations and explanations for various ma...
In source:services/api/config/application.default.yml, the explanation of max_compute_nodes is wrong. It suggests tha... Tom Clegg
02:23 pm Bug #12295 (New): [nodemanager] Only looking at first 100 queued jobs
I saw a case last night where there were 391 queued jobs (due to a different bug), but node manager was only looking ... Tom Morris
02:00 pm Bug #12107 (Resolved): [API] jobs.create should not do slow git operations
Applied in changeset arvados|commit:95000b5d6bb4264533a1770346342c8fd3dbe61a. Anonymous
01:57 pm Bug #12107: [API] jobs.create should not do slow git operations
Lucas Di Pentima wrote:
> ** Lines 176 & 181: I think those @must_git()@ calls could be condensed into one by using ...
Tom Clegg
01:57 pm Revision 95000b5d (arvados): Merge branch '12107-faster-git'
closes #12107
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
01:54 pm Revision 596534dd (arvados): 12107: Add protective comment.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:45 pm Revision 57e0d92c (arvados): Merge branch '12084-dispatch-stuck'
closes #12084
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
02:59 am Task #12201 (In Progress): Review 12073-nodemanager-stale-nodes-recs
Lucas Di Pentima
02:54 am Revision 0f1bac0c (arvados): 12073: Added tests
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com> Lucas Di Pentima
02:14 am Revision 0888c533 (arvados): 12084: Fix dispatcher getting bogged down on "too many open files".
Previously, handling the "too many open files" error from popen3
consisted of sleeping 1 second and trying the next j...
Tom Clegg
01:54 am Revision 6175b807 (arvados): 12084: Remove dead code.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:51 am Revision fa2f64c6 (arvados): 12084: Reap children whose threads exit abnormally (status == nil).
Ruby's thread status is false if the thread exited normally, nil if it
exited abnormally.
Arvados-DCO-1.1-Signed-off...
Tom Clegg

09/19/2017

10:18 pm Task #12263 (In Progress): Review 12247-no-failed-checksum
Lucas Di Pentima
10:14 pm Bug #12107: [API] jobs.create should not do slow git operations
Just one comment:
* File @services/api/app/models/commit.rb@
** Lines 176 & 181: I think those @must_git()@ calls...
Lucas Di Pentima
08:31 pm Story #12289 (New): Migrate to Slurm API
Currently nodemanager parses the output of Slurm command line utilities to get the information that it needs. This is... Tom Morris
07:12 pm Story #12288 (New): Status endpoint aggregator
Similar to #12260 which aggregates health checks for a cluster, we may want to also aggregate the results returned by... Tom Morris
06:18 pm Feature #11184: [Keep] Support multiple storage tiers
suggest
# specify desired functionality (user can push X buttons, result is Y)
# enumerate features/improvements ne...
Tom Clegg
06:02 pm Feature #12260: Healthcheck endpoint aggregator
Authenticated externally-visible endpoint that reports all of the health checks for all services that should be runni... Tom Clegg
02:54 pm Revision 4e85a19e (arvados): 12107: Fix test suite dependence on outer git config.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:48 pm Bug #12247: [keepproxy] Fix misleading log message when GET response is interrupted
12247-no-failed-checksum @ commit:8d9adcff3cfc57c775f136ef32dcad6b3860a5a3
Tom Clegg
02:11 pm Bug #12247 (In Progress): [keepproxy] Fix misleading log message when GET response is interrupted
Tom Clegg
02:47 pm Revision 8d9adcff (arvados): 12247: Simplify (Hash)Sum() usage.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:37 pm Revision 0a4df379 (arvados): 12247: Propagate write errors, don't hide them with "bad checksum".
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:02 pm Revision c7dd8c81 (arvados): 12107: Fix test suite dependence on outer git config.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:56 pm Revision b7b42350 (arvados): 12107: Fix broken commit-exists-in-internal-repo check.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:52 pm Revision ae931bec (arvados): 12107: Fix broken "git branch --contains" check.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:30 am Revision 499884be (arvados): 12073: Added actor for dispatching node record updates to the api se...
The Nodemanager daemon periodically checks for stale node records and
issues update commands to clean them up so they...
Lucas Di Pentima

09/18/2017

09:19 pm Task #12282 (Closed): Review 12279-selenium-keep-web
Lucas Di Pentima
05:19 pm Task #12282 (In Progress): Review 12279-selenium-keep-web
Lucas Di Pentima
04:57 pm Task #12282 (Closed): Review 12279-selenium-keep-web
Peter Amstutz
08:55 pm Bug #12107: [API] jobs.create should not do slow git operations
12107-faster-git @ commit:4e85a19e6746eec88885926b87495e729f631d3a
* initializes the internal.git repo at test setup...
Tom Clegg
08:46 pm Revision b1b8942e (arvados): 12107: Test fetch-and-tag on unreferenced and non-tip commits.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:46 pm Revision 71ad5890 (arvados): 12107: Use a fresh internal.git repo for each test run.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:09 pm Bug #12279 (Rejected): [Workbench] Use selenium for keep-web tests
It looks like upgrading Arvbox to PhantomJS 1.9.8 also solves the problem, so I'm going to close this. Peter Amstutz
04:58 pm Bug #12279: [Workbench] Use selenium for keep-web tests
Passed tests here:
https://ci.curoverse.com/job/developer-run-tests/458/
But now able to pass workbench tests i...
Peter Amstutz
02:24 pm Bug #12279 (In Progress): [Workbench] Use selenium for keep-web tests
Peter Amstutz
02:10 pm Bug #12279 (Rejected): [Workbench] Use selenium for keep-web tests
Keep-web fail when run in Arvbox, due either to bugs in PhantomJS or some other interaction with the container enviro... Peter Amstutz
08:00 pm Revision 5cbf8527 (arvados): Bump PhantomJS version no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
07:59 pm Revision 8cbc52c4 (arvados): Arvbox explicitly initializes postgres with en_US.UTF-8 locale. no ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
07:09 pm Revision a2b75f5a (arvados): Fix quoting in test_with_arvbox no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
06:33 pm Revision 3854e6bf (arvados): Merge branch 'master' into 12107-faster-git
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
06:30 pm Story #12197 (Resolved): Add PDH column and filter to trash display
Applied in changeset arvados|commit:a6d5c9b5a512e7c4b04e7f73fe2777bd81277602. Anonymous
06:20 pm Story #12197: Add PDH column and filter to trash display
Lucas Di Pentima wrote:
> something like “PDH (Content address)” would be a good header alternative?
Sure, went w...
Tom Clegg
02:11 pm Story #12197: Add PDH column and filter to trash display
A couple of minor comments:
* File @apps/workbench/app/views/trash_items/_show_recent_trash.html.erb@
** Line 47:...
Lucas Di Pentima
01:29 pm Story #12197: Add PDH column and filter to trash display
!12197-search-pdh-0923.png! Tom Clegg
01:04 pm Story #12197: Add PDH column and filter to trash display
12197-show-pdh-in-trash @ commit:0923fecbf907d2aaa7f35775eba9ecd947eed098
https://ci.curoverse.com/job/developer-r...
Tom Clegg
06:26 pm Task #12202 (Resolved): Review 12197-show-pdh-in-trash
Tom Clegg
01:43 pm Task #12202 (In Progress): Review 12197-show-pdh-in-trash
Lucas Di Pentima
06:25 pm Revision a6d5c9b5 (arvados): Merge branch '12197-show-pdh-in-trash'
closes #12197
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
06:25 pm Revision e596f2e3 (arvados): Merge branch 'master' into 12197-show-pdh-in-trash
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
06:12 pm Revision 6249668b (arvados): 12197: Update PDH column label for consistency.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:32 pm Feature #12216: [keep-web] machine-readable file listings
We should also consider providing an S3-compatible API. Peter Amstutz
02:15 pm Feature #10763 (Resolved): [arvbox] [arvados-ws] Make arvbox use the new arvados-ws
Peter Amstutz
02:13 pm Revision 349e4b5e (arvados): Remove -f from 'docker tag' due to Docker update refs #12234
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:11 pm Revision 8bbc411d (arvados): 12279: Use selenium for workbench tests that access keep-web.
Needed for workbench tests to pass in Arvbox (workaround for PhantomJS bug).
Arvados-DCO-1.1-Signed-off-by: Peter Am...
Peter Amstutz
01:55 pm Revision cab4d8ce (arvados): 12125: Restore "move trashed items to home" behavior for now.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
01:03 pm Revision 0923fecb (arvados): 12197: Test PDH search and display on trash page.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:03 pm Revision 36c50d46 (arvados): 12197: Remove trash/delete labels on content rows.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg

09/15/2017

06:16 pm Bug #12273 (New): [crunch] Should not try to upload special files
If the output directory contains special files (such as named pipes) they should be ignored by the uploader. Verify ... Peter Amstutz
03:06 pm Feature #8333: [SDKs] `arv keep docker` supports `repo:tag` image name scheme
Jeff Jasper from q^2 bumped into this problem. Can we fix this? Nico César
12:33 pm Revision d3c3e67f (arvados): 12125: Fix 404 page when not showing a specific object.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:11 am Revision d1814ec4 (arvados): 12125: Workbench 404 page checks if item is in the trash.
Provides a convenient button to untrash it.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
01:35 am Revision 4b76af1a (arvados): 12125: Can browse trashed projects & untrash them.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
12:36 am Revision bf04f060 (arvados): 12125: Initial work, separate collection and project trash tabs.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
12:22 am Revision 786a15e9 (arvados): Arvbox support for caching and offline install of npm packages. no ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz

09/14/2017

11:39 pm Revision 1962fd79 (arvados): 12032: Add missing files.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision dd61e1fb (arvados): 12032: Make queries to groups table a special case, streamlines perm...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision d29a9a49 (arvados): 12032: Add copyright notice
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 9f649ad2 (arvados): 12032: Bug fix so include_trash still respects permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision b5c3577e (arvados): 12032: Test for ensure_unique_name when untrashing groups.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 375d03c0 (arvados): 12032: Refactor readable_by to minimize subqueries.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision fcb7d171 (arvados): 12032: Log.readable_by uses permission_view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision cdff1d7e (arvados): 12032: Controller support for group trash.
Conttroller support and testing for contents, index, show, trash, untrash,
containers.
Arvados-DCO-1.1-Signed-off-by...
Peter Amstutz
11:39 pm Revision 568f53d1 (arvados): 12032: Adding controller tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision d5eb6a70 (arvados): 12032: Add test fixtures
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 4fec5ed8 (arvados): 12032: Fix hiding trashed groups directly owned by user.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 2c5abff2 (arvados): 12032: Tests for group delete behavior.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision a079a9f1 (arvados): 12032: Rename permission_view and remove Rails permission cache.
Always refresh permission view when permission graph changes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz...
Peter Amstutz
11:39 pm Revision b02ee3ad (arvados): 12032: Fix owner_check to include user_uuids and target_owner_uuid
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 01da62c6 (arvados): 12032: Update install guide to specify minimum Postgres version of 9.3
Include instructions for using SCL to get a newer Postgres on CentOS7.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz ...
Peter Amstutz
11:39 pm Revision fb19f9e7 (arvados): 12032: Restore create_permission_view.sql with note that it is only
present for migration reasons.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
11:39 pm Revision b2922040 (arvados): 12032: Fix down migration.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision f6b5fd14 (arvados): 12032: Database reset used by integration tests refreshes permission...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 2bbce020 (arvados): 12032: Container readable check uses subquery instead join to avoid ...
duplicate rows.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
11:39 pm Revision 45691d64 (arvados): 12032: Update structure.sql from master schema + migration only.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 7dad4d2b (arvados): 12032: Remove startnode from materialized_permission_view (again), t...
without it.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
11:39 pm Revision e824b828 (arvados): 12032: Refresh materialized_permission_view immediately after migrat...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 4c9661ef (arvados): 12032: Remove hopefully-unnecessary view refreshes between tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 087d67e1 (arvados): 12032: Remove unnecessary checks on user_uuids.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision bd89394a (arvados): 12032: Remove user_uuid special case from all_perms.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 678f1f40 (arvados): 12032: Add permission_refresh_lock
This ensures that when refreshing the permission view in a transaction, any
other transactions affecting permissions ...
Peter Amstutz
11:39 pm Revision 2bbc9d8d (arvados): 12032: Add comments to migration. Also special case api_client_auth...
in readable_by.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
11:39 pm Revision e8abbc51 (arvados): 12032: Ensure that permission_view is invalidated & refreshed
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 7f0699fc (arvados): 12032: Added migration for materialized view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision c0777df3 (arvados): 12032: Controller & integration test teardown invalidates permission...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 0e1f8c8b (arvados): 12032: Update structure.sql
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 08aa32b0 (arvados): 12032: Don't need to refresh permission view in database seeds, shou...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 6f445067 (arvados): 12032: Benchmark for group permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision 3d83ff92 (arvados): 12032: Use permission_view in subquery to filter objects readable by...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
11:39 pm Revision f965ac6e (arvados): 12032: Additional refactoring of readable_by. Refactor "trashable" ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
08:55 pm Bug #12268 (New): Update to standard libcloud 2.x
We want to stop using a private fork of libcloud, but we need the regression in the current version fixed and release... Tom Morris
08:53 pm Story #8999 (Closed): [node manager] Upgrade to libcloud 2.0
Tom Morris
08:13 pm Story #8999 (New): [node manager] Upgrade to libcloud 2.0
Lucas Di Pentima
08:50 pm Task #12266 (New): Review
Tom Clegg
08:50 pm Task #12265 (New): Review
Tom Clegg
08:50 pm Task #12264 (New): Review
Lucas Di Pentima
08:50 pm Task #12263 (Resolved): Review 12247-no-failed-checksum
Tom Clegg
08:37 pm Bug #9900 (Resolved): [Crunch2] [API] Add ephemeral "run token" for running containers
Resolved in #8128 with the @auth_uuid@ column, except that it doesn't limit scope. Tom Clegg
08:29 pm Feature #12260 (New): Healthcheck endpoint aggregator
Tom Morris
08:18 pm Story #10537 (Duplicate): [Workbench] Add support for Trash Bin
Tom Morris
08:14 pm Bug #12196 (Resolved): [crunchstat-summary] avoid opening too many files at once when working on ...
Fixed in #10472, commit:b0ec12e8f75cc2bd97d110f8cda055f34d04c4de Tom Clegg
08:09 pm Task #12250 (Resolved): Review 12248-crunch2-reversemap
Peter Amstutz
03:57 pm Task #12250 (In Progress): Review 12248-crunch2-reversemap
Lucas Di Pentima
08:06 pm Task #12069 (Closed): Review
Tom Clegg
08:06 pm Task #12203 (Resolved): Review 12194-search-always-valid
Tom Clegg
07:58 pm Story #12197 (In Progress): Add PDH column and filter to trash display
Tom Clegg
03:28 pm Story #12197: Add PDH column and filter to trash display
Looks pretty good. Let's get rid of the trash: and delete: labels since they just make the alignment even more ragged... Tom Morris
07:55 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
I'd say it's worth adding a comment in the transaction block assuring the reader that "lock table" really is necessar... Tom Clegg
06:28 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Instead of "update ... set x=x+1", we should just do "lock table permission_update_lock" before refreshing the permis... Tom Clegg
05:29 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Tom Clegg wrote:
> The problem in note-41 seems to be that the race-losing "refresh materialized view" has already d...
Peter Amstutz
04:51 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
The problem in note-41 seems to be that the race-losing "refresh materialized view" has already decided to use the st... Tom Clegg
04:10 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
|pg client1|pg client 2|
|dirty = 1|dirty = 1|
|refresh||
|dirty = 0||
|update blah||
|dirty = 1|refresh|
|comm...
Peter Amstutz
03:55 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Thanks for looking at this.
Unfortunately, "FOR SHARE" and "FOR UPDATE" can't be used with "UNION" and "WITH RECUR...
Peter Amstutz
02:35 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
This seems important, so I tried using the postgres console to find out how races are handled.
Where "check" means...
Tom Clegg
07:06 pm Revision 1a97222f (arvados): 12032: Add permission_refresh_lock
This ensures that when refreshing the permission view in a transaction, any
other transactions affecting permissions ...
Peter Amstutz
04:25 pm Bug #12248 (Resolved): Failing CWL test in reverse path mapping
Applied in changeset arvados|commit:8078724be30f3df89eca3252921a2d1b8d14bea3. Peter Amstutz
04:17 pm Bug #12248: Failing CWL test in reverse path mapping
This LGTM, please merge. Lucas Di Pentima
04:18 pm Revision 8078724b (arvados): Merge branch '12248-crunch2-reversemap' closes #12248
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:20 pm Revision f1999e53 (arvados): Merge branch '12236-libcloud-blob-storage-regression'
Refs #12236
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima
03:03 pm Revision d73fa228 (arvados): 12236: Bumped libcloud version dependency to 2.2.1.dev2
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com> Lucas Di Pentima
12:55 pm Revision ba81565d (arvados-dev): Add missing debian9 target
no issue #
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@veritasgenetics.com>
Javier Bértoli
12:01 am Bug #12246: Better crunch-run error when command not found
At a minimum, the error message should include a quoted & escape version of the program that it is attempting to run ... Tom Morris

09/13/2017

09:07 pm Revision da3b350b (arvados): Merge branch '12194-search-always-valid'
closes #12194
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
09:01 pm Story #12197: Add PDH column and filter to trash display
Haven't updated tests yet.
How does this look?
12197-show-pdh-in-trash @ commit:6ac4615d13060a19d8cafbe35b67838...
Tom Clegg
08:59 pm Revision 6ac4615d (arvados): 12197: Show UUID and PDH of trashed collections.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:27 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Tom Clegg wrote:
> If the materialized view isn't protected by transactions like everything else, how can we convi...
Peter Amstutz
06:52 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Peter Amstutz wrote:
> Tom Clegg wrote:
> > Why do we need to explicitly invalidate the permission cache in test te...
Tom Clegg
05:53 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Tom Clegg wrote:
> Why do we need to explicitly invalidate the permission cache in test teardown, instead of relying...
Peter Amstutz
03:10 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Why do we need to explicitly invalidate the permission cache in test teardown, instead of relying on transactions lik... Tom Clegg
08:21 pm Bug #12073: [Node manager] Clean up stale arvados node records
Peter Amstutz wrote:
> Lucas Di Pentima wrote:
> > Is the nodemanager periodically restarted? If some cloud node go...
Peter Amstutz
08:04 pm Bug #12073: [Node manager] Clean up stale arvados node records
Lucas Di Pentima wrote:
> Is the nodemanager periodically restarted? If some cloud node goes down and the nodemanage...
Peter Amstutz
08:00 pm Bug #12073: [Node manager] Clean up stale arvados node records
Is the nodemanager periodically restarted? If some cloud node goes down and the nodemanager immediately restarts befo... Lucas Di Pentima
07:06 pm Bug #12073: [Node manager] Clean up stale arvados node records
Lucas Di Pentima wrote:
> Following a related ticket note: https://dev.arvados.org/issues/12064#note-2
>
> Is it ...
Peter Amstutz
06:52 pm Bug #12073: [Node manager] Clean up stale arvados node records
Following a related ticket note: https://dev.arvados.org/issues/12064#note-2
Is it safe to assume that the correct...
Lucas Di Pentima
08:14 pm Revision 42f4a3b6 (arvados): 12032: Don't need to refresh permission view in database seeds, shou...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
08:03 pm Revision 777466ea (arvados): 12197: Add missing end tags.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:00 pm Bug #12194 (Resolved): [API] [Workbench] Colons and ampersands in search should not produce errors
Split API improvement to #12251 Tom Clegg
07:59 pm Revision 60709456 (arvados): 12032: Remove user_uuid special case from all_perms.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
07:50 pm Revision 92817fd6 (arvados): 12032: Remove unnecessary checks on user_uuids.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
07:48 pm Bug #12251 (New): [API] Strict checks for "@@" filter operand
The operand of a @@ filter should be checked against a well-defined format.
* If the operand does not follow this fo...
Tom Clegg
07:43 pm Revision b6e83fea (arvados): 12032: Remove hopefully-unnecessary view refreshes between tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
07:37 pm Revision a6877341 (arvados): Merge branch '12194-search-always-valid'
refs #12194
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
07:11 pm Bug #12107: [API] jobs.create should not do slow git operations
(continuing from note-11, which I saved mid-investigation)
In any case, experiments confirm we can't rely on fetch...
Tom Clegg
06:24 pm Task #12250 (Resolved): Review 12248-crunch2-reversemap
Peter Amstutz
06:01 pm Bug #12249 (New): Default workbench login page mentions Google, even when not using Google login.
Peter Amstutz
05:56 pm Revision ffd559e0 (arvados): 12248: Bugfix reversemap.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:55 pm Bug #12248 (In Progress): Failing CWL test in reverse path mapping
Peter Amstutz
05:55 pm Bug #12248 (Resolved): Failing CWL test in reverse path mapping
https://ci.curoverse.com/job/run-cwl-test-9tee4/348/ Peter Amstutz
05:20 pm Revision 7afb849b (arvados): 12032: Update structure.sql from master schema + migration only.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 1d5af2a1 (arvados): 12032: Remove startnode from materialized_permission_view (again), t...
without it.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
05:20 pm Revision 60703281 (arvados): 12032: Refresh materialized_permission_view immediately after migrat...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 1f3c006a (arvados): 12032: Container readable check uses subquery instead join to avoid ...
duplicate rows.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
05:20 pm Revision d56460ec (arvados): 12032: Test for ensure_unique_name when untrashing groups.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision e8fe2247 (arvados): 12032: Bug fix so include_trash still respects permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision af508784 (arvados): 12032: Refactor readable_by to minimize subqueries.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 16f0b499 (arvados): 12032: Log.readable_by uses permission_view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 4b3fa8db (arvados): 12032: Database reset used by integration tests refreshes permission...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 4f5d7db1 (arvados): 12032: Fix down migration.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 4ccdb93d (arvados): 12032: Controller & integration test teardown invalidates permission...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 14539b19 (arvados): 12032: Update install guide to specify minimum Postgres version of 9.3
Include instructions for using SCL to get a newer Postgres on CentOS7.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz ...
Peter Amstutz
05:20 pm Revision 0135533f (arvados): 12032: Add missing files.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision ed90eac5 (arvados): 12032: Rename permission_view and remove Rails permission cache.
Always refresh permission view when permission graph changes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz...
Peter Amstutz
05:20 pm Revision 44cfaac5 (arvados): 12032: Benchmark for group permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 9c01c884 (arvados): 12032: Use permission_view in subquery to filter objects readable by...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 2f01a496 (arvados): 12032: Additional refactoring of readable_by. Refactor "trashable" ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 519397c2 (arvados): 12032: Tests for group delete behavior.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 8466e0d5 (arvados): 12032: Fix hiding trashed groups directly owned by user.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 77749bfa (arvados): 12032: Add test fixtures
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision ee834c5f (arvados): 12032: Adding controller tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision ff5e8724 (arvados): 12032: Controller support for group trash.
Conttroller support and testing for contents, index, show, trash, untrash,
containers.
Arvados-DCO-1.1-Signed-off-by...
Peter Amstutz
05:20 pm Revision 6d9a5247 (arvados): 12032: Add copyright notice
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 74635275 (arvados): 12032: Make queries to groups table a special case, streamlines perm...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision ddcda9c9 (arvados): 12032: Fix owner_check to include user_uuids and target_owner_uuid
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 24cc0db7 (arvados): 12032: Ensure that permission_view is invalidated & refreshed
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 2a954156 (arvados): 12032: Added migration for materialized view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision e7ed51cb (arvados): 12032: Update structure.sql
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:20 pm Revision 49a1825d (arvados): 12032: Add comments to migration. Also special case api_client_auth...
in readable_by.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
05:20 pm Revision 4a2f6ec8 (arvados): 12032: Restore create_permission_view.sql with note that it is only
present for migration reasons.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
05:17 pm Revision a58021c2 (arvados): 12032: Refresh materialized_permission_view immediately after migrat...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:06 pm Bug #12247: [keepproxy] Fix misleading log message when GET response is interrupted
Reproduced with curl on a dev cluster:... Tom Clegg
04:57 pm Bug #12247 (Resolved): [keepproxy] Fix misleading log message when GET response is interrupted
Reported on mailing list:... Tom Clegg
04:57 pm Task #12188 (Resolved): Review 12186-cwl-no-nameroot
Peter Amstutz
04:51 pm Bug #12246 (In Progress): Better crunch-run error when command not found
If a container specifies a command not found, or specifies a script with a #! line that isn't found, the error is ver... Peter Amstutz
03:51 pm Revision 341b921a (arvados): 12032: Remove startnode from materialized_permission_view (again), t...
without it.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
03:32 pm Revision 190e2b69 (arvados): 12032: Update structure.sql from master schema + migration only.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:54 pm Revision 7ed59a34 (arvados): Merge branch '12236-libcloud-blob-storage-regression'
Refs #12236
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima
02:47 pm Revision 0b3981f9 (arvados): 12236: Bumped libcloud to 2.2.1.dev2 that fixes a regression
related to alternate cloud environments.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics...
Lucas Di Pentima
02:15 pm Revision 5230dcc7 (arvados): 12032: Update db/structure.sql.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:32 pm Revision bd5a371c (arvados): 12107: Fix unreliable use of git-fetch.
Git-fetch does not fetch by sha1. If we can't find and fetch a branch
containing the desired commit, we still need to...
Tom Clegg
10:08 am Feature #12244 (New): API server bulk transfers for keep-balance collection retrieval
In Issue 9998 (https://dev.arvados.org/issues/9998) we managed to improve performance of retrieving batches of collec... Joshua Randall

09/12/2017

08:28 pm Bug #12241 (New): logo.png in API server is Clinical Future logo
Peter Amstutz
07:25 pm Story #12239 (New): Allow templating of the collection sharing web page
As a system administrator for a cluster with custom branding, I would like to use templating on the collection sharin... Tom Morris
05:57 pm Story #12234 (Resolved): Update arvbox to Debian 9, Docker 17
Peter Amstutz
05:57 pm Task #12235 (Resolved): Review 12234-arvbox-stretch
Peter Amstutz
04:10 pm Task #10381 (Resolved): Review
Peter Amstutz
04:06 pm Revision 091e05c8 (arvados): Fix arvbox-demo (2nd try) refs #12234
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:50 pm Bug #12186 (Resolved): [cwl] cwl.input.yml contains "nameroot" and "nameext" fields, breaks reuse...
Applied in changeset arvados|commit:194df852b504214879c005a0b730ab1e00395160. Peter Amstutz
03:44 pm Bug #12186: [cwl] cwl.input.yml contains "nameroot" and "nameext" fields, breaks reuse with RunIn...
Lucas Di Pentima wrote:
> As far as I can tell, this looks good to me. One question: would it be too complex to make...
Peter Amstutz
03:37 pm Bug #12186: [cwl] cwl.input.yml contains "nameroot" and "nameext" fields, breaks reuse with RunIn...
As far as I can tell, this looks good to me. One question: would it be too complex to make a test to prove that reuse... Lucas Di Pentima
03:44 pm Revision 194df852 (arvados): Merge branch '12186-cwl-no-nameroot' closes #12186
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:25 pm Bug #10349 (Resolved): [DOC] add cookbook section with code snippets
Applied in changeset arvados|commit:7385689b6fd8df96434aadf7c0377d684c4abe1c. Peter Amstutz
02:09 pm Bug #10349: [DOC] add cookbook section with code snippets
The parent uuids are inconsistent, and should just be one example: qr1hi-xvhdp-zzzzzzzzzzzzzzz
Please change all p...
Bryan Cosca
03:18 pm Revision 7385689b (arvados): Merge branch '10349-cookbook' closes #10349
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:15 pm Revision d9e495b5 (arvados): 10349: Add support for syntax highlighting inline code blocks.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
01:52 pm Task #12188 (New): Review 12186-cwl-no-nameroot
Peter Amstutz
01:51 pm Task #12188 (In Progress): Review 12186-cwl-no-nameroot
Lucas Di Pentima
01:47 pm Revision ea137ac2 (arvados): 10349: Add code snippet for combining collections.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
01:36 pm Bug #12107: [API] jobs.create should not do slow git operations
Ok, I ran the tests on jenkins just to be sure, and they passed without issues. LGTM, thanks! Lucas Di Pentima

09/11/2017

11:05 pm Bug #12194: [API] [Workbench] Colons and ampersands in search should not produce errors
This LGTM, except for the fact that "or" queries are not included, as described on note-6. Just mentioning this in ca... Lucas Di Pentima
08:59 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Another try, I think this will be the one: https://ci.curoverse.com/job/developer-run-tests/448/ Peter Amstutz
12:15 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
jenkins run @ https://ci.curoverse.com/job/developer-run-tests/441/ Peter Amstutz
08:57 pm Revision 037ecde4 (arvados): 12032: Container readable check uses subquery instead join to avoid ...
duplicate rows.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
06:18 pm Revision 199ecdd6 (arvados): 12032: Database reset used by integration tests refreshes permission...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
06:04 pm Revision b35c837c (arvados): Fix arvbox-demo refs #12234
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:21 pm Revision 03d60b32 (arvados): Merge branch '12234-arvbox-stretch' refs #12234
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:34 pm Story #12234: Update arvbox to Debian 9, Docker 17
It's working for me, LGTM. Thanks! Lucas Di Pentima
12:09 pm Story #12234: Update arvbox to Debian 9, Docker 17
Lucas Di Pentima wrote:
> After a little fiddling on my newly-upgraded-to-stretch dev VM, I managed to build and run...
Peter Amstutz
04:12 pm Revision e1423c97 (arvados): 12032: Fix down migration.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision 56c9d0d2 (arvados): 12032: Adding controller tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision a52710e2 (arvados): 12032: Bug fix so include_trash still respects permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision 2a67dce8 (arvados): 12032: Make queries to groups table a special case, streamlines perm...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision 02a097ee (arvados): 12032: Test for ensure_unique_name when untrashing groups.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision eb0c522b (arvados): 12032: Refactor readable_by to minimize subqueries.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision c0d473a9 (arvados): 12032: Log.readable_by uses permission_view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision 6f9a1ca5 (arvados): 12032: Controller support for group trash.
Conttroller support and testing for contents, index, show, trash, untrash,
containers.
Arvados-DCO-1.1-Signed-off-by...
Peter Amstutz
03:59 pm Revision f35de188 (arvados): 12032: Add test fixtures
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision adcd2315 (arvados): 12032: Add copyright notice
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision bb826fa2 (arvados): 12032: Fix hiding trashed groups directly owned by user.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision dba406e0 (arvados): 12032: Tests for group delete behavior.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision 960edc92 (arvados): 12032: Additional refactoring of readable_by. Refactor "trashable" ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision b8aa78fe (arvados): 12032: Use permission_view in subquery to filter objects readable by...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision 2a1e89e9 (arvados): 12032: Benchmark for group permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision daa752d7 (arvados): 12032: Fix owner_check to include user_uuids and target_owner_uuid
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision c5d47581 (arvados): 12032: Restore create_permission_view.sql with note that it is only
present for migration reasons.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
03:59 pm Revision b5a56c9e (arvados): 12032: Rename permission_view and remove Rails permission cache.
Always refresh permission view when permission graph changes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz...
Peter Amstutz
03:59 pm Revision 2dcf9520 (arvados): 12032: Add missing files.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision d4e2172b (arvados): 12032: Update install guide to specify minimum Postgres version of 9.3
Include instructions for using SCL to get a newer Postgres on CentOS7.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz ...
Peter Amstutz
03:59 pm Revision 51e3bde8 (arvados): 12032: Ensure that permission_view is invalidated & refreshed
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision 2f5acf2d (arvados): 12032: Added migration for materialized view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision 88f4b3e2 (arvados): 12032: Update structure.sql
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:59 pm Revision 4981c40d (arvados): 12032: Add comments to migration. Also special case api_client_auth...
in readable_by.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
03:59 pm Revision ad8b15c6 (arvados): 12032: Controller & integration test teardown invalidates permission...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:57 pm Revision 7a61a3b1 (arvados): 10349: Fix formatting. Add link from user guide to improve discover...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:51 pm Revision 42f6376c (arvados): 12234: Need --system so pip installs SDK packages globally.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:00 pm Revision c4f252e7 (arvados): 10349: Add snippts for listing inputs/outputs of containers, failed ...
requests, list logs of request.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
03:00 pm Revision 7f108bc7 (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
03:00 pm Revision 38e6bfb6 (arvados): 10349: Add "Create a collection sharing link"
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:59 pm Revision 52905eb4 (arvados): 10349: Add snippts for listing inputs/outputs of containers, failed ...
requests, list logs of request.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
01:42 pm Task #12203 (In Progress): Review 12194-search-always-valid
Lucas Di Pentima
12:56 pm Bug #12107: [API] jobs.create should not do slow git operations
Not sure why the same tests didn't fail for me but I have been able to reproduce this with "git fetch".
I found th...
Tom Clegg
12:18 pm Bug #12186: [cwl] cwl.input.yml contains "nameroot" and "nameext" fields, breaks reuse with RunIn...
Jenkins run @ https://ci.curoverse.com/job/developer-run-tests/440/ Peter Amstutz
12:11 pm Revision 45054326 (arvados): 12186: Filter nameroot/nameext from RunInSingleContainer and update ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
12:11 pm Revision ecf3cf1e (arvados): 12186: Filter nameroot from runner-submitted input object.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
12:01 pm Revision d5007925 (arvados): 12234: Update arvbox to Debian stretch, Docker 17, Postgres 9.6
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz

09/08/2017

10:20 pm Story #12234: Update arvbox to Debian 9, Docker 17
After a little fiddling on my newly-upgraded-to-stretch dev VM, I managed to build and run arvbox.
Attached is a scr...
Lucas Di Pentima
04:58 pm Story #12234 (In Progress): Update arvbox to Debian 9, Docker 17
Peter Amstutz
04:58 pm Story #12234 (Resolved): Update arvbox to Debian 9, Docker 17
Peter Amstutz
07:21 pm Task #12235 (In Progress): Review 12234-arvbox-stretch
Lucas Di Pentima
05:12 pm Task #12235 (Resolved): Review 12234-arvbox-stretch
Lucas Di Pentima
07:19 pm Bug #12107: [API] jobs.create should not do slow git operations
Running @services/api@ tests on my Debian 9 VM produced a lot of errors, like this one:... Lucas Di Pentima
02:14 am Bug #12107 (In Progress): [API] jobs.create should not do slow git operations
Tom Clegg
02:14 am Bug #12107: [API] jobs.create should not do slow git operations
12107-faster-git @ commit:32341a4777692a28358f2af5afa0d9e975e2da73
This makes the first two proposed improvements:...
Tom Clegg
07:02 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Peter Amstutz wrote:
> I'm not sure exactly what you mean? The structure.sql that is committed in the branch is the...
Tom Clegg
06:44 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Argh workbench tests are failing on jenkins (but API server's own tests pass). Might be failing to start up API serv... Peter Amstutz
06:37 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Tom Clegg wrote:
> Also
> * Add entry to [[Upgrading to master]]: upgrade to Postgres &ge;9.3, with link to docs fo...
Peter Amstutz
05:27 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Also
* Add entry to [[Upgrading to master]]: upgrade to Postgres &ge;9.3, with link to docs for migrating db to the ...
Tom Clegg
03:47 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Remaining TODOs:
* Resolve why some tests fail on jenkins
* -Rename materialized view so it doesn't conflict with...
Peter Amstutz
06:51 pm Story #12197: Add PDH column and filter to trash display
As we discussed during grooming, let's go with the approach of stacking the two dates to free up space for the PDH. I... Tom Morris
01:14 pm Story #12197: Add PDH column and filter to trash display
Confirmed the "filter by PDH" part already works. It's inconvenient to test, and not obvious that it's working, just ... Tom Clegg
06:38 pm Task #12126 (Resolved): API server support for trash
Peter Amstutz
06:29 pm Revision 84756b16 (arvados): 12032: Restore create_permission_view.sql with note that it is only
present for migration reasons.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
05:59 pm Revision fdea2cf2 (arvados): 12032: Update install guide to specify minimum Postgres version of 9.3
Include instructions for using SCL to get a newer Postgres on CentOS7.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz ...
Peter Amstutz
04:58 pm Revision 277132fa (arvados): 12234: Update arvbox to Debian stretch, Docker 17, Postgres 9.6
Peter Amstutz
04:36 pm Revision 2f6af007 (arvados): 12032: Add missing files.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision 135db618 (arvados): 12032: Rename permission_view and remove Rails permission cache.
Always refresh permission view when permission graph changes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz...
Peter Amstutz
04:22 pm Revision bba9a9be (arvados): Merge branch '10472-csummary-cwl-pipeline'
closes #10472
closes #12221
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
04:20 pm Revision 4e517a7b (arvados): 12033: Fix npm sanity-check recipe.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
04:17 pm Revision 4785d4a2 (arvados): 10472: Use itervalues() instead of iteritems() if key is not used.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
03:31 pm Task #12128 (In Progress): Review 12107-faster-git
Lucas Di Pentima
02:05 pm Revision 820ad7e2 (arvados): 10472: Fix logging format.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:05 pm Revision f2060a00 (arvados): 12221: Merge branch '12221-crunchstat-summary-valueerror'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:50 pm Revision 81d4874a (arvados): 12194: Update comment.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:20 am Bug #12134 (Resolved): [arv-mount] Fix test deadlock by using new llfuse in test suite
No test deadlocks since merge. Tom Clegg
02:17 am Revision bbf2bc5c (arvados): 12194: Handle to_tsquery(null).
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:12 am Revision 32341a47 (arvados): 12107: Use git-fetch instead of pack|unpack, and only when needed.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:51 am Bug #12194: [API] [Workbench] Colons and ampersands in search should not produce errors
12194-search-always-valid @ commit:43eb8f415a1a28bfb721892d51b5ba002ac113ea
(from note-5) "munge (or not munge) th...
Tom Clegg
01:45 am Revision 43eb8f41 (arvados): 12194: Fix empty search case.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:09 am Revision 9a9e79d7 (arvados): 12194: Fix accidentally mutated argument.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:09 am Revision 059027a1 (arvados): 12194: Construct @@ operands more carefully to avoid bad API munge.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg

09/07/2017

09:44 pm Revision 4587f806 (arvados): 12032: Controller & integration test teardown invalidates permission...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
09:04 pm Revision 9aff8a36 (arvados): 10472: Merge branch 'master' into 10472-csummary-cwl-pipeline
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
09:03 pm Revision 80ffee29 (arvados): 10472: Add test for arvados-cwl-runner job tree.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:59 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
I only have one of the failures Jenkins had.... Tom Clegg
08:19 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Tom Clegg wrote:
> If refreshing the materialized view follows the usual rules of consistency/locking/transactions...
Peter Amstutz
07:01 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Peter Amstutz wrote:
> Tom Clegg wrote:
> > Postgresql docs say "only one REFRESH at a time may run against any one...
Tom Clegg
05:38 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Tom Clegg wrote:
> Postgresql docs say "only one REFRESH at a time may run against any one materialized view" but we...
Peter Amstutz
03:07 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Tom Clegg wrote:
> Peter Amstutz wrote:
> > There's a passing test that asserts the 404 with a note we might change...
Peter Amstutz
03:01 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
There's a bit of a refresh race bug here too: the view can become stale between "refresh materialized view" and "set ... Tom Clegg
02:27 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Postgresql docs say "only one REFRESH at a time may run against any one materialized view" but we have no locking her... Tom Clegg
01:47 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
||Database query time for 1000 items|For 1 item|
|12032|Collection Load (491.5ms)|Collection Load (6.0ms)|
|master|...
Peter Amstutz
03:58 am Story #12032: Allow projects to be deleted (ie placed in the trash can)
12032-project-trash @ commit:893b9849ee1f3d407778a666702dfa300e0cebbc
Make permission_view a materialized view, wi...
Peter Amstutz
03:32 am Story #12032: Allow projects to be deleted (ie placed in the trash can)
Using materialized permission & better indexes:... Peter Amstutz
05:45 pm Revision e3c4b6b1 (arvados): 12032: Benchmark for group permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision dc38303d (arvados): 12032: Use permission_view in subquery to filter objects readable by...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision de75d524 (arvados): 12032: Tests for group delete behavior.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision 70eff8f8 (arvados): 12032: Fix hiding trashed groups directly owned by user.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision e034e0fa (arvados): 12032: Add test fixtures
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision 906482f1 (arvados): 12032: Adding controller tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision 07036ebe (arvados): 12032: Additional refactoring of readable_by. Refactor "trashable" ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision 8e7a4a55 (arvados): 12032: Log.readable_by uses permission_view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision bb19b61b (arvados): 12032: Refactor readable_by to minimize subqueries.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision ef3c1bf7 (arvados): 12032: Test for ensure_unique_name when untrashing groups.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision 51a3a54e (arvados): 12032: Bug fix so include_trash still respects permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision 66f5e61f (arvados): 12032: Add copyright notice
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision 44666813 (arvados): 12032: Make queries to groups table a special case, streamlines perm...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision d3967494 (arvados): 12032: Controller support for group trash.
Conttroller support and testing for contents, index, show, trash, untrash,
containers.
Arvados-DCO-1.1-Signed-off-by...
Peter Amstutz
05:45 pm Revision 3188061b (arvados): 12032: Ensure that permission_view is invalidated & refreshed
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision 4e82a971 (arvados): 12032: Added migration for materialized view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision 50a40811 (arvados): 12032: Update structure.sql
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:45 pm Revision d03fcecb (arvados): 12032: Add comments to migration. Also special case api_client_auth...
in readable_by.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
05:45 pm Revision 26a45f49 (arvados): 12032: Fix owner_check to include user_uuids and target_owner_uuid
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:39 pm Revision 397c9079 (arvados): 12032: Add comments to migration. Also special case api_client_auth...
in readable_by.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz
02:59 pm Revision 9b94f9f3 (arvados): 12032: Update structure.sql
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
01:05 pm Revision 23d1b7c2 (arvados): 12033: Fix tests.
refs #12033
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
03:41 am Revision 893b9849 (arvados): 12032: Added migration for materialized view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:12 am Revision 034a8c0c (arvados): 12032: Ensure that permission_view is invalidated & refreshed
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:57 am Revision f308830a (arvados): 12033: browserify is needed in production env, for package-building.
refs #12033
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg

09/06/2017

10:54 pm Revision f471e098 (arvados): 12033: Fix tests.
refs #12033
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
10:33 pm Revision b71baee6 (arvados): 12033: Fix tests.
refs #12033
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
09:20 pm Revision bc4e237b (arvados): 10472: Un-bork text reports.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:25 pm Revision 56c5c336 (arvados): 10472: Follow job trees made by arvados-cwl-runner jobs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:20 pm Revision 1fb7f4b3 (arvados): 10472: Follow children recorded in job['components'].
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:14 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
So the "startnode" workaround is needed to distinguish between "iteratively explore edges (startnode=true)" and "prop... Peter Amstutz
07:16 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Hm. My note-16 doesn't account for items that are accessible through direct permission links (i.e., where there would... Tom Clegg
07:03 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Special casing groups, and doing a simpler subquery on permission_view:... Peter Amstutz
07:01 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
OK, it sounds like you're saying the "trashed" column in permission_view is not actually what we want it to be, despi... Tom Clegg
06:37 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Tom Clegg wrote:
> I don't think the permission bug existed, and the fix should be reverted. Here's my reasoning:
>...
Peter Amstutz
05:01 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
master branch:... Peter Amstutz
02:03 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
I don't think the permission bug existed, and the fix should be reverted. Here's my reasoning:
* If we were followin...
Tom Clegg
08:06 pm Revision b0ec12e8 (arvados): 10472: Conserve FDs by not opening collections until ready to read.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:02 pm Revision 0edcfd8f (arvados): 12032: Make queries to groups table a special case, streamlines perm...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
08:02 pm Revision d950b79a (arvados): 12032: Fix owner_check to include user_uuids and target_owner_uuid
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
07:02 pm Revision b2d825bd (arvados): Merge branch '12033-multisite-search'
refs #12033
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
04:33 pm Revision ea272326 (arvados): 12032: Test for ensure_unique_name when untrashing groups.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision beba5383 (arvados): 12032: Add copyright notice
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision 9b065ae4 (arvados): 12032: Bug fix so include_trash still respects permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision fabd3046 (arvados): 12032: Fix hiding trashed groups directly owned by user.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision 5f11500a (arvados): 12032: Refactor readable_by to minimize subqueries.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision b8885362 (arvados): 12032: Use permission_view in subquery to filter objects readable by...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision 7c4cf01d (arvados): 12032: Controller support for group trash.
Conttroller support and testing for contents, index, show, trash, untrash,
containers.
Arvados-DCO-1.1-Signed-off-by...
Peter Amstutz
04:33 pm Revision 298b3361 (arvados): 12032: Adding controller tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision 3b30af08 (arvados): 12032: Add test fixtures
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision 2d321e4c (arvados): 12032: Additional refactoring of readable_by. Refactor "trashable" ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision 6f36f258 (arvados): 12032: Tests for group delete behavior.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision 02e5b421 (arvados): 12032: Log.readable_by uses permission_view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:33 pm Revision c97d9a11 (arvados): 12032: Benchmark for group permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
03:44 pm Task #12131 (In Progress): Review 12032-project-trash
Tom Clegg
03:30 pm Bug #12222 (Resolved): Typo in python documentation
Applied in changeset arvados|commit:25ee930328d52f818f53ed8ccd2e289f235c33d1. Anonymous
03:29 pm Bug #12222: Typo in python documentation
Thanks for your attention to detail and for filing the ticket, this is now fixed! Ward Vandewege
10:24 am Bug #12222 (Resolved): Typo in python documentation
... Andrey Solomatin
03:24 pm Revision 25ee9303 (arvados): Fix typo in python documentation.
closes #12222
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege
03:09 pm Revision b86917a2 (arvados): 12033: Document one-SaveUIState-per-page limitation.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
03:06 pm Revision 91448ce4 (arvados): 12033: Document SaveUIState.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:49 pm Revision 22418ed6 (arvados): Apply a few gofmt -s fixes.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege
02:22 pm Task #12066 (Resolved): Review 12055-nodemanager-ec2-tags
Nico César
01:14 pm Bug #12073 (In Progress): [Node manager] Clean up stale arvados node records
Lucas Di Pentima
11:04 am Revision 7825bb39 (arvados-dev): Add stretch to freight
refs #11572
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@veritasgenetics.com>
Javier Bértoli

09/05/2017

09:23 pm Revision 62387cc9 (arvados): Add Running to excluded non-categories. Improve error
Tom Morris
09:02 pm Revision a1d09f06 (arvados): Merge branch '12212-aws-instance-profile'
refs #12212
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima
08:29 pm Revision 232feac2 (arvados): 12033: Skip "show" btn if guessed workbench link is obviously wrong.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:27 pm Revision 5c724cff (arvados): 12033: Merge branch 'master' into 12033-multisite-search
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
07:46 pm Bug #12212: [arvados-node-manager] Instance-profile ARN request
Also added the example to the online docs - commit:ef5d9a98b Lucas Di Pentima
05:02 pm Bug #12212: [arvados-node-manager] Instance-profile ARN request
Should I merge the small update (commit:fdfa24a94)? Lucas Di Pentima
04:10 pm Bug #12212 (Resolved): [arvados-node-manager] Instance-profile ARN request
Nico César
07:45 pm Revision ef5d9a98 (arvados): 12212: Added example on web documentation
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com> Lucas Di Pentima
07:39 pm Revision 6d3dc6bf (arvados): Merge branch '12190-s3-read-after-write'
refs #12190
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
07:20 pm Bug #12194: [API] [Workbench] Colons and ampersands in search should not produce errors
From discussion offline:
* API should support queries like "foo bar", "foo & bar", "foo*&bar*", "foo* bar", "foo|bar...
Tom Clegg
04:13 pm Bug #9223 (In Progress): [Node manager] Uses huge amount of RAM on AWS
resolved in #12163 Nico César

09/04/2017

08:48 pm Revision a77e3ab6 (arvados): 12190: Don't test block existence before first write.
"Amazon S3 provides read-after-write consistency for PUTS of new
objects in your S3 bucket in all regions with one ca...
Tom Clegg
07:23 pm Feature #12216 (New): [keep-web] machine-readable file listings
Currently, keep-web serves human-readable directory listings using an HTML template but does not offer machine-readab... Tom Clegg
04:39 pm Story #8999: [node manager] Upgrade to libcloud 2.0
This is resolved by our updates on #12055. Right now we're using our 2.2.1.dev1 fork while waiting for libcloud to re... Lucas Di Pentima
04:37 pm Story #8999 (In Progress): [node manager] Upgrade to libcloud 2.0
Lucas Di Pentima
04:10 pm Bug #12020 (Closed): [Tests] Flaky test in Python SDK tests.test_events.WebsocketTest.test_subscr...
Doesn't seem to be flaky lately. Closing this until it re-appears. Lucas Di Pentima
04:10 pm Bug #12215: arvados-docker-cleaner broken on ubuntu precise (12.04)
I've installed python 3.6 from source on all humgen-0x-0x nodes and arvados-docker-cleaner is now running out of a vi... Joshua Randall
02:41 pm Bug #12215: arvados-docker-cleaner broken on ubuntu precise (12.04)
haha, right - I meant to say precise (12.04) on which the newest python is indeed 3.2 - ARGH! Joshua Randall
02:40 pm Bug #12215: arvados-docker-cleaner broken on ubuntu precise (12.04)
Actually it looks like python 3.4 is available on trusty but it isn't required by docker-py (which apparently should ... Joshua Randall
02:34 pm Bug #12215: arvados-docker-cleaner broken on ubuntu precise (12.04)
My guess at a fix would be to pin the version of python3-docker-py built on trusty so that it uses an older version o... Joshua Randall
02:27 pm Bug #12215 (New): arvados-docker-cleaner broken on ubuntu precise (12.04)
arvados-docker-cleaner does not start on trusty (ubuntu 12.04).
this appears to be because one of its dependencie...
Joshua Randall
03:45 pm Revision a78396a5 (arvados): 12033: Merge branch 'master' into 12033-multisite-search
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
03:45 pm Bug #12212: [arvados-node-manager] Instance-profile ARN request
Added config example at commit:fdfa24a94 Lucas Di Pentima
03:37 pm Bug #12212: [arvados-node-manager] Instance-profile ARN request
Reading nodemanager's code I noticed this bit on @services/nodemanager/arvnodeman/config.py@:... Lucas Di Pentima
02:43 pm Bug #12212 (In Progress): [arvados-node-manager] Instance-profile ARN request
Lucas Di Pentima
03:43 pm Revision fdfa24a9 (arvados): 12212: Adding configuration example for apllying instance profiles t...
computed nodes.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima

09/02/2017

06:33 pm Bug #12194: [API] [Workbench] Colons and ampersands in search should not produce errors
Investigation results:
* Yes, users want to be able to find files called "example_abc123-FOO.bar" by searching "exam...
Tom Clegg

09/01/2017

10:10 pm Bug #12055 (Resolved): [node manager] ec2 set tags on create
Applied in changeset arvados|commit:2ac65228ff6b32921e6c8194b6c51ce9a710f385. Anonymous
08:12 pm Bug #12055: [node manager] ec2 set tags on create
Updates at commit:1ba39510d
Test run: https://ci.curoverse.com/job/developer-run-tests/425/
Retrieve the node ima...
Lucas Di Pentima
07:56 pm Bug #12055: [node manager] ec2 set tags on create
Testing libcloud-2.2.1.dev1 & a-n-m from commit:b13876638cf57b400bd59513a0a1811b3d2993a1 on 4xphq showed a high RAM u... Lucas Di Pentima
04:07 pm Bug #12055: [node manager] ec2 set tags on create
The script @build/run-build-packages-one-target.sh@ already makes the deb package from our libcloud fork. I tried to ... Lucas Di Pentima
03:15 pm Bug #12055: [node manager] ec2 set tags on create
review @ commit:b13876638cf57b400bd59513a0a1811b3d2993a1

we have to be able to package the libcloud and check ...
Nico César
02:30 pm Bug #12055: [node manager] ec2 set tags on create
Update: Building all the packages made the package test succeed Lucas Di Pentima
10:04 pm Revision 2ac65228 (arvados): 12055: Merge branch '12055-nodemanager-ec2-tags'
Closes #12055
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima
08:06 pm Revision 1ba39510 (arvados): 12055: Avoid RAM exhaustion on bootup by asking AWS only the AMI
list owned by 'self'. refs #9223 #12163
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics....
Lucas Di Pentima
03:42 pm Task #12187 (Resolved): Review 12134-llfuse-patch
Tom Clegg
03:40 pm Bug #12134: [arv-mount] Fix test deadlock by using new llfuse in test suite
We'll have to update arvbox to stretch to make it pass tests. Tom Clegg
03:39 pm Bug #12134 (Feedback): [arv-mount] Fix test deadlock by using new llfuse in test suite
Tom Clegg
03:29 pm Revision 84f5a47b (arvados): Merge branch '12134-llfuse-patch'
refs #12134
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
03:22 pm Bug #12212 (Resolved): [arvados-node-manager] Instance-profile ARN request
When creating a instance, is good to have the option of an instance-profile ARN so some policies con be applied ( for... Nico César

08/31/2017

10:11 pm Bug #12055: [node manager] ec2 set tags on create
Updates at commit:b13876638cf57b400bd59513a0a1811b3d2993a1
Created new 2.2.1.dev1 branch including the latest fixe...
Lucas Di Pentima
07:45 pm Bug #12055: [node manager] ec2 set tags on create
Also, make sure to test package building (this is how I noticed the versioning problems above).... Peter Amstutz
07:26 pm Bug #12055: [node manager] ec2 set tags on create
If the stable release of libcloud is 2.2.0, we need our fork to be 2.2.1.dev1. Right now we have a package filename ... Peter Amstutz
03:14 pm Bug #12055: [node manager] ec2 set tags on create
Running the entire test suite against the latest @libcloud 2.2.0.dev1@ changes: https://ci.curoverse.com/job/develope... Lucas Di Pentima
08:43 pm Bug #12194: [API] [Workbench] Colons and ampersands in search should not produce errors
I suspect losing prefix matching would be a regression. One of the use cases for full text search is searching for s... Peter Amstutz
07:55 pm Bug #12194: [API] [Workbench] Colons and ampersands in search should not produce errors
12194-fulltext-plain-query @ commit:9e433e06ab2a11fbaaf73c5082c2a64eff596856
Tom Clegg
08:40 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Peter Amstutz wrote:
> There's a passing test that asserts the 404 with a note we might change it later. We can mak...
Tom Clegg
08:03 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Tom Clegg wrote:
> Following through users is the desired behavior when there's a group&rarr;user "manage" link. W...
Peter Amstutz
07:50 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
Asking for a few clarifications before looking at the code:
Peter Amstutz wrote:
> * Fix bug in permission_view w...
Tom Clegg
05:44 pm Story #12032: Allow projects to be deleted (ie placed in the trash can)
12032-project-trash @ commit:dfcbdd5823bf85a462305a58df79a0112d3020d8
* Updates permission_view to propagate "tras...
Peter Amstutz
08:16 pm Revision b1387663 (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
08:15 pm Revision 25c27bf2 (arvados): 12055: Updated dev version number & dependency scripts
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com> Lucas Di Pentima
06:58 pm Revision 3cc3a2f5 (arvados): 12032: Add copyright notice
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
06:50 pm Revision dfcbdd58 (arvados): 12032: Bug fix so include_trash still respects permissions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
05:37 pm Revision 9e433e06 (arvados): 12194: Use plainto_tsquery() for full-text search.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
05:37 pm Revision 69c60233 (arvados): 12194: Test colons in fulltext search.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
04:10 pm Revision 1b077e15 (arvados): 12032: Test for ensure_unique_name when untrashing groups.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:59 pm Bug #12134: [arv-mount] Fix test deadlock by using new llfuse in test suite
Tried to run the tests repeatedly on my VM, but @llfuse@ requires @cython 0.24+@ and Debian Jessie doesn't have it.
...
Lucas Di Pentima
02:41 pm Revision 5b0057c6 (arvados): 12032: Log.readable_by uses permission_view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:41 pm Revision d901415a (arvados): 12032: Refactor readable_by to minimize subqueries.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:41 pm Revision 549a1cc8 (arvados): 12032: Adding controller tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:41 pm Revision 5e161d86 (arvados): 12032: Controller support for group trash.
Conttroller support and testing for contents, index, show, trash, untrash,
containers.
Arvados-DCO-1.1-Signed-off-by...
Peter Amstutz
02:41 pm Revision 0365e9f3 (arvados): 12032: Additional refactoring of readable_by. Refactor "trashable" ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:41 pm Revision 724da26e (arvados): 12032: Fix hiding trashed groups directly owned by user.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:41 pm Revision 9620f75a (arvados): 12032: Tests for group delete behavior.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:41 pm Revision 4e40ff2a (arvados): 12032: Use permission_view in subquery to filter objects readable by...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:41 pm Revision 61ba951a (arvados): 12032: Add test fixtures
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:37 pm Revision d0700464 (arvados): 12032: Refactor readable_by to minimize subqueries.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
02:18 pm Revision 87ba27e4 (arvados): 10472: Ignore "Running [command]" log message from crunchstat.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg

08/30/2017

09:33 pm Revision d62a499c (arvados): 10349: Add "Create a collection sharing link"
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
08:49 pm Revision d5bdc7be (arvados): 12194: Use plainto_tsquery() for full-text search.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
08:41 pm Bug #12194 (In Progress): [API] [Workbench] Colons and ampersands in search should not produce er...
Tom Clegg
01:46 pm Bug #12194 (Resolved): [API] [Workbench] Colons and ampersands in search should not produce errors
Currently, typing "bcbio:latest" in the Workbench search box results in a filter like ["any","@@","bcbio:latest"], wh... Tom Clegg
08:10 pm Task #12205 (New): Review
Peter Amstutz
08:09 pm Task #12203 (Resolved): Review 12194-search-always-valid
Tom Clegg
08:09 pm Task #12202 (Resolved): Review 12197-show-pdh-in-trash
Tom Clegg
08:09 pm Task #12126 (In Progress): API server support for trash
Peter Amstutz
08:09 pm Task #12201 (In Progress): Review 12073-nodemanager-stale-nodes-recs
Lucas Di Pentima
08:09 pm Task #12200 (New): Review
Peter Amstutz
08:05 pm Bug #12199 (New): Don't schedule jobs on nodes which are bigger than requested
Tom Morris
07:50 pm Bug #10584: [FUSE] high memory consumption (possible leak) in long-running arv-mount
Might be worth running the "retry PUT" test many times in a row. At least once I've seen the test suite get stuck the... Tom Clegg
07:45 pm Bug #12198 (New): Copying a project with a docker image doesn't copy the docker metadata
Tom Morris
07:03 pm Story #12197 (Resolved): Add PDH column and filter to trash display
Tom Morris
06:47 pm Story #12032 (In Progress): Allow projects to be deleted (ie placed in the trash can)
Peter Amstutz
06:46 pm Bug #11925 (Resolved): [Nodemanager] Fix unit tests
Peter Amstutz
06:45 pm Bug #12196 (Resolved): [crunchstat-summary] avoid opening too many files at once when working on ...
The new --threads argument limits CPU and memory use, so now instead of crashing on a large (500+ container) workflow... Tom Clegg
06:38 pm Task #12187 (In Progress): Review 12134-llfuse-patch
Lucas Di Pentima
06:38 pm Bug #10359 (Resolved): [crunchstat-summary] Limit concurrency to keep memory use under control
Tom Clegg
05:13 pm Revision 37fce338 (arvados): 12032: Log.readable_by uses permission_view
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
04:59 pm Task #12143 (Resolved): Exercise test suite with patched llfuse
Tom Clegg
03:34 pm Bug #12055: [node manager] ec2 set tags on create
Stress test run successful at: https://workbench.4xphq.arvadosapi.com/pipeline_instances/4xphq-d1hrv-mspsxk8tgxfmwhd Lucas Di Pentima
11:17 am Bug #12055: [node manager] ec2 set tags on create
Created a new branch on our @libcloud@ fork, based against upstream version 2.2: https://github.com/curoverse/libclou... Lucas Di Pentima
03:30 pm Revision b29fdd27 (arvados): 4878: Fix whitespace and missing </p> tag.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
03:19 pm Revision 526f3e54 (arvados): 12033: Avoid startsWith(), unsupported in test suite.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
03:15 pm Revision 582ba85e (arvados): 12033: Disable/hide multi-site search by default.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
03:14 pm Revision ba244db1 (arvados): 12033: Add Object.assign polyfill for test suite.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
03:06 pm Revision 18d29e3e (arvados): 12032: Controller support for group trash.
Conttroller support and testing for contents, index, show, trash, untrash,
containers.
Arvados-DCO-1.1-Signed-off-by...
Peter Amstutz
01:30 pm Revision c46c3134 (arvados): Merge branch '11898-no-distinct'
refs #11898
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
11:10 am Revision 83e42852 (arvados): 12055: Changed nodemanager's libcloud dependency to use our v2.2
fork.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima
01:09 am Revision 4f05fc9a (arvados): Workbench: when showing the detail for script_parameters in the pipe...
instance or work unit view, do not limit that field to half the screen
for no reason.
No issue #
Arvados-DCO-1.1-Si...
Ward Vandewege

08/29/2017

06:50 pm Story #12191 (New): Support SLURM parameter passthrough from CWL jobs
The list of arguments which can be specified by users is configurable by the site admins with the default list being ... Tom Morris
06:10 pm Feature #12167: [SDKs] [API] [keepstore] [keepproxy] Facilitate request tracing for arv-put
This should be done in such a way that all clients can benefit from it, although the one we're most interested in is ... Tom Clegg
06:01 pm Story #12189 (New): Support generic resource requests for run time constraints
In a similar fashion to the way SLURM does for Generic Resource Scheduling https://slurm.schedmd.com/gres.html
Bas...
Tom Morris
04:59 pm Bug #12186 (In Progress): [cwl] cwl.input.yml contains "nameroot" and "nameext" fields, breaks re...
Peter Amstutz
01:48 pm Bug #12186 (Resolved): [cwl] cwl.input.yml contains "nameroot" and "nameext" fields, breaks reuse...
Peter Amstutz
04:58 pm Task #12188 (Resolved): Review 12186-cwl-no-nameroot
Peter Amstutz
03:19 pm Bug #12020: [Tests] Flaky test in Python SDK tests.test_events.WebsocketTest.test_subscribe_poll
I ran this test locally 400 times without a failure, nevertheless on Jenkins it fails from time to time. Could it be ... Lucas Di Pentima
02:01 pm Bug #12020 (In Progress): [Tests] Flaky test in Python SDK tests.test_events.WebsocketTest.test_s...
Lucas Di Pentima
02:45 pm Revision d047c1cb (arvados): 12033: Add config to link multi-site search to a remote site.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:05 pm Task #12187 (Resolved): Review 12134-llfuse-patch
Tom Clegg
01:29 pm Revision 99c19e15 (arvados): 12134: Minimize multiprocessing worker startups.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
01:29 pm Revision 545ea1b1 (arvados): 12134: Use fixed/unreleased llfuse in test suite.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com> Tom Clegg
01:26 pm Bug #12134: [arv-mount] Fix test deadlock by using new llfuse in test suite
at commit:7c92bc77b, ran fuse tests 50 times in a row with no deadlocks, interrupted by this (non-deadlocking) failur... Tom Clegg
05:30 am Revision bb91f86e (arvados): Merge branch 'master' into 11898-no-distinct
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg

08/28/2017

02:16 pm Bug #12183 (New): [crunch-run] Handle symlinks with absolute paths into output directory
This is suspicious:
2017-08-28T11:09:17.982121623Z CMD: ln -s /var/spool/cwl/STAR-Fusion_outdir/star-fusion.prelim...
Peter Amstutz
01:59 pm Bug #12178: Activating an account (setting is_active from false to true) does not email the new user
I tested with a new user on a customer cluster. Bryan Cosca
01:57 pm Revision dc480344 (arvados): Bump cwltool to eliminate nameext/nameroot in output. refs #12100
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
01:57 pm Task #11894 (Resolved): Review 11309-crunchstat-summary-containers
Lucas Di Pentima
01:57 pm Revision f0fe91a7 (arvados): 12032: Adding controller tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz

08/26/2017

02:18 am Revision ecaf4e93 (arvados): 12033: Improve multi-site search navigation a bit.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg
02:15 am Revision 04123029 (arvados): 12033: Canary query before initiating login procedure.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com> Tom Clegg

08/25/2017

09:41 pm Bug #12178: Activating an account (setting is_active from false to true) does not email the new user
All users and clusters? I'm pretty sure this used to work. Tom Morris
07:04 pm Bug #12178 (New): Activating an account (setting is_active from false to true) does not email the...
Bryan Cosca
06:39 pm Bug #10349: [DOC] add cookbook section with code snippets
Ideas to add: (These are things I think I know how to do, but think other people would want) This all comes from a de... Bryan Cosca
06:23 pm Revision f1834827 (arvados): 12032: Add test fixtures
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
01:16 pm Bug #12170 (New): crunch-run handling non-group readable files in output directory
Some tools apply a 0200 mask to their output. This breaks crunch-run which relies on group rw permission to be able ... Peter Amstutz
01:58 am Revision 01b6cbdf (arvados): 12032: Fix hiding trashed groups directly owned by user.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz

08/24/2017

09:09 pm Revision 6b928cd8 (arvados): 12032: Tests for group delete behavior.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
08:22 pm Revision a263160f (arvados): 12032: Additional refactoring of readable_by. Refactor "trashable" ...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz
07:40 pm Story #4305: [Node Manager] Investigate and try to address RAM use
see #12163
Nico César
05:32 pm Feature #12167 (New): [SDKs] [API] [keepstore] [keepproxy] Facilitate request tracing for arv-put
h2. Background
When an arv-put process is slow or broken, it is useful to grep logs for related server-side activi...
Nico César
04:03 pm Revision 59d6af85 (arvados): 12032: Use permission_view in subquery to filter objects readable by...
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com> Peter Amstutz

08/22/2017

05:53 pm Revision 12b7c5ad (arvados-dev): Remove obsolete script, add dependencies for cwl tests.
refs #12157 Javier Bértoli
03:30 pm Revision 3389110d (arvados): Update test to match new log message.
refs #11309
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg
02:43 pm Story #11309 (Resolved): [Crunch2] crunchstat-summary --container UUID should summarize container...
Tom Clegg
 

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