radhika [Wed, 7 Jun 2017 14:30:22 +0000 (10:30 -0400)]
closes #11652
Merge branch '11652-recursive-contents-wb'
radhika [Wed, 7 Jun 2017 14:29:30 +0000 (10:29 -0400)]
11652: fix comment on test
Tom Clegg [Wed, 7 Jun 2017 14:27:59 +0000 (10:27 -0400)]
11809: Prune collection cache asynchronously.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Wed, 7 Jun 2017 14:27:06 +0000 (10:27 -0400)]
11809: Rename FooEntries -> MaxFooEntries in cache config.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Wed, 7 Jun 2017 14:23:41 +0000 (10:23 -0400)]
11809: Add /status.json handler.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Lucas Di Pentima [Wed, 7 Jun 2017 13:45:53 +0000 (10:45 -0300)]
11557: Merge branch 'master' into 11557-acr-output-col-perms
radhika [Tue, 6 Jun 2017 19:49:34 +0000 (15:49 -0400)]
Merge branch 'master' into 11652-recursive-contents-wb
Tom Clegg [Tue, 6 Jun 2017 19:22:57 +0000 (15:22 -0400)]
Merge branch '11652-recursive-contents'
refs #11652
Tom Clegg [Tue, 6 Jun 2017 19:21:28 +0000 (15:21 -0400)]
11809: More cache tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Tue, 6 Jun 2017 19:12:53 +0000 (15:12 -0400)]
11809: Add unit test for cache.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Tue, 6 Jun 2017 17:53:36 +0000 (13:53 -0400)]
11652: Merge branch 'master' into 11652-recursive-contents
Tom Clegg [Tue, 6 Jun 2017 17:53:25 +0000 (13:53 -0400)]
11652: Add tests for non-recursive and home-project cases.
radhika [Tue, 6 Jun 2017 17:06:19 +0000 (13:06 -0400)]
11652: use "recursive=true" in workbench search requests
Tom Clegg [Tue, 6 Jun 2017 15:57:34 +0000 (11:57 -0400)]
11809: Cache permission and collection lookups.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
radhika [Tue, 6 Jun 2017 15:17:29 +0000 (11:17 -0400)]
Merge branch 'master' into 11652-recursive-contents
radhika [Tue, 6 Jun 2017 15:07:36 +0000 (11:07 -0400)]
closes #9587
Merge branch '9587-trash-page'
radhika [Tue, 6 Jun 2017 15:01:06 +0000 (11:01 -0400)]
9587: rename pane name to "Recent trash"
Peter Amstutz [Tue, 6 Jun 2017 13:31:46 +0000 (09:31 -0400)]
10312: Add services/nodemanager-integration to test list
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>
radhika [Tue, 6 Jun 2017 00:40:46 +0000 (20:40 -0400)]
9587: sort the trash page rows by trash_at timestamp
radhika [Tue, 6 Jun 2017 00:29:18 +0000 (20:29 -0400)]
Merge branch 'master' into 9587-trash-page
radhika [Mon, 5 Jun 2017 22:58:03 +0000 (18:58 -0400)]
closes #9587
Merge branch '9587-trash-page'
radhika [Fri, 2 Jun 2017 21:31:04 +0000 (17:31 -0400)]
9587: sort order issue
radhika [Wed, 31 May 2017 19:03:53 +0000 (15:03 -0400)]
9587: expose untrash api
radhika [Tue, 30 May 2017 22:35:06 +0000 (18:35 -0400)]
9587: trash page
Peter Amstutz [Mon, 5 Jun 2017 20:40:30 +0000 (16:40 -0400)]
10312: Fix unit tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>
Peter Amstutz [Fri, 2 Jun 2017 21:35:15 +0000 (17:35 -0400)]
10312: Tests pass for booting single node, multiple nodes, hitting quota, quota
probe. Add node manager integration to run-tests.sh.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>
radhika [Mon, 5 Jun 2017 17:00:02 +0000 (13:00 -0400)]
closes #4921
Merge branch '4921-clear-modal-preview-pane'
Tom Clegg [Mon, 5 Jun 2017 14:06:26 +0000 (10:06 -0400)]
Merge branch '9005-share-discovery'
closes #9005
Lucas Di Pentima [Mon, 5 Jun 2017 13:43:07 +0000 (10:43 -0300)]
11557: Don't assume log, output and components are always present on a job record.
This was causing some tests to fail.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima [Mon, 5 Jun 2017 12:54:29 +0000 (09:54 -0300)]
11557: Create can_read link on reused jobs
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Lucas Di Pentima [Mon, 5 Jun 2017 12:20:20 +0000 (09:20 -0300)]
11557: Added log collection copying to local project when reusing jobs
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
radhika [Sat, 3 Jun 2017 15:08:39 +0000 (11:08 -0400)]
4921: also clear preview pane when a project is selected from projects dropdown menu
radhika [Fri, 2 Jun 2017 21:45:06 +0000 (17:45 -0400)]
9587: show trash page contents in Recent tab pane
radhika [Fri, 2 Jun 2017 21:31:04 +0000 (17:31 -0400)]
9587: sort order issue
Tom Clegg [Fri, 2 Jun 2017 19:43:28 +0000 (15:43 -0400)]
9005: Serve keep_services/accessible regardless of auth status.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Fri, 2 Jun 2017 18:58:28 +0000 (14:58 -0400)]
11652: Update API docs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Fri, 2 Jun 2017 18:53:20 +0000 (14:53 -0400)]
11652: Add "recursive" flag to groups#contents controller.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
radhika [Fri, 2 Jun 2017 17:55:06 +0000 (13:55 -0400)]
closes #4921
Merge branch '4921-clear-modal-preview-pane'
Peter Amstutz [Fri, 2 Jun 2017 15:58:55 +0000 (11:58 -0400)]
10312: Integration test framework for node manager, runs full node manager with
fake cloud driver and monitors logging output.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>
Lucas Di Pentima [Fri, 2 Jun 2017 02:15:37 +0000 (23:15 -0300)]
11557: Copy reused job's output to a collection on specified project (or Home project by default)
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Tom Clegg [Thu, 1 Jun 2017 21:37:37 +0000 (17:37 -0400)]
9005: Replace matchTrue regexp with StringBool func.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Peter Amstutz [Thu, 1 Jun 2017 21:37:09 +0000 (17:37 -0400)]
10312: Adding ability to substitute fake libcloud driver but run full node manager for integration testing.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>
radhika [Thu, 1 Jun 2017 20:09:24 +0000 (16:09 -0400)]
4921: clear preview pane when the selectable container is cleared
Tom Clegg [Thu, 1 Jun 2017 19:31:26 +0000 (15:31 -0400)]
9005: Restore "refresh services on SIGHUP" to keepproxy.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Thu, 1 Jun 2017 19:26:42 +0000 (15:26 -0400)]
9005: Rename ClearCache to RefreshServiceDiscovery
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Peter Amstutz [Thu, 1 Jun 2017 14:07:49 +0000 (10:07 -0400)]
10312: Identify error message that look like we are hitting a quota or account limit. Set soft node quota in order to stop trying to boot new nodes until the total node count goes down. Probe node quota upward when at the soft limit and able to boot nodes successfully.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>
radhika [Thu, 1 Jun 2017 18:05:46 +0000 (14:05 -0400)]
9587: include "owner" in trash rows; update trash icon.
radhika [Thu, 1 Jun 2017 16:59:57 +0000 (12:59 -0400)]
9587: test /trash page
Lucas Di Pentima [Thu, 1 Jun 2017 14:53:31 +0000 (11:53 -0300)]
11557: Simplifying conditional usage
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@curoverse.com>
Tom Clegg [Thu, 1 Jun 2017 01:49:43 +0000 (21:49 -0400)]
9005: Tidy up test suite.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Thu, 1 Jun 2017 01:48:52 +0000 (21:48 -0400)]
9005: Fix test cases to accommodate service discovery changes.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
radhika [Wed, 31 May 2017 21:16:48 +0000 (17:16 -0400)]
9587: cleanup trashed_items method
radhika [Wed, 31 May 2017 20:54:57 +0000 (16:54 -0400)]
9587: display name instead of clickable link and remove tags
Tom Clegg [Wed, 31 May 2017 18:16:43 +0000 (14:16 -0400)]
9005: Keep service discovery up to date automatically.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Tue, 30 May 2017 19:24:45 +0000 (15:24 -0400)]
9005: De-duplicate arvadosclient setup.
Fix ignored KeepServiceURIs when using an arvados.Client to create an
arvadosclient.ArvadosClient.
Fix ARVADOS_API_HOST_INSECURE=no or =false interpreted as "insecure
mode" in arvados.Client setup.
Log & ignore invalid entries in ARVADOS_KEEP_SERVICES in
arvados.Client setup. Handle extra separator chars more gracefully.
Tom Clegg [Tue, 30 May 2017 19:22:21 +0000 (15:22 -0400)]
11720: Fix go test recipe so *_test=-check.vv uses vendor dir, too.
Tom Clegg [Wed, 31 May 2017 20:13:50 +0000 (16:13 -0400)]
Merge branch '9005-keep-http-client'
refs #9005
Tom Clegg [Wed, 31 May 2017 20:12:44 +0000 (16:12 -0400)]
9005: Modify default transport instead of building from scratch.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Tom Clegg [Wed, 31 May 2017 19:46:29 +0000 (15:46 -0400)]
9005: Remove periodic CloseIdleConnections().
This is unnecessary now that the transport has a non-zero
IdleConnTimeout.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
radhika [Wed, 31 May 2017 19:03:53 +0000 (15:03 -0400)]
9587: expose untrash api
Tom Clegg [Wed, 31 May 2017 19:03:10 +0000 (15:03 -0400)]
9005: Copy default transport if possible. Move magics to consts.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
Peter Amstutz [Wed, 31 May 2017 18:26:01 +0000 (14:26 -0400)]
Merge branch '11766-workflow-deadlock' closes #11766
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>
radhika [Wed, 31 May 2017 17:33:54 +0000 (13:33 -0400)]
Merge branch 'master' into 9587-trash-page
radhika [Wed, 31 May 2017 17:33:19 +0000 (13:33 -0400)]
9587: untrash option
radhika [Wed, 31 May 2017 15:22:43 +0000 (11:22 -0400)]
9587: tab line buttons in trash page
radhika [Tue, 30 May 2017 22:35:06 +0000 (18:35 -0400)]
9587: trash page
Lucas Di Pentima [Tue, 30 May 2017 21:24:23 +0000 (18:24 -0300)]
Merge branch '11684-unsigned-locator-fix'
Closes #11684
Lucas Di Pentima [Tue, 30 May 2017 20:56:07 +0000 (17:56 -0300)]
11684: ArvadosFile.flush() now check if it is the only owner of a bufferblock before deleting it, so the extra argument is not required.
On commit_all(), always check if the owner attribute is an instance of ArvadosFile before calling flush()
Fixed a couple tests that were mocking bufferblock.owner so that they work with this new behavior.
Peter Amstutz [Tue, 30 May 2017 18:42:34 +0000 (14:42 -0400)]
Merge branch '11767-squeue-reasons' refs #11767
Peter Amstutz [Tue, 30 May 2017 18:34:39 +0000 (14:34 -0400)]
11767: Make squeue format output pipe (|) delimited so that it doesn't get
confused by spaces in the "Reasons" column
Lucas Di Pentima [Tue, 30 May 2017 17:07:41 +0000 (14:07 -0300)]
11684: Merge branch 'master' into 11684-unsigned-locator-fix
Peter Amstutz [Tue, 30 May 2017 15:18:41 +0000 (11:18 -0400)]
Merge branch '11769-scancel-jobs-only' closes #11769
Tom Clegg [Mon, 29 May 2017 22:15:24 +0000 (18:15 -0400)]
9005: Share http Transports and Clients across KeepClients.
radhika [Mon, 29 May 2017 19:56:26 +0000 (15:56 -0400)]
closes #11739 , #11751
Merge branch '11739-container-requests-in-dashboard'
radhika [Mon, 29 May 2017 17:19:05 +0000 (13:19 -0400)]
11739: preload containers and children of all container_requests in dashboard display.
11751: in /container_requests page, use the column name "Name" and display either name of uuid of the object.
Lucas Di Pentima [Mon, 29 May 2017 16:59:14 +0000 (13:59 -0300)]
11684: Instead of fiddling with ArvadosFile object's internals from the BlockManager
put threads to update the segments locators when committing synchronously a block
built from smaller blocks, take advantage of ArvadosFile.flush() existing mechanism
to update unrealized segments locators by building a list of bufferblock owners
and calling all owner's flush() method on commit_all().
To avoid calling delete_bufferblock() many times on a single bufferblock, added
a flag on flush() and delete the bufferblock after flushing all owners.
Peter Amstutz [Fri, 26 May 2017 17:29:45 +0000 (13:29 -0400)]
11766: Bump cwltool version for deadlock fix.
Peter Amstutz [Fri, 26 May 2017 20:22:10 +0000 (16:22 -0400)]
Fix crunch script to set trash_intermediate and intermediate_output_ttl refs #11100
Peter Amstutz [Fri, 26 May 2017 19:49:32 +0000 (15:49 -0400)]
11769: HasUuid::UUID_REGEX matches anything that looks like an Arvados uuid. As a result, if crunchv1 and crunchv2 dispatchers are on the same cluster, crunch-dispatch.rb will try to scancel containers thinking they are "orphan jobs". Tighten the regex to only match job uuids.
Peter Amstutz [Fri, 26 May 2017 19:32:46 +0000 (15:32 -0400)]
Merge branch '11767-slurm-units' refs #11767
Peter Amstutz [Fri, 26 May 2017 19:31:57 +0000 (15:31 -0400)]
11767: Test cases that it will convert fractional values from squeue.
Peter Amstutz [Fri, 26 May 2017 19:25:56 +0000 (15:25 -0400)]
11767: Slurm apparently will print out half values (like 2.5G).
Peter Amstutz [Fri, 26 May 2017 19:14:12 +0000 (15:14 -0400)]
11767: Recognize lowercase suffixes, just in case future versions of slurm
change the format again.
Peter Amstutz [Fri, 26 May 2017 18:48:16 +0000 (14:48 -0400)]
11767: Correctly parse values with unit suffixes printed by squeue.
Peter Amstutz [Fri, 26 May 2017 18:21:34 +0000 (14:21 -0400)]
Merge branch '11100-cwl-set-output-ttl' closes #11100
Peter Amstutz [Fri, 26 May 2017 18:21:01 +0000 (14:21 -0400)]
Merge branch 'master' into 11100-cwl-set-output-ttl
Peter Amstutz [Fri, 26 May 2017 16:13:25 +0000 (12:13 -0400)]
11100: Fix test
Peter Amstutz [Fri, 26 May 2017 15:06:35 +0000 (11:06 -0400)]
11100: Add ciso8601 dependency
Peter Amstutz [Fri, 26 May 2017 14:42:47 +0000 (10:42 -0400)]
11100: Add test for --trash-intermediate. Add log message when intermediate
outputs are scheduled for trash.
Lucas Di Pentima [Fri, 26 May 2017 02:34:59 +0000 (23:34 -0300)]
11684: When packing small blocks into one, save references of the files
included on the block when committing it asynchronously, so that the
segment's locators can be updated at the put thread after the block is
committed and the permission token is returned from the API Server.
Jiayong Li [Fri, 26 May 2017 01:49:26 +0000 (21:49 -0400)]
closes #11362 Merge branch '11362-missing-input-sdk/cwl'
Jiayong Li [Fri, 26 May 2017 01:47:59 +0000 (21:47 -0400)]
Change visit in pathmapper.py to raise OSError if input file is not found, change test_pathmapper.py to test it, and update python client version in setup.py
Jiayong Li [Fri, 26 May 2017 01:38:12 +0000 (21:38 -0400)]
refs #11362 Merge branch '11362-missing-input-sdk/python'
Jiayong Li [Fri, 26 May 2017 01:36:51 +0000 (21:36 -0400)]
Change statfile in run.py to be able to raise OSError, and change the mock in test_pathmapper.py accordingly
Lucas Di Pentima [Wed, 24 May 2017 18:10:53 +0000 (15:10 -0300)]
Merge branch '11501-job-stats-discrepancy'
Closes #11501
Lucas Di Pentima [Wed, 24 May 2017 16:51:47 +0000 (13:51 -0300)]
11501: Simplified helper method call. Changed wording of run time description.
Peter Amstutz [Wed, 24 May 2017 14:56:49 +0000 (10:56 -0400)]
Merge branch '11543-collection-per-tool' closes #11543
Peter Amstutz [Wed, 24 May 2017 14:36:40 +0000 (10:36 -0400)]
11100: Separate "trash intermediate on success" behavior from "output intermediate TTL" option. Update documentation.
Lucas Di Pentima [Wed, 24 May 2017 13:47:56 +0000 (10:47 -0300)]
11501: Don't filter out reused children when calculating running time.
Use always wall time when saying how much time passed after completion/failure.
Lucas Di Pentima [Tue, 23 May 2017 23:11:14 +0000 (20:11 -0300)]
11501: When calculating a work unit's running time, only include 'leaf' children, filtering those that were reused.
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