Tom Clegg [Wed, 3 May 2017 14:20:52 +0000 (10:20 -0400)]
Merge branch '11606-rails4-no-munge'
closes #11606
Tom Clegg [Wed, 3 May 2017 14:20:35 +0000 (10:20 -0400)]
11308: Stop test suite if api etc. cannot be started.
Peter Amstutz [Wed, 3 May 2017 13:52:41 +0000 (09:52 -0400)]
11469: All {kind: tmp} mounts set up under host tempdir, don't try to use
Docker volumes.
Peter Amstutz [Wed, 3 May 2017 02:53:28 +0000 (22:53 -0400)]
11369: Fix tests. Tweak test fixture to include a mounts entry with capacity.
Peter Amstutz [Wed, 3 May 2017 01:26:55 +0000 (21:26 -0400)]
11369: Log node sizes at startup. Fix setting of scratch disk size.
radhika [Wed, 3 May 2017 04:24:41 +0000 (00:24 -0400)]
10645: add test for container_request display with input mounts
Peter Amstutz [Wed, 3 May 2017 03:06:28 +0000 (23:06 -0400)]
11369: Containers API: Add capacity to tmp and output mounts. Also support {outputDirType: keep_output_dir} of RuntimeConstraints.
Peter Amstutz [Wed, 3 May 2017 02:21:36 +0000 (22:21 -0400)]
11369: RAM request includes keep cache RAM. Add request for temp disk.
radhika [Wed, 3 May 2017 01:05:25 +0000 (21:05 -0400)]
Merge branch 'master' into 10645-cr-mounts-display
radhika [Tue, 2 May 2017 20:03:28 +0000 (16:03 -0400)]
8019: need to check and write log if things are closing down
Tom Clegg [Tue, 2 May 2017 17:02:32 +0000 (13:02 -0400)]
11308: Merge branch 'master' into 11308-python3
Conflicts:
sdk/python/arvados/arvfile.py
sdk/python/arvados/commands/put.py
sdk/python/tests/test_collections.py
Lucas Di Pentima [Tue, 2 May 2017 15:44:26 +0000 (12:44 -0300)]
Merge branch '11185-wb-disable-reuse'
Closes #11185
Tom Clegg [Tue, 2 May 2017 15:39:52 +0000 (11:39 -0400)]
11606: Disable deep_munge behavior. Rename test so it runs in test suite.
Lucas Di Pentima [Tue, 2 May 2017 15:24:14 +0000 (12:24 -0300)]
Merge branch '11579-arvput-follow-symlinks'
Closes #11579
Lucas Di Pentima [Tue, 2 May 2017 14:56:56 +0000 (11:56 -0300)]
11185: Merge branch 'master' into 11185-wb-disable-reuse
Lucas Di Pentima [Tue, 2 May 2017 14:55:02 +0000 (11:55 -0300)]
11579: Merge branch 'master' into 11579-arvput-follow-symlinks
Lucas Di Pentima [Tue, 2 May 2017 14:52:44 +0000 (11:52 -0300)]
11579: Added assertion on test to check for file symlinks to be copied by default.
Don't treat a PathDoesNotExist exception as an abnormal termination, just log the proper error message, and quit.
radhika [Tue, 2 May 2017 01:43:37 +0000 (21:43 -0400)]
10645: container request mounts display
Lucas Di Pentima [Mon, 1 May 2017 21:05:02 +0000 (18:05 -0300)]
11579: Removed feature about not uploading a symlinked dir twice.
When using --no-follow-links parameter, symlinked files will be also ignored.
Updated tests.
Lucas Di Pentima [Mon, 1 May 2017 19:58:48 +0000 (16:58 -0300)]
11185: Removed newly added completed-acr fixture and modified the already existing completed-older CR
to be able to use it on the tests.
Change the reset_form() JS function to something more specific to this usage, to avoid future
conflicts.
Tom Clegg [Mon, 1 May 2017 18:03:24 +0000 (14:03 -0400)]
Merge branch '10988-document-ubuntu1604-support'
closes #10988
Tom Clegg [Mon, 1 May 2017 17:57:43 +0000 (13:57 -0400)]
10988: Remove apt.arvados.org repo priority: we no longer publish/require the older packages.
Ward Vandewege [Thu, 26 Jan 2017 22:33:05 +0000 (17:33 -0500)]
10988: Document our Ubuntu 16.04 support.
Peter Amstutz [Mon, 1 May 2017 17:29:49 +0000 (13:29 -0400)]
Merge branch 'master' into origin-8019-crunchrun-log-throttle
Peter Amstutz [Mon, 1 May 2017 16:44:54 +0000 (12:44 -0400)]
Merge branch '11469-volume-tmp' refs #11469
Peter Amstutz [Mon, 1 May 2017 14:36:44 +0000 (10:36 -0400)]
Crunch script doesn't fail in file/directory literals that don't have a 'location'. refs #11549
Peter Amstutz [Mon, 1 May 2017 14:02:56 +0000 (10:02 -0400)]
11469: Docker-managed volumes go in "Volumes" not "Binds".
Lucas Di Pentima [Fri, 28 Apr 2017 19:18:56 +0000 (16:18 -0300)]
11185: Addressed several requests:
* Added '...' to 'Re-run' button's title to indicate it will show a dialog.
* Corrected comment.
* Added javascript code so that the 'Cancel' and 'x' buttons on the dialog reset the checkbox.
* Expanded test cases to cover CRs that both do and don't use arvados-cwl-runner command, with
and without container reuse.
Peter Amstutz [Fri, 28 Apr 2017 18:50:38 +0000 (14:50 -0400)]
8019: Rework partial line throttling. Fix sending flush when buffer is ready
so it does not block.
Tom Clegg [Fri, 28 Apr 2017 16:59:08 +0000 (12:59 -0400)]
Merge branch '11537-keepproxy-loop'
closes #11537
Lucas Di Pentima [Fri, 28 Apr 2017 15:25:01 +0000 (12:25 -0300)]
11579: Check if paths exist, raise meaningful exception if not.
Added test for this case.
Peter Amstutz [Fri, 28 Apr 2017 14:40:06 +0000 (10:40 -0400)]
Merge branch '11549-cwl-smarter-mounts' closes #11549
Tom Clegg [Thu, 27 Apr 2017 19:24:41 +0000 (15:24 -0400)]
11537: Add Via header to get/head/post/put responses.
Tom Clegg [Thu, 27 Apr 2017 14:51:49 +0000 (10:51 -0400)]
11537: Add Via header to proxied keepstore requests.
Propagate keepclient PUT error messages to caller.
Tom Clegg [Thu, 27 Apr 2017 20:55:45 +0000 (16:55 -0400)]
Merge branch '7709-rails-observers'
refs #7709
Tom Clegg [Thu, 27 Apr 2017 20:51:46 +0000 (16:51 -0400)]
7709: Add rails-observers gem so plugins can use it.
Lucas Di Pentima [Thu, 27 Apr 2017 20:15:53 +0000 (17:15 -0300)]
11579: Explicitly following links on test.
Lucas Di Pentima [Thu, 27 Apr 2017 20:12:56 +0000 (17:12 -0300)]
11579: Tests added.
Lucas Di Pentima [Thu, 27 Apr 2017 19:51:31 +0000 (16:51 -0300)]
11579: Added symlinked dir traversal as the default behavior.
Added flag to disable this and ignore symlinked dirs: --no-follow-links.
radhika [Thu, 27 Apr 2017 19:44:37 +0000 (15:44 -0400)]
8019: partial line throttling etc
Peter Amstutz [Thu, 27 Apr 2017 18:24:43 +0000 (14:24 -0400)]
11549: Fix container requests so it doesn't mount each file individually,
instead mount common collections/subdirectories.
Peter Amstutz [Thu, 27 Apr 2017 18:05:00 +0000 (14:05 -0400)]
11549: Test that containers don't mount each file individually, instead mount
common collections/subdirectories.
Tom Clegg [Thu, 27 Apr 2017 16:59:06 +0000 (12:59 -0400)]
Merge branch '7709-api-rails4'
closes #7709
Lucas Di Pentima [Thu, 27 Apr 2017 16:54:32 +0000 (13:54 -0300)]
11579: Test proving the bug: arv-put does not follow symlinks.
Lucas Di Pentima [Thu, 27 Apr 2017 15:42:49 +0000 (12:42 -0300)]
11185: When re-run, the default behaviour is to copy reuse disabled. Changed modal dialog to allow
the user to enable reuse.
Updated tests.
Lucas Di Pentima [Thu, 27 Apr 2017 13:55:26 +0000 (10:55 -0300)]
11185: Now we only have one "Re-run" button that will give the user the option to disable container reuse on a modal dialog.
Updated test.
Lucas Di Pentima [Wed, 26 Apr 2017 18:56:00 +0000 (15:56 -0300)]
Merge branch '10111-cr-provenance-graph'
Closes #10111
Lucas Di Pentima [Wed, 26 Apr 2017 18:55:03 +0000 (15:55 -0300)]
10111: Merge branch 'master' into 10111-cr-provenance-graph
Lucas Di Pentima [Wed, 26 Apr 2017 18:29:20 +0000 (15:29 -0300)]
10111: Replaced graph edges names: cr->child & mounts->input.
Nico Cesar [Wed, 26 Apr 2017 18:25:22 +0000 (14:25 -0400)]
Merge branch '11305-migrate-docker19-doc'
Documentation for the migration process from Docker 1.9 or less to Docker 1.10+
Docker changed the format of the images, and there is an arvados tool arvados-migrate-docker19,
this commit explains how to migrate
refs #11305
Lucas Di Pentima [Wed, 26 Apr 2017 16:28:06 +0000 (13:28 -0300)]
10111: If there is no cwl.input.json object as part of a CR mount list, search for input PDHs on the entire mount list
radhika [Wed, 26 Apr 2017 16:15:24 +0000 (12:15 -0400)]
10112: add Run button to workflow#show page
Tom Clegg [Wed, 26 Apr 2017 14:33:13 +0000 (10:33 -0400)]
7709: Merge branch 'master' into 7709-api-rails4
Lucas Di Pentima [Wed, 26 Apr 2017 14:03:35 +0000 (11:03 -0300)]
11185: On re-run without reuse, assign 'false' to CR.use_existing. Added related test.
Lucas Di Pentima [Wed, 26 Apr 2017 11:56:01 +0000 (08:56 -0300)]
10111: Only include those mounts that are declared on the cwl input definition.
Removed trailing spaces.
Lucas Di Pentima [Wed, 26 Apr 2017 02:04:49 +0000 (23:04 -0300)]
11185: Added "Re-run without reuse" button to the completed CR page, so that it
copies the CR modifying the arvados-cwl-runner arguments to avoid container
reuse.
Expanded related test.
radhika [Tue, 25 Apr 2017 20:43:47 +0000 (16:43 -0400)]
8019: load log throttling config params during NewContainerRunner
Lucas Di Pentima [Tue, 25 Apr 2017 19:26:38 +0000 (16:26 -0300)]
10111: Added "child" CRs to the graph, and removed container image and requesting container elements.
radhika [Tue, 25 Apr 2017 19:05:31 +0000 (15:05 -0400)]
8019: rateLimit method signature
radhika [Tue, 25 Apr 2017 18:08:14 +0000 (14:08 -0400)]
Merge branch 'master' into 8019-crunchrun-log-throttle
radhika [Tue, 25 Apr 2017 18:06:55 +0000 (14:06 -0400)]
8019: load rate limiting config parameters from discovery document once per log writer creation.
Tom Clegg [Tue, 25 Apr 2017 17:22:44 +0000 (13:22 -0400)]
Merge branch '11544-bad-collection-id-500'
closes #11544
Tom Clegg [Tue, 25 Apr 2017 16:57:11 +0000 (12:57 -0400)]
11544: Return 404 instead of 500 for malformed collection IDs.
Peter Amstutz [Tue, 25 Apr 2017 15:58:34 +0000 (11:58 -0400)]
Merge branch '11507-deleted-bufferblocks' refs #11507
Peter Amstutz [Fri, 21 Apr 2017 20:36:21 +0000 (16:36 -0400)]
11507: Move repack_writes() method from ArvadosFile to BufferBlock.
Tom Clegg [Tue, 25 Apr 2017 05:14:23 +0000 (01:14 -0400)]
7709: Merge branch 'master' into 7709-api-rails4
Conflicts:
services/api/db/structure.sql
Lucas Di Pentima [Tue, 25 Apr 2017 03:50:31 +0000 (00:50 -0300)]
10111: Tests added
radhika [Mon, 24 Apr 2017 21:21:52 +0000 (17:21 -0400)]
8019: more testing
radhika [Mon, 24 Apr 2017 20:42:20 +0000 (16:42 -0400)]
8019: add tests and address issues identified
Lucas Di Pentima [Mon, 24 Apr 2017 20:07:19 +0000 (17:07 -0300)]
10111: Merge branch 'master' into 10111-cr-provenance-graph
Lucas Di Pentima [Mon, 24 Apr 2017 19:30:00 +0000 (16:30 -0300)]
10111: Added provenance graph for container requests.
Tom Clegg [Mon, 24 Apr 2017 18:57:41 +0000 (14:57 -0400)]
Fix panic in test case (overwriting a locked sync.Mutex with an unlocked one).
No issue #
Tom Clegg [Mon, 24 Apr 2017 18:05:20 +0000 (14:05 -0400)]
Merge branch '11517-no-count-logs'
refs #11517
Tom Clegg [Mon, 24 Apr 2017 18:02:54 +0000 (14:02 -0400)]
11517: Add test for count=none.
Tom Clegg [Mon, 24 Apr 2017 18:00:45 +0000 (14:00 -0400)]
11517: Skip database reset in some workbench unit tests.
Reduces unit test suite time by half.
Tom Clegg [Mon, 24 Apr 2017 17:42:31 +0000 (13:42 -0400)]
11517: Comment with_count() method
Nico Cesar [Mon, 24 Apr 2017 17:02:15 +0000 (13:02 -0400)]
11305: added kernel and module dependency for docker migration in doc
refs #11305
radhika [Mon, 24 Apr 2017 14:05:32 +0000 (10:05 -0400)]
Merge branch 'master' into 8019-crunchrun-log-throttle
Tom Clegg [Fri, 21 Apr 2017 19:17:46 +0000 (15:17 -0400)]
11517: Use count=none when retrieving logs.
Nico Cesar [Mon, 24 Apr 2017 12:43:55 +0000 (08:43 -0400)]
we need the tagged image to do this
Tom Clegg [Sat, 22 Apr 2017 06:29:00 +0000 (02:29 -0400)]
11308: Fix arvfile append mode: write() changes the file pointer.
Tom Clegg [Sat, 22 Apr 2017 06:26:59 +0000 (02:26 -0400)]
11308: Fix bytes vs. strings from recent merge.
radhika [Fri, 21 Apr 2017 21:25:03 +0000 (17:25 -0400)]
8019: rateLimit crunch-run logging using API configuration parameters
Tom Clegg [Fri, 21 Apr 2017 20:02:50 +0000 (16:02 -0400)]
11308: Merge branch 'master' into 11308-python3
Conflicts:
sdk/python/arvados/arvfile.py
sdk/python/arvados/commands/get.py
sdk/python/arvados/commands/migrate19.py
sdk/python/tests/test_arv_get.py
sdk/python/tests/test_arvfile.py
Peter Amstutz [Fri, 21 Apr 2017 18:48:15 +0000 (14:48 -0400)]
11507: Put self._pending_write_size update back under the lock.
Peter Amstutz [Fri, 21 Apr 2017 18:31:49 +0000 (14:31 -0400)]
11507: More small block packing fixes:
* Repack writes before small block merging.
* Update segments of file with new locator/segment offset instead of replacing
entire file contents.
Peter Amstutz [Fri, 21 Apr 2017 13:55:00 +0000 (09:55 -0400)]
11507: Cleanup
Peter Amstutz [Thu, 20 Apr 2017 21:45:37 +0000 (17:45 -0400)]
11507: Put bufferblocks into DELETED state when deleted so they don't get
reused accidentally if there are dangling references. When packing small
blocks, update segments with the block hash instead of the bufferblock id to
avoid dangling references.
Peter Amstutz [Thu, 20 Apr 2017 21:10:30 +0000 (17:10 -0400)]
11507: Test cases that reproduce bug
Peter Amstutz [Thu, 20 Apr 2017 18:18:44 +0000 (14:18 -0400)]
Merge branch '11510-sdk-extend-files' refs #11510
Peter Amstutz [Thu, 20 Apr 2017 18:15:49 +0000 (14:15 -0400)]
11510: Tweak interface to better match Pythons "io.IOBase" class.
Tom Clegg [Thu, 20 Apr 2017 18:10:50 +0000 (14:10 -0400)]
Merge branch '11470-update-task-fields'
refs #11470
Peter Amstutz [Thu, 20 Apr 2017 17:25:56 +0000 (13:25 -0400)]
11510: Fix truncate() to not change file pointer. Additional tests.
Peter Amstutz [Thu, 20 Apr 2017 14:41:05 +0000 (10:41 -0400)]
11510: Repack writes any time there's more than one segment referencing the same bufferblock.
Peter Amstutz [Tue, 18 Apr 2017 21:54:57 +0000 (17:54 -0400)]
11510: Fix longstanding bug in replace_range() when appending data from a buffer that was written out of order.
Tom Clegg [Thu, 20 Apr 2017 02:12:42 +0000 (22:12 -0400)]
11470: Fix identifiers to conventional Go.
Tom Clegg [Thu, 20 Apr 2017 02:09:45 +0000 (22:09 -0400)]
11470: Fix accidentally cleared fields during job_task update.
Updating with a Task struct had the effect of clearing job_uuid,
created_by_job_task_uuid, and parameters fields, and resetting
sequence to 0.
Lucas Di Pentima [Wed, 19 Apr 2017 20:42:26 +0000 (17:42 -0300)]
Merge branch '11502-unstripped-manifest-fix'
Closes #11502, #11511
Lucas Di Pentima [Wed, 19 Apr 2017 19:38:30 +0000 (16:38 -0300)]
11502: Merge branch 'master' into 11502-unstripped-manifest-fix
Lucas Di Pentima [Wed, 19 Apr 2017 19:28:26 +0000 (16:28 -0300)]
11502: Instead of asking for a stripped manifest, replace the tokens with some constant string to do the comparison.
projects / arvados.git / log