radhika [Fri, 30 Sep 2016 14:40:41 +0000 (10:40 -0400)]
10078: Update recent_collections so that the collection query it is not executed twice, once in this method and once in show_dashboard for r[:collections].each statement.
radhika [Fri, 30 Sep 2016 14:36:07 +0000 (10:36 -0400)]
10078: Update the Node.filter so that this query is not executed three times: once for nodes.sort_by and twice in compute_node_summary for nodes.select
Peter Amstutz [Fri, 7 Oct 2016 18:32:15 +0000 (14:32 -0400)]
Merge branch '8018-container-retry' closes #8018
Peter Amstutz [Fri, 7 Oct 2016 18:30:30 +0000 (14:30 -0400)]
Bump cwltool version for bugfix https://github.com/common-workflow-language/cwltool/pull/206
refs #10203
Tom Morris [Thu, 6 Oct 2016 21:45:58 +0000 (17:45 -0400)]
Merge branch '10077-workbench-integration-tests' closes #10077
Tom Morris [Thu, 6 Oct 2016 21:43:56 +0000 (17:43 -0400)]
Add explanatory comment about FIXME
Peter Amstutz [Thu, 6 Oct 2016 20:50:16 +0000 (16:50 -0400)]
Enumerate Directory contents in output when --compute-checksum is
provided (needed to pass CWL conformance tests). No issue #
Peter Amstutz [Thu, 6 Oct 2016 16:54:28 +0000 (12:54 -0400)]
8018: Additional assertions checking when container_uuid changes/does not change.
Peter Amstutz [Thu, 6 Oct 2016 15:36:27 +0000 (11:36 -0400)]
Merge branch '9307-cwl-use-tmp-output' closes #9307 closes #9308
Peter Amstutz [Thu, 6 Oct 2016 15:34:34 +0000 (11:34 -0400)]
Merge branch 'master' into 9307-cwl-use-tmp-output
Conflicts:
sdk/cwl/tests/test_job.py
Peter Amstutz [Thu, 6 Oct 2016 15:25:53 +0000 (11:25 -0400)]
9307: Improve crunchrunner error handling. Fix typo.
Peter Amstutz [Wed, 5 Oct 2016 19:55:35 +0000 (15:55 -0400)]
Bump schema-salad & cwltool version for cwl document validation bugfix. no issue #
Peter Amstutz [Wed, 5 Oct 2016 18:08:52 +0000 (14:08 -0400)]
9307: Bump tests to use v1.0 and make sure that arvados_cwl.add_arv_hints() is called.
Peter Amstutz [Wed, 5 Oct 2016 15:08:40 +0000 (11:08 -0400)]
9308: Set task.keepTmpOutput: true when outputDirType is keep_output_dir.
Peter Amstutz [Wed, 5 Oct 2016 17:52:23 +0000 (13:52 -0400)]
9308: Add test for KeepTmpOutput flag.
Peter Amstutz [Wed, 5 Oct 2016 17:16:54 +0000 (13:16 -0400)]
8018: Add migration script for "container_count" field.
Peter Amstutz [Wed, 5 Oct 2016 15:09:37 +0000 (11:09 -0400)]
Merge branch '10165-cwl-outputs' closes #10165
Peter Amstutz [Tue, 4 Oct 2016 22:30:06 +0000 (18:30 -0400)]
9308: Add 'keepTmpOutput' option to crunchrunner
Peter Amstutz [Tue, 4 Oct 2016 20:24:46 +0000 (16:24 -0400)]
10165: Add --output-name option to set name of output collection.
Peter Amstutz [Tue, 4 Oct 2016 19:56:55 +0000 (15:56 -0400)]
8018: Fix state transition checks. Add test of retry and fix other tests to
not retry.
Peter Amstutz [Tue, 4 Oct 2016 15:06:11 +0000 (11:06 -0400)]
Merge branch '9001-summary-skip-malformed-lines' closes #9001
Peter Amstutz [Mon, 3 Oct 2016 18:48:36 +0000 (14:48 -0400)]
10165: Add test for make_output_collection
Peter Amstutz [Mon, 3 Oct 2016 16:59:51 +0000 (12:59 -0400)]
10165: Pass around keep client object instead of creating new client per
Collection.
Peter Amstutz [Fri, 30 Sep 2016 21:35:52 +0000 (17:35 -0400)]
10165: Handle copying complete collection contents into subdirectory.
Peter Amstutz [Fri, 30 Sep 2016 21:00:34 +0000 (17:00 -0400)]
10165: DRY key cleanup.
Peter Amstutz [Fri, 30 Sep 2016 19:59:51 +0000 (15:59 -0400)]
10165: Add FinalOutputPathMapper. Delete basename/size/listing from output object because that information is captured by the enclosing Collection. Sort keys.
Peter Amstutz [Fri, 30 Sep 2016 18:59:32 +0000 (14:59 -0400)]
Merge branch '9857-cwl-acceptlist-re' refs #9857
Peter Amstutz [Fri, 30 Sep 2016 18:16:32 +0000 (14:16 -0400)]
10165: Always make an output collection when a workflow completes.
Peter Amstutz [Fri, 30 Sep 2016 17:21:56 +0000 (13:21 -0400)]
Merge branch '10032-cwl-spinup' refs #10032
Peter Amstutz [Fri, 30 Sep 2016 15:58:49 +0000 (11:58 -0400)]
10032: Fix test to include --preserve-entire-environment
Peter Amstutz [Fri, 30 Sep 2016 15:24:53 +0000 (11:24 -0400)]
10032: Update schema salad and cwltool packages to get document validation optimizations.
Peter Amstutz [Fri, 30 Sep 2016 15:24:15 +0000 (11:24 -0400)]
Drill down on metrics on job submission.
Tom Morris [Thu, 29 Sep 2016 16:33:49 +0000 (12:33 -0400)]
Fix negative Capybara assertion/matcher
Tom Morris [Thu, 29 Sep 2016 16:33:40 +0000 (12:33 -0400)]
Fix not present test for Capybara
Tom Morris [Thu, 29 Sep 2016 16:33:27 +0000 (12:33 -0400)]
Fix long wait for Capybara test
Tom Morris [Thu, 29 Sep 2016 16:33:01 +0000 (12:33 -0400)]
Fix row selection logic to not wait
Tom Morris [Thu, 29 Sep 2016 16:33:16 +0000 (12:33 -0400)]
Restore Capybara.default_max_wait_time side effect
Tom Morris [Thu, 29 Sep 2016 16:31:48 +0000 (12:31 -0400)]
Fix and simplify wait_for_ajax
Don't change global Capybara.default_max_wait_time
Sleep so we're not competing with thread(s) doing work
Tom Clegg [Thu, 29 Sep 2016 16:11:45 +0000 (12:11 -0400)]
Increase timeout and allow early success on download test. No issue #
radhika [Thu, 29 Sep 2016 15:09:30 +0000 (11:09 -0400)]
refs #9498 Fix failing workbench integration test due to containers fixture update.
Peter Amstutz [Thu, 29 Sep 2016 14:31:08 +0000 (10:31 -0400)]
Merge branch '10151-cwl-dir-listing' closes #10151
Peter Amstutz [Thu, 29 Sep 2016 14:30:30 +0000 (10:30 -0400)]
10032: Add more metrics
Peter Amstutz [Wed, 28 Sep 2016 20:26:45 +0000 (16:26 -0400)]
10151: Ensure that job_order_object is normalized and Directory listings are enumerated.
Tom Clegg [Wed, 28 Sep 2016 20:20:00 +0000 (16:20 -0400)]
Merge branch '9848-copy-container-output' refs #9848
Tom Clegg [Tue, 27 Sep 2016 16:49:49 +0000 (12:49 -0400)]
9848: Set expiry time on container output and log collections.
Tom Clegg [Tue, 27 Sep 2016 16:48:16 +0000 (12:48 -0400)]
9848: Use pointer receiver for all arvadosclient.ArvadosClient methods.
This makes it possible for all methods to satisfy a single interface.
Tom Clegg [Tue, 27 Sep 2016 03:18:24 +0000 (23:18 -0400)]
9848: Copy the output and log collections (if any) when finalizing a container request.
When reusing a container, ensure log and output are readable.
Tom Clegg [Tue, 27 Sep 2016 03:23:01 +0000 (23:23 -0400)]
9848: group some assertions into bigger test cases.
Tom Clegg [Wed, 28 Sep 2016 20:19:03 +0000 (16:19 -0400)]
Merge branch '9953-dockercleaner-config' closes #9953
Tom Clegg [Wed, 28 Sep 2016 20:18:00 +0000 (16:18 -0400)]
9953: Add arvados-docker-cleaner.service to MANIFEST.in.
Fixes error during `setup.py install`:
Command "/tmp/tmp.lpB0zPHYWs/VENV3DIR/bin/python3 -u -c "import setuptools, tokenize;__file__=/tmp/pip-6gqvw70n-build/setup.py;exec(compile(getattr(tokenize, open, open)(__file__).read().replace(rn, n), __file__, exec))" install --record /tmp/pip-ljhdcczu-record/install-record.txt --single-version-externally-managed --compile --install-headers /tmp/tmp.lpB0zPHYWs/VENV3DIR/include/site/python3.4/arvados-docker-cleaner" failed with error code 1 in /tmp/pip-6gqvw70n-build/
Tom Clegg [Wed, 28 Sep 2016 15:13:40 +0000 (11:13 -0400)]
9950: 9953: 9954: 9955: 9957: Add AssertPathExists= to unit file to avoid startup until config file exists.
Tom Clegg [Wed, 28 Sep 2016 15:12:11 +0000 (11:12 -0400)]
9950: Fix arvados-git-httpd executable path. Update config path to /etc/arvados/git-httpd/.
Tom Clegg [Wed, 28 Sep 2016 14:47:36 +0000 (10:47 -0400)]
9953: Update default config path.
Tom Clegg [Wed, 28 Sep 2016 13:44:07 +0000 (09:44 -0400)]
9953: If config cannot be read/parsed, show just the error without the stack trace.
Tom Clegg [Fri, 23 Sep 2016 20:47:29 +0000 (16:47 -0400)]
9953: Install/remove systemd unit files wherever systemd exists, even if it is not running.
Tom Clegg [Fri, 23 Sep 2016 20:41:01 +0000 (16:41 -0400)]
9953: Update build scripts to Go 1.7.1.
Tom Clegg [Fri, 23 Sep 2016 20:40:37 +0000 (16:40 -0400)]
9953: De-duplicate Go and Python postinst/prerm scripts.
Tom Clegg [Fri, 23 Sep 2016 20:08:37 +0000 (16:08 -0400)]
9953: Add systemd unit file for arvados-docker-cleaner.
Tom Clegg [Fri, 23 Sep 2016 20:09:03 +0000 (16:09 -0400)]
9953: Install python data files to /usr/share/... not /usr/data/share/...
Tom Clegg [Fri, 23 Sep 2016 14:26:10 +0000 (10:26 -0400)]
9953: PEP-8
Tom Clegg [Fri, 23 Sep 2016 14:17:59 +0000 (10:17 -0400)]
9953: Load config from file.
Tom Clegg [Fri, 23 Sep 2016 03:58:30 +0000 (23:58 -0400)]
9953: Ignore non-container events (volume, network) and events with no status, instead of crashing.
Ward Vandewege [Wed, 28 Sep 2016 17:35:56 +0000 (13:35 -0400)]
Use our cached copy of phantomjs-1.9.7 instead of pulling it from https
upstream with flakey connectivity.
closes #10130
Tom Clegg [Wed, 28 Sep 2016 13:59:36 +0000 (09:59 -0400)]
Merge branch '9990-workbench-client-timeout' closes #9990
Tom Clegg [Thu, 8 Sep 2016 14:41:37 +0000 (10:41 -0400)]
9990: Add configs for Workbench API client timeouts.
Peter Amstutz [Tue, 27 Sep 2016 21:18:06 +0000 (17:18 -0400)]
8018: Create new container if there are retriable container requests.
Peter Amstutz [Tue, 27 Sep 2016 20:36:58 +0000 (16:36 -0400)]
Merge branch '10129-cwl-remove-listing' closes #10129
Peter Amstutz [Tue, 27 Sep 2016 20:30:27 +0000 (16:30 -0400)]
10129: Rename del_listing to trim_listing and add docstring about what it is
for.
Tom Clegg [Tue, 27 Sep 2016 20:11:22 +0000 (16:11 -0400)]
Merge branch '9912-config-yaml' closes #9912
Peter Amstutz [Tue, 27 Sep 2016 19:57:40 +0000 (15:57 -0400)]
10129: Ensure that directory literals get preserved when trimming keep directory listings.
Tom Clegg [Tue, 27 Sep 2016 18:00:21 +0000 (14:00 -0400)]
9912: Support YAML config files. Change default config file paths to /etc/arvados/foo/foo.yml.
Peter Amstutz [Tue, 27 Sep 2016 17:42:04 +0000 (13:42 -0400)]
Fix #10133, use "resolved" (keep reference) instead of target (filesystem
path). I think this was a merge conflict mistake.
Peter Amstutz [Mon, 26 Sep 2016 20:49:27 +0000 (16:49 -0400)]
10129: Trim listing from Directory objects that are keep references, because
they can get very large.
Peter Amstutz [Tue, 27 Sep 2016 14:59:42 +0000 (10:59 -0400)]
8018: Add container_count field.
Peter Amstutz [Mon, 26 Sep 2016 21:17:35 +0000 (17:17 -0400)]
Merge branch '10081-update-cwl-runner' refs #10081
Peter Amstutz [Mon, 26 Sep 2016 21:04:29 +0000 (17:04 -0400)]
10081: Fix renamed methods.
radhika [Mon, 26 Sep 2016 20:03:17 +0000 (16:03 -0400)]
closes #9514
Merge branch '9514-only-delete-old-container-logs'
Peter Amstutz [Mon, 26 Sep 2016 19:30:39 +0000 (15:30 -0400)]
Merge branch '9988-cwl-arv-hints' closes #9988
Peter Amstutz [Mon, 26 Sep 2016 19:30:17 +0000 (15:30 -0400)]
Fix typo.
Tom Clegg [Mon, 26 Sep 2016 17:44:16 +0000 (13:44 -0400)]
Merge branch '9950-arv-git-httpd-config' closes #9950
Tom Clegg [Mon, 26 Sep 2016 16:24:46 +0000 (12:24 -0400)]
9950: Remove uses of environment variables.
Tom Clegg [Wed, 21 Sep 2016 18:34:05 +0000 (14:34 -0400)]
9950: Propagate Client.Insecure config to arvadosclient library via ARVADOS_API_HOST_INSECURE env var.
Tom Clegg [Wed, 21 Sep 2016 01:28:00 +0000 (21:28 -0400)]
9950: Add systemd unit file arv-git-httpd.service.
Tom Clegg [Wed, 21 Sep 2016 13:35:27 +0000 (09:35 -0400)]
9950: Rename Root config to RepoRoot.
Tom Clegg [Wed, 21 Sep 2016 01:27:32 +0000 (21:27 -0400)]
9950: Load config from /etc/arvados/arv-git-httpd/config.json.
radhika [Mon, 26 Sep 2016 14:53:38 +0000 (10:53 -0400)]
refs #10028
Merge branch '10028-search-uuid-prefix'
radhika [Mon, 26 Sep 2016 14:15:33 +0000 (10:15 -0400)]
9514: update delete_old_job_logs task also to use the better performing sql.
Peter Amstutz [Mon, 26 Sep 2016 12:42:43 +0000 (08:42 -0400)]
Merge branch '10081-cwl-run-same-job' closes #10081
radhika [Sat, 24 Sep 2016 23:31:09 +0000 (19:31 -0400)]
9514: Use sql to issue delete sql without getting ids in batch.
Tom Clegg [Sat, 24 Sep 2016 02:31:54 +0000 (22:31 -0400)]
Merge branch '10124-fix-sleepy-tests' closes #10124
Tom Clegg [Fri, 23 Sep 2016 18:50:23 +0000 (14:50 -0400)]
10124: Replace "sleep 1, then assert" with "retry assertion for up to 10 seconds".
Peter Amstutz [Fri, 23 Sep 2016 20:22:10 +0000 (16:22 -0400)]
Bump cwltool version in fpm_build refs #10088
Peter Amstutz [Fri, 23 Sep 2016 20:20:07 +0000 (16:20 -0400)]
Merge branch '10081-cwl-run-same-job' into 9988-cwl-arv-hints
Peter Amstutz [Fri, 23 Sep 2016 20:18:39 +0000 (16:18 -0400)]
Merge branch 'master' into 10081-cwl-run-same-job
Conflicts:
sdk/cwl/arvados_cwl/runner.py
Peter Amstutz [Fri, 23 Sep 2016 20:14:06 +0000 (16:14 -0400)]
Merge branch '10088-cwl-dedup-deps' refs #10088
Peter Amstutz [Fri, 23 Sep 2016 18:27:35 +0000 (14:27 -0400)]
10081: Change logical identifier for Arvados schema to arvados.org/cwl.
Improve exception text when checking that locations are keep references.
radhika [Fri, 23 Sep 2016 18:09:20 +0000 (14:09 -0400)]
9514: if logs are not found in logs table, do not show the log div for a completed container.
Peter Amstutz [Fri, 23 Sep 2016 02:38:06 +0000 (22:38 -0400)]
10088: Updated cwltool deduplicates dependencies to avoid creating separate
collections for subdirectories. Don't try to update file literals that arn't
in scandeps.
Tom Clegg [Fri, 23 Sep 2016 16:06:54 +0000 (12:06 -0400)]
Use longer timeout for flaky test.
No issue #
Tom Clegg [Fri, 23 Sep 2016 15:34:14 +0000 (11:34 -0400)]
gofmt. refs #9955
projects / arvados.git / log