Tom Clegg [Tue, 31 Mar 2020 17:52:23 +0000 (13:52 -0400)]
16053: Merge branch 'master'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 31 Mar 2020 17:51:31 +0000 (13:51 -0400)]
16053: Error out on unimplemented install in production mode.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Lucas Di Pentima [Fri, 27 Mar 2020 15:04:07 +0000 (12:04 -0300)]
Merge branch '16265-security-updates'
Closes #16265
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Fri, 27 Mar 2020 14:21:36 +0000 (11:21 -0300)]
Merge branch '16266-wb1-xss-fix'
Closes #16266
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Thu, 26 Mar 2020 17:02:40 +0000 (14:02 -0300)]
16265: Merge branch 'dependabot/bundler/services/api/nokogiri-1.10.8' into 16265-security-updates
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Thu, 26 Mar 2020 17:02:24 +0000 (14:02 -0300)]
Merge branch '16265-security-updates' into dependabot/bundler/services/api/nokogiri-1.10.8
Lucas Di Pentima [Thu, 26 Mar 2020 16:59:58 +0000 (13:59 -0300)]
16265: Merge branch 'dependabot/bundler/apps/workbench/loofah-2.3.1' into 16265-security-updates
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Thu, 26 Mar 2020 16:59:19 +0000 (13:59 -0300)]
Merge branch '16265-security-updates' into dependabot/bundler/apps/workbench/loofah-2.3.1
Lucas Di Pentima [Thu, 26 Mar 2020 16:56:37 +0000 (13:56 -0300)]
16265: Merge branch 'dependabot/bundler/apps/workbench/nokogiri-1.10.8' into 16265-security-updates
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Thu, 26 Mar 2020 16:56:18 +0000 (13:56 -0300)]
Merge branch '16265-security-updates' into dependabot/bundler/apps/workbench/nokogiri-1.10.8
Lucas Di Pentima [Thu, 26 Mar 2020 16:54:26 +0000 (13:54 -0300)]
16265: Merge branch 'dependabot/bundler/apps/workbench/rake-13.0.1' into 16265-security-updates
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Thu, 26 Mar 2020 16:54:07 +0000 (13:54 -0300)]
Merge branch '16265-security-updates' into dependabot/bundler/apps/workbench/rake-13.0.1
Lucas Di Pentima [Thu, 26 Mar 2020 16:46:52 +0000 (13:46 -0300)]
16265: Merge branch 'dependabot/bundler/services/api/rake-13.0.1' into 16265-security-updates
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Thu, 26 Mar 2020 16:45:27 +0000 (13:45 -0300)]
Merge branch '16265-security-updates' into dependabot/bundler/services/api/rake-13.0.1
Lucas Di Pentima [Mon, 23 Mar 2020 21:07:56 +0000 (18:07 -0300)]
16266: Applies monkeypatch to fix CVE-2020-5267 on workbench1.
As adviced on https://github.com/advisories/GHSA-65cv-r6x7-79hv
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Thu, 26 Mar 2020 16:29:40 +0000 (13:29 -0300)]
16266: Adds tests exposing potential XSS vulnerability on escape_javascript()
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Tom Clegg [Wed, 25 Mar 2020 18:57:42 +0000 (14:57 -0400)]
16053: Specify utf8 encoding when creating databases.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Wed, 25 Mar 2020 18:35:51 +0000 (14:35 -0400)]
Merge branch '16138-fix-arv-copy' refs #16138
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Wed, 25 Mar 2020 17:53:25 +0000 (13:53 -0400)]
Merge branch 'Majewski/feature/links-client' refs #16260
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Tue, 24 Mar 2020 19:40:59 +0000 (15:40 -0400)]
16053: Add ca-certificates to deps.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 24 Mar 2020 16:12:30 +0000 (12:12 -0400)]
16053: Add example script for installing from scratch.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 24 Mar 2020 16:03:36 +0000 (12:03 -0400)]
16053: Add scripts for running tests in docker.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Tue, 24 Mar 2020 19:35:38 +0000 (15:35 -0400)]
16138: Remove additional/code references to copying pipelines
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 24 Mar 2020 17:23:01 +0000 (13:23 -0400)]
Remove python2 arvados-cwl-runner package build, only python3
refs #12409
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Mon, 23 Mar 2020 21:40:29 +0000 (17:40 -0400)]
16053: Fix check for installed bundler versions.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 23 Mar 2020 20:30:55 +0000 (16:30 -0400)]
16053: Fix test for already-installed en_US.UTF-8 locale.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 23 Mar 2020 19:21:44 +0000 (15:21 -0400)]
15063: Fix tests to accommodate curl speed check granularity.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 23 Mar 2020 18:19:10 +0000 (14:19 -0400)]
16053: Fix keepstore tests that fail when running as root.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 23 Mar 2020 18:02:57 +0000 (14:02 -0400)]
16053: Upgrade mockito for JDK 11 compatibility.
Fixes:
17:19:59.486 [DEBUG] [TestEventLogger] org.arvados.client.logic.keep.FileDownloaderTest STARTED
17:19:59.573 [DEBUG] [TestEventLogger]
17:19:59.573 [DEBUG] [TestEventLogger] org.arvados.client.logic.keep.FileDownloaderTest > classMethod STARTED
17:19:59.593 [DEBUG] [TestEventLogger]
17:19:59.594 [DEBUG] [TestEventLogger] org.arvados.client.logic.keep.FileDownloaderTest > classMethod FAILED
17:19:59.594 [DEBUG] [TestEventLogger] org.mockito.exceptions.base.MockitoException:
17:19:59.594 [DEBUG] [TestEventLogger] Mockito cannot mock this class: class org.arvados.client.api.client.CollectionsApiClient.
17:19:59.594 [DEBUG] [TestEventLogger]
17:19:59.594 [DEBUG] [TestEventLogger] If you're not sure why you're getting this error, please report to the mailing list.
17:19:59.594 [DEBUG] [TestEventLogger]
17:19:59.594 [DEBUG] [TestEventLogger]
17:19:59.594 [DEBUG] [TestEventLogger] Java : 11
17:19:59.595 [DEBUG] [TestEventLogger] JVM vendor name : Debian
17:19:59.595 [DEBUG] [TestEventLogger] JVM vendor version : 11.0.6+10-post-Debian-1deb10u1
17:19:59.595 [DEBUG] [TestEventLogger] JVM name : OpenJDK 64-Bit Server VM
17:19:59.595 [DEBUG] [TestEventLogger] JVM version : 11.0.6+10-post-Debian-1deb10u1
17:19:59.595 [DEBUG] [TestEventLogger] JVM info : mixed mode, sharing
17:19:59.595 [DEBUG] [TestEventLogger] OS name : Linux
17:19:59.595 [DEBUG] [TestEventLogger] OS version : 4.9.0-12-amd64
17:19:59.595 [DEBUG] [TestEventLogger]
17:19:59.595 [DEBUG] [TestEventLogger]
17:19:59.595 [DEBUG] [TestEventLogger] You are seeing this disclaimer because Mockito is configured to create inlined mocks.
17:19:59.595 [DEBUG] [TestEventLogger] You can learn about inline mocks and their limitations under item #39 of the Mockito class javadoc.
17:19:59.595 [DEBUG] [TestEventLogger]
17:19:59.595 [DEBUG] [TestEventLogger] Underlying exception : org.mockito.exceptions.base.MockitoException: Could not modify all classes [class java.lang.Object, class org.arvados.client.api.client.BaseApiClient, class org.arvados.client.api.client.CollectionsApiClient, class org.arvados.client.api.client.BaseStandardApiClient]
17:19:59.595 [DEBUG] [TestEventLogger] at org.mockito.internal.runners.DefaultInternalRunner$1.withBefores(DefaultInternalRunner.java:38)
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 23 Mar 2020 16:42:14 +0000 (12:42 -0400)]
16053: Pass along test args to gradle in java-v2 test suite.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 23 Mar 2020 16:39:37 +0000 (12:39 -0400)]
16053: Install java runtime and jdk.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Mon, 23 Mar 2020 15:00:07 +0000 (11:00 -0400)]
16138: Remove additional pipelines related code
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Fri, 20 Mar 2020 21:04:38 +0000 (17:04 -0400)]
16053: Install gradle.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Fri, 20 Mar 2020 19:47:00 +0000 (15:47 -0400)]
16138: whitelist fields for arv-copy
Also removed code for copying
PipelineTemplate/PipelineInstance (obsolete jobs API).
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Thu, 19 Mar 2020 20:29:50 +0000 (16:29 -0400)]
16053: Fix warnings when installer cwd is not readable by postgres.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 19 Mar 2020 18:57:26 +0000 (14:57 -0400)]
16053: Fix permissions for test db user.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 19 Mar 2020 17:35:23 +0000 (13:35 -0400)]
16053: Run initdb, start postgresql, and add arvados user if needed.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 19 Mar 2020 17:34:57 +0000 (13:34 -0400)]
16053: Install all three needed versions of bundler.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 19 Mar 2020 17:34:35 +0000 (13:34 -0400)]
16053: Make CONFIGSRC optional again.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Wed, 18 Mar 2020 19:15:27 +0000 (15:15 -0400)]
Merge branch '12409-cwl-v1.2' refs #12409
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 17 Mar 2020 21:08:44 +0000 (17:08 -0400)]
12409: Bump cwltool version for more bugfixing.
The tests pass, and the tests confirm that the packed workflow is the
original version and not the upgraded version, which is what we
wanted.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Tue, 17 Mar 2020 13:37:15 +0000 (09:37 -0400)]
16053: Remove unneeded GOPATH mangling.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 17 Mar 2020 13:28:15 +0000 (09:28 -0400)]
16053: Note test timeout trap.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Krzysztof Majewski [Tue, 17 Mar 2020 07:52:50 +0000 (08:52 +0100)]
Add Links API client.
Arvados-DCO-1.1-Signed-off-by: Krzysztof Majewski <majewski.kielce@gmail.com>
Krzysztof Majewski [Tue, 17 Mar 2020 07:49:50 +0000 (08:49 +0100)]
Merge pull request #1 from arvados/master
update
Tom Clegg [Mon, 16 Mar 2020 21:00:21 +0000 (17:00 -0400)]
16053: Add debian:10 install-and-boot test.
Run with "go test -check.vv -tags docker".
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 16 Mar 2020 20:22:21 +0000 (16:22 -0400)]
16053: Install en_US.UTF-8 locale.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 16 Mar 2020 20:22:09 +0000 (16:22 -0400)]
16053: Less verbose wget progress bars.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 16 Mar 2020 20:21:28 +0000 (16:21 -0400)]
16053: Prefer dependencies in /var/lib/arvados/bin if they exist.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 16 Mar 2020 20:20:51 +0000 (16:20 -0400)]
16053: Use setuidgid instead of sudo to drop privileges.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 16 Mar 2020 20:04:31 +0000 (16:04 -0400)]
16053: Add boot flags: -timeout and -shutdown.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Lucas Di Pentima [Mon, 16 Mar 2020 13:56:28 +0000 (10:56 -0300)]
Merge branch '16029-arvboot-wss-fix'. Refs #16029
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Mon, 16 Mar 2020 13:08:15 +0000 (10:08 -0300)]
16029: Makes gofmt happy.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Sat, 14 Mar 2020 14:01:45 +0000 (11:01 -0300)]
16029: Fixes Websockets' ExternalURL config on arvados-boot.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Tom Clegg [Sat, 14 Mar 2020 01:16:56 +0000 (21:16 -0400)]
16053: Add "install" command.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Sat, 14 Mar 2020 01:16:36 +0000 (21:16 -0400)]
16053: Run postgresql as "postgres" user if supervisor is root.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Sat, 14 Mar 2020 01:13:37 +0000 (21:13 -0400)]
16053: 15954: Use auto-generated certificates in nginx config.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Fri, 13 Mar 2020 17:45:07 +0000 (13:45 -0400)]
Merge branch '16129-scoped-token-doc' refs #16129
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Fri, 13 Mar 2020 17:17:43 +0000 (13:17 -0400)]
16129: Improve text and add links from comments
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Thu, 12 Mar 2020 21:46:21 +0000 (17:46 -0400)]
16129: Link to collection sharing link example.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Thu, 12 Mar 2020 21:10:59 +0000 (17:10 -0400)]
16129: Revise scoped token docs a bit, more examples
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Thu, 12 Mar 2020 20:12:31 +0000 (16:12 -0400)]
Merge branch '16221-arv-mount-api-1.x'
fixes #16221
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Thu, 12 Mar 2020 19:06:09 +0000 (15:06 -0400)]
12409: Fix packing bug in cwltool, bump dependency on cwltool
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Thu, 12 Mar 2020 13:41:55 +0000 (09:41 -0400)]
Merge branch '16217-ws-ping'
refs #16217
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 12 Mar 2020 04:15:16 +0000 (00:15 -0400)]
16221: Fix test for config endpoint.
x['configs'] raises KeyError on an old discovery doc -- test
x.get('configs', False) instead.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 20:52:04 +0000 (16:52 -0400)]
Fix instance IDs in arvados-dispatch-cloud log messages.
Some logs had {"Instance": {}} instead of the provider's instance ID.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Wed, 11 Mar 2020 20:05:48 +0000 (16:05 -0400)]
12409: Preserve CWL document version when using RunInSingleContainer
Also update cwltool dependency and remove the workaround from #16169
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 10 Mar 2020 22:24:19 +0000 (18:24 -0400)]
16129: Scoped token doc WIP
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 10 Mar 2020 20:53:41 +0000 (16:53 -0400)]
12409: Update schema-salad pin to latest
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 10 Mar 2020 19:55:50 +0000 (15:55 -0400)]
12409: Bump ruamel.yaml version pin on python sdk
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Tue, 10 Mar 2020 18:01:36 +0000 (14:01 -0400)]
Merge branch '15954-boot-test-cluster'
refs #15954
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 15:15:49 +0000 (11:15 -0400)]
15954: Merge branch 'master'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 14:51:41 +0000 (10:51 -0400)]
15954: Turn off exec bits on temp config file mode.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 14:48:12 +0000 (10:48 -0400)]
15954: Add comment about stdout.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 14:41:31 +0000 (10:41 -0400)]
15954: Dedup find-available-port logic.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 14:41:01 +0000 (10:41 -0400)]
15954: Fix wrong func name in comment.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 14:40:45 +0000 (10:40 -0400)]
15954: Fix style, handle errors first.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 14:40:25 +0000 (10:40 -0400)]
15954: Remove superfluous argument to autofillConfig.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 14:40:04 +0000 (10:40 -0400)]
15954: Use logger instead of writing to stderr.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 14:39:41 +0000 (10:39 -0400)]
15954: Turn off group/other-write bits, even if permitted by umask.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Mon, 9 Mar 2020 22:07:03 +0000 (18:07 -0400)]
12409: Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Thu, 27 Feb 2020 23:10:22 +0000 (18:10 -0500)]
12409: Interactive mode testargs works for py3
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Wed, 26 Feb 2020 19:18:53 +0000 (14:18 -0500)]
12409: Only run sdk/cwl tests py3
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Wed, 26 Feb 2020 18:55:46 +0000 (13:55 -0500)]
12409: Add --devcwl
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Wed, 26 Feb 2020 18:38:05 +0000 (13:38 -0500)]
12409: test_with_arvbox work in progress
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Thu, 5 Mar 2020 23:00:15 +0000 (18:00 -0500)]
Pin version of launchy gem while we still support Ruby 2.3
refs #16215
Need to do it for login-sync too.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Thu, 5 Mar 2020 21:46:42 +0000 (16:46 -0500)]
Merge branch '16219-insufficient-scratch'
fixes #16219
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 21:42:39 +0000 (16:42 -0500)]
16219: Test populated container fields.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Thu, 5 Mar 2020 21:27:33 +0000 (16:27 -0500)]
Pin version of launchy gem while we still support Ruby 2.3
refs #16215
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Thu, 5 Mar 2020 19:44:22 +0000 (14:44 -0500)]
16219: Load all fields needed to compute node size.
Without ContainerImage and Mounts, the scratch size requirement can't
be computed correctly.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 4 Mar 2020 22:15:10 +0000 (17:15 -0500)]
Fix type of ContainerRequestState consts.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 18:16:43 +0000 (13:16 -0500)]
16217: Error out if (*pq.Listener)Ping() fails.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 18:12:52 +0000 (13:12 -0500)]
16217: Close http server before closing listener when shutting down.
Changes log message from "accept tcp ...: use of closed network
connection" to "http: Server closed".
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Wed, 4 Mar 2020 20:17:49 +0000 (15:17 -0500)]
Fix error reporting bug in User.redirect_to
Also improve error logging when User.register fails.
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
dependabot[bot] [Tue, 3 Mar 2020 21:27:30 +0000 (21:27 +0000)]
Bump rake from 12.3.2 to 13.0.1 in /apps/workbench
Bumps [rake](https://github.com/ruby/rake) from 12.3.2 to 13.0.1.
- [Release notes](https://github.com/ruby/rake/releases)
- [Changelog](https://github.com/ruby/rake/blob/master/History.rdoc)
- [Commits](https://github.com/ruby/rake/compare/v12.3.2...v13.0.1)
Signed-off-by: dependabot[bot] <support@github.com>
dependabot[bot] [Tue, 3 Mar 2020 21:27:27 +0000 (21:27 +0000)]
Bump rake from 12.3.2 to 13.0.1 in /services/api
Bumps [rake](https://github.com/ruby/rake) from 12.3.2 to 13.0.1.
- [Release notes](https://github.com/ruby/rake/releases)
- [Changelog](https://github.com/ruby/rake/blob/master/History.rdoc)
- [Commits](https://github.com/ruby/rake/compare/v12.3.2...v13.0.1)
Signed-off-by: dependabot[bot] <support@github.com>
Peter Amstutz [Tue, 3 Mar 2020 21:17:38 +0000 (16:17 -0500)]
Remove Gemfile.lock from login-sync
no issue #
To be consistent with sdk/ruby sdk/cli behavior.
There's a circular dependency where the version number of the gem is
embedded in Gemfile.lock, but the version number is derived from the
git commit timestamp, so when it updates Gemfile.lock it creates a new
version, which requires a updating Gemfile.lock, and so on.
However, unlike the Ruby on Rails deb/rpm packages, when we create
gems (dev or production) it does not include Gemfile.lock, so there's
no benefit to having it checked in.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 3 Mar 2020 20:34:05 +0000 (15:34 -0500)]
Ruby gems respect ARVADOS_BUILDING_VERSION
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 2 Mar 2020 19:05:06 +0000 (14:05 -0500)]
Merge branch '16169-cwl-hints' refs #16169
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Fri, 28 Feb 2020 17:07:35 +0000 (12:07 -0500)]
16169: Monkey patch load_tool.resolve_and_validate_document to fix bug
There is a bug in upstream cwltool where the version updater needs to
replace the document fragments in the loader index with the updated
ones, but actually it only does it for the root document. Normally we
just fix the bug in upstream but that's challenging because current
cwltool dropped support for Python 2.7 and we're still supporting py2
in Arvados 2.0 (although py2 support will most likely be dropped in
Arvados 2.1). Making a bugfix fork comes with its own
complications (it would need to be added to PyPi) so monkey patching
is the least disruptive fix (and is relatively safe because our
cwltool dependency is pinned to a specific version). This
should be removed as soon as a bugfix goes into upstream cwltool and
we upgrade to it.
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