arvados.git
4 years ago16263: Generalize "local_user_list" flag to "no_federation"
Peter Amstutz [Tue, 31 Mar 2020 02:14:23 +0000 (22:14 -0400)]
16263: Generalize "local_user_list" flag to "no_federation"

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago16263: UserMerge shouldn't be federated
Peter Amstutz [Mon, 30 Mar 2020 21:12:17 +0000 (17:12 -0400)]
16263: UserMerge shouldn't be federated

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago16263: Fix omitempty placement
Peter Amstutz [Mon, 30 Mar 2020 18:50:06 +0000 (14:50 -0400)]
16263: Fix omitempty placement

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago16263: Add omitempty to GetOptions
Peter Amstutz [Mon, 30 Mar 2020 18:43:36 +0000 (14:43 -0400)]
16263: Add omitempty to GetOptions

Don't try to migrate if activate_remote_user fails.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago16263: Add local_user_list to boolParams
Peter Amstutz [Sat, 28 Mar 2020 01:36:09 +0000 (21:36 -0400)]
16263: Add local_user_list to boolParams

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago16263: Add local_user_list flag to bypass LoginCluster behavior
Peter Amstutz [Fri, 27 Mar 2020 21:08:48 +0000 (17:08 -0400)]
16263: Add local_user_list flag to bypass LoginCluster behavior

Required by federation migrate script.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago16263: Decodes JSON numbers as strings instead of float64.
Lucas Di Pentima [Thu, 26 Mar 2020 14:46:34 +0000 (11:46 -0300)]
16263: Decodes JSON numbers as strings instead of float64.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago16263: Adds unit test case confirming 'limit' bug.
Lucas Di Pentima [Wed, 25 Mar 2020 19:35:18 +0000 (16:35 -0300)]
16263: Adds unit test case confirming 'limit' bug.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago16263: Adds test exposing a bug when using 'limit' with the max int64 value.
Lucas Di Pentima [Wed, 25 Mar 2020 14:26:55 +0000 (11:26 -0300)]
16263: Adds test exposing a bug when using 'limit' with the max int64 value.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago16263: Bool filter bug fix.
Lucas Di Pentima [Tue, 24 Mar 2020 20:39:01 +0000 (17:39 -0300)]
16263: Bool filter bug fix.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago16263: Adds test exposing a bug on filter unmarshalling.
Lucas Di Pentima [Tue, 24 Mar 2020 21:03:34 +0000 (18:03 -0300)]
16263: Adds test exposing a bug on filter unmarshalling.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago16263: Makes gofmt happy.
Lucas Di Pentima [Mon, 23 Mar 2020 19:20:41 +0000 (16:20 -0300)]
16263: Makes gofmt happy.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago16263: Don't cache modified_by_*_uuid fields when using LoginCluster.
Lucas Di Pentima [Mon, 23 Mar 2020 18:32:59 +0000 (15:32 -0300)]
16263: Don't cache modified_by_*_uuid fields when using LoginCluster.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago16263: Adds nullify behavior to users's batch_update endpoint.
Lucas Di Pentima [Mon, 23 Mar 2020 15:27:18 +0000 (12:27 -0300)]
16263: Adds nullify behavior to users's batch_update endpoint.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago16263: Assigns nil to select attributes when receiving empty values.
Lucas Di Pentima [Thu, 19 Mar 2020 21:15:52 +0000 (18:15 -0300)]
16263: Assigns nil to select attributes when receiving empty values.

Controller may translate NULL values to "" on certain object string fields.
The same with integers, NULLs are converted to 0.
When controller retrieves objects from railsAPI and uses the data to create
or update objects, some of those fields should get converted back to NULL.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago16263: Adds test exposing the bug.
Lucas Di Pentima [Thu, 19 Mar 2020 16:18:05 +0000 (13:18 -0300)]
16263: Adds test exposing the bug.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years agoMerge branch '12409-cwl-v1.2' refs #12409
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>

4 years ago12409: Bump cwltool version for more bugfixing.
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>

4 years agoMerge branch '16029-arvboot-wss-fix'. Refs #16029
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>

4 years ago16029: Makes gofmt happy.
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>

4 years ago16029: Fixes Websockets' ExternalURL config on arvados-boot.
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>

4 years agoMerge branch '16129-scoped-token-doc' refs #16129
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>

4 years ago16129: Improve text and add links from comments
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>

4 years ago16129: Link to collection sharing link example.
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>

4 years ago16129: Revise scoped token docs a bit, more examples
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>

4 years agoMerge branch '16221-arv-mount-api-1.x'
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>

4 years ago12409: Fix packing bug in cwltool, bump dependency on cwltool
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>

4 years agoMerge branch '16217-ws-ping'
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>

4 years ago16221: Fix test for config endpoint.
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>

4 years agoFix instance IDs in arvados-dispatch-cloud log messages.
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>

4 years ago12409: Preserve CWL document version when using RunInSingleContainer
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>

4 years ago16129: Scoped token doc WIP
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>

4 years ago12409: Update schema-salad pin to latest
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>

4 years ago12409: Bump ruamel.yaml version pin on python sdk
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>

4 years agoMerge branch '15954-boot-test-cluster'
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>

4 years ago15954: Merge branch 'master'
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>

4 years ago15954: Turn off exec bits on temp config file mode.
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>

4 years ago15954: Add comment about stdout.
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>

4 years ago15954: Dedup find-available-port logic.
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>

4 years ago15954: Fix wrong func name in comment.
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>

4 years ago15954: Fix style, handle errors first.
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>

4 years ago15954: Remove superfluous argument to autofillConfig.
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>

4 years ago15954: Use logger instead of writing to stderr.
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>

4 years ago15954: Turn off group/other-write bits, even if permitted by umask.
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>

4 years ago12409: Fix tests
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>

4 years ago12409: Interactive mode testargs works for py3
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>

4 years ago12409: Only run sdk/cwl tests py3
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>

4 years ago12409: Add --devcwl
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>

4 years ago12409: test_with_arvbox work in progress
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>

4 years agoPin version of launchy gem while we still support Ruby 2.3
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>

4 years agoMerge branch '16219-insufficient-scratch'
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>

4 years ago16219: Test populated container fields.
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>

4 years agoPin version of launchy gem while we still support Ruby 2.3
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>

4 years ago16219: Load all fields needed to compute node size.
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>

4 years agoFix type of ContainerRequestState consts.
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>

4 years ago16217: Error out if (*pq.Listener)Ping() fails.
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>

4 years ago16217: Close http server before closing listener when shutting down.
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>

4 years agoFix error reporting bug in User.redirect_to
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>

4 years agoRemove Gemfile.lock from login-sync
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>

4 years agoRuby gems respect ARVADOS_BUILDING_VERSION
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>

4 years agoMerge branch '16169-cwl-hints' refs #16169
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>

4 years ago16169: Monkey patch load_tool.resolve_and_validate_document to fix bug
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.

4 years ago16169: Adds test exposing the requirement propagation bug.
Lucas Di Pentima [Wed, 26 Feb 2020 23:58:59 +0000 (20:58 -0300)]
16169: Adds test exposing the requirement propagation bug.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years agoUse new version tag to avoid tag whose checksum changed.
Tom Clegg [Mon, 2 Mar 2020 17:45:28 +0000 (12:45 -0500)]
Use new version tag to avoid tag whose checksum changed.

refs #12308

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoMerge branch '14990-support-email-exported-config'
Lucas Di Pentima [Fri, 28 Feb 2020 21:24:37 +0000 (18:24 -0300)]
Merge branch '14990-support-email-exported-config'

Refs #14990

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago14990: Adds exported config section on the API documentation.
Lucas Di Pentima [Fri, 28 Feb 2020 18:40:32 +0000 (15:40 -0300)]
14990: Adds exported config section on the API documentation.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago14990: Exports Mail.SupportEmailAddress config so that WB2 can use it.
Lucas Di Pentima [Fri, 28 Feb 2020 18:28:22 +0000 (15:28 -0300)]
14990: Exports Mail.SupportEmailAddress config so that WB2 can use it.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

4 years ago15954: Merge branch 'master'
Tom Clegg [Fri, 28 Feb 2020 18:10:02 +0000 (13:10 -0500)]
15954: Merge branch 'master'

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Fix nginx listener addresses.
Tom Clegg [Fri, 28 Feb 2020 06:59:12 +0000 (01:59 -0500)]
15954: Fix nginx listener addresses.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Skip database.yml when running under arvados-server boot.
Tom Clegg [Fri, 28 Feb 2020 05:51:44 +0000 (00:51 -0500)]
15954: Skip database.yml when running under arvados-server boot.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Ignore warnings from passenger-config validate-install.
Tom Clegg [Thu, 27 Feb 2020 21:39:02 +0000 (16:39 -0500)]
15954: Ignore warnings from passenger-config validate-install.

Otherwise, an existing passenger installation (system-wide or in an
rvm gemset) causes cluster startup to fail.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoMerge branch '16202-shell-suffix' refs #16202
Peter Amstutz [Thu, 27 Feb 2020 20:48:37 +0000 (15:48 -0500)]
Merge branch '16202-shell-suffix' refs #16202

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years agoMerge branch '16177-trust-all-content'
Peter Amstutz [Thu, 27 Feb 2020 20:46:47 +0000 (15:46 -0500)]
Merge branch '16177-trust-all-content'

refs #16177
refs #16151

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago15954: Fix api pidfile race.
Tom Clegg [Thu, 27 Feb 2020 20:30:47 +0000 (15:30 -0500)]
15954: Fix api pidfile race.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoNodemanager and crunchstat-summary sync with pysdk version
Peter Amstutz [Thu, 27 Feb 2020 18:56:49 +0000 (13:56 -0500)]
Nodemanager and crunchstat-summary sync with pysdk version

refs #16151

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago15954: Don't touch GEM_ vars if rvm is in use.
Tom Clegg [Thu, 27 Feb 2020 18:47:19 +0000 (13:47 -0500)]
15954: Don't touch GEM_ vars if rvm is in use.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago16177: Don't run pip --quiet to get more information about what it is doing
Peter Amstutz [Thu, 27 Feb 2020 18:38:37 +0000 (13:38 -0500)]
16177: Don't run pip --quiet to get more information about what it is doing

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago16177: Fix tests, test server config now has TrustAllContent: false
Peter Amstutz [Thu, 27 Feb 2020 17:21:34 +0000 (12:21 -0500)]
16177: Fix tests, test server config now has TrustAllContent: false

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago15954: Fix config for login tests.
Tom Clegg [Thu, 27 Feb 2020 17:05:10 +0000 (12:05 -0500)]
15954: Fix config for login tests.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Fix test.
Tom Clegg [Thu, 27 Feb 2020 16:58:48 +0000 (11:58 -0500)]
15954: Fix test.

The following "setup user" call was only succeeding because the "uuid"
param was being ignored and the call was processed as a no-op ("admin
account is already set up, nothing to do").

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Don't send copious "rake test" logs to stdout.
Tom Clegg [Thu, 27 Feb 2020 16:19:28 +0000 (11:19 -0500)]
15954: Don't send copious "rake test" logs to stdout.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Fix railsapi startup in run_test_server.py.
Tom Clegg [Thu, 27 Feb 2020 15:22:54 +0000 (10:22 -0500)]
15954: Fix railsapi startup in run_test_server.py.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoMerge branch '16177-trust-all-content' refs #16177
Peter Amstutz [Thu, 27 Feb 2020 15:17:51 +0000 (10:17 -0500)]
Merge branch '16177-trust-all-content' refs #16177

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago16202: Add Workbench.SSHHelpHostSuffix
Peter Amstutz [Wed, 26 Feb 2020 21:12:22 +0000 (16:12 -0500)]
16202: Add Workbench.SSHHelpHostSuffix

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago15954: Merge branch 'master'
Tom Clegg [Thu, 27 Feb 2020 14:25:20 +0000 (09:25 -0500)]
15954: Merge branch 'master'

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Remove unused LibPath.
Tom Clegg [Thu, 27 Feb 2020 14:23:24 +0000 (09:23 -0500)]
15954: Remove unused LibPath.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Check addr/port for unsupported configs.
Tom Clegg [Wed, 26 Feb 2020 21:56:18 +0000 (16:56 -0500)]
15954: Check addr/port for unsupported configs.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago16177: Use correct config item Collections.TrustAllContent
Peter Amstutz [Wed, 26 Feb 2020 20:31:58 +0000 (15:31 -0500)]
16177: Use correct config item Collections.TrustAllContent

Also added fallback error handler, if view or download link doesn't
work, render error text (otherwise you get a very confusing Rails
crash page).

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years agoarvbox now installs python tools with python3
Peter Amstutz [Wed, 26 Feb 2020 19:16:14 +0000 (14:16 -0500)]
arvbox now installs python tools with python3

Also adjust 'geo' config for local/public mode.

refs #12409

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years agoFix web shell.
Ward Vandewege [Wed, 26 Feb 2020 18:49:28 +0000 (13:49 -0500)]
Fix web shell.

refs #16203

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@jhvc.com>

4 years agoMerge branch '16172-remote-token-validation'
Tom Clegg [Wed, 26 Feb 2020 15:31:10 +0000 (10:31 -0500)]
Merge branch '16172-remote-token-validation'

fixes #16172

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Tidy up federation test.
Tom Clegg [Wed, 26 Feb 2020 15:18:16 +0000 (10:18 -0500)]
15954: Tidy up federation test.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Move PortableDataHash func to sdk/go/arvados.
Tom Clegg [Wed, 26 Feb 2020 15:17:32 +0000 (10:17 -0500)]
15954: Move PortableDataHash func to sdk/go/arvados.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Fix up logging prefix.
Tom Clegg [Wed, 26 Feb 2020 15:16:38 +0000 (10:16 -0500)]
15954: Fix up logging prefix.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: More careful about finding available ports.
Tom Clegg [Wed, 26 Feb 2020 07:01:33 +0000 (02:01 -0500)]
15954: More careful about finding available ports.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Rename booter to supervisor, tidy up.
Tom Clegg [Tue, 25 Feb 2020 23:44:48 +0000 (18:44 -0500)]
15954: Rename booter to supervisor, tidy up.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoFix wrong token expected at keepproxy health check endpoint.
Tom Clegg [Tue, 25 Feb 2020 18:26:30 +0000 (13:26 -0500)]
Fix wrong token expected at keepproxy health check endpoint.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Propagate remote param.
Tom Clegg [Tue, 25 Feb 2020 17:14:32 +0000 (12:14 -0500)]
15954: Propagate remote param.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Allow activating user using an admin token.
Tom Clegg [Tue, 25 Feb 2020 16:12:58 +0000 (11:12 -0500)]
15954: Allow activating user using an admin token.

This was intended to work already, but didn't.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15954: Fixup federation test.
Tom Clegg [Tue, 25 Feb 2020 16:11:47 +0000 (11:11 -0500)]
15954: Fixup federation test.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>