arvados.git
3 years agoFix OS package iteration number in run-build-docker-jobs-image.sh
Ward Vandewege [Mon, 23 Nov 2020 19:48:35 +0000 (14:48 -0500)]
Fix OS package iteration number in run-build-docker-jobs-image.sh

refs #17012

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

3 years agoUpdate error checking in run-build-docker-jobs-image.sh
Ward Vandewege [Mon, 23 Nov 2020 16:51:21 +0000 (11:51 -0500)]
Update error checking in run-build-docker-jobs-image.sh

refs #17012

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

3 years agoRemove now-unneeded code from sdk/cwl/test_with_arvbox.sh, add comment
Ward Vandewege [Mon, 23 Nov 2020 16:47:53 +0000 (11:47 -0500)]
Remove now-unneeded code from sdk/cwl/test_with_arvbox.sh, add comment
to clarify that calculate_python_sdk_cwl_package_versions now outputs
python-style package suffixes.

refs #17012

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

3 years ago17154: Add comment. Use strings.HasPrefix
Peter Amstutz [Mon, 23 Nov 2020 15:59:06 +0000 (10:59 -0500)]
17154: Add comment.  Use strings.HasPrefix

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

3 years ago17154: Copy updates on federated users to local cluster
Peter Amstutz [Fri, 20 Nov 2020 21:01:25 +0000 (16:01 -0500)]
17154: Copy updates on federated users to local cluster

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

3 years ago17154: Make sure most current user record is loaded.
Peter Amstutz [Fri, 20 Nov 2020 20:25:27 +0000 (15:25 -0500)]
17154: Make sure most current user record is loaded.

Convert 'option' items (which are symbols) to strings for value comparison

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

3 years agoNow that calculate_python_sdk_cwl_package_versions returns python-style
Ward Vandewege [Mon, 23 Nov 2020 14:20:56 +0000 (09:20 -0500)]
Now that calculate_python_sdk_cwl_package_versions returns python-style
version string suffixes (.dev/rc), make sure the 2 scripts that use that
function are adapted accordingly.

refs #17012

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

3 years agoMove the handle_python_package() function from run-library.sh to
Ward Vandewege [Sun, 22 Nov 2020 13:35:06 +0000 (08:35 -0500)]
Move the handle_python_package() function from run-library.sh to
run-build-packages-python-and-ruby.sh, it is only used in the latter.
Update it to call python3 instead of just 'python'.

refs #15888

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

3 years agoFix more golint warnings.
Ward Vandewege [Sat, 21 Nov 2020 20:53:01 +0000 (15:53 -0500)]
Fix more golint warnings.

No issue #

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

3 years agoRemove one more python2 remnant. This is a fix for the
Ward Vandewege [Fri, 20 Nov 2020 22:31:50 +0000 (17:31 -0500)]
Remove one more python2 remnant. This is a fix for the
python3-arvados-cwl-runner package, it now installs /usr/bin/cwltool
again.

refs #15888

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

3 years ago17015: Ensure that containers belong to this cluster
Peter Amstutz [Thu, 19 Nov 2020 20:36:29 +0000 (15:36 -0500)]
17015: Ensure that containers belong to this cluster

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

3 years ago17009: Mention S3 considerations in keep-web install doc.
Tom Clegg [Thu, 19 Nov 2020 21:48:15 +0000 (16:48 -0500)]
17009: Mention S3 considerations in keep-web install doc.

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

3 years ago17009: Support accessing S3 with virtual hosted-style URLs.
Tom Clegg [Wed, 18 Nov 2020 22:35:29 +0000 (17:35 -0500)]
17009: Support accessing S3 with virtual hosted-style URLs.

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

3 years agoFix more golint warnings.
Ward Vandewege [Tue, 17 Nov 2020 01:40:47 +0000 (20:40 -0500)]
Fix more golint warnings.

No issue #

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

3 years ago17012: switch calculate_python_sdk_cwl_package_versions() to use the
Ward Vandewege [Tue, 17 Nov 2020 22:35:31 +0000 (17:35 -0500)]
17012: switch calculate_python_sdk_cwl_package_versions() to use the
       python version calculation code. This effectively is bash calling
       python calling bash, which I don't like, but the code is simpler.

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

3 years ago17012: update calculation of python version number in run-library.sh
Ward Vandewege [Tue, 17 Nov 2020 15:26:58 +0000 (10:26 -0500)]
17012: update calculation of python version number in run-library.sh
       (used by a few docker image scripts).

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

3 years ago17012: remove old gittaggers.py files.
Ward Vandewege [Tue, 17 Nov 2020 14:52:53 +0000 (09:52 -0500)]
17012: remove old gittaggers.py files.

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

3 years ago17012: when calculating the version of our Python packages, take the
Ward Vandewege [Mon, 16 Nov 2020 20:08:26 +0000 (15:08 -0500)]
17012: when calculating the version of our Python packages, take the
       build directory into account.

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

3 years ago16950: switch to os.UserHomeDir(), and send all output to stderr.
Ward Vandewege [Wed, 18 Nov 2020 21:20:40 +0000 (16:20 -0500)]
16950: switch to os.UserHomeDir(), and send all output to stderr.

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

3 years ago16950: make specifying of the output directory mandatory (remove
Ward Vandewege [Wed, 18 Nov 2020 15:09:51 +0000 (10:09 -0500)]
16950: make specifying of the output directory mandatory (remove
       default).

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

3 years ago16950: refactor caching; use ~/.cache/arvados/costanalyzer for that
Ward Vandewege [Sat, 14 Nov 2020 18:22:50 +0000 (13:22 -0500)]
16950: refactor caching; use ~/.cache/arvados/costanalyzer for that
       purpose.

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

3 years ago16950: more changes after review.
Ward Vandewege [Fri, 13 Nov 2020 21:22:57 +0000 (16:22 -0500)]
16950: more changes after review.

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

3 years ago16950: changes after review.
Ward Vandewege [Thu, 12 Nov 2020 03:07:48 +0000 (22:07 -0500)]
16950: changes after review.

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

3 years ago16950: add tests for the costanalyzer.
Ward Vandewege [Tue, 3 Nov 2020 21:34:16 +0000 (16:34 -0500)]
16950: add tests for the costanalyzer.

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

3 years ago16950: add the costanalyzer to arvados-client.
Ward Vandewege [Sat, 3 Oct 2020 17:58:50 +0000 (13:58 -0400)]
16950: add the costanalyzer to arvados-client.

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

3 years ago16950: a few cleanups for our container request fixtures: attach a real
Ward Vandewege [Fri, 30 Oct 2020 20:29:40 +0000 (16:29 -0400)]
16950: a few cleanups for our container request fixtures: attach a real
       log collection, and define CompletedContainerRequestUUID in
       arvadostest (go).

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

3 years agoadded TestCreateRemoteContainerRequestCheckSetRuntimeToken
Nico Cesar [Thu, 10 Dec 2020 19:46:05 +0000 (14:46 -0500)]
added TestCreateRemoteContainerRequestCheckSetRuntimeToken

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoChanged the way we test mock
Nico Cesar [Thu, 10 Dec 2020 19:04:55 +0000 (14:04 -0500)]
Changed the way we test mock

After a long discussion as a result of https://dev.arvados.org/issues/17014#note-18
Tom Clegg and Nico Cesar agreed that TestCreateRemoteContainerRequestCheckRuntimeToken
was expecting the same sent json object in the mock

the process is
client -> zzzzz cluster -> zmock

and we expect to have a random runtime_token in the zmock cluster

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoSystemRootToken was missing in the test
Nico Cesar [Tue, 8 Dec 2020 23:03:10 +0000 (18:03 -0500)]
SystemRootToken was missing in the test

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoadded 'shell' to arvbox
Nico Cesar [Tue, 8 Dec 2020 21:44:37 +0000 (16:44 -0500)]
added 'shell' to arvbox

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoadding an old friend: TestCreateRemoteContainerRequestCheckRuntimeToken
Nico Cesar [Tue, 8 Dec 2020 16:16:20 +0000 (11:16 -0500)]
adding an old friend: TestCreateRemoteContainerRequestCheckRuntimeToken

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agouser context is needed to pass tests ..
Nico Cesar [Fri, 4 Dec 2020 22:40:27 +0000 (17:40 -0500)]
user context is needed to pass tests ..

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoadded a test that fails to prove rpc.Conn is not DTRT
Nico Cesar [Fri, 4 Dec 2020 20:25:28 +0000 (15:25 -0500)]
added a test that fails to prove rpc.Conn is not DTRT

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years ago17014: Add mock response to users/current. 17014-controller-container-requests-TC
Tom Clegg [Tue, 1 Dec 2020 17:14:16 +0000 (12:14 -0500)]
17014: Add mock response to users/current.

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

3 years agoadding failing TestCreateRemoteContainerRequest
Nico Cesar [Mon, 30 Nov 2020 17:09:54 +0000 (12:09 -0500)]
adding failing TestCreateRemoteContainerRequest

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agomaking old tests pass
Nico Cesar [Mon, 30 Nov 2020 17:01:21 +0000 (12:01 -0500)]
making old tests pass

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoAdding old tests that fail
Nico Cesar [Thu, 19 Nov 2020 16:46:21 +0000 (11:46 -0500)]
Adding old tests that fail

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoNew name of output collection is null or empty
Nico Cesar [Wed, 18 Nov 2020 21:08:30 +0000 (16:08 -0500)]
New name of output collection is null or empty

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years ago17014: making cr.container_uuid a string
Nico Cesar [Wed, 18 Nov 2020 20:35:36 +0000 (15:35 -0500)]
17014: making cr.container_uuid a string

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years ago17014: Munge list items in controller responses. 17014-controller-container-requests-mungeitems
Tom Clegg [Wed, 18 Nov 2020 20:04:28 +0000 (15:04 -0500)]
17014: Munge list items in controller responses.

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

3 years agoBetter comments
Nico Cesar [Tue, 17 Nov 2020 19:14:32 +0000 (14:14 -0500)]
Better comments

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoaddressing https://dev.arvados.org/issues/17014#note-8 Tests
Nico Cesar [Tue, 17 Nov 2020 17:32:39 +0000 (12:32 -0500)]
addressing https://dev.arvados.org/issues/17014#note-8 Tests

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoaddressing https://dev.arvados.org/issues/17014#note-8 Tests
Nico Cesar [Tue, 17 Nov 2020 17:23:09 +0000 (12:23 -0500)]
addressing https://dev.arvados.org/issues/17014#note-8 Tests

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoaddressing https://dev.arvados.org/issues/17014#note-8 Tests
Nico Cesar [Tue, 17 Nov 2020 17:15:23 +0000 (12:15 -0500)]
addressing https://dev.arvados.org/issues/17014#note-8 Tests

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years ago17014: expires_at and Filters feedback. Comments improvement
Nico Cesar [Mon, 16 Nov 2020 22:13:44 +0000 (17:13 -0500)]
17014: expires_at and Filters feedback. Comments improvement

more changes addressing https://dev.arvados.org/issues/17014#note-8

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agofollowing https://dev.arvados.org/issues/17014#note-8
Nico Cesar [Mon, 16 Nov 2020 19:58:41 +0000 (14:58 -0500)]
following https://dev.arvados.org/issues/17014#note-8

removed "len(token) < 41" case

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years ago17014: rebase with master and adaptation changes
Nico Cesar [Mon, 16 Nov 2020 19:43:38 +0000 (14:43 -0500)]
17014: rebase with master and adaptation changes

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>17014: rebase
with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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with master and adaptation changes

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Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoFix more golint warnings.
Ward Vandewege [Sun, 15 Nov 2020 19:18:40 +0000 (14:18 -0500)]
Fix more golint warnings.

No issue #

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

3 years ago17111: Deselect unsigned_manifest_text by default in groups#contents.
Tom Clegg [Fri, 13 Nov 2020 20:44:43 +0000 (15:44 -0500)]
17111: Deselect unsigned_manifest_text by default in groups#contents.

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

3 years agoFix more golint warnings.
Ward Vandewege [Fri, 13 Nov 2020 01:02:56 +0000 (20:02 -0500)]
Fix more golint warnings.

No issue #

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

3 years agocontainer requests in the new codepath for controller
Nico Cesar [Tue, 10 Nov 2020 14:00:52 +0000 (09:00 -0500)]
container requests in the new codepath for controller

Controller's "new" codepath is a step towards sunsetting railsapi. This
commit is the initial work to get Container Requests in that path

The reason for deleting some tests is intentional. This is part of the migration
from
   apps/workbench/test/controllers/container_requests_controller_test.rb
to
   lib/controller/integration_test.go

This single-commit is the result of collaboration with Lucas Di Pentima
and Tom Clegg in the branch 17014-controller-cr

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <nico@curii.com>

3 years agoFix more golint warnings.
Ward Vandewege [Sun, 8 Nov 2020 21:41:21 +0000 (16:41 -0500)]
Fix more golint warnings.

No issue #

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

3 years agoMerge branch '17086-add-focal-fossa' into master
Ward Vandewege [Sat, 7 Nov 2020 13:45:42 +0000 (08:45 -0500)]
Merge branch '17086-add-focal-fossa' into master

closes #17086

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

3 years ago17086: Merge branch 'master' into 17086-add-focal-fossa
Ward Vandewege [Sat, 7 Nov 2020 13:45:09 +0000 (08:45 -0500)]
17086: Merge branch 'master' into 17086-add-focal-fossa

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

3 years agoFix require path in the 'script/rails' script for api server.
Ward Vandewege [Fri, 6 Nov 2020 13:34:38 +0000 (08:34 -0500)]
Fix require path in the 'script/rails' script for api server.

closes #17094

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

3 years ago17086: build packages for Ubuntu 20.04, Focal Fossa.
Ward Vandewege [Thu, 5 Nov 2020 19:43:37 +0000 (14:43 -0500)]
17086: build packages for Ubuntu 20.04, Focal Fossa.

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

3 years agoMerge branch '17090-exclusive-lock' refs #17090
Peter Amstutz [Thu, 5 Nov 2020 20:15:13 +0000 (15:15 -0500)]
Merge branch '17090-exclusive-lock' refs #17090

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

3 years ago17090: Migration to refresh_permissions
Peter Amstutz [Thu, 5 Nov 2020 19:55:35 +0000 (14:55 -0500)]
17090: Migration to refresh_permissions

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

3 years ago17090: Use EXCLUSIVE lock for permission updates
Peter Amstutz [Thu, 5 Nov 2020 16:09:30 +0000 (11:09 -0500)]
17090: Use EXCLUSIVE lock for permission updates

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

3 years agoFix more golint warnings.
Ward Vandewege [Thu, 5 Nov 2020 00:52:42 +0000 (19:52 -0500)]
Fix more golint warnings.

No issue #

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

3 years agoMerge branch '17040-slow-query' refs #17040
Peter Amstutz [Tue, 3 Nov 2020 18:29:21 +0000 (13:29 -0500)]
Merge branch '17040-slow-query' refs #17040

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

3 years ago17040: Update structure.sql
Peter Amstutz [Tue, 3 Nov 2020 18:01:57 +0000 (13:01 -0500)]
17040: Update structure.sql

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

3 years ago17040: RefreshTrashedGroups migration, clear_permissions calls forget_cached_group_perms
Peter Amstutz [Tue, 3 Nov 2020 17:12:59 +0000 (12:12 -0500)]
17040: RefreshTrashedGroups migration, clear_permissions calls forget_cached_group_perms

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

3 years ago17040: Cache results of User.group_permissions
Peter Amstutz [Mon, 2 Nov 2020 21:20:02 +0000 (16:20 -0500)]
17040: Cache results of User.group_permissions

When requesting a list of groups (either directly, or with the
"shared" endpoint) it calls writable_by for each group.  This
indirectly calls User.group_permissions, which makes a database query.
When it does this for every group (with a database query each time),
which gets very expensive.

To address this, this commit caches the result of group_permissions on
the user object.

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

3 years ago17040: Get user_uuids and embed them as a constant in the main query
Peter Amstutz [Mon, 2 Nov 2020 19:25:28 +0000 (14:25 -0500)]
17040: Get user_uuids and embed them as a constant in the main query

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

3 years agoFix more golint warnings.
Ward Vandewege [Sun, 1 Nov 2020 22:27:04 +0000 (17:27 -0500)]
Fix more golint warnings.

No issue #

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

3 years agoMerge branch '17047-centos-remove-rh-python-dependencies' into master
Javier Bértoli [Wed, 28 Oct 2020 19:56:29 +0000 (16:56 -0300)]
Merge branch '17047-centos-remove-rh-python-dependencies' into master

closes #17047
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@curii.com>

3 years ago17047: bugfixes, and add an entry to the upgrade notes about the
Ward Vandewege [Wed, 28 Oct 2020 19:29:58 +0000 (15:29 -0400)]
17047: bugfixes, and add an entry to the upgrade notes about the
       packaging change.

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

3 years agofeat(centos): use centos-provided python3
Javier Bértoli [Tue, 27 Oct 2020 13:13:53 +0000 (10:13 -0300)]
feat(centos): use centos-provided python3

Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@curii.com>

3 years agobuild: Remove remaining references to the SSO server packages.
Ward Vandewege [Tue, 27 Oct 2020 15:24:23 +0000 (11:24 -0400)]
build: Remove remaining references to the SSO server packages.

No issue #

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

3 years agodocumentation: Mention distribution packages on the "Install the Slurm
Ward Vandewege [Tue, 27 Oct 2020 15:23:05 +0000 (11:23 -0400)]
documentation: Mention distribution packages on the "Install the Slurm
dispatcher" page.

closes #16883

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

3 years agoMerge branch '17044-remove-debian-stretch' into master
Ward Vandewege [Tue, 27 Oct 2020 15:14:15 +0000 (11:14 -0400)]
Merge branch '17044-remove-debian-stretch' into master

closes #17044

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

3 years ago17040: Refactor trash check
Peter Amstutz [Tue, 27 Oct 2020 02:55:46 +0000 (22:55 -0400)]
17040: Refactor trash check

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

3 years ago17044: implement review comments (part 2): update cwl tests to use
Ward Vandewege [Mon, 26 Oct 2020 23:35:12 +0000 (19:35 -0400)]
17044: implement review comments (part 2): update cwl tests to use
       Debian buster.

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

3 years ago17044: implement review comments (part 1).
Ward Vandewege [Mon, 26 Oct 2020 23:33:10 +0000 (19:33 -0400)]
17044: implement review comments (part 1).

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

3 years ago17044: remove Debian "stretch" from the build infrastructure. Update
Ward Vandewege [Mon, 26 Oct 2020 19:14:37 +0000 (15:14 -0400)]
17044: remove Debian "stretch" from the build infrastructure. Update
       documentation to mark stretch as EOL post the last release in the
       2.1.X series.

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

3 years agoMerge branch '16996-add-dispatch-local-service-file' into master
Javier Bértoli [Mon, 26 Oct 2020 18:32:23 +0000 (15:32 -0300)]
Merge branch '16996-add-dispatch-local-service-file' into master

closes #16996
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@curii.com>

3 years agofeat(crunch-dispatch-local): add crunch-run dependency
Javier Bértoli [Mon, 26 Oct 2020 15:28:29 +0000 (12:28 -0300)]
feat(crunch-dispatch-local): add crunch-run dependency

refs #16995
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@curii.com>

3 years agofix(crunch-dispatch-local): add missing service file
Javier Bértoli [Mon, 19 Oct 2020 13:06:18 +0000 (10:06 -0300)]
fix(crunch-dispatch-local): add missing service file

refs #16996
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@curii.com>

3 years agoFix more golint warnings.
Ward Vandewege [Sun, 25 Oct 2020 15:42:59 +0000 (11:42 -0400)]
Fix more golint warnings.

No issue #

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

3 years agoFix more golint warnings.
Ward Vandewege [Sun, 25 Oct 2020 00:28:04 +0000 (20:28 -0400)]
Fix more golint warnings.

No issue #

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

3 years agoMerge branch '16930-tagging' into master
Ward Vandewege [Fri, 23 Oct 2020 20:40:35 +0000 (16:40 -0400)]
Merge branch '16930-tagging' into master

closes #16930

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

3 years ago16930: remove local 'latest' tag before pushing.
Ward Vandewege [Fri, 23 Oct 2020 18:31:14 +0000 (14:31 -0400)]
16930: remove local 'latest' tag before pushing.

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

3 years agoFix author e-mail addresses in our gemspecs.
Ward Vandewege [Fri, 23 Oct 2020 17:01:55 +0000 (13:01 -0400)]
Fix author e-mail addresses in our gemspecs.

No issue #

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

3 years ago17040: Swap the order of where clauses in the readable_by query
Peter Amstutz [Fri, 23 Oct 2020 00:44:15 +0000 (20:44 -0400)]
17040: Swap the order of where clauses in the readable_by query

This seems work around a query planner bug in Postgres 9.5.

A hotfix provided to a customer resulted in dramatically better
performance.

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

3 years agoMake run-build-docker-images.sh a little smarter, allow building just
Ward Vandewege [Wed, 21 Oct 2020 15:10:00 +0000 (11:10 -0400)]
Make run-build-docker-images.sh a little smarter, allow building just
one type of arvbox images.

refs #16930

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

3 years agoMerge branch '17010-re-run-workflow' refs #17010
Peter Amstutz [Thu, 22 Oct 2020 18:45:17 +0000 (14:45 -0400)]
Merge branch '17010-re-run-workflow' refs #17010

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

3 years ago17010: Use !! instead of (? true : false)
Peter Amstutz [Thu, 22 Oct 2020 18:44:37 +0000 (14:44 -0400)]
17010: Use !! instead of (? true : false)

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

3 years ago17010: Don't double up --enable-reuse
Peter Amstutz [Thu, 22 Oct 2020 02:27:14 +0000 (22:27 -0400)]
17010: Don't double up --enable-reuse

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

3 years ago17010: Fix tests. Tests check that --enable-reuse is set
Peter Amstutz [Thu, 22 Oct 2020 02:16:26 +0000 (22:16 -0400)]
17010: Fix tests.  Tests check that --enable-reuse is set

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

3 years ago17010: Fix tests
Peter Amstutz [Wed, 21 Oct 2020 21:19:05 +0000 (17:19 -0400)]
17010: Fix tests

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

3 years ago17010: Fix debug comment
Peter Amstutz [Wed, 21 Oct 2020 20:37:17 +0000 (16:37 -0400)]
17010: Fix debug comment

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

3 years ago17010: When running workflow from workbench, enable reuse by default
Peter Amstutz [Wed, 21 Oct 2020 20:13:50 +0000 (16:13 -0400)]
17010: When running workflow from workbench, enable reuse by default

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

3 years ago17010: Redesign "Re-run..." button to choose project to run in
Peter Amstutz [Wed, 21 Oct 2020 20:02:12 +0000 (16:02 -0400)]
17010: Redesign "Re-run..." button to choose project to run in

Also move workflow step reuse to the "Inputs" tab instead of a modal.

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

3 years agoMake run-build-docker-images.sh a little smarter, allow building just
Ward Vandewege [Wed, 21 Oct 2020 16:06:26 +0000 (12:06 -0400)]
Make run-build-docker-images.sh a little smarter, allow building just
one type of arvbox images (part 2).

refs #16930

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

3 years agoMerge branch '16471-install-using-salt' into master
Javier Bértoli [Wed, 21 Oct 2020 15:47:09 +0000 (12:47 -0300)]
Merge branch '16471-install-using-salt' into master

closes #16471
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@curii.com>

3 years agoMerge branch '16669-oidc-access-token'
Tom Clegg [Wed, 21 Oct 2020 14:11:37 +0000 (10:11 -0400)]
Merge branch '16669-oidc-access-token'

refs #16669

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

3 years ago16669: Fix test.
Tom Clegg [Thu, 24 Sep 2020 14:05:30 +0000 (10:05 -0400)]
16669: Fix test.

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

3 years ago16669: Fix pass-through of cached remote token.
Tom Clegg [Wed, 23 Sep 2020 21:37:34 +0000 (17:37 -0400)]
16669: Fix pass-through of cached remote token.

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

3 years ago16669: Fix access token cache panic.
Tom Clegg [Tue, 22 Sep 2020 15:03:45 +0000 (11:03 -0400)]
16669: Fix access token cache panic.

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