arvados.git
11 months agoMerge branch '20825-cwl-separate-runner' refs #20825
Peter Amstutz [Thu, 19 Oct 2023 18:44:52 +0000 (14:44 -0400)]
Merge branch '20825-cwl-separate-runner' refs #20825

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

11 months agoMerge branch '20933-arv-copy-cwl' refs #20933
Peter Amstutz [Thu, 12 Oct 2023 14:00:13 +0000 (10:00 -0400)]
Merge branch '20933-arv-copy-cwl'  refs #20933

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

11 months agoMerge branch '20984-instance-capacity'
Tom Clegg [Tue, 24 Oct 2023 19:32:49 +0000 (15:32 -0400)]
Merge branch '20984-instance-capacity'

fixes #20984

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

11 months agoMerge branch '20885-pdoc-style'
Brett Smith [Thu, 28 Sep 2023 23:56:43 +0000 (19:56 -0400)]
Merge branch '20885-pdoc-style'

Closes #20885.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

11 months ago20885: Update argument docstrings after pdoc migration
Brett Smith [Fri, 20 Oct 2023 15:57:45 +0000 (11:57 -0400)]
20885: Update argument docstrings after pdoc migration

Update arvados.api_resources to use our new function argument format.

Refs #20885.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

11 months agoMerge branch '19818-api-pydoc'
Brett Smith [Fri, 29 Sep 2023 15:28:50 +0000 (11:28 -0400)]
Merge branch '19818-api-pydoc'

Closes #19818.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

11 months agoMerge branch '20937-arv-copy-http' refs #20937
Peter Amstutz [Wed, 11 Oct 2023 13:20:29 +0000 (09:20 -0400)]
Merge branch '20937-arv-copy-http' refs #20937

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

11 months agoMerge branch '20990-name-btree' refs #20990
Peter Amstutz [Tue, 3 Oct 2023 13:54:30 +0000 (09:54 -0400)]
Merge branch '20990-name-btree' refs #20990

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

13 months agoFix 2.7.0 date in upgrading notes, refs #20769 2.7.0
Peter Amstutz [Thu, 21 Sep 2023 13:14:54 +0000 (09:14 -0400)]
Fix 2.7.0 date in upgrading notes, refs #20769

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

14 months agoNeed to have nvidia installed so singularity detects it
Peter Amstutz [Wed, 20 Sep 2023 21:15:20 +0000 (17:15 -0400)]
Need to have nvidia installed so singularity detects it

refs #20769

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

14 months agoCheck out singularity from git to get submodules
Peter Amstutz [Wed, 20 Sep 2023 21:08:10 +0000 (17:08 -0400)]
Check out singularity from git to get submodules

refs #20769

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

14 months agoAdd singularity build deps libglib2.0-dev and libseccomp-dev to packer
Peter Amstutz [Wed, 20 Sep 2023 20:56:15 +0000 (16:56 -0400)]
Add singularity build deps libglib2.0-dev and libseccomp-dev to packer

refs #20769

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

14 months agoSet 2.7.0 release date, refs #20769
Peter Amstutz [Wed, 20 Sep 2023 17:23:22 +0000 (13:23 -0400)]
Set 2.7.0 release date, refs #20769

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

14 months agoFix cwltest version pin, refs #20973
Peter Amstutz [Tue, 19 Sep 2023 21:24:47 +0000 (17:24 -0400)]
Fix cwltest version pin, refs #20973

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

14 months agoMerge branch '20973-cwltest' refs #20973
Peter Amstutz [Mon, 18 Sep 2023 15:29:27 +0000 (11:29 -0400)]
Merge branch '20973-cwltest' refs #20973

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

14 months agoMerge branch '20497-updating-wgs-tutorial'
Brett Smith [Mon, 18 Sep 2023 14:45:02 +0000 (10:45 -0400)]
Merge branch '20497-updating-wgs-tutorial'

Closes #20497.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20497: Typo fixes 20497-updating-wgs-tutorial
Brett Smith [Mon, 18 Sep 2023 14:44:04 +0000 (10:44 -0400)]
20497: Typo fixes

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20497: Give brief instructions for reviewing subprocess output
Brett Smith [Mon, 18 Sep 2023 14:35:42 +0000 (10:35 -0400)]
20497: Give brief instructions for reviewing subprocess output

This was previously discussed in the same paragraph as the main workflow
download collection. Moving it here means we don't jump back and forth
as much between the main workflow process and a subprocess.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20497: Clarify collection view/download
Brett Smith [Mon, 18 Sep 2023 13:37:52 +0000 (09:37 -0400)]
20497: Clarify collection view/download

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20497: Clean up section 5 opening paragraph
Brett Smith [Mon, 18 Sep 2023 13:34:55 +0000 (09:34 -0400)]
20497: Clean up section 5 opening paragraph

There used to be multiple navigation options listed here. Now that
there's only one, the introduction needs to be updated to match.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months agoPin cwltest version that we package, refs #20973 20973-cwltest
Peter Amstutz [Mon, 18 Sep 2023 13:32:11 +0000 (09:32 -0400)]
Pin cwltest version that we package, refs #20973

The subsequent release of cwltest confirms that files exist on disk,
since our files are in Keep, all the tests fail.  We should add
[optional] Arvados support to cwltest so it can access Keep but for
the time being just package the last working version.

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

14 months ago20497: Direct the reader to the tutorial project via Public Favorites
Brett Smith [Mon, 18 Sep 2023 13:31:14 +0000 (09:31 -0400)]
20497: Direct the reader to the tutorial project via Public Favorites

Unfortunately searching for the project raises a couple of issues:

* The search results return two copies of the project, one from pirca
  and one from jutro. If the reader picks the jutro one, they'll be
  prompted to log in again, losing their progress and kicking them off the
  happy path.

* The search results also return the finished demo workflow process we
  publish for people, "(start here) Example WGS processing workflow". This
  is attractive to people because it says "(start here)", has a bright
  green "Completed" badge next to it, and the difference between a process
  and a project may not be clear to people who are just getting started
  with Arvados.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20497: Add missing paragraph break
Brett Smith [Mon, 18 Sep 2023 13:29:24 +0000 (09:29 -0400)]
20497: Add missing paragraph break

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20497: Make button text consistent with Workbench 2 UI
Brett Smith [Mon, 18 Sep 2023 13:28:20 +0000 (09:28 -0400)]
20497: Make button text consistent with Workbench 2 UI

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months agoMerge branch '20955-log-update-doc' refs #20955
Peter Amstutz [Mon, 18 Sep 2023 13:21:13 +0000 (09:21 -0400)]
Merge branch '20955-log-update-doc' refs #20955

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

14 months ago20955: Typo fixes throughout 20955-log-update-doc
Brett Smith [Mon, 18 Sep 2023 02:47:57 +0000 (22:47 -0400)]
20955: Typo fixes throughout

* "superceded"→"superseded"
* "via[d] the" repetition
* "database" echoed twice in one sentence
* Link hardcoded to doc.arvados.org→site.baseurl

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20955: Update documentation about the new and legacy container logging systems
Peter Amstutz [Fri, 15 Sep 2023 20:47:12 +0000 (16:47 -0400)]
20955: Update documentation about the new and legacy container logging systems

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

14 months ago20955: Reorder upgrade notes in rough order of disruptiveness
Peter Amstutz [Fri, 15 Sep 2023 17:47:51 +0000 (13:47 -0400)]
20955: Reorder upgrade notes in rough order of disruptiveness

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

14 months agoAdd note about api_client_authorization deprecated fields refs #20951
Peter Amstutz [Fri, 15 Sep 2023 15:11:07 +0000 (11:11 -0400)]
Add note about api_client_authorization deprecated fields refs #20951

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

14 months agoMerge branch '20926-installer-pg-client-version'. Closes #20926
Lucas Di Pentima [Thu, 14 Sep 2023 21:04:06 +0000 (18:04 -0300)]
Merge branch '20926-installer-pg-client-version'. Closes #20926

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20926: Makes regex for postgres.client state more strict. 20926-installer-pg-client-version
Lucas Di Pentima [Thu, 14 Sep 2023 21:02:44 +0000 (18:02 -0300)]
20926: Makes regex for postgres.client state more strict.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months agoMerge branch '20932-wb2-docs'
Brett Smith [Thu, 14 Sep 2023 16:00:42 +0000 (12:00 -0400)]
Merge branch '20932-wb2-docs'

Closes #20932.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20926: Sets default PG version when when using single host deployment.
Lucas Di Pentima [Thu, 14 Sep 2023 14:46:30 +0000 (11:46 -0300)]
20926: Sets default PG version when when using single host deployment.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20926: Sets PostgreSQL v15 the default version.
Lucas Di Pentima [Thu, 14 Sep 2023 14:23:00 +0000 (11:23 -0300)]
20926: Sets PostgreSQL v15 the default version.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20926: Requires manually setting PG version when not using the 'database' role.
Lucas Di Pentima [Wed, 13 Sep 2023 22:27:13 +0000 (19:27 -0300)]
20926: Requires manually setting PG version when not using the 'database' role.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months agoMerge branch '20930-websocket'
Tom Clegg [Wed, 13 Sep 2023 19:53:59 +0000 (15:53 -0400)]
Merge branch '20930-websocket'

fixes #20930
fixes #20507

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agoMerge branch '20850-wb1-deprecated' refs #20850
Peter Amstutz [Wed, 13 Sep 2023 19:28:12 +0000 (15:28 -0400)]
Merge branch '20850-wb1-deprecated' refs #20850

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

14 months ago20850: Fix capitalization and indentation
Peter Amstutz [Wed, 13 Sep 2023 19:26:28 +0000 (15:26 -0400)]
20850: Fix capitalization and indentation

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

14 months ago20932: Update un/trash instructions for Workbench 2 20932-wb2-docs
Brett Smith [Wed, 13 Sep 2023 18:29:43 +0000 (14:29 -0400)]
20932: Update un/trash instructions for Workbench 2

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20932/20850/20890: Remove switch instructions from Workbench migration guide
Brett Smith [Wed, 13 Sep 2023 18:16:19 +0000 (14:16 -0400)]
20932/20850/20890: Remove switch instructions from Workbench migration guide

The switch feature has been removed from Workbench 2, and a deprecation
notice in Workbench 1 now prominently leads you to switch. See #20890
and #20850, respectively.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20497: Updating documentation
Alex Coleman [Wed, 13 Sep 2023 04:24:09 +0000 (22:24 -0600)]
20497: Updating documentation

Updating screenshots, adding additional screenshot, rewording several sections, and adding more relevant
information for Workbench2.

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

14 months ago20926: Allows the database version to be configurable from local.params.
Lucas Di Pentima [Tue, 12 Sep 2023 22:35:36 +0000 (19:35 -0300)]
20926: Allows the database version to be configurable from local.params.

Also, installs postgresql-client on the controller nodes from the salt
formula, so that its version matches the configured value.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20840: Typo fixes.
Brett Smith [Tue, 12 Sep 2023 21:53:32 +0000 (17:53 -0400)]
20840: Typo fixes.

Refs #20840.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months agoFix flaky dispatchcloud test.
Tom Clegg [Tue, 12 Sep 2023 17:52:24 +0000 (13:52 -0400)]
Fix flaky dispatchcloud test.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agoMerge branch '20840-api-deprecate-notice' refs #20840
Peter Amstutz [Tue, 12 Sep 2023 15:46:54 +0000 (11:46 -0400)]
Merge branch '20840-api-deprecate-notice' refs #20840

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

14 months ago20930: Fix deadlock in notify/listen event loop. 20930-websocket
Tom Clegg [Tue, 12 Sep 2023 13:49:35 +0000 (09:49 -0400)]
20930: Fix deadlock in notify/listen event loop.

See TestManyEventsAndSubscribers comment in previous commit.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20930: Test many clients connecting and disonnecting.
Tom Clegg [Sun, 10 Sep 2023 02:01:22 +0000 (22:01 -0400)]
20930: Test many clients connecting and disonnecting.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20930: Concurrency optimization.
Tom Clegg [Sun, 10 Sep 2023 02:02:29 +0000 (22:02 -0400)]
20930: Concurrency optimization.

In handler, create the eventSink later, and call Stop() sooner, to
avoid needlessly blocking other sinks during other setup/teardown.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agoMerge branch '20888-encrypted-cert-key-doc'. Closes #20888
Lucas Di Pentima [Fri, 8 Sep 2023 21:00:19 +0000 (18:00 -0300)]
Merge branch '20888-encrypted-cert-key-doc'. Closes #20888

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20888: Applies suggested improvements. 20888-encrypted-cert-key-doc
Lucas Di Pentima [Fri, 8 Sep 2023 20:59:03 +0000 (17:59 -0300)]
20888: Applies suggested improvements.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20930: Fix passing arvados.Client (with a sync.Mutex) by value.
Tom Clegg [Fri, 8 Sep 2023 20:06:57 +0000 (16:06 -0400)]
20930: Fix passing arvados.Client (with a sync.Mutex) by value.

Copying could occur while the original arvados.Client was being used
to fetch the discovery doc and had its Mutex locked.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20930: Fix unhelpful test failure output.
Tom Clegg [Fri, 8 Sep 2023 20:31:39 +0000 (16:31 -0400)]
20930: Fix unhelpful test failure output.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20888: Expands the encrypted cert key feature's documentation.
Lucas Di Pentima [Fri, 8 Sep 2023 19:59:10 +0000 (16:59 -0300)]
20888: Expands the encrypted cert key feature's documentation.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months agoAvoid Python3.7 incompatibility introduced in typing_extensions 4.8.
Tom Clegg [Fri, 8 Sep 2023 13:39:38 +0000 (09:39 -0400)]
Avoid Python3.7 incompatibility introduced in typing_extensions 4.8.

refs #20905

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agoMerge branch '20889-installer-fixes'. Closes #20889
Lucas Di Pentima [Thu, 7 Sep 2023 13:07:18 +0000 (10:07 -0300)]
Merge branch '20889-installer-fixes'. Closes #20889

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months agoMerge branch '20750-sharing-token-scopes'
Brett Smith [Tue, 5 Sep 2023 20:50:09 +0000 (16:50 -0400)]
Merge branch '20750-sharing-token-scopes'

Closes #20750.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20750/20927: Add TODO about network error handling
Brett Smith [Tue, 5 Sep 2023 20:46:54 +0000 (16:46 -0400)]
20750/20927: Add TODO about network error handling

The commit message for 9717f88d29310067fa70e19fb9afb3679c036bc4 says:

> This may also provide better behavior in cases of network hiccups or
> other remote server turbulence.

This was written with the expectation that those problems would raise
`HTTPClient::BadResponseError`. That was mistaken. Those problems
actually raise lower-level socket exceptions instead.

We now have a ticket to improve the error handling here. It's out of
scope for #20750, since the error handling is no worse than it was
before the branch.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20750: Fix comment typo
Brett Smith [Tue, 5 Sep 2023 20:46:48 +0000 (16:46 -0400)]
20750: Fix comment typo

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months agoMerge branch '20612-diag-ctr-api-access'
Tom Clegg [Tue, 5 Sep 2023 19:46:17 +0000 (15:46 -0400)]
Merge branch '20612-diag-ctr-api-access'

closes #20612

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20612: Fix up punctuation/capitalization in docs.
Tom Clegg [Tue, 5 Sep 2023 19:39:33 +0000 (15:39 -0400)]
20612: Fix up punctuation/capitalization in docs.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20840: Fix broken url 20840-api-deprecate-notice
Peter Amstutz [Tue, 5 Sep 2023 18:06:49 +0000 (14:06 -0400)]
20840: Fix broken url

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

14 months agoMerge branch '20919-fix-proxy-url'
Tom Clegg [Mon, 4 Sep 2023 14:11:32 +0000 (10:11 -0400)]
Merge branch '20919-fix-proxy-url'

fixes #20919

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20850: Don't show wb2 deprecation notice to anonymous users 20850-wb1-deprecated
Peter Amstutz [Sun, 3 Sep 2023 17:52:40 +0000 (13:52 -0400)]
20850: Don't show wb2 deprecation notice to anonymous users

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

14 months ago20840: Add deprecations to upgrade notes
Peter Amstutz [Sun, 3 Sep 2023 17:36:49 +0000 (13:36 -0400)]
20840: Add deprecations to upgrade notes

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

14 months ago20840: Add warning boxes to legacy APIs and rearrange API listing
Peter Amstutz [Sun, 3 Sep 2023 17:27:03 +0000 (13:27 -0400)]
20840: Add warning boxes to legacy APIs and rearrange API listing

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

14 months ago20850: Fix test selector
Peter Amstutz [Sun, 3 Sep 2023 16:44:34 +0000 (12:44 -0400)]
20850: Fix test selector

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

14 months ago20850: Add deprecation notice & wb2 redirect to every page
Peter Amstutz [Fri, 1 Sep 2023 21:26:28 +0000 (17:26 -0400)]
20850: Add deprecation notice & wb2 redirect to every page

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

14 months ago20612: Document diagnostics image building / container options. 20612-diag-ctr-api-access
Tom Clegg [Fri, 1 Sep 2023 18:22:51 +0000 (14:22 -0400)]
20612: Document diagnostics image building / container options.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20612: Set DEBIAN_FRONTEND=noninteractive for container build.
Tom Clegg [Fri, 1 Sep 2023 17:47:08 +0000 (13:47 -0400)]
20612: Set DEBIAN_FRONTEND=noninteractive for container build.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agogithub-207: Fix outgoing Host header in proxy request. github-207
Tom Clegg [Wed, 30 Aug 2023 18:30:27 +0000 (14:30 -0400)]
github-207: Fix outgoing Host header in proxy request.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20915: Add missing import to _pycurlhelper
Brett Smith [Thu, 31 Aug 2023 13:27:03 +0000 (09:27 -0400)]
20915: Add missing import to _pycurlhelper

Closes #20915.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months agoFix for cached files from arvados-controller
George Chlipala [Mon, 28 Aug 2023 21:57:06 +0000 (16:57 -0500)]
Fix for cached files from arvados-controller
Arvados-DCO-1.1-Signed-off-by: George Chlipala <gchlip2@uic.edu>

14 months agoMerge branch '20877-trashed-priority' refs #20877
Peter Amstutz [Tue, 29 Aug 2023 18:15:08 +0000 (14:15 -0400)]
Merge branch '20877-trashed-priority' refs #20877

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

14 months agoMerge branch '20839-pysdk-deprecations'
Brett Smith [Tue, 29 Aug 2023 15:41:10 +0000 (11:41 -0400)]
Merge branch '20839-pysdk-deprecations'

Closes #20839.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20877: Do not create log or output collections if parent is frozen or trashed 20877-trashed-priority
Peter Amstutz [Tue, 29 Aug 2023 15:04:03 +0000 (11:04 -0400)]
20877: Do not create log or output collections if parent is frozen or trashed

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

14 months agoMerge branch '20757-ctr-shell-settings'
Tom Clegg [Tue, 29 Aug 2023 13:16:00 +0000 (09:16 -0400)]
Merge branch '20757-ctr-shell-settings'

fixes #20757

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20836: Update test_select for Py<3.8 compatibility 20839-pysdk-deprecations
Brett Smith [Mon, 28 Aug 2023 20:26:41 +0000 (16:26 -0400)]
20836: Update test_select for Py<3.8 compatibility

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20839: Mark deprecated PySDK functions as such
Brett Smith [Sun, 27 Aug 2023 02:13:39 +0000 (22:13 -0400)]
20839: Mark deprecated PySDK functions as such

This is in preparation to remove these from the SDK in Arvados 3.0.

These changes exacerbated the circular import between the top-level
arvados and util, which had knock-off effects on other import
statements, causing them to see the world differently (like whether
`arvados.api` is a module or function). Most of the import-related
shuffling is meant to mitigate all that.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20839: Add order_key to select in keyset_list_all
Brett Smith [Sun, 27 Aug 2023 03:59:21 +0000 (23:59 -0400)]
20839: Add order_key to select in keyset_list_all

Like uuid, the main loop requires this field.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20839: Replace arvados.util.mkdir_dash_p calls throughout
Brett Smith [Sun, 27 Aug 2023 02:52:13 +0000 (22:52 -0400)]
20839: Replace arvados.util.mkdir_dash_p calls throughout

In preparation to deprecate the function.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20839: Replace arvados.util.list_all calls throughout
Brett Smith [Sun, 27 Aug 2023 02:01:32 +0000 (22:01 -0400)]
20839: Replace arvados.util.list_all calls throughout

In preparation to deprecate this function. This does leave a couple
calls in arv-docker-migrate19, but that command will also be deprecated
and removed at least as soon as the function.

The changes to the the sdk/cwl/tests/test_submit.py mocks are necessary
because of mechanical differences between list_all and keyset_list_all.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

test fixup

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20757: Split tests into separate funcs. 20757-ctr-shell-settings
Tom Clegg [Mon, 28 Aug 2023 18:40:05 +0000 (14:40 -0400)]
20757: Split tests into separate funcs.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20612: Run diagnostics from inside the test container too.
Tom Clegg [Mon, 28 Aug 2023 14:23:34 +0000 (10:23 -0400)]
20612: Run diagnostics from inside the test container too.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months ago20839: Optimize list sort
Brett Smith [Sun, 27 Aug 2023 01:55:39 +0000 (21:55 -0400)]
20839: Optimize list sort

Trivial optimization I noticed while working around here.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20839: Replace arvados.util.run_command calls in arv-copy
Brett Smith [Sun, 27 Aug 2023 01:42:20 +0000 (21:42 -0400)]
20839: Replace arvados.util.run_command calls in arv-copy

In preparation for deprecating this function.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20839: Remove old Python 2 TextIOWrapper shim
Brett Smith [Sat, 26 Aug 2023 23:32:53 +0000 (19:32 -0400)]
20839: Remove old Python 2 TextIOWrapper shim

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

14 months ago20889: Fixes Keep S3 bucket instructions. 20889-installer-fixes
Lucas Di Pentima [Fri, 25 Aug 2023 19:20:08 +0000 (16:20 -0300)]
20889: Fixes Keep S3 bucket instructions.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20889: Adds documentation explaining the use of TLS cert keys encryption.
Lucas Di Pentima [Fri, 25 Aug 2023 19:13:22 +0000 (16:13 -0300)]
20889: Adds documentation explaining the use of TLS cert keys encryption.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20889: Fixes installer.sh indentation to match the how provision.sh is written.
Lucas Di Pentima [Fri, 25 Aug 2023 18:30:04 +0000 (15:30 -0300)]
20889: Fixes installer.sh indentation to match the how provision.sh is written.

It had a mix of space-based and tab-based indentation that made code a bit
difficult to read.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20889: Checks that cert files are present before trying to use them.
Lucas Di Pentima [Fri, 25 Aug 2023 18:22:56 +0000 (15:22 -0300)]
20889: Checks that cert files are present before trying to use them.

Also, some documentation fixes.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20757: `arvados-client shell` uses settings.conf if present.
Tom Clegg [Fri, 25 Aug 2023 16:28:56 +0000 (12:28 -0400)]
20757: `arvados-client shell` uses settings.conf if present.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

14 months agoMerge branch '20877-trashed-priority' refs #20877
Peter Amstutz [Fri, 25 Aug 2023 14:49:33 +0000 (10:49 -0400)]
Merge branch '20877-trashed-priority' refs #20877

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

14 months agoMerge branch '20894-instances-default' refs #20894
Peter Amstutz [Fri, 25 Aug 2023 14:04:25 +0000 (10:04 -0400)]
Merge branch '20894-instances-default' refs #20894

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

14 months ago20889: Fixes a bug when database & controller roles are on a single node.
Lucas Di Pentima [Fri, 25 Aug 2023 13:30:11 +0000 (10:30 -0300)]
20889: Fixes a bug when database & controller roles are on a single node.

The database role gets handled first, so the controller node gets removed
from the list and then when checking if multiple nodes were available, the
code path for a single controller didn't checked if the node was already
removed from the node list.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20889: Allows customization on database name and user.
Lucas Di Pentima [Thu, 24 Aug 2023 21:47:26 +0000 (18:47 -0300)]
20889: Allows customization on database name and user.

Also, allows specifying external PG service for the single host cases.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20889: Allows configurable S3 bucket name and IAM profile for Keep backend.
Lucas Di Pentima [Thu, 24 Aug 2023 21:05:10 +0000 (18:05 -0300)]
20889: Allows configurable S3 bucket name and IAM profile for Keep backend.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20889: Adds config handling of external database service.
Lucas Di Pentima [Thu, 24 Aug 2023 20:56:05 +0000 (17:56 -0300)]
20889: Adds config handling of external database service.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20889: Removes unnecessary documentation about rolling upgrades.
Lucas Di Pentima [Thu, 24 Aug 2023 20:35:39 +0000 (17:35 -0300)]
20889: Removes unnecessary documentation about rolling upgrades.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20889: Removes DISABLED_CONTROLLER from the user-editable local.params file.
Lucas Di Pentima [Thu, 24 Aug 2023 19:31:45 +0000 (16:31 -0300)]
20889: Removes DISABLED_CONTROLLER from the user-editable local.params file.

As the rolling upgrade procedure is done automatically, this is not needed
and could cause confusion by being on local.params

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

14 months ago20750: Fix documentation link typo 20750-sharing-token-scopes
Brett Smith [Thu, 24 Aug 2023 19:11:32 +0000 (15:11 -0400)]
20750: Fix documentation link typo

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>