arvados.git
6 months ago19821: Convert CollectionWriter.open docstring to Markdown 19821-collection-docstrings
Brett Smith [Thu, 12 Oct 2023 18:06:19 +0000 (14:06 -0400)]
19821: Convert CollectionWriter.open docstring to Markdown

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

6 months ago19821: Fully qualify docstring types
Brett Smith [Thu, 12 Oct 2023 18:00:49 +0000 (14:00 -0400)]
19821: Fully qualify docstring types

This gets pdoc to hyperlink the type.

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

6 months ago19821: Bugfix type declarations for compatibility with Python<3.9
Brett Smith [Wed, 11 Oct 2023 16:40:55 +0000 (12:40 -0400)]
19821: Bugfix type declarations for compatibility with Python<3.9

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

6 months ago19821: Improve consistency of Properties type
Brett Smith [Wed, 11 Oct 2023 16:40:18 +0000 (12:40 -0400)]
19821: Improve consistency of Properties type

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

6 months ago19821: Document the arvados.collection module
Brett Smith [Tue, 10 Oct 2023 20:24:12 +0000 (16:24 -0400)]
19821: Document the arvados.collection module

* Add docstrings and type signatures to all public methods.

* Mark all deprecated classes and methods. Move them to the bottom of
  the module for better organization of web documentation.

* Mark all internal classes and methods.

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

6 months agoClose span
Peter Amstutz [Wed, 11 Oct 2023 14:25:41 +0000 (10:25 -0400)]
Close span

refs #20937

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

6 months agoRemove duplicated ~$
Peter Amstutz [Wed, 11 Oct 2023 14:16:44 +0000 (10:16 -0400)]
Remove duplicated ~$

refs #20937

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

6 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>

6 months ago20937: Simplify use of logger.error
Peter Amstutz [Wed, 11 Oct 2023 13:19:24 +0000 (09:19 -0400)]
20937: Simplify use of logger.error

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

6 months ago20937: Improve error handling 20937-arv-copy-http
Peter Amstutz [Tue, 10 Oct 2023 17:49:15 +0000 (13:49 -0400)]
20937: Improve error handling

Also clean up docs a bit

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

6 months agoMerge branch '20949-wb-redirects-improvements'. Closes #20949
Lucas Di Pentima [Tue, 10 Oct 2023 15:29:34 +0000 (12:29 -0300)]
Merge branch '20949-wb-redirects-improvements'. Closes #20949

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

6 months ago20949: Adds query string based redirections from wb1's actions controller. 20949-wb-redirects-improvements
Lucas Di Pentima [Fri, 6 Oct 2023 17:23:20 +0000 (14:23 -0300)]
20949: Adds query string based redirections from wb1's actions controller.

Matches '/actions?uuid=X' URLs and redirects to an appropriate WB2 URL.

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

6 months ago20937: Update documentation
Peter Amstutz [Fri, 6 Oct 2023 14:42:11 +0000 (10:42 -0400)]
20937: Update documentation

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

6 months ago20937: Return same tuple consistently from http_to_keep
Peter Amstutz [Fri, 6 Oct 2023 14:01:40 +0000 (10:01 -0400)]
20937: Return same tuple consistently from http_to_keep

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

6 months ago20937: fix deadlock with duplicated blocks
Peter Amstutz [Mon, 11 Sep 2023 20:45:44 +0000 (16:45 -0400)]
20937: fix deadlock with duplicated blocks

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

6 months ago20937: Set limit on 'put' queue
Peter Amstutz [Mon, 11 Sep 2023 20:10:08 +0000 (16:10 -0400)]
20937: Set limit on 'put' queue

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

6 months ago20937: Fix in -> is typo
Peter Amstutz [Mon, 11 Sep 2023 19:57:53 +0000 (15:57 -0400)]
20937: Fix in -> is typo

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

6 months ago20937: Handle None result
Peter Amstutz [Mon, 11 Sep 2023 19:56:18 +0000 (15:56 -0400)]
20937: Handle None result

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

6 months ago20937: Fix pathmapper use of http_to_keep
Peter Amstutz [Mon, 11 Sep 2023 17:02:42 +0000 (13:02 -0400)]
20937: Fix pathmapper use of http_to_keep

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

6 months ago20937: Add error handling to threaded collection copy
Peter Amstutz [Mon, 11 Sep 2023 14:02:26 +0000 (10:02 -0400)]
20937: Add error handling to threaded collection copy

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

6 months ago20937: Better handling of repeated blocks
Peter Amstutz [Fri, 8 Sep 2023 02:46:44 +0000 (22:46 -0400)]
20937: Better handling of repeated blocks

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

6 months ago20937: Fix progress writer
Peter Amstutz [Fri, 8 Sep 2023 02:33:51 +0000 (22:33 -0400)]
20937: Fix progress writer

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

6 months ago20937: Parallel collection copy
Peter Amstutz [Thu, 5 Oct 2023 19:14:31 +0000 (15:14 -0400)]
20937: Parallel collection copy

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

6 months ago20937: Add http import capability to arv-copy
Peter Amstutz [Fri, 8 Sep 2023 01:52:14 +0000 (21:52 -0400)]
20937: Add http import capability to arv-copy

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

6 months agoMerge branch 'main' from workbench2.git
Tom Clegg [Thu, 5 Oct 2023 15:46:31 +0000 (11:46 -0400)]
Merge branch 'main' from workbench2.git

refs #18874

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

6 months agoMerge branch '21002-restore-banner-adjust-width'
Lisa Knox [Thu, 5 Oct 2023 14:45:32 +0000 (10:45 -0400)]
Merge branch '21002-restore-banner-adjust-width'

closes #21002

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

6 months agoMerge branch '21033-wb2-dependency-upgrades'. Closes #21033
Lucas Di Pentima [Tue, 3 Oct 2023 20:52:35 +0000 (17:52 -0300)]
Merge branch '21033-wb2-dependency-upgrades'. Closes #21033

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

6 months ago21033: Applies dependency upgrades.
Lucas Di Pentima [Tue, 3 Oct 2023 18:59:23 +0000 (15:59 -0300)]
21033: Applies dependency upgrades.

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

7 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>

7 months ago21028: Build Ruby from source on rocky8
Brett Smith [Fri, 29 Sep 2023 22:48:41 +0000 (18:48 -0400)]
21028: Build Ruby from source on rocky8

Same rationale as fe8da34676be7c6fbb1042fcfcabee19bfa424d0.

Refs #21028.

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

7 months agoNote that groups/contents API can accept a user UUID
Brett Smith [Fri, 29 Sep 2023 19:35:21 +0000 (15:35 -0400)]
Note that groups/contents API can accept a user UUID

This is very helpful for generalizing project walk code and I don't
think it's documented anywhere.

No issue #.

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

7 months ago21028: Build Ruby from source on rocky8
Brett Smith [Fri, 29 Sep 2023 19:23:56 +0000 (15:23 -0400)]
21028: Build Ruby from source on rocky8

Without this, RVM downloads a binary Ruby with a bunch of configuration
options turned on. This can lead to problems building extensions when
Ruby thinks a certain feature is supported but our Docker image doesn't
have the headers to support it. Right now we're seeing that in the zlib
gem: it has extra code to turn on when Ruby supports Valgrind, but we
don't have the Valgrind headers necessary to build that code.

Closes #21028.

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

7 months ago20878: Bugfix missing variable sigil
Brett Smith [Fri, 29 Sep 2023 19:22:13 +0000 (15:22 -0400)]
20878: Bugfix missing variable sigil

Without this, the test compared against the constant string "TARGET" and
never tried to reuse built RPMs.

Refs #20878.

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

7 months agoMerge branch '18874-merge-wb2'
Tom Clegg [Fri, 29 Sep 2023 17:46:58 +0000 (13:46 -0400)]
Merge branch '18874-merge-wb2'

refs #18874

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

7 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>

7 months ago20932: Update API index for Workbench 2 default
Brett Smith [Fri, 29 Sep 2023 14:21:50 +0000 (10:21 -0400)]
20932: Update API index for Workbench 2 default

* Just call it "Workbench," not "Workbench 2" or "new Workbench."
* Remove reference to Workbench 1 Advanced tab.

Refs #20932.

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

7 months ago19818: Document arvados.api module 19818-api-pydoc
Brett Smith [Fri, 29 Sep 2023 02:04:46 +0000 (22:04 -0400)]
19818: Document arvados.api module

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

7 months ago19818: Deprecate arvados.api.OrderedJsonModel
Brett Smith [Fri, 29 Sep 2023 01:35:38 +0000 (21:35 -0400)]
19818: Deprecate arvados.api.OrderedJsonModel

Python dictionaries started preserving insertion order in CPython 3.6,
and that became a specified feature of the language in Python 3.7. That
means the default model has the same behavior as OrderedJsonModel on
every platform supported by Arvados. Deprecate the class accordingly.

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

7 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>

7 months ago21002: set banner maxWidth to 50% Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa...
Lisa Knox [Thu, 28 Sep 2023 19:23:33 +0000 (15:23 -0400)]
21002: set banner maxWidth to 50% Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

7 months ago21002: fixed notif menu clickboxes Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa...
Lisa Knox [Thu, 28 Sep 2023 16:03:05 +0000 (12:03 -0400)]
21002: fixed notif menu clickboxes Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

7 months ago18874: Merge commit '6f8dcb2b13f3058db656908fb26b09e23b527f08' into 18874-merge-wb2
Tom Clegg [Thu, 28 Sep 2023 15:24:01 +0000 (11:24 -0400)]
18874: Merge commit '6f8dcb2b13f3058db656908fb26b09e23b527f08' into 18874-merge-wb2

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

7 months ago21002: fixed tooltip focus on notificatoin icon Arvados-DCO-1.1-Signed-off-by: Lisa...
Lisa Knox [Thu, 28 Sep 2023 14:30:25 +0000 (10:30 -0400)]
21002: fixed tooltip focus on notificatoin icon Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

7 months ago20885: Update PySDK docstrings after pdoc migration 20885-pdoc-style
Brett Smith [Mon, 25 Sep 2023 20:26:46 +0000 (16:26 -0400)]
20885: Update PySDK docstrings after pdoc migration

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

7 months ago20885: Add our own pdoc wrapper
Brett Smith [Mon, 25 Sep 2023 21:31:24 +0000 (17:31 -0400)]
20885: Add our own pdoc wrapper

Mainly to support admonitions. See the documentation and comments in
pysdk_pdoc.py for details.

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

7 months ago20885: Clean up run-tests Python install env
Brett Smith [Mon, 25 Sep 2023 20:40:56 +0000 (16:40 -0400)]
20885: Clean up run-tests Python install env

Most of this code duplicates sdk/python/setup.py and should no longer be
necessary with modern pip. Invoking pip so often also makes it slower
than it needs to be.

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

7 months agoMerge branch '20862-google-api-client'
Tom Clegg [Mon, 25 Sep 2023 18:17:41 +0000 (14:17 -0400)]
Merge branch '20862-google-api-client'

fixes #20862

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

7 months ago20862: Update docs on google-api-client fork. 20862-google-api-client
Tom Clegg [Mon, 25 Sep 2023 18:14:37 +0000 (14:14 -0400)]
20862: Update docs on google-api-client fork.

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

7 months ago20862: Emit notice about skipping sdk/ruby-google-api-client tests.
Tom Clegg [Mon, 25 Sep 2023 15:56:48 +0000 (11:56 -0400)]
20862: Emit notice about skipping sdk/ruby-google-api-client tests.

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

7 months ago20862: Merge branch 'main' into 20862-google-api-client
Tom Clegg [Mon, 25 Sep 2023 15:46:36 +0000 (11:46 -0400)]
20862: Merge branch 'main' into 20862-google-api-client

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

7 months ago20990: Add btree index on name for groups & collections 20990-name-btree
Peter Amstutz [Fri, 22 Sep 2023 20:22:44 +0000 (16:22 -0400)]
20990: Add btree index on name for groups & collections

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

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 months agoMerge branch '19359-optional-enum' refs #19359
Peter Amstutz [Fri, 15 Sep 2023 14:03:21 +0000 (10:03 -0400)]
Merge branch '19359-optional-enum' refs #19359

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

7 months ago19359: Can select empty item to clear optional enum input
Peter Amstutz [Thu, 14 Sep 2023 21:06:11 +0000 (17:06 -0400)]
19359: Can select empty item to clear optional enum input

Sets the field value to null, which means "use default value" in CWL.

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

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 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>

7 months ago19359: Support 'optional' enum type parameters
Peter Amstutz [Fri, 8 Sep 2023 20:06:37 +0000 (16:06 -0400)]
19359: Support 'optional' enum type parameters

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

7 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>

7 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>