arvados.git
9 months ago20300: Use Rails 6.0 config defaults.
Tom Clegg [Thu, 21 Sep 2023 02:05:32 +0000 (22:05 -0400)]
20300: Use Rails 6.0 config defaults.

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

9 months ago20300: Update symbols to strings in relations.
Tom Clegg [Tue, 19 Sep 2023 14:04:16 +0000 (10:04 -0400)]
20300: Update symbols to strings in relations.

In Rails 6.1 the column names are converted to strings internally, so
checking for "foreign_key == :owner_uuid" no longer works.

Using symbols continues to work when declaring relations, but they are
updated to strings anyway for clarity, and to match
canonical/documented usage.

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

9 months ago20300: Use Rails 5.2 config defaults.
Tom Clegg [Tue, 19 Sep 2023 13:44:52 +0000 (09:44 -0400)]
20300: Use Rails 5.2 config defaults.

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

9 months ago20300: Rail 6.1 app:update.
Tom Clegg [Tue, 19 Sep 2023 04:04:45 +0000 (00:04 -0400)]
20300: Rail 6.1 app:update.

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

9 months ago20300: Update bundle to rails 6.1.
Tom Clegg [Tue, 19 Sep 2023 03:56:57 +0000 (23:56 -0400)]
20300: Update bundle to rails 6.1.

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

9 months ago20300: Update test to new Rails API.
Tom Clegg [Tue, 19 Sep 2023 03:55:46 +0000 (23:55 -0400)]
20300: Update test to new Rails API.

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

9 months ago20300: Mark belongs_to relations as optional.
Tom Clegg [Mon, 18 Sep 2023 20:06:29 +0000 (16:06 -0400)]
20300: Mark belongs_to relations as optional.

Temporary migration switch is no longer effective.

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

9 months ago20300: Rails 6.0 app:update
Tom Clegg [Mon, 25 Sep 2023 18:36:56 +0000 (14:36 -0400)]
20300: Rails 6.0 app:update

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

9 months ago20300: Add rails-generated files to .licenseignore.
Tom Clegg [Thu, 14 Sep 2023 13:37:26 +0000 (09:37 -0400)]
20300: Add rails-generated files to .licenseignore.

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

9 months ago20300: Fix key order sensitivity in test, part 2.
Tom Clegg [Thu, 7 Sep 2023 18:01:24 +0000 (14:01 -0400)]
20300: Fix key order sensitivity in test, part 2.

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

9 months ago20300: Fix key order sensitivity in test, part 1.
Tom Clegg [Thu, 7 Sep 2023 17:45:13 +0000 (13:45 -0400)]
20300: Fix key order sensitivity in test, part 1.

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

9 months ago20300: Update expected content-type in test.
Tom Clegg [Thu, 7 Sep 2023 14:13:53 +0000 (10:13 -0400)]
20300: Update expected content-type in test.

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

9 months ago20300: Fix where(nil, ...) case.
Tom Clegg [Thu, 7 Sep 2023 13:39:34 +0000 (09:39 -0400)]
20300: Fix where(nil, ...) case.

Rails 5 accepted where(nil, ...) as a no-op, but in Rails 6 that's an
error.

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

9 months ago20300: Fix YAML usage.
Tom Clegg [Thu, 7 Sep 2023 13:37:56 +0000 (09:37 -0400)]
20300: Fix YAML usage.

YAML.safe_load_file does not exist until Ruby 3.

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

9 months ago20300: Remove obsolete uses of set_attribute_was.
Tom Clegg [Thu, 7 Sep 2023 17:53:41 +0000 (13:53 -0400)]
20300: Remove obsolete uses of set_attribute_was.

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

9 months ago20300: Change deprecated update_attributes to update.
Tom Clegg [Wed, 6 Sep 2023 21:21:50 +0000 (17:21 -0400)]
20300: Change deprecated update_attributes to update.

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

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 months ago20891: corrected navigation function in renderer Arvados-DCO-1.1-Signed-off-by:...
Lisa Knox [Wed, 27 Sep 2023 19:48:18 +0000 (15:48 -0400)]
20891: corrected navigation function in renderer  Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago20382: refined menukind narrowing Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa...
Lisa Knox [Wed, 27 Sep 2023 13:13:51 +0000 (09:13 -0400)]
20382: refined menukind narrowing Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago20382: works for admins Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii...
Lisa Knox [Tue, 26 Sep 2023 20:33:12 +0000 (16:33 -0400)]
20382: works for admins Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago20382: cancel in context menu works for non-admins Arvados-DCO-1.1-Signed-off-by...
Lisa Knox [Tue, 26 Sep 2023 19:36:21 +0000 (15:36 -0400)]
20382: cancel in context menu works for non-admins Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: fixed open-in-new-tab test Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa...
Lisa Knox [Tue, 26 Sep 2023 13:52:39 +0000 (09:52 -0400)]
15768: fixed open-in-new-tab test Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>

9 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>

9 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>

9 months ago20300: Call safe_load explicitly instead of using safe_yaml gem.
Tom Clegg [Wed, 6 Sep 2023 21:20:11 +0000 (17:20 -0400)]
20300: Call safe_load explicitly instead of using safe_yaml gem.

safe_yaml breaks new i18n.

ArgumentError: wrong number of arguments (given 2, expected 1)
/home/tom/.gem/ruby/2.7.0/gems/safe_yaml-1.0.5/lib/safe_yaml.rb:37:in `unsafe_load_file'
/home/tom/.gem/ruby/2.7.0/gems/i18n-1.14.1/lib/i18n/backend/base.rb:254:in `load_yml'
...

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

9 months ago20300: Remove extra Time.parse(), which Rails 6 does implicitly.
Tom Clegg [Tue, 5 Sep 2023 13:49:33 +0000 (09:49 -0400)]
20300: Remove extra Time.parse(), which Rails 6 does implicitly.

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

9 months ago20300: Remove obsolete i18n version pin.
Tom Clegg [Tue, 5 Sep 2023 13:40:44 +0000 (09:40 -0400)]
20300: Remove obsolete i18n version pin.

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

9 months ago20300: Update gemfiles to rails 6.
Tom Clegg [Mon, 18 Sep 2023 18:36:54 +0000 (14:36 -0400)]
20300: Update gemfiles to rails 6.

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

9 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>

9 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>

9 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>

9 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>

9 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>

9 months ago15768: removed errant .only from spec Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa...
Lisa Knox [Fri, 22 Sep 2023 19:55:22 +0000 (15:55 -0400)]
15768: removed errant .only from spec Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: process outputs no longer disappear on reload Arvados-DCO-1.1-Signed-off-by...
Lisa Knox [Fri, 22 Sep 2023 19:52:43 +0000 (15:52 -0400)]
15768: process outputs no longer disappear on reload Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago20225: Correct cypress test names / add terminal newline (style)
Stephen Smith [Fri, 22 Sep 2023 14:35:34 +0000 (10:35 -0400)]
20225: Correct cypress test names / add terminal newline (style)

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

9 months ago20225: Remove unused imports / dead code
Stephen Smith [Fri, 22 Sep 2023 14:35:13 +0000 (10:35 -0400)]
20225: Remove unused imports / dead code

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

9 months ago20225: Add subdirectory selection support to directory array picker
Stephen Smith [Fri, 22 Sep 2023 14:12:42 +0000 (10:12 -0400)]
20225: Add subdirectory selection support to directory array picker

Adds cascade flag to tree picker to disable recursive directory selection

Reworks initProjectsTreePicker to support initializing multiple selections.
Loads each selection's ancestor tree in parallel, combines updates to same tree
pickers before inserting the ancestor tree, then loads necessary collections in
parallel

Changes checkbox visibility logic to show collection selection checkbox even
when collection is not loaded/expanded when cascade mode is off - since the
selection won't cascade there is no need to require the collection to be opened

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

9 months ago20225: Add subdirectory selection support to directory input
Stephen Smith [Thu, 21 Sep 2023 19:02:10 +0000 (15:02 -0400)]
20225: Add subdirectory selection support to directory input

Converts getFileOperationLocation into a dispatchable helper so it can access
the store to augment FileOperationLocations with a PDH

Converts DirectoryTreePickerField into a connected class component in order to
use getFileOperationLocation

Change DirectoryInputComponent to include directories in the picker and use
getFileOperationLocation to pass FileOperationLocation instead of Collection
objects so that the subpath within the collection can be embedded in the
Directory object

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

9 months ago15768: fixed search test spec Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox...
Lisa Knox [Thu, 21 Sep 2023 18:57:37 +0000 (14:57 -0400)]
15768: fixed search test spec Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: fixed search test spec Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox...
Lisa Knox [Thu, 21 Sep 2023 17:25:59 +0000 (13:25 -0400)]
15768: fixed search test spec Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>

9 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>

9 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>

9 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>

9 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>

9 months ago15768: fixed copytoclipboard from search results Arvados-DCO-1.1-Signed-off-by: Lisa...
Lisa Knox [Wed, 20 Sep 2023 16:43:22 +0000 (12:43 -0400)]
15768: fixed copytoclipboard from search results Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: added manual form submit in searchbar spec Arvados-DCO-1.1-Signed-off-by:...
Lisa Knox [Wed, 20 Sep 2023 14:56:16 +0000 (10:56 -0400)]
15768: added manual form submit in searchbar spec Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: virtual machine spec pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox...
Lisa Knox [Wed, 20 Sep 2023 13:18:00 +0000 (09:18 -0400)]
15768: virtual machine spec pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: fixed rerun bug Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii...
Lisa Knox [Tue, 19 Sep 2023 22:33:57 +0000 (18:33 -0400)]
15768: fixed rerun bug Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>

9 months ago15768: all favorites specs pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox...
Lisa Knox [Mon, 18 Sep 2023 23:05:53 +0000 (19:05 -0400)]
15768: all favorites specs pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: all collection specs pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox...
Lisa Knox [Mon, 18 Sep 2023 19:58:21 +0000 (15:58 -0400)]
15768: all collection specs pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: all collection specs pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox...
Lisa Knox [Mon, 18 Sep 2023 17:02:48 +0000 (13:02 -0400)]
15768: all collection specs pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 months ago15768: collection spec passes Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox...
Lisa Knox [Sun, 17 Sep 2023 22:19:10 +0000 (18:19 -0400)]
15768: collection spec passes Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: get_items on single collection copy Arvados-DCO-1.1-Signed-off-by: Lisa Knox...
Lisa Knox [Sun, 17 Sep 2023 21:12:21 +0000 (17:12 -0400)]
15768: get_items on single collection copy Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: fixed dialog not closing on single collection copy Arvados-DCO-1.1-Signed...
Lisa Knox [Sun, 17 Sep 2023 21:07:07 +0000 (17:07 -0400)]
15768: fixed dialog not closing on single collection copy Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 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>

9 months ago15768: testing Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>
Lisa Knox [Thu, 14 Sep 2023 15:18:04 +0000 (11:18 -0400)]
15768: testing Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>

9 months ago15768: testing Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>
Lisa Knox [Thu, 14 Sep 2023 14:44:48 +0000 (10:44 -0400)]
15768: testing Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>

9 months ago15768: fixed 422 err showing in browser Arvados-DCO-1.1-Signed-off-by: Lisa Knox...
Lisa Knox [Thu, 14 Sep 2023 14:10:42 +0000 (10:10 -0400)]
15768: fixed 422 err showing in browser Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: fixed checkbox undefined Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox...
Lisa Knox [Thu, 14 Sep 2023 01:25:02 +0000 (21:25 -0400)]
15768: fixed checkbox undefined Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 months ago15768: fixed double error messages Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa...
Lisa Knox [Wed, 13 Sep 2023 23:35:58 +0000 (19:35 -0400)]
15768: fixed double error messages Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>

9 months ago15768: all tests pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>
Lisa Knox [Wed, 13 Sep 2023 21:00:43 +0000 (17:00 -0400)]
15768: all tests pass Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>

9 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>

9 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>

9 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>

9 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>

9 months ago15768: last test Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>
Lisa Knox [Wed, 13 Sep 2023 18:16:05 +0000 (14:16 -0400)]
15768: last test Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

9 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>