Merge branch '22693-docker-28'

Closes #22693.

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

22693: Update Docker pin to version 28

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

22605: finished first of 2 new tests on wf project picker

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

22605: fixed collection details display in picker

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

22605: started writing tests

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

Merge branch '22652-axios-upgrade' into main. Closes #22652

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

20650: Tinkering with AWS credentials

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

20650: Implemented s3_to_keep

Added support importing from s3 to arv-copy

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

20650: Initial refactor spitting up http_to_keep to share code

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

Build Java SDK with jdk11, refs #22084

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

22605: fixed eslint linting cy.js files

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

22652: Bump axios-mock-adapter to latest

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

22652: Bump axios to latest to address CVE-2025-27152

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

22652: First upgrade axios depended on by wait-on to address CVE-2025-27152

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

22605: users now prohibited from running wfs in other users root projects

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

Merge branch '22689-bump-babel-dependencies' into main. Closes #22689

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

22689: Bump @babel/runtime-corejs2 to address CVE-2025-27789

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

22689: Bump @babel/helpers to address CVE-2025-27789

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

22689: Bump @babel/runtime to address CVE-2025-27789

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

22605: added separate state for intermediate selection

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

21926: Add upgrade note about cuda→gpu API changes

Refs #21926.

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

22605 added update function to treePicker componentDidUpdate

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

Merge branch '22621-upload-error-message' into main. Closes #22621

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

22605: clean up state when input unmounts

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

22605: fixed accidental reset of default target wf run owner

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

22621: Change collection file upload error to be generic

Upload errors do not generate any reason in the exceptions so we are unable to
display specific error reasons.

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

22605: fixed wf owner overwrite when lacking perms

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

22605: fixed initial tree picker load

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

Merge branch '22320-cached-only'

Refs #22320. Closes #22344.

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

Merge branch '22228-separate-expire-and-refresh'

fixes #22228

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

Merge branch '22655-keepclient-test'

closes #22655

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

22320: Add tests for CachedOnly.

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

22320: Add CheckCacheOnly option to BlockReadOptions.

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

Merge branch '22320-repack-small-blocks'

refs #22320

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

22655: Fix Python 3 usage -- raise exceptions, not strings.

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

22655: Fix func signature to force kwargs, remove unused arg.

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

Merge branch '22602-arv-copy' refs #22602

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

22320: Check final blocksInManifest.

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

22320: Run slow tests and write chart data only if env var is set.

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

22602: DRY search() to use search_paths() and add test

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

22320: Fix comment typo.

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

22228: Update comments.

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

22228: Test that remote expires_at is preserved in local cache.

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

Merge branch '22660-acr-cred-leak' refs #22660

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

22228: Update tests to use refreshes_at to induce cache refresh.

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

22228: Add refreshes_at field, preserve upstream expires_at.

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

22660: Simpler sanitize implementation from brett

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

22605: picker now expands Home Projects

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

22602: Further improve error reporting for getting cluster creds

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

22602: Fix test

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

22602: Improve error handling when instance info is wrong

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

22660: Sanitize the git remote URL

Remove the username/password section of the netloc part of the URL, if
present.  This was reported by a user that it was leaking github
tokens, as one way of providing a github token is write it as

https://x-access-token:blahblahblah@github.com/foo/bar.git

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

22605: default project now highlights and expands in the picker, except for user root projects

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

22605: fixed isValid after cancel button click

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

22655: Propagate errors running run_test_servers.py from Go suites.

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

22655: Don't keep waiting for a subprocess to listen after it exits.

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

22655: In test environment, retry in-use addr for 5 minutes.

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

22605: fixed edge case where user does not have write perm in wf original owener

* The target owner already switches to the user's root project if the user does not have write access, this change just ensures the parent redux-form aligns with that change

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

Bump rack from 3.1.10 to 3.1.12 in /services/api

refs #22657

Bumps [rack](https://github.com/rack/rack) from 3.1.10 to 3.1.12.
- [Release notes](https://github.com/rack/rack/releases)
- [Changelog](https://github.com/rack/rack/blob/main/CHANGELOG.md)
- [Commits](https://github.com/rack/rack/compare/v3.1.10...v3.1.12)

---
updated-dependencies:
- dependency-name: rack
  dependency-type: indirect
...

Arvados-DCO-1.1-Signed-off-by: dependabot[bot] <support@github.com>

22655: Try a bit harder to detect port conflicts.

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

22655: Avoid needlessly changing global state in test suites.

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

Merge branch '17209-http-forward'

closes #17209

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

17209: Remove unused commented-out code.

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

Merge branch '22644-arvados-server-install-singularity'

Refs #22644.

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

22602: arv-copy checks config file first then falls back on default creds

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

22605: fixed favorites test

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

22605: fixed create-workflow test

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

Merge branch '22647-postinst-ignores-gem-install-errors'

Closes #22647, #22648.

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

22647: Wordsmith comment and status message

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

22320: Export Repack() method.

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

22320: Remove unimplemented Underutilized option.

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

22320: Add test cases for 32MiB and 32MiB-1 sized blocks.

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

22320: Fix maxBlockSize restored to wrong value after tests.

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

22647: Ignore `gem install` errors in RailsAPI postinst

See comments for rationale.

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

22605 changed the title of the form

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

22605: default project populates when starting from workflow panel

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

22320: Fix test case cheating by repeating content.

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

22320: Implement full-repack, like old tests expected.

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

22320: Parameterize RepackCost test.

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

22320: Improve stats output.

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

22320: Fix mkdir in test.

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

22320: Fix test panic.

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

22320: Write more stats for charting.

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

22320: Refine repacking algorithm to handle a range of block sizes.

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

22320: Fix Repack bug causing segment replacements to be skipped.

repackTree must call replaceSegments with the newly computed
replacements -- not the merged set of new replacements plus
previously-applied replacements.  If it passes the merged set to
replaceSegments, some of the new replacements will be skipped.

For example, if a previous repack applied A->B, and the current repack
applies B->D and C->D, then the merged set includes A->D, and A is no
longer referenced, so replaceSegments will skip any->D.

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

22320: Refactor test case.

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

22320: Add repack-after-write test.

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

22320: Track repack results.

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

22320: Naive Repack implementation.

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

22605: project picker opens automatically on step 2 of run process

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

22644: Install Singularity from archive instead of Git

Ansible is already doing this, and it looks like something has maybe
happened with one of the submodules so it no longer gets cloned
correctly. Using the source archive is less error-prone.

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

22605: input displays processOwner from redux store instead of local state

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

22608: Add PowerTools setup to the API install docs

Mirroring the upgrade note. Refs #22608.

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

22605: moved SET_PROCESS_OWNER_UUID call to input component

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

22605: default project now populates even on f5 on run-process-panel

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

Merge branch '22608-enable-powertools'

Refs #22608.

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

22605: cancel button now works

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

22605: user root projects now selectable

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

22605: Target project input now shows the default selection

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

22608: Add upgrade note about libyaml/PowerTools dependency

This is a consequence of the upgrade to Rails 7.1.

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