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[pull] dev from galaxyproject:dev #948

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[pull] dev from galaxyproject:dev #948

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mvdbeek and others added 26 commits September 12, 2024 10:59
[24.1] Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1
Also:
- Remove unnecessary `unicodify()` calls
[24.1] Fix copying workflow with subworkflow step for step that you own
…le_handling

[24.1] Fix response if dataset requested by display application is deleted
Parse stored config details to script-based visualizations
Bumps [express](https://github.com/expressjs/express) from 4.19.2 to 4.21.0.
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/4.21.0/History.md)
- [Commits](expressjs/express@4.19.2...4.21.0)

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

Signed-off-by: dependabot[bot] <support@github.com>
[24.1] Use smtplib send_message to support utf-8 chars in to and from
…nDialog` directory and updated import paths accordingly
wm75 and others added 30 commits September 24, 2024 11:27
[24.1] Fix data_column ref to nested collection
…client/dompurify-3.1.3

Bump dompurify from 3.0.6 to 3.1.3 in /client
Add unique constraints to the email and username fields in the galaxy_user table
Backend handling of setting user-role, user-group, and group-role associations
When upgrading back to a valid revision, upgrade to head, not the
revision under test: we need the latest version of the model definition
in the database for the test to cleanup correctly.
- Do not explicitly import fixtures (a little duplication is safer/cleaner)
- Move dangerous fixture into module to prevent accidental usage from other modules
- Ensure only one database is used for all tests in module
Implement Pydantic model for workflow test format.
that support pagination to 10000. Clients can always request more data via offset
requests, but since this is not a streaming API we need to build the
response in memory before we can start sending.
data_column params: offer same columns with and without use_header_names
[24.1] Limit max number of items in dataproviders
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
Refactor migration testing setup code
Surprised (or not actually ...) that mypy didn't catch this.
- Allow class: File and class: Collection on file and collection test descriptions.
- Allow collection_type: <type> in collection test descriptions. Implement this.
- Update test workflows to reflect these two things as best practices.
Raise exception if CompressedFile used on incompatible file
Enable ``ignore-without-code`` mypy error code
Improvements to Planemo test format based on feedback/discussions.
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