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@KochTobi KochTobi commented Oct 6, 2025

What's Changed

New Features 🚀

Bugfixes 🪲

Documentation & CI 🪂

Others 🧃

Full Changelog: 1.11.0...1.11.2

sven1103 and others added 11 commits September 24, 2025 11:08
Introduces the maven pgp verify plugin and activates it for every module that has a src/main directory.

Builds will now fail, if the signature does not validate and there is no rule specified for it in the pgp-keys.override.list.

To skip manual curation of known maven artifacts, we use a pgp-keys-map from org.simplify4u.
Enables user to filter for a subset of raw datasets to prepare the download URL list.

Introduces database view SQL statements for aggregated information to address this user story: information about the raw dataset and the referenced samples.

Introduces a scheduled synchronization for fetching raw dataset from a remote source (e.g., openBIS) and creates a local cache table with information to improve query performance.
Use a more FOSS preserving license.
Will no generate a full software bill of materials for each module. License texts are included as well.
Removes some smelling code that can produce race conditions for the UI update. Also passes now the current UI instance as reference for background jobs with reactor. Ui getters are not thread-safe and are not guaranteed to return the intended UI reference. According to Vaadin's documentation, it is better to fetch the UI reference in the main thread and pass it to background threads explicitly.

Also, this PR enforces the server to push changes to the UI, since with automatic polling we see that the UI is not always updated despite this should be the expected behaviour when the user session lock is released. This resulted in ui components not being updated from background tasks (validation, registration pending task toast, etc) and the update was waiting for a ui interaction from the user.
@KochTobi KochTobi requested a review from a team as a code owner October 6, 2025 07:45
sven1103 and others added 2 commits October 6, 2025 09:47
* Preserve order of levels

* make it compile again

* wip

* wip

* section off regions and add borders

* Replace ontology-term CSS class

* Remove CSS classes

Replace `.vertical-list` by `.flex-vertical .width-full`
Replace `.trailing-margin-large` by `.margin-bottom-07`
Replace `.trailing-margin-normal` by `.margin-bottom-05`
Replace `.trailing-margin-small` by `.margin-bottom-03`

* wip

* add missing variables

* replace lumo with custom variables

* move ButtonFactory

* add icon button factory method

* update demo

* Fix label css

* replace with classes

* introduce delete event

* wip

* add restoration option for deleted variables

* Add Nullable annotation to DialogBody.java#with method

* remove test button

* Fix value handling of level field

* Add paste behaviour

* address code smells

* hide public constructor

* simplify memento interface

removes Speculative Generality

* Handle validation

* Make InputValidation combinable

* require all snapshots to be serializable

* adapt validation to validate multivariable constraints

adds validation for duplicate variable names.

* wip

* Add DragDropList.java

* Push UI code

* extract classes and add add dialog

* Load values and call the service

missing check for deleted variables and changes to levels.
Adding, deleting, renaming and changing the unit of a variable are functional now.

* remove unused method

* Add empty input if no variables exist

* Add variable deletion confirm dialog

* add bold css class

* add tooltip to locked levels

Co-authored-by: Shraddha Pawar <[email protected]>

* extract change records

* add scroll css classes

* make drag-drop configurable

* replace lumo var with own variable definition

Replaces the lumo variable with a custom variable. The custom variable has the same value as the lumo variable without depending on lumo and makes editing css in editors easier (as the variable is defined in the project scope and not only after compilation)

* remove duplicate css classes

* use correct css class

* Fix import

* propagate level changes

address code smells

* Cleanup methods

* Fix inverted boolean

* respect enabled state when adding and removing items

* use correct variable name in changes

* Prevent unintended modification on card collection

Remove domain ExperimentalGroup from UI component

* reload experimental variables upon completion

* address code smells

* enhance dragdrop

hides the dragged element during dragging

* reload information on attach event

* remove unused code

* return experimental variables sorted by variable name

* Correct icon colors

* update indexes

* change dialog size back to medium

* remove unused css

* fix border colors

borders in dialogs have a specific color.
borders can be specifically set to not have any color.

Co-authored-by: Shraddha Pawar <[email protected]>

* Trim variable name input

* Fix padding for linked orcid account

* Change message for duplicate variable names

Co-authored-by: Shraddha Pawar <[email protected]>

* address wrong padding

Co-authored-by: Shraddha Pawar <[email protected]>

* Remove specific border color for choice box

Co-authored-by: Shraddha Pawar <[email protected]>

* Clarify error colors

* Add dialog with dangerous confirm action

* Ask directly instead of restore option

Instead of presenting the user with the list of deleted experimental variables in the end, directly ask them when they delete the variable. Removes the need for the restore option as they only get removed when users confirm the intended action.

* Improve check for defined variables

Ignores leading and tailing whitespace when comparing variable name to existing variable names.

* Do not silently remove dupliate levels in experimental variable

Co-authored-by: Sven F. <[email protected]>

* address review

Co-authored-by: Sven F. <[email protected]>

* address review

* Fix sorting of variables

* Remove duplicate error when level value changes

Co-authored-by: Shraddha Pawar <[email protected]>

* Remove error message for duplicate variable name

When editing a duplicated variable name, the error message is removed.

* replace choice-box css

* Change error text

Co-authored-by: Shraddha Pawar <[email protected]>

* update dev.bundle

* Fix css color

* Change delete confirm text

Co-authored-by: Shraddha Pawar <[email protected]>

* Link javadoc

Co-authored-by: Sven F. <[email protected]>

* Add clarifying javadoc

Co-authored-by: Sven F. <[email protected]>

* remove all the generics from javadoc

Co-authored-by: Sven F. <[email protected]>

* address review

* add missed change

* address exception

Co-authored-by: Sven F. <[email protected]>

* Use deep copy instead of inplace modification

Co-authored-by: Sven F. <[email protected]>

* Remove comment

I removed the comment and we will encounter the issue again if and when we try to implement a drag handle. Tracking it with our own github issue is not necessary as maybe another solution is found at a future time.

* Provide exception supplier

* Use UIHandle

---------

Co-authored-by: KochTobi <[email protected]>
Co-authored-by: Shraddha Pawar <[email protected]>
Co-authored-by: Sven F. <[email protected]>
Co-authored-by: Sven F. <[email protected]>
Co-authored-by: Sven Fillinger <[email protected]>
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2 participants