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updates #5

Merged
merged 34 commits into from
Sep 16, 2024
Merged

updates #5

merged 34 commits into from
Sep 16, 2024

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arfazhxss
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Mandatory checks

  • Change in CHANGELOG.md described in a way that is understandable for the average user (if applicable)
  • Tests created for changes (if applicable)
  • Manually tested changed features in running JabRef (always required)
  • Screenshots added in PR description (for UI changes)
  • Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
  • Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.

leaf-soba and others added 30 commits September 8, 2024 08:47
* Rename "Show 'Ai Chat' tab" to "Show tab 'AI Chat'"

solve #11708

* add unit test and refactor parseArgument

add unit test and refactor AbstractParamLayoutFormatter.parseArgument

* rewrite the test method name

rewrite the test method name
* Initial requirement

* Initial requirement

* Add OpenFastTrace

* Fix linting

* Remove wrong disable rule
* Move cut and copy out of MainTable into LibraryTab

* Move ImportHandler to LibraryTab and Reword methods

* Seperated notifications

* l10n

* CHANGELOG.md

* Wording consistency
* Remove unnecessary AI dependencies

* Remove AiApiKeyProvider.java

* Fix checkers
* Refine JavaDoc

* Add TODOs

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>

* Fix typos

* Reoder settings

* Fix arch flaw

Co-authored-by: Christoph <siedlerkiller@gmail.com>
Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>

* Fix checkstyle and formatting

---------

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
Co-authored-by: Christoph <siedlerkiller@gmail.com>
* New translations jabref_en.properties (French)

* New translations jabref_en.properties (Polish)

* New translations jabref_en.properties (Portuguese, Brazilian)

* New translations jabref_en.properties (Spanish)

* New translations jabref_en.properties (Arabic)

* New translations jabref_en.properties (Danish)

* New translations jabref_en.properties (German)

* New translations jabref_en.properties (Greek)

* New translations jabref_en.properties (Finnish)

* New translations jabref_en.properties (Italian)

* New translations jabref_en.properties (Japanese)

* New translations jabref_en.properties (Korean)

* New translations jabref_en.properties (Dutch)

* New translations jabref_en.properties (Norwegian)

* New translations jabref_en.properties (Portuguese)

* New translations jabref_en.properties (Russian)

* New translations jabref_en.properties (Swedish)

* New translations jabref_en.properties (Turkish)

* New translations jabref_en.properties (Ukrainian)

* New translations jabref_en.properties (Chinese Simplified)

* New translations jabref_en.properties (Chinese Traditional)

* New translations jabref_en.properties (Vietnamese)

* New translations jabref_en.properties (Indonesian)

* New translations jabref_en.properties (Persian)

* New translations jabref_en.properties (Tagalog)
* Fixed an exception when searching for unlinked files.

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* Update CHANGELOG.md

---------

Co-authored-by: Christoph <siedlerkiller@gmail.com>
* Add option to disable keeping download url

Refs https://discourse.jabref.org/t/import-adds-pdf-link-and-url-to-file-entry/4484/

* Fix checkstyle

* Compilefix

* add default

* Update CHANGELOG.md

* add addtional check

* fix ui

* fix test

* fix fcking test

---------

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
* Add volume information

* Add pages

* Fix OpenAccessDOITest

* Revert openaccesssdoifetcher result

* Change test openAccess article

* remove .pdf extension from expected arg
* Remove AI service from OpenOfficePanel

* Remove unused import

* Revert

* Remove correct import

---------

Co-authored-by: Subhramit Basu Bhowmick <subhramit.bb@live.in>
…11738)

Bumps [dev.langchain4j:langchain4j-hugging-face](https://github.com/langchain4j/langchain4j) from 0.33.0 to 0.34.0.
- [Release notes](https://github.com/langchain4j/langchain4j/releases)
- [Commits](langchain4j/langchain4j@0.33.0...0.34.0)

---
updated-dependencies:
- dependency-name: dev.langchain4j:langchain4j-hugging-face
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [org.yaml:snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 2.2 to 2.3.
- [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-2.3..snakeyaml-2.2)

---
updated-dependencies:
- dependency-name: org.yaml:snakeyaml
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…11741)

Bumps [org.openrewrite.recipe:rewrite-recipe-bom](https://github.com/openrewrite/rewrite-recipe-bom) from 2.17.0 to 2.18.0.
- [Release notes](https://github.com/openrewrite/rewrite-recipe-bom/releases)
- [Commits](openrewrite/rewrite-recipe-bom@v2.17.0...v2.18.0)

---
updated-dependencies:
- dependency-name: org.openrewrite.recipe:rewrite-recipe-bom
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [io.github.stefanbratanov:jvm-openai](https://github.com/StefanBratanov/jvm-openai) from 0.10.0 to 0.11.0.
- [Release notes](https://github.com/StefanBratanov/jvm-openai/releases)
- [Commits](StefanBratanov/jvm-openai@v0.10.0...v0.11.0)

---
updated-dependencies:
- dependency-name: io.github.stefanbratanov:jvm-openai
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [src/main/resources/csl-styles](https://github.com/citation-style-language/styles) from `2b15b1f` to `4e0902d`.
- [Release notes](https://github.com/citation-style-language/styles/releases)
- [Commits](citation-style-language/styles@2b15b1f...4e0902d)

---
updated-dependencies:
- dependency-name: src/main/resources/csl-styles
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [buildres/abbrv.jabref.org](https://github.com/JabRef/abbrv.jabref.org) from `b69f1d6` to `234cce8`.
- [Release notes](https://github.com/JabRef/abbrv.jabref.org/releases)
- [Commits](JabRef/abbrv.jabref.org@b69f1d6...234cce8)

---
updated-dependencies:
- dependency-name: buildres/abbrv.jabref.org
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* New translations jabref_en.properties (French)

* New translations jabref_en.properties (Polish)

* New translations jabref_en.properties (Portuguese, Brazilian)

* New translations jabref_en.properties (Italian)
* Rename "Show 'Ai Chat' tab" to "Show tab 'AI Chat'"

solve #11708

* Update Server.java

1. remove superfluous URISyntaxException
2. change System.out.printf to LOGGER.debug
3. use `createSSLContext(boolean)` instead of deprecated API `createSSLContext()`
Bumps [com.dlsc.gemsfx:gemsfx](https://github.com/dlsc-software-consulting-gmbh/GemsFX) from 2.43.0 to 2.48.0.
- [Release notes](https://github.com/dlsc-software-consulting-gmbh/GemsFX/releases)
- [Changelog](https://github.com/dlsc-software-consulting-gmbh/GemsFX/blob/master/jreleaser.yml)
- [Commits](dlsc-software-consulting-gmbh/GemsFX@v2.43.0...v2.48.0)

---
updated-dependencies:
- dependency-name: com.dlsc.gemsfx:gemsfx
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
* refactor BstTextPrefixer.textPrefix

1. add more unit test about nested brace cases
2. refactor the `textPrefix` method to make it clear

* rewrite unit test

use @ParameterizedTest and @CsvSource to rewrite unit test
1. move `parse` into `MetaDataParser`
2. move `getAsStringList` into `MetaDataSerializer`
3. some minor fix
Signed-off-by: gradle-update-robot <gradle-update-robot@regolo.cc>
Co-authored-by: gradle-update-robot <gradle-update-robot@regolo.cc>
* Use @tempdir for index path

* Add closeAndWait for LuceneManager

* Add `waitOnClose` to the LuceneManager constructor

* Fix test

* Revert "Add `waitOnClose` to the LuceneManager constructor"

This reverts commit 81a30ff,
3fa71f4
* Add Gemini LLM model

* Fix bugs

* Fix privacy policy notice

* Fix table formatting

---------

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
…#11627)

* Refactor EprintCleanup to handle institution, version, and EID fields

* Add test for cleanup with VERSION, INSTITUTION, and EID

* Add version to EPRINT if not present

* Modify test to retain INSTITUTION as "tbd"; include documentation link

* clear institution field if it is "arXiv" else keep it as it is.

* Complied to OpenRewrite to ensure "modern" Java coding practices.

* Update CHANGELOG.md

* Add "real" hyperlink

---------

Co-authored-by: Subhramit Basu Bhowmick <subhramit.bb@live.in>
Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
* add unit test to generateInstitutionKey

prepare to refactor this method

* Update BracketedPatternTest.java
* Add setting to always add "Cited on pages" text in JStyle Citations.

* Add setting: always add "Cited on pages" text to JStyles.

* Add changelog.

* Add change to Changelog.

* Fix translation key. Ensure checkstyle conformity.

* Correct option text, position, & hiding behavior.

The new option's presence now based on selected style, with presence
being ensured only if the style is a JStyle. The option now appears
always first from the top, using index based insertion to achieve this.

The text has been updated to reference bibliographic entries as opposed
to citations, which was factually incorrect.

* Cited on pages... text now appears.

Reference existing preference in OOBibBase to properly propagate
setting, so that "Cited on pages" text literal will appear when user has
it configured.

Remove accomplished TODOs.

* Shift changelog entry, fix setting string, misc. formatting

* Attempt to update submodules to origin/master state.

* Attempt to fix submodule hashes.

* Re-ignore submodules.

* Fix spacing.

---------

Co-authored-by: Subhramit Basu Bhowmick <subhramit.bb@live.in>
* Enable/Disable the undo and redo toolbar/menu buttons correctly

* Add changelog entry
* New translations jabref_en.properties (French)

* New translations jabref_en.properties (Polish)

* New translations jabref_en.properties (Portuguese, Brazilian)

* New translations jabref_en.properties (German)

* New translations jabref_en.properties (Italian)
* Refine JavaDoc

* Add TODOs

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>

* Fix typos

* Reoder settings

* Fix arch flaw

Co-authored-by: Christoph <siedlerkiller@gmail.com>
Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>

* Fix checkstyle and formatting

* Make BackgroundTask independent from UI

* Move BackgroundTask from gui to logic

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* protected -> public

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* Move CurrentThreadTaskExecutor from gui to logic

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* protected/package private -> public

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* Fix formatting

* Make ArchitectureTest "real"

* Fix typo in "cancelled"

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* Fix JavaDoc

* Move execute(JavaFX Task) down to UiTaskExecutor

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* Fixed an exception when searching for unlinked files.

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* Fix CHANGELOG

* Move TaskExecutor from gui to logic

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* Fix more checkstyle

* Introduce NotifcationService

Also:

- Move openAiChat from AiService (logic) to GroupTree (gui)

* move unlinked files filter to logic

* Inline JabRefDesktop.get*Directory() (to avoid dependency to gui from logic)

* move search display mode enum

* Introduce "Directories"

* Remove unused variables

* Move ChatHistoryService to UI

* move fallback exception handler to logic and add consumer for thread execution

* remove dialog service from logic class

* Route ChatHistoryService correctly

* Do not do architecture tests for test classes

* remove dialog service in test

* Fix checkstyle

* Sort and shelve preferences objects

* Fix CHANGELOG

* Checkstyle imports

* Refactor NativeDesktop

- Integrate OS into NativeDesktop
- Integrate JabRefDesktop into NativeDesktop

* Compile fix

* Introduce OS (and move things from NativeDesktop)

* Move FilePreferences to logic

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>

* Fix imports

* More optimize imports...

* One more...

* Move externalFileTypes from FilePreferences to ExternalApplicationPreferences

* Adapt classes to new structure of ExternalApplicatoinPreferences

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>

* Move MrDlibPreferences

* Move AutoCompleteFirstNameMode to logic.preferences

* Move detectProgramPath to OS

* Rename "PreferenceService" to "Preferences"

* Adapt name of factory

* Move class - we do it differently in main JabRef

* Move Preferences to logic (to prepare split up in gui / non-gui)

* Infrastructore for gui / non-gui

* Rename Preferences to CliPreferences

* Fix names - begin to move getEntryEditorPreferences()

* Rename GuiPreferences to CoreGuiPreferences

* Fix CliPreferences - GuiPreferences

* Move constants

* Move "getMergeDialogPreferences()" to GuiPreferences

* Make LinkedFile independent from Gui

* Push down AutoCompletePreferences

* Pull down CoreGuiPreferences and Workspace preferences

* Fix empty line

* Push getUnlinkedFilesDialogPreferences() down

* Push down ExternalApplicationsPreferences

* Adapt code

* fix imports

* fix more imports

* checkstyle

* fix more imports

* rewrite

* Fix imports

* Push down SidePanePreferences

* Adapt code

* Fix variable location

* Push down GroupsPreferences

* Adapt classes

* Push down getSpecialFieldsPreferences()

* Adapt code

* Push down PreviewPreferences

* Adapt code

* Push down PushToApplicationPreferences

* Push down NameDisplayPreferences

* ADapt code

* Push down main table preference, main table column preferences, and search dialog column preferences

* Push down KeyBindingsRepository

* Add warning if file could not be deleted

* Remove some calls to NativeDesktop

* Remove NativeDesktop from JabRefCliPreferences

* Introduce constants (and migrations may be accessed by GUI)

* Fix wrong logger

* Relax migrations

* Move PreferencesFilter to gui

* Move LuceneIndexer to logic

* Remove preferences package from tests

* Fix imports

* Fix checkstyle

* Fix compile error

* Fix logger

* Add workaround

* Discard changes to src/test/resources/org/jabref/logic/exporter/ModsExportFormatTestOnlyRequiredFields.xml

* Discard changes to src/test/resources/org/jabref/logic/exporter/ModsExportFormatTestAllFields.xml

* Reset *.xml to main

* Creaate LastFilesOpenedPreferences

* Re-activate code for Server

* NativeDesktop use is not restricted

* Fix architecture test

---------

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
Co-authored-by: Christoph <siedlerkiller@gmail.com>
@arfazhxss arfazhxss merged commit 7d3f66c into arfazhxss:main Sep 16, 2024
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