Fix issue warning message #1

juliusalberto · 2024-10-15T02:33:29Z

Ref JabRef#10121. Based on the suggestions of the repo maintainer I have:

Passes down the NotificationService to CleanupWorker. I called the notification service directly from the CleanupWorker but I'm not sure as I added error formatting in the CleanupWorker. Ideally, there will be another method in the DialogService class that can take a list of exceptions and print it in the dialog window.
Added strings in the Jabref_en.properties file

Mandatory checks

I own the copyright of the code submitted and I licence it under the MIT license
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.

JxCl-L · 2024-10-15T06:28:12Z

Looks good to me! Your changes address the issue effectively. Nice work on implementation and updating the necessary files. Ready for merge in my opinion.

juliusalberto · 2024-10-15T11:10:57Z

Looks good to me! Your changes address the issue effectively. Nice work on implementation and updating the necessary files. Ready for merge in my opinion.

Do you think I should move the formatting logic in the org.jabref.logic.cleanupworker to somewhere in the DialogService class? I'm not sure about it - I really don't want to change the codebase too much. I think it's better to create a pull request - and then ask the maintainer how they want to proceed with it. What do you think? @JxCl-L

Noah-Martin1 · 2024-10-16T05:08:10Z

Why are 4 of the checks failing?

# Conflicts: # src/main/resources/l10n/JabRef_en.properties

* Switch priorities * Add link to PR

Co-authored-by: Christoph <[email protected]>

…r#findAssociatedFiles (JabRef#11994) Co-authored-by: Christoph <[email protected]>

* remove Deprecated getText() remove Deprecated getText() * Fix the code to pass unit test Maybe I should add more unit test based on my change? * Add more unit test to support my change 1. more unit test 2. rollback logic to follow old code which assumed that databaseContext is never null * change to @ParameterizedTest test change to @ParameterizedTest test * update follow requested change 1. remove test prefix 2. remove unnecessary inline the helper method 3. fix a type 4. two minor refactor in both files. * remove unused import remove import org.jspecify.annotations.Nullable; --------- Co-authored-by: Oliver Kopp <[email protected]>

* 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)

* Output error if requirements tracing fails * Add word to dict * Fix requirements chain * Fix casing

JabRef#12009) * Rewrite handleStringData to use CompositeIdFetcher JabRef#12004 add a no-args constructor to CompositeIdFetcher.java * delete the no-args constructor. --------- Co-authored-by: u7744550 <[email protected]>

* Add "After submission of a pull request" * Fix space

* Update takanome-dev/assign-issue-action to beta * Update actions to test actions * Add required "maitnainers" field

* fix typos and update to MADR 4.0.0 * update to MADR 4.0.0 * improve readability * remove redundant escape characters

* Try other template format * Even shorter

JabRef#12014) * "Converted test cases in FileNameCleanerTest to use @CsvSource for improved readability. Added additional test cases for Linux to handle file name restrictions. * Fixed checkstyle error * Removed empytline for checkstyle * Fixed CSV parsing issues by enclosing values containing commas in double quotes. Test case was failing so had to fix * Changed the custom test * Fixed custom test * Fixed custom test (again) * Revised custom test * Fixed the ordering of expected and input * Swapped for all test cases * Added removed test case * Added forgotten comma * Added singlequotes so csvSource can differentiate the 2 strings

Bumps [org.mockito:mockito-core](https://github.com/mockito/mockito) from 5.14.1 to 5.14.2. - [Release notes](https://github.com/mockito/mockito/releases) - [Commits](mockito/mockito@v5.14.1...v5.14.2) --- updated-dependencies: - dependency-name: org.mockito:mockito-core dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…f#12051) Bumps [src/main/resources/csl-styles](https://github.com/citation-style-language/styles) from `b413a77` to `5cfc7ae`. - [Release notes](https://github.com/citation-style-language/styles/releases) - [Commits](citation-style-language/styles@b413a77...5cfc7ae) --- updated-dependencies: - dependency-name: src/main/resources/csl-styles dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…ef#12052) Bumps [src/main/resources/csl-locales](https://github.com/citation-style-language/locales) from `8bc2af1` to `4753e3a`. - [Release notes](https://github.com/citation-style-language/locales/releases) - [Commits](citation-style-language/locales@8bc2af1...4753e3a) --- updated-dependencies: - dependency-name: src/main/resources/csl-locales dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> 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 `d870374` to `50edbd5`. - [Release notes](https://github.com/JabRef/abbrv.jabref.org/releases) - [Commits](JabRef/abbrv.jabref.org@d870374...50edbd5) --- updated-dependencies: - dependency-name: buildres/abbrv.jabref.org dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…e-warning-message

* Readd `@deprecated` annotation * Fix casing

Refs cli/cli#6274

* Convert to record * Add embedded-postgres dependency * Setup embedded postgre server * Indexing entries with Postgres * Remove Lucene bib fields indexer * Use PreparedStatement to fix escaping characters * Rename LuceneManager to IndexManager * Begin to implement "new" search syntax Co-authored-by: Loay Ghreeb <[email protected]> Co-authored-by: Carl Christian Snethlage <[email protected]> * Some new operators * Change log level of EmbeddedPostgres * Handle search flags * Fix default field * Fix handling of anyfield (and add "any" as alias) * Openrewrite... * More test cases * Remove non-covered libraries * Use LIKE syntax as default instead of regex Disabled exact match * Update module-info.java * Create "query" package * Postgres searcher * Return back the exact match operator * checkstyle * Add link * WIP * Fix compilation * WIP * Intermediate result Co-authored-by: Loay Ghreeb <[email protected]> * Query should be OK Co-authored-by: Loay Ghreeb <[email protected]> * Indexing of split values Co-authored-by: Loay Ghreeb <[email protected]> * Fix tests compile * Use first name Last name for authors * Refactor SQL query visitor * Adapt tests * Use join with EXACT_MATCH only * Update to Postgres 17 * Attempt to use sub-queries with CTEs * Fix CTEs sub-queries and grouping TODO: EXCAT_MATCH to search in split table * group matches by entry_id * Use NOT IN for negation queries * Fix unary NOT operator * Use split values table for EXACT_MATCH queries * Prepare for linked files index (full-text) * Prepare linked files tables * Fix searching * Use multi column index * fix merged module issues * Fix update event * Remove postgres linked files indexer * Remove and insert field on update event * Remove search score column * Update search groups matches * Remove search_score from tale preferences * Migrate search groups flags to new syntax * Localization * Fix dialog message * Ignores groups field from default searches Fixes JabRef#7996 * Use TYPE_HEADER field for entrytype * Search to Lucene query for linked files searching * Marge linked files and bib fields results * Searching in background task * Fix search to SQL tests * Localization test * Fix DatabaseSearcherTest * Fix DatabaseSearcherWithBibFilesTest * Fix exportMatches test * Update src/main/java/org/jabref/model/entry/BibEntry.java Co-authored-by: Oliver Kopp <[email protected]> * Add SINGLE_ENTRY_LINK to latex field * Remove changelog entries * Remove groups migration from localization * Extract search terms from query (ignore negated terms) * Fix architecture test * Highlight Preview viewer with Postgres regexp_replace * OpenRewrite * Remove onRunning * Set search query listener in the constructor * Fix preview tab scrolling * Use prepared statement to fix escaping * Use prepared statement for sql query * Store the start and end positions for every field * WIP highlight source tab * Fix source tab highlighting * Return regex, case-sensitive flags back to the search bar * Use for search bar flags for unfielded terms * Skip migrations for unfieleded terms * Return regex, case-sensitive CheckBox to search groups dialog * Apply suggestions from code review Co-authored-by: Oliver Kopp <[email protected]> * Update JabRef_en.properties * Fix search grammar to support special chars * Create SearchQueryTest.java * Adapt SQL visitor with new grammar * Allow to use quotes without escaping * escape SQL wildcard chars * Reorder methods * Adapt SearchFlagsToExpressionVisitor * Adapt SearchToLuceneVisitor * Adapt SearchQueryExtractorVisitor * Fix tests * Fix DatabaseSearcherTest * Fix search terms patten for highlighting * Highlight source tab field by field according to the search query * Apply suggestions from code review * Update src/main/java/org/jabref/gui/importer/actions/SearchGroupsMigrationAction.java Co-authored-by: Oliver Kopp <[email protected]> * Set default operator to AND * remove debug --------- Co-authored-by: Oliver Kopp <[email protected]> Co-authored-by: Carl Christian Snethlage <[email protected]> Co-authored-by: Siedlerchr <[email protected]>

* New translations jabref_en.properties (French) * New translations jabref_en.properties (Spanish) * New translations jabref_en.properties (Polish) * New translations jabref_en.properties (Portuguese, Brazilian) * New translations jabref_en.properties (Danish) * New translations jabref_en.properties (German) * New translations jabref_en.properties (Greek) * 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 (Chinese Simplified) * New translations jabref_en.properties (Vietnamese) * New translations jabref_en.properties (Indonesian) * New translations jabref_en.properties (Tagalog)

* Fix comments * Improve comment * Fix variable name * Add list of entries to ImportFilesResultItemViewModel If any error, no double entries in result set * Fix support to move files into library * Handle existing files in the case of "Copy" * Add link to PR * Fix mocking for CitationsRelationTabViewModelTest * Use Files.isSameFile * Clean filenames at "getValidFileName" * Add JavaDoc comment * Rewrite LinkedFileHandler to do the renaming, too * Remove unused method * Introduce DragDrop.handleDropOfFiles (to avoid code duplication) * Group file related methods together (in BibEntry) * Remove unused methods * Refine CHANGELOG.md * Avoid double-addition when linking files * Fix condition * Fix flag * Add notification also on move/copy if file exists * Fix checkstyle error * Streamline code * Fix target directory creation * Fix compilation, and remove Index Manager from ImportHandler * Remove IndexManager from EntryEditor * Update CommentsTabTest.java --------- Co-authored-by: Loay Ghreeb <[email protected]>

* Also add message on failing tests * Add check for forks

* Add template engine ADR * Update docs/decisions/0039-template-engine.md Co-authored-by: Oliver Kopp <[email protected]> * Update docs/decisions/0039-template-engine.md Co-authored-by: Oliver Kopp <[email protected]> * Update docs/decisions/0039-template-engine.md Co-authored-by: Oliver Kopp <[email protected]> * Update from code review * Add examples * Update examples * Update from code review * Fix wording * Add chosen option * Add chosen option * Remove blank line --------- Co-authored-by: Oliver Kopp <[email protected]>

Refs JabRef#12063

…f#12043) * Add RfcId to handle RFC url link to support quick import * Refactor RFC URL parsing Add JavaDoc comments Remove unnecessary lowercase * Refactor RFC URL parsing Add JavaDoc comments Remove unnecessary lowercase * Adjust code style * Adjust code style * According to CI test feedback: - Removed RFC entry from identifier list(StandardField.java) - Modified RfcId class to extend EprintIdentifier * Accorfing to maintainer feedback to fix: - Replaced RfcId name with RFC class for consistency and clarity. - Updated RFC parsing logic to support both plain RFC IDs (e.g., "rfc7276") and full URLs (e.g., "https://www.rfc-editor.org/rfc/rfc7276.html"). - Added tests in RFCTest to validate proper parsing of RFC identifiers from both formats. - Removed unnecessary method (isValid) improved code clarity. - Adjusted the CompositeIdFetcher to integrate the new RFC class functionalities. * Refactored RFCTest to adhere to the suggestions provided: - Converted `testParsePlainRfcId` to a `@ParameterizedTest` using `@CsvSource`. - Adjusted `testInvalidRfc` to use `assertEquals(Optional.empty(), rfc)`. - Updated `testGetExternalUri` to verify the URI using `Optional.of()` for consistent checks. * adjust code format according to CI test(checkstyle) * Swap expected and input * Fix OpenRewrite issues * fix code style according to checkstyle --------- Co-authored-by: Cheng <[email protected]> Co-authored-by: Oliver Kopp <[email protected]>

…abRef#12038) * Caught an error when accessing an invalid path. fixes JabRef#10548 * Fixed typo in issue num * Moved changelog entry to unreleased section * Moved try-catch and added tests * Fix checkstyle * Fix checkstyle again * Fix checkstyle fr this time * Discard changes to external-libraries.md * Result of "rewriteRun" * Add link to issue * Use VisibleForTesting annotation * Remove Jimfs depdencency --------- Co-authored-by: Tom Martin <[email protected]> Co-authored-by: Oliver Kopp <[email protected]>

* First version of the double click issue * First version to use double click to open TeXstudio * change the click count to two * I set the GitHub page for the test * Replace exec() with ProcessBuilder and printStackTrace() with LOGGER * change some useless functions * I solve the csl-styles submodel problem * Solve the avvrv.jabref.org conflict * The double click function works fine for the emacs external program * The double click function works fine for the TeXworks external program * I changed the required code. I also delete some useless comment. I make TeXworks works for this feature * finished texWorks and delete some comments * delete some comments * solve untrack files * I make Sublime Text works for this feature * I make WinEdt works for this feature * delete some command and change jumpString to jumpToLineCommandlineArguments * Fix csl-styles Please enter the commit message for your changes. Lines starting * Fix abbrv.jabref.org submodules * I make Vim works for this feature * I rewrite jumpToLine for TexShop. But I don't hava a Mac OS machine. I hope it's working. * Delete the JumpToLine in TeXshop and a comment line in TeXstudio * Fix submodules (and wrong file) * Fix empty lines * Default should be TeXstudio * Remvoe "Integer.format" (and add test) * Fix PushToVim * Cleanup PushToLyx * Refactor PushToVim * Add CHANGELOG.md entry --------- Co-authored-by: Oliver Kopp <[email protected]>

* Identifier: Rename "getNormalized" to "asString" (and replace getDOI by asString) * Fix method name * Fix checkstyle * Fix method name * Fix methodname ... agian ... * Adapt to new method names * Fix method name ... again ...

Fixes

…JabRef#12037) * Change enum & localisation preferences from "General File Directory" to "Library File Directory" * change 'generalFileDirectory' to 'libraryFileDirectory' in codebase * change 'generalFileDirectory' to 'libraryFileDirectory' in test code * change 'General file directory' to 'Library file directory' in places that were previously missed. * amendment to prior commits: should show up in GUI as "Library-specific File Directory". Have followed convention for "User-Specific File Directory" where this is referred to outside of UI prompts as "Library File Directory" * update CHANGELOG.md to document activity in this branch. * Additional/missed locations: change 'General File Directory' to 'Library-specific File Directory' * Per Koppor's instructions: unify front/back end to "Library-specific File Directory" * update code comments to reflect change from library file directory to library-specific file directory * updated en localisation per unit tests: 1. removed unused general file directory key 2. made Library-specific file directory key all-lowercase per unit test requirements. --------- Co-authored-by: rl712 <[email protected]>

…e-warning-message

…d methods

juliusalberto added 3 commits October 15, 2024 00:55

implement showing warning message in the cleanupworker

beaf0f5

Edited changelog

6c78f9f

Merge branch 'JabRef:main' into fix-issue-warning-message

a617549

juliusalberto and others added 24 commits October 16, 2024 22:41

Merge branch 'main' into fix-issue-warning-message

6a7754f

# Conflicts: # src/main/resources/l10n/JabRef_en.properties

Add missing Localization

a4f0b53

Edited casting

d9c3998

Test WIP version of action (JabRef#11989)

1e91b29

Revert "Test WIP version of action (JabRef#11989)" (JabRef#11990)

25635de

Switch priorities: XMP over Grobid (JabRef#11992)

e6c3602

* Switch priorities * Add link to PR

Streamline text of DownloadFullTextAction (JabRef#11993)

624570b

Co-authored-by: Christoph <[email protected]>

Streamline code of org.jabref.logic.util.io.CitationKeyBasedFileFinde…

d258f18

…r#findAssociatedFiles (JabRef#11994) Co-authored-by: Christoph <[email protected]>

Fix link in CONTRIBUTING.md (JabRef#11995)

7ef35ad

Fix typo (JabRef#12002)

6537bc9

Ignore rsync errors on uploading (JabRef#12008)

04255d0

Update 0011-test-external-links-in-documentation.md (JabRef#12006)

a2122bd

Output error if requirements tracing fails (JabRef#12003)

1a0e44e

* Output error if requirements tracing fails * Add word to dict * Fix requirements chain * Fix casing

Add "After submission of a pull request" (JabRef#12010)

b4d5db4

* Add "After submission of a pull request" * Fix space

Update to javafx 23.0.1 (JabRef#12013)

9025778

Update takanome-dev/assign-issue-action to beta (JabRef#12012)

705629e

* Update takanome-dev/assign-issue-action to beta * Update actions to test actions * Add required "maitnainers" field

Update to MADR 4.0.0 (JabRef#12016)

30d0409

* fix typos and update to MADR 4.0.0 * update to MADR 4.0.0 * improve readability * remove redundant escape characters

Fix removing comments (JabRef#12019)

72b5ec0

Try other template format (JabRef#12011)

a3f13aa

* Try other template format * Even shorter

clarify After submission of a pull request in CONTRIBUTING.md

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dependabot bot and others added 30 commits October 21, 2024 14:52

Replace @deprecated by explaining text (JabRef#12055)

a6db811

Merge branch 'main' of https://github.com/JabRef/jabref into fix-issu…

e30b201

…e-warning-message

Implemented the suggestion, moved the showFailure() to the GUI package

5d72058

Readd @deprecated annotation (JabRef#12056)

8cf8959

* Readd `@deprecated` annotation * Fix casing

Fix wrong permission

4ec8bed

Fix permissions (again)

ed4be93

Try more permissions

b663e25

Debug: Does it fail because the label does not exist?

7dda643

Does not work - even with "permissions: write-all"

3ad5812

Refs cli/cli#6274

Fix link to contribution guide (JabRef#12064)

bffdb8b

Also add message on failing tests (JabRef#12063)

ae85bd5

* Also add message on failing tests * Add check for forks

Try github.token

a8d3305

Refs JabRef#12063

Change casing and improve naming of Background tasks (JabRef#12066)

a94dd11

Fixes

Disable meta data elements in adr-template (JabRef#12074)

ee5d78b

New Crowdin updates (JabRef#12075)

4ce83c4

Merge branch 'main' of https://github.com/JabRef/jabref into fix-issu…

8c8cfe8

…e-warning-message

Implemented suggestions to use collectors, removed unused comments an…

702820e

…d methods

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Fix issue warning message #1

Fix issue warning message #1

juliusalberto commented Oct 15, 2024 •

edited

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JxCl-L commented Oct 15, 2024

juliusalberto commented Oct 15, 2024

Noah-Martin1 commented Oct 16, 2024

Fix issue warning message #1

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Fix issue warning message #1

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juliusalberto commented Oct 15, 2024 • edited Loading

Mandatory checks

JxCl-L commented Oct 15, 2024

juliusalberto commented Oct 15, 2024

Noah-Martin1 commented Oct 16, 2024

juliusalberto commented Oct 15, 2024 •

edited

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