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Merge remote-tracking branch 'upstream/main' into fix-8010
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* upstream/main: (101 commits)
  Fixed tests by reverting development artifact
  Fixed checkstyle
  Fixed test
  remove empty lines
  move to entry editor prefs
  Reduced use of Globals for fileUpdateMonitor, removed unused themeManager vars
  reformulate
  Update src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
  fix checkstyle
  Modernize tests at BibtexParserTest
  Removed ImportFormatReader from Globals at all
  Fixes some JavaDoc errors
  Add newline
  Really fix order
  Fix CHANGELOG.md order
  Fix checkstyle
  Update CHANGELOG.md
  move to entry editor editor tab
  add javadoc
  checkstyle
  ...

# Conflicts:
#	CHANGELOG.md
#	src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
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@Siedlerchr
Siedlerchr committed May 18, 2023
2 parents f33c540 + 00399f7 commit 76c776f
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2 changes: 2 additions & 0 deletions .github/workflows/tests-fetchers.yml
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Expand Up @@ -7,6 +7,8 @@ on:
paths:
- 'src/main/java/org/jabref/logic/importer/fetcher/**'
- 'src/test/java/org/jabref/logic/importer/fetcher/**'
- 'src/main/java/org/jabref/logic/crawler/**'
- 'src/test/java/org/jabref/logic/crawler/**'
- '.github/workflows/tests-fetchers.yml'
- 'build.gradle'
pull_request:
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39 changes: 22 additions & 17 deletions CHANGELOG.md
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Expand Up @@ -20,9 +20,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We added support for more biblatex date formats for parsing dates [#2753](https://github.com/JabRef/issues/2753).
- We added support for multiple languages for exporting to and importing references from MS Office. [#9699](https://github.com/JabRef/jabref/issues/9699)
- We enabled scrolling in the groups list when dragging a group on another group. [#2869](https://github.com/JabRef/jabref/pull/2869)
- We added the option to automatically download online files when a new entry is created from an existing ID (e.g. DOI). The option can be disabled in the preferences under "Import and Export" [#9756](https://github.com/JabRef/jabref/issues/9756)
- We added the option to automatically download online files when a new entry is created from an existing ID (e.g., DOI). The option can be disabled in the preferences under "Import and Export". [#9756](https://github.com/JabRef/jabref/issues/9756)
- We added a new Integrity check for unscaped ampersands. [koppor#585](https://github.com/koppor/jabref/issues/585)
- We added the possibility to automatically fetch entries when an IBSN is pasted on the main table [#9864](https://github.com/JabRef/jabref/issues/9864)
- We added support for parsing `$\backslash$` in file paths (as exported by Mendeley). [forum#3470](https://discourse.jabref.org/t/mendeley-bib-import-with-linked-files/3470)
- We added the possibility to automatically fetch entries when an ISBN is pasted on the main table. [#9864](https://github.com/JabRef/jabref/issues/9864)
- We added the option to disable the automatic linking of files in the entry editor [#5105](https://github.com/JabRef/jabref/issues/5105)

### Changed

Expand All @@ -46,8 +48,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We reorganized the order of tabs and settings in the library properties. [#9836](https://github.com/JabRef/jabref/pull/9836)
- We changed the handling of an "overflow" of authors at `[authIniN]`: JabRef uses `+` to indicate an overflow. Example: `[authIni2]` produces `A+` (instead of `AB`) for `Aachen and Berlin and Chemnitz`. [#9703](https://github.com/JabRef/jabref/pull/9703)
- We moved the preferences option to open the last edited files on startup to the 'General' tab. [#9808](https://github.com/JabRef/jabref/pull/9808)
- We improved the recognition of DOIs when pasting a link containing a DOI on the maintable. [#9864](https://github.com/JabRef/jabref/issues/9864s)
- We reordered the preferences dialog. [#9839](https://github.com/JabRef/jabref/pull/9839)
- We split the 'Import and Export' tab into 'Web Search' and 'Export'. [#9839](https://github.com/JabRef/jabref/pull/9839)
- We improved the recognition of DOIs when pasting a link containing a DOI on the maintable [#9864](https://github.com/JabRef/jabref/issues/9864s)
- We moved the option to run JabRef in memory stick mode into the preferences dialog toolbar. [#9866](https://github.com/JabRef/jabref/pull/9866)
- In case the library contains empty entries, they are not written to disk. [#8645](https://github.com/JabRef/jabref/issues/8645)
- The formatter `remove_unicode_ligatures` is now called `replace_unicode_ligatures`. [#9890](https://github.com/JabRef/jabref/pull/9890)

### Fixed

Expand All @@ -67,14 +73,16 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed the double paste issue when <kbd>Cmd</kbd> + <kbd>v</kbd> is pressed on 'New entry from plaintext' dialog. [#9367](https://github.com/JabRef/jabref/issues/9367)
- We fixed an issue where the pin button on the Global Search dialog was located at the bottom and not at the top. [#9362](https://github.com/JabRef/jabref/issues/9362)
- We fixed the log text color in the event log console when using dark mode. [#9732](https://github.com/JabRef/jabref/issues/9732)
- We fixed an issue where searching for unlinked files would include the current library's .bib file [#9735](https://github.com/JabRef/jabref/issues/9735)
- We fixed an issue where it was no longer possible to connect to a shared mysql database due to an exception [#9761](https://github.com/JabRef/jabref/issues/9761)
- We fixed an issue where an exception was thrown for the user after <kbd>Ctrl</kbd>+<kbd>Z</kbd> command [#9737](https://github.com/JabRef/jabref/issues/9737)
- We fixed an issue where searching for unlinked files would include the current library's .bib file. [#9735](https://github.com/JabRef/jabref/issues/9735)
- We fixed an issue where it was no longer possible to connect to a shared mysql database due to an exception. [#9761](https://github.com/JabRef/jabref/issues/9761)
- We fixed an issue where an exception was thrown for the user after <kbd>Ctrl</kbd>+<kbd>Z</kbd> command. [#9737](https://github.com/JabRef/jabref/issues/9737)
- We fixed the citation key generation for (`[authors]`, `[authshort]`, `[authorsAlpha]`, `authIniN`, `authEtAl`, `auth.etal`)[https://docs.jabref.org/setup/citationkeypatterns#special-field-markers] to handle `and others` properly. [koppor#626](https://github.com/koppor/jabref/issues/626)
- We fixed the Save/save as file type shows BIBTEX_DB instead of "Bibtex library" [#9372](https://github.com/JabRef/jabref/issues/9372)
- We fixed the Save/save as file type shows BIBTEX_DB instead of "Bibtex library". [#9372](https://github.com/JabRef/jabref/issues/9372)
- We fixed the default main file directory for non-English Linux users. [#8010](https://github.com/JabRef/jabref/issues/8010)
- We fixed an issue regarding recording redundant prefixes in search history. [#9685](https://github.com/JabRef/jabref/issues/9685)
- We fixed an issue where passing a URL containing a DOI led to a "No entry found" notification. [#9821](https://github.com/JabRef/jabref/issues/9821)
- We fixed some minor visual inconsistencies and issues in the preferences dialog. [#9866](https://github.com/JabRef/jabref/pull/9866)
- The order of save actions is now retained. [#9890](https://github.com/JabRef/jabref/pull/9890)

### Removed

Expand All @@ -83,9 +91,6 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We removed the options menu, because the two contents were moved to the File menu or the properties of the library. [#9768](https://github.com/JabRef/jabref/pull/9768)
- We removed the 'File' tab in the preferences and moved its contents to the 'Export' tab. [#9839](https://github.com/JabRef/jabref/pull/9839)




## [5.9] - 2023-01-06

### Added
Expand Down Expand Up @@ -114,7 +119,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed an issue where entering a date in the format "YYYY/MM" in the entry editor date field caused an exception. [#9492](https://github.com/JabRef/jabref/issues/9492)
- For portable versions, the `.deb` file now works on plain debian again. [#9472](https://github.com/JabRef/jabref/issues/9472)
- We fixed an issue where the download of linked online files failed after an import of entries for certain urls. [#9518](https://github.com/JabRef/jabref/issues/9518)
- We fixed an issue where an exception occured when manually downloading a file from an URL in the entry editor. [#9521](https://github.com/JabRef/jabref/issues/9521)
- We fixed an issue where an exception occurred when manually downloading a file from an URL in the entry editor. [#9521](https://github.com/JabRef/jabref/issues/9521)
- We fixed an issue with open office csv file formatting where commas in the abstract field where not escaped. [#9087][https://github.com/JabRef/jabref/issues/9087]
- We fixed an issue with deleting groups where subgroups different from the selected group were deleted. [#9281][https://github.com/JabRef/jabref/issues/9281]

Expand Down Expand Up @@ -366,7 +371,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve

### Added

- We added confirmation dialog when user wants to close a library where any empty entires are detected. [#8096](https://github.com/JabRef/jabref/issues/8096)
- We added confirmation dialog when user wants to close a library where any empty entries are detected. [#8096](https://github.com/JabRef/jabref/issues/8096)
- We added import support for CFF files. [#7945](https://github.com/JabRef/jabref/issues/7945)
- We added the option to copy the DOI of an entry directly from the context menu copy submenu. [#7826](https://github.com/JabRef/jabref/issues/7826)
- We added a fulltext search feature. [#2838](https://github.com/JabRef/jabref/pull/2838)
Expand Down Expand Up @@ -413,7 +418,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
### Fixed

- We fixed an issue where an exception occurred when pasting an entry with a publication date-range of the form 1910/1917 [#7864](https://github.com/JabRef/jabref/issues/7864)
- We fixed an issue where an exception occured when a preview style was edited and afterwards another preview style selected. [#8280](https://github.com/JabRef/jabref/issues/8280)
- We fixed an issue where an exception occurred when a preview style was edited and afterwards another preview style selected. [#8280](https://github.com/JabRef/jabref/issues/8280)
- We fixed an issue where the actions to move a file to a directory were incorrectly disabled. [#7908](https://github.com/JabRef/jabref/issues/7908)
- We fixed an issue where an exception occurred when a linked online file was edited in the entry editor [#8008](https://github.com/JabRef/jabref/issues/8008)
- We fixed an issue when checking for a new version when JabRef is used behind a corporate proxy. [#7884](https://github.com/JabRef/jabref/issues/7884)
Expand Down Expand Up @@ -497,11 +502,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve

### Fixed

- We fixed an isuse where some texts (e.g. descriptionss) in dialogs could not be translated [#7854](https://github.com/JabRef/jabref/issues/7854)
- We fixed an issue where some texts (e.g. descriptions) in dialogs could not be translated [#7854](https://github.com/JabRef/jabref/issues/7854)
- We fixed an issue where import hangs for ris files with "ER - " [#7737](https://github.com/JabRef/jabref/issues/7737)
- We fixed an issue where getting bibliograhpic data from DOI or another identifer did not respect the library mode (BibTeX/biblatex)[#1018](https://github.com/JabRef/jabref/issues/6267)
- We fixed an issue where importing entries would not respect the library mode (BibTeX/biblatex)[#1018](https://github.com/JabRef/jabref/issues/1018)
- We fixed an issue where an exception occured when importing entries from a web search [#7606](https://github.com/JabRef/jabref/issues/7606)
- We fixed an issue where an exception occurred when importing entries from a web search [#7606](https://github.com/JabRef/jabref/issues/7606)
- We fixed an issue where the table column sort order was not properly stored and resulted in unsorted eports [#7524](https://github.com/JabRef/jabref/issues/7524)
- We fixed an issue where the value of the field `school` or `institution` would be printed twice in the HTML Export [forum#2634](https://discourse.jabref.org/t/problem-with-exporting-techreport-phdthesis-mastersthesis-to-html/2634)
- We fixed an issue preventing to connect to a shared database. [#7570](https://github.com/JabRef/jabref/pull/7570)
Expand Down Expand Up @@ -726,11 +731,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed an issue where long directory names created from patterns could create an exception. [#3915](https://github.com/JabRef/jabref/issues/3915)
- We fixed an issue where sort on numeric cases was broken. [#6349](https://github.com/JabRef/jabref/issues/6349)
- We fixed an issue where year and month fields were not cleared when converting to biblatex [#6224](https://github.com/JabRef/jabref/issues/6224)
- We fixed an issue where an "Not on FX thread" exception occured when saving on linux [#6453](https://github.com/JabRef/jabref/issues/6453)
- We fixed an issue where an "Not on FX thread" exception occurred when saving on linux [#6453](https://github.com/JabRef/jabref/issues/6453)
- We fixed an issue where the library sort order was lost. [#6091](https://github.com/JabRef/jabref/issues/6091)
- We fixed an issue where brackets in regular expressions were not working. [6469](https://github.com/JabRef/jabref/pull/6469)
- We fixed an issue where multiple background task popups stacked over each other.. [#6472](https://github.com/JabRef/jabref/issues/6472)
- We fixed an issue where LaTeX citations for specific commands (\autocites) of biblatex-mla were not recognized. [#6476](https://github.com/JabRef/jabref/issues/6476)
- We fixed an issue where LaTeX citations for specific commands (`\autocite`s) of biblatex-mla were not recognized. [#6476](https://github.com/JabRef/jabref/issues/6476)
- We fixed an issue where drag and drop was not working on empty database. [#6487](https://github.com/JabRef/jabref/issues/6487)
- We fixed an issue where the name fields were not updated after the preferences changed. [#6515](https://github.com/JabRef/jabref/issues/6515)
- We fixed an issue where "null" appeared in generated BibTeX keys. [#6459](https://github.com/JabRef/jabref/issues/6459)
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15 changes: 8 additions & 7 deletions build.gradle
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Expand Up @@ -117,11 +117,11 @@ dependencies {
implementation 'org.apache.pdfbox:fontbox:3.0.0-RC1'
implementation 'org.apache.pdfbox:xmpbox:3.0.0-RC1'

implementation 'org.apache.lucene:lucene-core:9.5.0'
implementation 'org.apache.lucene:lucene-queryparser:9.5.0'
implementation 'org.apache.lucene:lucene-queries:9.5.0'
implementation 'org.apache.lucene:lucene-analysis-common:9.5.0'
implementation 'org.apache.lucene:lucene-highlighter:9.5.0'
implementation 'org.apache.lucene:lucene-core:9.6.0'
implementation 'org.apache.lucene:lucene-queryparser:9.6.0'
implementation 'org.apache.lucene:lucene-queries:9.6.0'
implementation 'org.apache.lucene:lucene-analysis-common:9.6.0'
implementation 'org.apache.lucene:lucene-highlighter:9.6.0'

implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.10.0'
implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
Expand Down Expand Up @@ -179,8 +179,8 @@ dependencies {
implementation 'com.konghq:unirest-java:3.14.2'

implementation 'org.slf4j:slf4j-api:2.0.7'
implementation "org.tinylog:tinylog-api:2.6.1"
implementation "org.tinylog:slf4j-tinylog:2.6.1"
implementation "org.tinylog:tinylog-api:2.6.2"
implementation "org.tinylog:slf4j-tinylog:2.6.2"
implementation "org.tinylog:tinylog-impl:2.6.1"

implementation 'de.undercouch:citeproc-java:3.0.0-beta.2'
Expand Down Expand Up @@ -494,6 +494,7 @@ checkstyle {
rewrite {
activeRecipe(
'org.jabref.config.rewrite.cleanup',
'org.openrewrite.java.logging.slf4j.LoggersNamedForEnclosingClass',
'org.openrewrite.java.logging.slf4j.ParameterizedLogging',
'org.openrewrite.java.logging.slf4j.Slf4jLogShouldBeConstant'
)
Expand Down
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