Merge remote-tracking branch 'upstream/main' into improveSearchPerfor…

…mance * upstream/main: Bump gittools/actions from 1.2.0 to 2.0.0 (JabRef#11529) Bump src/main/resources/csl-styles from `fd6cb3e` to `bf2926b` (JabRef#11528) Bump org.openrewrite.rewrite from 6.16.3 to 6.16.4 (JabRef#11527) Bump org.apache.commons:commons-lang3 from 3.14.0 to 3.15.0 (JabRef#11525) Bump org.jspecify:jspecify from 0.3.0 to 1.0.0 (JabRef#11523) Bump com.github.andygoossens.modernizer from 1.9.2 to 1.9.3 (JabRef#11524) Always show star for local unsaved library (JabRef#11519) Update to javafx 22.02 (JabRef#11518) Try to use "release" (made in fork) (JabRef#11517) Fix NPE when saving preferences (JabRef#11515) New translations jabref_en.properties (Portuguese, Brazilian) (JabRef#11516) Add OpenAI privacy policy (JabRef#11511) import PMID field in Pubmed (JabRef#11513) New Crowdin updates (JabRef#11514)
LoayGhreeb · Jul 24, 2024 · 21eb34a · 21eb34a
2 parents 839bf79 + fed6bde
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diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -66,12 +66,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v1.2.0
+        uses: gittools/actions/gitversion/setup@v2.0.0
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v1.2.0
+        uses: gittools/actions/gitversion/execute@v2.0.0
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

diff --git a/.github/workflows/deployment-jdk-ea.yml b/.github/workflows/deployment-jdk-ea.yml
@@ -84,12 +84,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v1.2.0
+        uses: gittools/actions/gitversion/setup@v2.0.0
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v1.2.0
+        uses: gittools/actions/gitversion/execute@v2.0.0
 
       # JDK
       - name: 'Set up JDK ${{ matrix.jdk }}'

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -79,12 +79,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v1.2.0
+        uses: gittools/actions/gitversion/setup@v2.0.0
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v1.2.0
+        uses: gittools/actions/gitversion/execute@v2.0.0
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,13 +17,15 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Changed
 
+- The Pubmed/Medline Plain importer now imports the PMID field as well [#11488](https://github.com/JabRef/jabref/issues/11488)
 - The 'Check for updates' menu bar button is now always enabled. [#11485](https://github.com/JabRef/jabref/pull/11485)
 - JabRef respects the [configuration for storing files relative to the .bib file](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#directories-for-files) in more cases. [#11492](https://github.com/JabRef/jabref/pull/11492)
 
 ### Fixed
 
 - We fixed an issue where the 'Check for updates' preference was not saved. [#11485](https://github.com/JabRef/jabref/pull/11485)
-- We fixed an issue where an exception was thrown after changing "show preview as a tab" in the preferences. [#11509](https://github.com/JabRef/jabref/pull/11509)
+- We fixed an issue where an exception was thrown after changing "show preview as a tab" in the preferences. [#11515](https://github.com/JabRef/jabref/pull/11515)
+- We fixed an issue where a new unsaved library was not marked with an asterisk [#11519](https://github.com/JabRef/jabref/pull/11519)
 
 ### Removed
 

diff --git a/PRIVACY.md b/PRIVACY.md
@@ -38,41 +38,42 @@ These third parties may log additional information besides your IP address and t
 
 These third-party services are the following:
 
-| Service                                                                                                         | Privacy Policy |
-|-----------------------------------------------------------------------------------------------------------------|----------------|
-| [ACM](https://www.acm.org/)                                                                                     | <https://www.acm.org/privacy-policy> |
-| [ACS Publications](https://pubs.acs.org/)                                                                       | <https://www.acs.org/privacy.html> |
-| [APS Advancing Physics](https://harvest.aps.org/)                                                               | <https://www.aps.org/about/privacy.cfm#privacy> |
-| [arXiv.org](https://arxiv.org/)                                                                                 | <https://info.arxiv.org/help/policies/privacy_policy.html> |
-| [Bibliotheksverbund Bayern](https://www.bib-bvb.de/)                                                            | <https://www.bib-bvb.de/web/guest/datenschutzerklaerung-bvb-homepage> |
-| [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/)                                           | <https://www.si.edu/Privacy> |
-| [Collection of Computer Science Bibliographies](https://en.wikipedia.org/wiki/Collection_of_Computer_Science_Bibliographies)                                     | **currently unavailable**, offline  |
-| [CrossRef](https://www.crossref.org/)                                                                           | <https://www.crossref.org/operations-and-sustainability/privacy/> |
-| [dblp](https://dblp.uni-trier.de/)                                                                              | <https://dblp.uni-trier.de/db/about/privacy.html> |
-| [Directory of Open Access Books](https://www.doabooks.org/)                                                     | <https://www.doabooks.org/en/resources/accessibility> |
-| [Digitala Vetenskapliga Arkivet](https://www.diva-portal.org/)                                                  | <https://www.uu.se/en/about-uu/data-protection-policy/> |
-| [DOI Foundation](https://www.doi.org/)                                                                          | <https://www.doi.org/privacy-policy/> |
-| [Elsevier](https://www.elsevier.com/)                                                                           | <https://www.elsevier.com/legal/privacy-policy> |
-| [Google Scholar](https://scholar.google.com/)                                                                   | <https://policies.google.com/privacy> |
-| [Gemeinsamer Verbundkatalog](https://www.gbv.de/)                                                               | <https://www.gbv.de/datenschutz> |
-| [IACR](https://www.iacr.org/)                                                                                   | <https://www.iacr.org/privacy.html> |
-| [IEEEXplore](https://ieeexplore.ieee.org/Xplore/home.jsp)                                                       | <https://www.ieee.org/security-privacy.html> |
-| [INSPIRE](https://inspirehep.net/)                                                                              | <https://cern.service-now.com/service-portal?id=privacy_policy&se=INSPIRE-Online&notice=main> |
-| [JSTOR](https://www.jstor.org/)                                                                                 | <https://www.ithaka.org/privacypolicy/> |
-| [Library of Congress](https://lccn.loc.gov/)                                                                    | <https://www.loc.gov/legal/> |
-| [National Library of Medicine](https://www.ncbi.nlm.nih.gov/)                                                   | <https://www.nlm.nih.gov/web_policies.html> |
-| [MathSciNet](http://www.ams.org/mathscinet)                                                                     | <https://www.ams.org/about-us/privacy> |
-| [mEDRA](https://www.medra.org/)                                                                                     | <https://<https://www.medra.org/stdoc/en/Servizio_DOI_Informativa_ENG.pdf> |
-| [Mr. DLib](https://mr-dlib.org/) [1]                                                                            | <https://support.dataverse.harvard.edu/harvard-dataverse-privacy-policy> |
-| [Openlibrary](https://openlibrary.org)                                                                          | <https://archive.org/about/terms.php> |
-| [ResearchGate](https://www.researchgate.net/)                                                                   | <https://www.researchgate.net/privacy-policy> |
-| [IETF Datatracker](https://datatracker.ietf.org/)                                                               | <https://www.ietf.org/privacy-statement/> |
-| [Semantic Scholar](https://www.semanticscholar.org/), powered by [Allen Institute for AI](https://allenai.org/) | <https://allenai.org/privacy-policy> |
-| [Springer Nature](https://dev.springernature.com/)                                                              | <https://dev.springernature.com/privacy-policy/> |
-| [The SAO/NASA Astrophysics Data System](https://ui.adsabs.harvard.edu/)                                         | <https://ui.adsabs.harvard.edu/help/privacy/> |
-| [Unpaywall](https://unpaywall.org/)                                                                             | <https://unpaywall.org/legal/privacy> |
-| [zbMATH Open](https://www.zbmath.org)                                                                           | <https://zbmath.org/privacy-policy/> |
-| [ISIDORE](https://isidore.science/)                                                                             | <https://isidore.science/credit> |
+| Service                                                                                                                      | Privacy Policy |
+|------------------------------------------------------------------------------------------------------------------------------|----------------|
+| [ACM](https://www.acm.org/)                                                                                                  | <https://www.acm.org/privacy-policy> |
+| [ACS Publications](https://pubs.acs.org/)                                                                                    | <https://www.acs.org/privacy.html> |
+| [APS Advancing Physics](https://harvest.aps.org/)                                                                            | <https://www.aps.org/about/privacy.cfm#privacy> |
+| [arXiv.org](https://arxiv.org/)                                                                                              | <https://info.arxiv.org/help/policies/privacy_policy.html> |
+| [Bibliotheksverbund Bayern](https://www.bib-bvb.de/)                                                                         | <https://www.bib-bvb.de/web/guest/datenschutzerklaerung-bvb-homepage> |
+| [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/)                                                        | <https://www.si.edu/Privacy> |
+| [Collection of Computer Science Bibliographies](https://en.wikipedia.org/wiki/Collection_of_Computer_Science_Bibliographies) | **currently unavailable**, offline  |
+| [CrossRef](https://www.crossref.org/)                                                                                        | <https://www.crossref.org/operations-and-sustainability/privacy/> |
+| [dblp](https://dblp.uni-trier.de/)                                                                                           | <https://dblp.uni-trier.de/db/about/privacy.html> |
+| [Directory of Open Access Books](https://www.doabooks.org/)                                                                  | <https://www.doabooks.org/en/resources/accessibility> |
+| [Digitala Vetenskapliga Arkivet](https://www.diva-portal.org/)                                                               | <https://www.uu.se/en/about-uu/data-protection-policy/> |
+| [DOI Foundation](https://www.doi.org/)                                                                                       | <https://www.doi.org/privacy-policy/> |
+| [Elsevier](https://www.elsevier.com/)                                                                                        | <https://www.elsevier.com/legal/privacy-policy> |
+| [Google Scholar](https://scholar.google.com/)                                                                                | <https://policies.google.com/privacy> |
+| [Gemeinsamer Verbundkatalog](https://www.gbv.de/)                                                                            | <https://www.gbv.de/datenschutz> |
+| [IACR](https://www.iacr.org/)                                                                                                | <https://www.iacr.org/privacy.html> |
+| [IEEEXplore](https://ieeexplore.ieee.org/Xplore/home.jsp)                                                                    | <https://www.ieee.org/security-privacy.html> |
+| [INSPIRE](https://inspirehep.net/)                                                                                           | <https://cern.service-now.com/service-portal?id=privacy_policy&se=INSPIRE-Online&notice=main> |
+| [JSTOR](https://www.jstor.org/)                                                                                              | <https://www.ithaka.org/privacypolicy/> |
+| [Library of Congress](https://lccn.loc.gov/)                                                                                 | <https://www.loc.gov/legal/> |
+| [National Library of Medicine](https://www.ncbi.nlm.nih.gov/)                                                                | <https://www.nlm.nih.gov/web_policies.html> |
+| [MathSciNet](http://www.ams.org/mathscinet)                                                                                  | <https://www.ams.org/about-us/privacy> |
+| [mEDRA](https://www.medra.org/)                                                                                              | <https://www.medra.org/stdoc/en/Servizio_DOI_Informativa_ENG.pdf> |
+| [Mr. DLib](https://mr-dlib.org/) [1]                                                                                         | <https://support.dataverse.harvard.edu/harvard-dataverse-privacy-policy> |
+| [OpenAI](https://openai.com/)                                                                                                | <https://openai.com/policies/privacy-policy/> |
+| [Openlibrary](https://openlibrary.org)                                                                                       | <https://archive.org/about/terms.php> |
+| [ResearchGate](https://www.researchgate.net/)                                                                                | <https://www.researchgate.net/privacy-policy> |
+| [IETF Datatracker](https://datatracker.ietf.org/)                                                                            | <https://www.ietf.org/privacy-statement/> |
+| [Semantic Scholar](https://www.semanticscholar.org/), powered by [Allen Institute for AI](https://allenai.org/)              | <https://allenai.org/privacy-policy> |
+| [Springer Nature](https://dev.springernature.com/)                                                                           | <https://dev.springernature.com/privacy-policy/> |
+| [The SAO/NASA Astrophysics Data System](https://ui.adsabs.harvard.edu/)                                                      | <https://ui.adsabs.harvard.edu/help/privacy/> |
+| [Unpaywall](https://unpaywall.org/)                                                                                          | <https://unpaywall.org/legal/privacy> |
+| [zbMATH Open](https://www.zbmath.org)                                                                                        | <https://zbmath.org/privacy-policy/> |
+| [ISIDORE](https://isidore.science/)                                                                                          | <https://isidore.science/credit> |
 
 [1]: *Note: The Mr. DLib service is used for the related articles tab in the entry editor and collects also your language, your browser and operating system (by default*disabled*).*
 

diff --git a/build.gradle b/build.gradle
@@ -6,12 +6,12 @@ import org.jabref.build.xjc.XjcTask
 plugins {
     id 'application'
 
-    id 'com.github.andygoossens.modernizer' version '1.9.2'
+    id 'com.github.andygoossens.modernizer' version '1.9.3'
 
     id 'me.champeau.jmh' version '0.7.2'
 
     // This is https://github.com/java9-modularity/gradle-modules-plugin/pull/282
-    id 'com.github.koppor.gradle-modules-plugin' version 'jitpack-SNAPSHOT'
+    id 'com.github.koppor.gradle-modules-plugin' version 'v1.8.15-cmd-1'
 
     id 'org.openjfx.javafxplugin' version '0.1.0'
 
@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.16.3'
+    id 'org.openrewrite.rewrite' version '6.16.4'
 }
 
 // Enable following for debugging
@@ -134,7 +134,7 @@ dependencyLocking {
 }
 
 javafx {
-    version = "22.0.1"
+    version = "22.0.2"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -166,7 +166,7 @@ dependencies {
     implementation "org.apache.lucene:lucene-highlighter:$luceneVersion"
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.11.0'
-    implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
+    implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.15.0'
     implementation group: 'org.apache.commons', name: 'commons-text', version: '1.12.0'
     implementation 'commons-logging:commons-logging:1.3.3'
     implementation 'com.h2database:h2-mvstore:2.2.224'
@@ -297,7 +297,7 @@ dependencies {
     // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'
 
     // Because of GraalVM quirks, we need to ship that. See https://github.com/jspecify/jspecify/issues/389#issuecomment-1661130973 for details
-    implementation 'org.jspecify:jspecify:0.3.0'
+    implementation 'org.jspecify:jspecify:1.0.0'
 
     // parse plist files
     implementation 'com.googlecode.plist:dd-plist:1.28'

diff --git a/src/main/java/org/jabref/gui/LibraryTab.java b/src/main/java/org/jabref/gui/LibraryTab.java
@@ -415,13 +415,8 @@ public void updateTabTitle(boolean isChanged) {
             uniquePathPart.ifPresent(part -> tabTitle.append(" \u2013 ").append(part));
         } else {
             if (databaseLocation == DatabaseLocation.LOCAL) {
+                tabTitle.append('*');
                 tabTitle.append(Localization.lang("untitled"));
-                if (bibDatabaseContext.getDatabase().hasEntries()) {
-                    // if the database is not empty and no file is assigned,
-                    // the database came from an import and has to be treated somehow
-                    // -> mark as changed
-                    tabTitle.append('*');
-                }
             } else {
                 addSharedDbInformation(tabTitle, bibDatabaseContext);
                 addSharedDbInformation(toolTipText, bibDatabaseContext);

diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -147,6 +147,12 @@ public EntryEditor(LibraryTab libraryTab, UndoAction undoAction, RedoAction redo
                 activeTab.notifyAboutFocus(currentlyEditedEntry);
             }
         });
+        EasyBind.listen(preferencesService.getPreviewPreferences().showPreviewAsExtraTabProperty(),
+                (obs, oldValue, newValue) -> {
+                    if (currentlyEditedEntry != null) {
+                        adaptVisibleTabs();
+                    }
+                });
     }
 
     private void setupDragAndDrop(LibraryTab libraryTab) {
@@ -384,9 +390,6 @@ public void setCurrentlyEditedEntry(BibEntry currentlyEditedEntry) {
             getSelectedTab().notifyAboutFocus(currentlyEditedEntry);
         });
 
-        EasyBind.listen(preferencesService.getPreviewPreferences().showPreviewAsExtraTabProperty(),
-                (obs, oldValue, newValue) -> adaptVisibleTabs());
-
         adaptVisibleTabs();
         setupToolBar();
 

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java
@@ -149,6 +149,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
 
                 // store the fields in a map
                 Map<String, Field> hashMap = new HashMap<>();
+                hashMap.put("PMID", StandardField.PMID);
                 hashMap.put("PG", StandardField.PAGES);
                 hashMap.put("PL", StandardField.ADDRESS);
                 hashMap.put("PHST", new UnknownField("history"));

diff --git a/src/main/resources/csl-styles b/src/main/resources/csl-styles
diff --git a/src/main/resources/l10n/JabRef_de.properties b/src/main/resources/l10n/JabRef_de.properties
@@ -503,7 +503,6 @@ Docs\ (This\ Year)=Dokumente (Dieses Jahr)
 Incorrect\ ISSN\ format=Ungültiges ISSN-Format
 Error\ accessing\ catalog=Fehler beim Katalogzugriff
 
-Check\ for\ latest\ version\ online=Prüfe online auf die neueste Version
 If\ you\ encounter\ an\ issue\ or\ a\ bug,\ please\ check\ the\ latest\ version,\ whether\ the\ issue\ is\ still\ present.=Wenn Sie auf ein Problem oder einen Fehler stoßen, testen Sie bitte die neueste Version und prüfen, ob das Problem noch vorhanden ist.
 
 Keep\ both=Beide behalten

diff --git a/src/main/resources/l10n/JabRef_es.properties b/src/main/resources/l10n/JabRef_es.properties
@@ -486,7 +486,6 @@ Docs\ (This\ Year)=Documentos (Este Año)
 Incorrect\ ISSN\ format=Formato ISSN incorrecto
 Error\ accessing\ catalog=Error al acceder al catálogo
 
-Check\ for\ latest\ version\ online=Busque la última versión en línea
 
 Keep\ both=Mantener ambos