Merge remote-tracking branch 'upstream/main' into writebackupToTemp

* upstream/main: Main instead of master Custom DOI base address fix (#7569) Change export to save (#7518) Bump unoloader from 7.1.1 to 7.1.2 (#7609) Bump org.beryx.jlink from 2.23.5 to 2.23.6 (#7610) Bump com.adarshr.test-logger from 2.1.1 to 3.0.0 (#7611) Bump libreoffice from 7.1.1 to 7.1.2 (#7612) Squashed 'buildres/csl/csl-styles/' changes from e1acabe..bfa3b6d (#7603) Rename master to main
JabRef · Apr 11, 2021 · 5b2b64c · 5b2b64c
2 parents 80b4f98 + 132f232
commit 5b2b64c
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -19,11 +19,11 @@ JabRef version <!-- version as shown in the about box --> on <!-- Windows 10|Ubu
 <!-- 
       Please always test if the bug is still reproducible in the latest development version.
       We are constantly improving JabRef and some bugs may already be fixed.
-      You can download the development version at: http://builds.jabref.org/master/
+      You can download the development version at: http://builds.jabref.org/main
       Please make a backup of your library before you try out this version.
       If you already use a development version, ensure that you use the latest one.
  -->
-- [ ] **Mandatory**: I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists
+- [ ] **Mandatory**: I have tested the latest development version from http://builds.jabref.org/main and the problem persists
 
 <!-- Add a clear and concise description of what the bug is. -->
 

diff --git a/build.gradle b/build.gradle
@@ -14,10 +14,10 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.38.0'
     id 'org.javamodularity.moduleplugin' version '1.7.0'
     id 'org.openjfx.javafxplugin' version '0.0.9'
-    id 'org.beryx.jlink' version '2.23.5'
+    id 'org.beryx.jlink' version '2.23.6'
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
-    id 'com.adarshr.test-logger' version '2.1.1'
+    id 'com.adarshr.test-logger' version '3.0.0'
 }
 
 gradle.startParameter.showStacktrace = org.gradle.api.logging.configuration.ShowStacktrace.ALWAYS
@@ -115,8 +115,8 @@ dependencies {
 
     implementation 'commons-cli:commons-cli:1.4'
 
-    implementation 'org.libreoffice:libreoffice:7.1.1'
-    implementation 'org.libreoffice:unoloader:7.1.1'
+    implementation 'org.libreoffice:libreoffice:7.1.2'
+    implementation 'org.libreoffice:unoloader:7.1.2'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.9'
     implementation 'info.debatty:java-string-similarity:2.0.0'

diff --git a/buildres/csl/csl-styles/archives-of-hand-and-microsurgery.csl b/buildres/csl/csl-styles/archives-of-hand-and-microsurgery.csl
@@ -0,0 +1,158 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
+  <info>
+    <title>Archives of Hand and Microsurgery</title>
+    <title-short>AHM</title-short>
+    <id>http://www.zotero.org/styles/archives-of-hand-and-microsurgery</id>
+    <link href="http://www.zotero.org/styles/archives-of-hand-and-microsurgery" rel="self"/>
+    <link href="http://www.zotero.org/styles/the-pan-african-medical-journal" rel="template"/>
+    <link href="https://submit.handmicro.org/about/Author.php" rel="documentation"/>
+    <author>
+      <name>Patrick O'Brien</name>
+    </author>
+    <category citation-format="numeric"/>
+    <category field="medicine"/>
+    <issn>2586-3290</issn>
+    <eissn>2586-3533</eissn>
+    <updated>2021-03-30T14:44:29+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="author">
+    <names variable="author" suffix=". ">
+      <name delimiter-precedes-et-al="always" delimiter-precedes-last="always" initialize-with="" name-as-sort-order="all" sort-separator=" "/>
+      <label form="short" prefix=" (" suffix=")"/>
+      <substitute>
+        <names variable="editor"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="editor">
+    <names variable="editor">
+      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always" delimiter-precedes-et-al="never"/>
+      <label prefix=", "/>
+    </names>
+  </macro>
+  <macro name="publisher">
+    <group delimiter=": ">
+      <text variable="publisher-place"/>
+      <text variable="publisher"/>
+    </group>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="page" match="none">
+        <choose>
+          <if type="article-journal">
+            <choose>
+              <if match="none" variable="page volume">
+                <text variable="DOI" prefix="https://doi.org/"/>
+              </if>
+            </choose>
+          </if>
+          <else-if type="webpage post post-weblog">
+            <group delimiter=". ">
+              <text variable="URL"/>
+              <group delimiter=" ">
+                <text term="accessed" text-case="capitalize-first"/>
+                <date variable="accessed">
+                  <date-part name="day" prefix=" "/>
+                  <date-part name="month" strip-periods="true" prefix=" "/>
+                  <date-part name="year" prefix=" "/>
+                </date>
+              </group>
+            </group>
+          </else-if>
+        </choose>
+      </if>
+    </choose>
+  </macro>
+  <macro name="journal-title">
+    <choose>
+      <if type="article-journal article-magazine" match="any">
+        <text variable="container-title" form="short" strip-periods="true" suffix="."/>
+      </if>
+      <else>
+        <text variable="container-title" suffix=". "/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="title">
+    <choose>
+      <if type="book thesis" match="any">
+        <text variable="title" font-style="italic"/>
+      </if>
+      <else>
+        <text variable="title"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if is-numeric="edition">
+        <group delimiter=" ">
+          <number variable="edition" form="ordinal"/>
+          <text term="edition" form="short"/>
+        </group>
+      </if>
+      <else>
+        <text variable="edition" suffix="."/>
+      </else>
+    </choose>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout vertical-align="baseline" delimiter="," prefix="[" suffix="]">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography et-al-min="7" et-al-use-first="6" second-field-align="flush">
+    <layout suffix=".">
+      <text variable="citation-number" suffix="."/>
+      <text macro="author"/>
+      <text macro="title" suffix=". "/>
+      <choose>
+        <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+          <group delimiter=" " prefix=" ">
+            <text macro="edition"/>
+            <text macro="publisher"/>
+          </group>
+        </if>
+        <else-if type="chapter paper-conference" match="any">
+          <group delimiter=". " prefix=" ">
+            <group>
+              <text term="in" suffix=": " text-case="capitalize-first"/>
+              <text macro="editor"/>
+            </group>
+            <text variable="container-title" font-style="italic"/>
+            <date variable="issued">
+              <date-part name="year"/>
+            </date>
+            <text macro="publisher"/>
+            <group delimiter=" ">
+              <label plural="never" variable="page" form="short"/>
+              <text variable="page"/>
+            </group>
+          </group>
+        </else-if>
+        <else>
+          <text macro="journal-title"/>
+          <group delimiter=";" suffix=".">
+            <date variable="issued" prefix=" ">
+              <date-part name="year"/>
+            </date>
+            <group delimiter=":">
+              <group>
+                <text variable="volume"/>
+                <text variable="issue" prefix="(" suffix=")"/>
+              </group>
+              <text variable="page"/>
+            </group>
+          </group>
+        </else>
+      </choose>
+      <text macro="access" prefix=" "/>
+    </layout>
+  </bibliography>
+</style>
diff --git a/buildres/csl/csl-styles/canadian-biosystems-engineering.csl b/buildres/csl/csl-styles/canadian-biosystems-engineering.csl
@@ -16,7 +16,7 @@
     <issn>1492-9058</issn>
     <eissn>1492-9066</eissn>
     <summary>Style for online journal Canadian Biosystems Engineering</summary>
-    <updated>2020-09-26T15:27:23+00:00</updated>
+    <updated>2020-12-05T19:18:31+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <locale xml:lang="en-US">
@@ -275,6 +275,15 @@
       <else-if type="webpage chapter paper-conference article-journal article-magazine article-newspaper" match="any">
         <text variable="title"/>
       </else-if>
+      <else-if type="patent">
+        <group delimiter=". ">
+          <text variable="title"/>
+          <group delimiter=", ">
+            <text variable="authority"/>
+            <text variable="number"/>
+          </group>
+        </group>
+      </else-if>
       <else-if type="motion_picture broadcast" match="any"/>
       <else>
         <choose>

diff --git a/buildres/csl/csl-styles/journal-of-accounting-research.csl b/buildres/csl/csl-styles/journal-of-accounting-research.csl
@@ -15,10 +15,6 @@
       <name>Xuanheng Huang</name>
       <email>huangxuanheng@gmail.com</email>
     </contributor>
-    <contributor>
-      <name>Vito Ferrulli</name>
-      <email>vitof970@gmail.com</email>
-    </contributor>
     <category citation-format="author-date"/>
     <category field="generic-base"/>
     <issn>0021-8456</issn>
@@ -161,7 +157,7 @@
         <if type="legal_case" match="none">
           <choose>
             <if variable="DOI">
-              <text variable="DOI" prefix="Available at https://doi.org/"/>
+              <text variable="DOI" prefix="https://doi.org/"/>
             </if>
             <else>
               <text variable="URL" prefix="Available at "/>

diff --git a/snap/snapcraft.yaml b/snap/snapcraft.yaml
@@ -52,7 +52,7 @@ environment:
 parts:
   jabref:
     plugin: dump
-    source: https://builds.jabref.org/master/JabRef-5.3-portable_linux.tar.gz
+    source: https://builds.jabref.org/main/JabRef-5.3-portable_linux.tar.gz
     stage-packages:
       - x11-utils
     override-build: |

diff --git a/src/main/java/org/jabref/gui/commonfxcontrols/SaveOrderConfigPanel.fxml b/src/main/java/org/jabref/gui/commonfxcontrols/SaveOrderConfigPanel.fxml
@@ -16,12 +16,12 @@
         <ToggleGroup fx:id="saveOrderToggleGroup"/>
     </fx:define>
 
-    <RadioButton fx:id="exportInOriginalOrder" text="%Export entries in their original order"
+    <RadioButton fx:id="exportInOriginalOrder" text="%Keep original order"
                  toggleGroup="$saveOrderToggleGroup"/>
-    <RadioButton fx:id="exportInTableOrder" text="%Export in current table sort order"
+    <RadioButton fx:id="exportInTableOrder" text="%Use current table sort order"
                  toggleGroup="$saveOrderToggleGroup"/>
     <RadioButton fx:id="exportInSpecifiedOrder"
-                 text="%Export entries ordered as specified" toggleGroup="$saveOrderToggleGroup"/>
+                 text="%Use specified order" toggleGroup="$saveOrderToggleGroup"/>
 
     <GridPane hgap="10.0" vgap="4.0">
         <columnConstraints>

diff --git a/src/main/java/org/jabref/gui/commonfxcontrols/SaveOrderConfigPanel.java b/src/main/java/org/jabref/gui/commonfxcontrols/SaveOrderConfigPanel.java
@@ -11,7 +11,6 @@
 
 import org.jabref.gui.util.FieldsUtil;
 import org.jabref.gui.util.ViewModelListCellFactory;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.field.Field;
 
 import com.airhacks.afterburner.views.ViewLoader;
@@ -70,12 +69,6 @@ private void initialize() {
         saveTerDesc.selectedProperty().bindBidirectional(viewModel.saveTertiaryDescPropertySelected());
     }
 
-    public void changeExportDescriptionToSave() {
-        exportInOriginalOrder.setText(Localization.lang("Save entries in their original order"));
-        exportInSpecifiedOrder.setText(Localization.lang("Save entries ordered as specified"));
-        exportInTableOrder.setText(Localization.lang("Save in current table sort order"));
-    }
-
     public BooleanProperty saveInOriginalProperty() {
         return viewModel.saveInOriginalProperty();
     }

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -10,6 +10,7 @@
 import java.util.Optional;
 import java.util.regex.Pattern;
 
+import org.jabref.gui.DialogService;
 import org.jabref.gui.Globals;
 import org.jabref.gui.JabRefGUI;
 import org.jabref.gui.desktop.os.DefaultDesktop;
@@ -19,6 +20,7 @@
 import org.jabref.gui.desktop.os.Windows;
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.logic.importer.util.IdentifierParser;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
 import org.jabref.model.database.BibDatabaseContext;
@@ -27,6 +29,7 @@
 import org.jabref.model.entry.identifier.DOI;
 import org.jabref.model.entry.identifier.Eprint;
 import org.jabref.model.util.FileHelper;
+import org.jabref.preferences.PreferencesService;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -107,6 +110,19 @@ private static void openDoi(String doi) throws IOException {
         openBrowser(link);
     }
 
+    public static void openCustomDoi(String link, PreferencesService preferences, DialogService dialogService) {
+        IdentifierParser.parse(StandardField.DOI, link)
+                        .map(identifier -> (DOI) identifier)
+                        .flatMap(doi -> doi.getExternalURIWithCustomBase(preferences.getDOIPreferences().getDefaultBaseURI()))
+                        .ifPresent(uri -> {
+                            try {
+                                JabRefDesktop.openBrowser(uri);
+                            } catch (IOException e) {
+                                dialogService.showErrorDialogAndWait(Localization.lang("Unable to open link."), e);
+                            }
+                        });
+    }
+
     /**
      * Open an external file, attempting to use the correct viewer for it.
      *
@@ -203,9 +219,8 @@ public static void openBrowser(URI url) throws IOException {
     }
 
     /**
-     * Opens the url with the users standard Browser.
-     * If that fails a popup will be shown to instruct the user to open the link manually
-     * and the link gets copied to the clipboard
+     * Opens the url with the users standard Browser. If that fails a popup will be shown to instruct the user to open the link manually and the link gets copied to the clipboard
+     *
      * @param url the URL to open
      */
     public static void openBrowserShowPopup(String url) {

diff --git a/src/main/java/org/jabref/gui/fieldeditors/IdentifierEditorViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/IdentifierEditorViewModel.java
@@ -36,7 +36,7 @@ public class IdentifierEditorViewModel extends AbstractEditorViewModel {
     private final TaskExecutor taskExecutor;
     private final DialogService dialogService;
     private final Field field;
-    private PreferencesService preferences;
+    private final PreferencesService preferences;
 
     public IdentifierEditorViewModel(Field field, SuggestionProvider<?> suggestionProvider, TaskExecutor taskExecutor, DialogService dialogService, FieldCheckers fieldCheckers, PreferencesService preferences) {
         super(field, suggestionProvider, fieldCheckers);
@@ -75,8 +75,8 @@ public BooleanProperty validIdentifierIsNotPresentProperty() {
 
     public void openExternalLink() {
         if (field.equals(StandardField.DOI) && preferences.getDOIPreferences().isUseCustom()) {
-            String baseURI = preferences.getDOIPreferences().getDefaultBaseURI();
-            openDOIWithCustomBase(baseURI);
+            identifier.get().map(identifier -> (DOI) identifier).map(DOI::getDOI)
+                      .ifPresent(s -> JabRefDesktop.openCustomDoi(s, preferences, dialogService));
         } else {
             openExternalLinkDefault();
         }
@@ -94,18 +94,6 @@ public void openExternalLinkDefault() {
         );
     }
 
-    public void openDOIWithCustomBase(String baseURI) {
-        identifier.get().map(identifier -> (DOI) identifier).flatMap(doi -> doi.getExternalURIWithCustomBase(baseURI)).ifPresent(
-                uri -> {
-                    try {
-                        JabRefDesktop.openBrowser(uri);
-                    } catch (IOException ex) {
-                        dialogService.showErrorDialogAndWait(Localization.lang("Unable to open link."), ex);
-                    }
-                }
-        );
-    }
-
     public boolean getIdentifierLookupInProgress() {
         return identifierLookupInProgress.get();
     }

diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -80,7 +80,7 @@
                 <CheckBox fx:id="protect"
                           text="%Refuse to save the library before external changes have been reviewed."/>
 
-                <Label styleClass="sectionHeader" text="%Export sort order"/>
+                <Label styleClass="sectionHeader" text="%Save sort order"/>
                 <SaveOrderConfigPanel fx:id="saveOrderConfigPanel"/>
 
                 <Label styleClass="sectionHeader" text="%Save actions"/>

diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -79,7 +79,6 @@ private void initialize() {
         protect.disableProperty().bind(viewModel.protectDisableProperty());
         protect.selectedProperty().bindBidirectional(viewModel.libraryProtectedProperty());
 
-        saveOrderConfigPanel.changeExportDescriptionToSave();
         saveOrderConfigPanel.saveInOriginalProperty().bindBidirectional(viewModel.saveInOriginalProperty());
         saveOrderConfigPanel.saveInTableOrderProperty().bindBidirectional(viewModel.saveInTableOrderProperty());
         saveOrderConfigPanel.saveInSpecifiedOrderProperty().bindBidirectional(viewModel.saveInSpecifiedOrderProperty());