Merge remote-tracking branch 'upstream/master' into winBuild

* upstream/master: Jstor Fetcher (#6992) Group: "Searching for keywords" searches for a single keyword ==> use singular (#6995) Merge parsing of bracketed patterns (#6989) 6848 fixed the issue of clicking collapse all expanding tree (#6993) Enable auto sync per default for Open/Libre Office (#6985) Bump unirest-java from 3.11.00 to 3.11.01 (#7001) Bump byte-buddy-parent from 1.10.16 to 1.10.17 (#7004) Bump lucene-queryparser from 8.6.2 to 8.6.3 (#7002) Bump postgresql from 42.2.16 to 42.2.17 (#7005) Bump pascalgn/automerge-action from v0.11.0 to v0.12.0 (#7006) Bump flowless from 0.6.1 to 0.6.2 (#7003)
JabRef · Oct 14, 2020 · 99f4de9 · 99f4de9
2 parents 439924c + 170e900
commit 99f4de9
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diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -16,7 +16,7 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.11.0
+        uses: pascalgn/automerge-action@v0.12.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "squash"

diff --git a/AUTHORS b/AUTHORS
@@ -113,6 +113,7 @@ Eiswindyeti
 Ellen Reitmayr
 Erdem Derebasoglu
 Erdem Derebaşoğlu
+Eric Lau
 Erik Putrycz
 Ervin Kolenovic
 Escoul
@@ -179,6 +180,7 @@ Jens Döcke
 joeyzgraggen
 Johannes Hupe
 Johannes Manner
+Johannes Theiner
 John David
 John Relph
 John Zedlewski

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,9 +15,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a query parser and mapping layer to enable conversion of queries formulated in simplified lucene syntax by the user into api queries. [#6799](https://github.com/JabRef/jabref/pull/6799)
 - We added some basic functionality to customise the look of JabRef by importing a css theme file. [#5790](https://github.com/JabRef/jabref/issues/5790)
 - We added connection check function in network preference setting [#6560](https://github.com/JabRef/jabref/issues/6560)
+- We added a new fetcher to enable users to search jstor.org [#6627](https://github.com/JabRef/jabref/issues/6627)
 
 ### Changed
 
+- We changed the default preferences for OpenOffice/LibreOffice integration to automatically sync the bibliography when
+inserting new citations in a OpenOffic/LibreOffice document. [#6957](https://github.com/JabRef/jabref/issues/6957)
 - We restructured the 'File' tab and extracted some parts into the 'Linked files' tab [#6779](https://github.com/JabRef/jabref/pull/6779)
 - JabRef now offers journal lists from <https://abbrv.jabref.org>. JabRef the lists which use a dot inside the abbreviations. [#5749](https://github.com/JabRef/jabref/pull/5749)
 - We removed two useless preferences in the groups preferences dialog. [#6836](https://github.com/JabRef/jabref/pull/6836)
@@ -33,6 +36,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We improved the detection of "short" DOIs [6880](https://github.com/JabRef/jabref/issues/6880)
 - We improved the duplicate detection when identifiers like DOI or arxiv are semantiaclly the same, but just syntactically differ (e.g. with or without http(s):// prefix). [#6707](https://github.com/JabRef/jabref/issues/6707)
 - We changed in the group interface "Generate groups from keywords in a BibTeX field" by "Generate groups from keywords in the following field". [#6983](https://github.com/JabRef/jabref/issues/6983)
+- We changed the name of a group type from "Searching for keywords" to "Searching for a keyword". [6995](https://github.com/JabRef/jabref/pull/6995)
 
 ### Fixed
 
@@ -48,6 +52,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where it was impossible to connect to OpenOffice/LibreOffice on Mac OSX. [#6970](https://github.com/JabRef/jabref/pull/6970)
 - We fixed an issue with the python script used by browser plugins that failed to locate JabRef if not installed in its default location. [#6963](https://github.com/JabRef/jabref/pull/6963/files)
 - We fixed an issue where identity column header had incorrect foreground color in the  Dark theme. [#6796](https://github.com/JabRef/jabref/issues/6796)
+- We fixed an issue where clicking on Collapse All button in the Search for Unlinked Local Files expanded the directory structure erroneously [#6848](https://github.com/JabRef/jabref/issues/6848)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -137,13 +137,13 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.8-1'
     implementation 'org.antlr:antlr4-runtime:4.8-1'
 
-    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.6.2') {
+    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.6.3') {
         exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
     }
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.0'
 
-    implementation 'org.postgresql:postgresql:42.2.16'
+    implementation 'org.postgresql:postgresql:42.2.17'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -163,14 +163,14 @@ dependencies {
     implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.1.0'
-    implementation 'org.fxmisc.flowless:flowless:0.6.1'
+    implementation 'org.fxmisc.flowless:flowless:0.6.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.10.4'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.10'
     implementation 'org.controlsfx:controlsfx:11.0.2'
 
     implementation 'org.jsoup:jsoup:1.13.1'
-    implementation 'com.konghq:unirest-java:3.11.00'
+    implementation 'com.konghq:unirest-java:3.11.01'
 
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -204,7 +204,7 @@ dependencies {
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.0'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.16'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.17'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
     testImplementation 'org.mockito:mockito-core:3.5.13'

diff --git a/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java b/src/main/java/org/jabref/gui/externalfiles/FindUnlinkedFilesDialog.java
@@ -165,7 +165,7 @@ private void initialize() {
         buttonOptionCollapseAll.setOnAction(event -> {
             CheckBoxTreeItem<FileNodeWrapper> root = (CheckBoxTreeItem<FileNodeWrapper>) tree.getRoot();
             expandTree(root, false);
-            root.setExpanded(true);
+            root.setExpanded(false);
         });
 
         textfieldDirectoryPath = new TextField();

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.fxml b/src/main/java/org/jabref/gui/groups/GroupDialog.fxml
@@ -71,7 +71,7 @@
                         </tooltip>
                     </RadioButton>
                     <RadioButton fx:id="keywordsRadioButton" toggleGroup="$type" wrapText="true"
-                                 text="%Searching for keywords">
+                                 text="%Searching for a keyword">
                         <tooltip>
                             <Tooltip text="%Dynamically group entries by searching a field for a keyword"/>
                         </tooltip>

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java b/src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java
@@ -170,20 +170,20 @@ private void setupValidation() {
                     }
                 },
                 ValidationMessage.error(String.format("%s > %n %s %n %n %s",
-                        Localization.lang("Searching for keywords"),
+                        Localization.lang("Searching for a keyword"),
                         Localization.lang("Keywords"),
                         Localization.lang("Invalid regular expression."))));
 
         keywordFieldEmptyValidator = new FunctionBasedValidator<>(
                 keywordGroupSearchFieldProperty,
                 StringUtil::isNotBlank,
-                ValidationMessage.error(Localization.lang("Please enter a field name to search for keywords.")));
+                ValidationMessage.error(Localization.lang("Please enter a field name to search for a keyword.")));
 
         keywordSearchTermEmptyValidator = new FunctionBasedValidator<>(
                 keywordGroupSearchTermProperty,
                 input -> !StringUtil.isNullOrEmpty(input),
                 ValidationMessage.error(String.format("%s > %n %s %n %n %s",
-                        Localization.lang("Searching for keywords"),
+                        Localization.lang("Searching for a keyword"),
                         Localization.lang("Keywords"),
                         Localization.lang("Search term is empty.")
                 )));

diff --git a/src/main/java/org/jabref/logic/citationkeypattern/BracketedPattern.java b/src/main/java/org/jabref/logic/citationkeypattern/BracketedPattern.java
@@ -172,6 +172,43 @@ public String expand(BibEntry bibentry, Character keywordDelimiter, BibDatabase
     public static String expandBrackets(String pattern, Character keywordDelimiter, BibEntry entry, BibDatabase database) {
         Objects.requireNonNull(pattern);
         Objects.requireNonNull(entry);
+        return expandBrackets(pattern, expandBracketContent(keywordDelimiter, entry, database));
+    }
+
+    /**
+     * Utility method creating a function taking the string representation of the content of a bracketed expression and
+     * expanding it.
+     *
+     * @param keywordDelimiter The keyword delimiter to use
+     * @param entry            The {@link BibEntry} to use for expansion
+     * @param database         The {@link BibDatabase} for field resolving. May be null.
+     * @return a function accepting a bracketed expression and returning the result of expanding it
+     */
+    private static Function<String, String> expandBracketContent(Character keywordDelimiter, BibEntry entry, BibDatabase database) {
+        return (String bracket) -> {
+            String expandedPattern;
+            List<String> fieldParts = parseFieldAndModifiers(bracket);
+            // check whether there is a modifier on the end such as
+            // ":lower":
+            expandedPattern = getFieldValue(entry, fieldParts.get(0), keywordDelimiter, database);
+            if (fieldParts.size() > 1) {
+                // apply modifiers:
+                expandedPattern = applyModifiers(expandedPattern, fieldParts, 1);
+            }
+            return expandedPattern;
+        };
+    }
+
+    /**
+     * Expands a pattern.
+     *
+     * @param pattern               The pattern to expand
+     * @param bracketContentHandler A function taking the string representation of the content of a bracketed pattern
+     *                              and expanding it
+     * @return The expanded pattern. Not null.
+     */
+    public static String expandBrackets(String pattern, Function<String, String> bracketContentHandler) {
+        Objects.requireNonNull(pattern);
         StringBuilder expandedPattern = new StringBuilder();
         StringTokenizer parsedPattern = new StringTokenizer(pattern, "\\[]\"", true);
 
@@ -181,23 +218,14 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
                 case "\"" -> appendQuote(expandedPattern, parsedPattern);
                 case "[" -> {
                     String fieldMarker = contentBetweenBrackets(parsedPattern, pattern);
-
-                    List<String> fieldParts = parseFieldMarker(fieldMarker);
-                    // check whether there is a modifier on the end such as
-                    // ":lower":
-                    if (fieldParts.size() <= 1) {
-                        expandedPattern.append(getFieldValue(entry, fieldMarker, keywordDelimiter, database));
-                    } else {
-                        // apply modifiers:
-                        String fieldValue = getFieldValue(entry, fieldParts.get(0), keywordDelimiter, database);
-                        expandedPattern.append(applyModifiers(fieldValue, fieldParts, 1));
-                    }
+                    expandedPattern.append(bracketContentHandler.apply(fieldMarker));
                 }
                 case "\\" -> {
                     if (parsedPattern.hasMoreTokens()) {
                         expandedPattern.append(parsedPattern.nextToken());
+                    } else {
+                        LOGGER.warn("Found a \"\\\" that is not part of an escape sequence");
                     }
-                    // FIXME: else -> raise exception or log? (S.G.)
                 }
                 default -> expandedPattern.append(token);
             }
@@ -1069,7 +1097,7 @@ public static String lastPage(String pages) {
      * @param arg The argument string.
      * @return An array of strings representing the parts of the marker
      */
-    protected static List<String> parseFieldMarker(String arg) {
+    protected static List<String> parseFieldAndModifiers(String arg) {
         List<String> parts = new ArrayList<>();
         StringBuilder current = new StringBuilder();
         boolean escaped = false;