Importing of BibDesk Groups and Linked Files (#10968)

* Add test to check parsing of BibDesk Static Groups

* Add test to check parsing of BibDesk Static Groups

* Change isExpanded attribute to false in expected groups

* remove extra blank line

* Add tests to check parsing of BibDesk Smart and mixed groups

* Add parsing of BibDesk Files

* Attempts at plist

* Now parses bdsk-file and shows it as a file in JabRef

* Add test for parsing a bdsk-file field

* Fix formatting

* Add dd-plist library to documentation

---------

Co-authored-by: Tian0602 <[email protected]>

* Add creation of static JabRef group from a BibDesk file

* Creates an empty ExplicitGroup from BibDesk comment

* Adds citations to new groups
modifies group creations to support multiple groups in the same BibDeskFile

* Fix requested changes
Refactor imports since they did not match with main
Add safety check in addBibDeskGroupEntriesToJabRefGroups

---------

Co-authored-by: Filippa Nilsson <[email protected]>

* Refactor newline to match main branch

Co-authored-by: Filippa Nilsson <[email protected]>

* Add changes to CHANGELOG.md

* Reformat indentation to match previous

* Revert external libraries

Adjust groups serializing

* checkstyle and optional magic

* fix

* fix tests

* fix

* fix dangling do

* better group tree metadata setting

* merge group trees, prevent duplicate group assignment in entry
Add new BibDesk group

Fix IOB for change listeing

* fix tests, and extract constant

* return early

* fixtest and checkstyle

---------

Co-authored-by: Anna Maartensson <[email protected]>
Co-authored-by: Tian0602 <[email protected]>
Co-authored-by: LottaJohnsson <[email protected]>
Co-authored-by: Filippa Nilsson <[email protected]>
Co-authored-by: Filippa Nilsson <[email protected]>
Co-authored-by: Oliver Kopp <[email protected]>
Co-authored-by: Siedlerchr <[email protected]>

Author: 8 people

CHANGELOG.md

@@ -24,6 +24,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - When pasting HTML into the abstract or a comment field, the hypertext is automatically converted to Markdown. [#10558](https://github.com/JabRef/jabref/issues/10558)
 - We added the possibility to redownload files that had been present but are no longer in the specified location. [#10848](https://github.com/JabRef/jabref/issues/10848)
 - We added the citation key pattern `[camelN]`. Equivalent to the first N words of the `[camel]` pattern.
+- We added importing of static groups and linked files from BibDesk .bib files. [#10381](https://github.com/JabRef/jabref/issues/10381)
 - We added ability to export in CFF (Citation File Format) [#10661](https://github.com/JabRef/jabref/issues/10661).
 - We added ability to push entries to TeXworks. [#3197](https://github.com/JabRef/jabref/issues/3197)
 - We added the ability to zoom in and out in the document viewer using <kbd>Ctrl</kbd> + <kbd>Scroll</kbd>. [#10964](https://github.com/JabRef/jabref/pull/10964)

build.gradle

@@ -242,6 +242,9 @@ dependencies {
     // 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'
 
+    // parse plist files
+    implementation 'com.googlecode.plist:dd-plist:1.23'
+
     testImplementation 'io.github.classgraph:classgraph:4.8.168'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'

licenses/com.googlecode.plist_ddplist.txt

@@ -0,0 +1,20 @@
+dd-plist - An open source library to parse and generate property lists
+Copyright (C) 2016 Daniel Dreibrodt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

src/main/java/module-info.java

@@ -144,4 +144,5 @@
     requires org.libreoffice.uno;
     requires de.saxsys.mvvmfx.validation;
     requires com.jthemedetector;
+    requires dd.plist;
 }

src/main/java/org/jabref/logic/bibtex/comparator/BibDatabaseDiff.java

@@ -49,6 +49,11 @@ private static EntryComparator getEntryComparator() {
     private static List<BibEntryDiff> compareEntries(List<BibEntry> originalEntries, List<BibEntry> newEntries, BibDatabaseMode mode) {
         List<BibEntryDiff> differences = new ArrayList<>();
 
+        // Prevent IndexOutOfBoundException
+        if (newEntries.isEmpty()) {
+            return differences;
+        }
+
         // Create a HashSet where we can put references to entries in the new
         // database that we have matched. This is to avoid matching them twice.
         Set<Integer> used = new HashSet<>(newEntries.size());
@@ -88,7 +93,6 @@ private static List<BibEntryDiff> compareEntries(List<BibEntry> originalEntries,
                     }
                 }
             }
-
             BibEntry bestEntry = newEntries.get(bestMatchIndex);
             if (bestMatch > MATCH_THRESHOLD
                     || hasEqualCitationKey(originalEntry, bestEntry)

src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java

@@ -18,6 +18,11 @@ public class MetadataSerializationConfiguration {
      */
     public static final char GROUP_QUOTE_CHAR = '\\';
 
+    /**
+     * Group Type suffix (part of the GroupType)
+     */
+    public static final String GROUP_TYPE_SUFFIX = ":";
+
     /**
      * For separating units (e.g. name and hierarchic context) in the string representation
      */

src/main/java/org/jabref/logic/util/MetadataSerializationConfiguration.java

@@ -23,6 +23,12 @@ public boolean equals(Object o) {
         return o instanceof AllEntriesGroup aeg && Objects.equals(aeg.getName(), getName());
     }
 
+    /**
+     * Always returns true for any BibEntry!
+     *
+     * @param entry The @{@link BibEntry} to check
+     * @return Always returns true
+     */
     @Override
     public boolean contains(BibEntry entry) {
         return true;

src/main/java/org/jabref/model/groups/AllEntriesGroup.java

@@ -135,6 +135,13 @@ public int hashCode() {
         return Objects.hash(group);
     }
 
+    /**
+     * Get only groups containing all the entries or just groups containing any of the
+     *
+     * @param entries    List of {@link BibEntry} to search for
+     * @param requireAll Whether to return only groups that must contain all entries
+     * @return List of {@link GroupTreeNode} containing the matches. {@link AllEntriesGroup} is always contained}
+     */
     public List<GroupTreeNode> getContainingGroups(List<BibEntry> entries, boolean requireAll) {
         List<GroupTreeNode> groups = new ArrayList<>();
 
@@ -197,6 +204,11 @@ public List<BibEntry> getEntriesInGroup(List<BibEntry> entries) {
         return result;
     }
 
+    /**
+     * Get the name of the underlying group
+     *
+     * @return String the name of the group
+     */
     public String getName() {
         return group.getName();
     }

src/main/java/org/jabref/model/groups/GroupTreeNode.java

@@ -48,6 +48,7 @@ public class MetaData {
     public static final String FILE_DIRECTORY_LATEX = "fileDirectoryLatex";
     public static final String PROTECTED_FLAG_META = "protectedFlag";
     public static final String SELECTOR_META_PREFIX = "selector_";
+    public static final String BIBDESK_STATIC_FLAG = "BibDesk Static Groups";
 
     public static final char ESCAPE_CHARACTER = '\\';
     public static final char SEPARATOR_CHARACTER = ';';