Fix journal abbbrev checker for curly braces (#9504)

* Fix journal abbbrev checker for curly braces Escape any curly braces Also use latex free fields Fixes #9475 Fixes #9503 * refactor abbreviation checker to latex free entry checker * adjust test cases * checkstyle * checkstyle * Streamline tests and add tests for 9475 and 9503 Co-authored-by: Christoph <siedlerkiller@gmail.com> Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com> * Rename Medline to Dotless and add translations for the menu actions * On our way Co-authored-by: Christoph <siedlerkiller@gmail.com> * Add misisng test Co-authored-by: Christoph <siedlerkiller@gmail.com> * Try to use full MVMap in groovy script * Fix path * Streamline action * Try to commit changes * Revert "Streamline action" This reverts commit 626e41a. * Try to fix action * Debug: show branch * Stay on current branch * Fix action * Remove bad files * Serizalizabe version 1 * Fix duplicate handling * Add trigger on braches * fix * Fix wrong comment * Some debug maybe? * debug * Add warning * Try to use a single MV store only * Fix import * CamleCase to dash-case * Fix brace * Update journal abbrev list * Remove debug output * Internalize loading * Disable workflow * Update CHANGELOG.md * Remove initialization hack * Update journal abbrev list * No need to fetch * Use right WoS file * Update journal abbrev list * fix l10n and reorder Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com> Co-authored-by: koppor <koppor@users.noreply.github.com>
JabRef · Jan 2, 2023 · 88c9f56 · 88c9f56
1 parent f626c72
commit 88c9f56
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Showing 25 changed files with 346 additions and 287 deletions.
diff --git a/.github/workflows/refresh-journal-lists.yml b/.github/workflows/refresh-journal-lists.yml
@@ -1,8 +1,8 @@
 name: Refresh Journal Lists
 
 on:
+  # Allow to run manually
   workflow_dispatch:
-    # Allow to run manually
 
 permissions:
   contents: read
@@ -15,12 +15,9 @@ jobs:
     name: Refresh Journal List Files
     runs-on: ubuntu-latest
     steps:
-      - name: Fetch all history for all tags and branches
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v3
         with:
-          ref: main
-          persist-credentials: false
-          fetch-depth: 0
+          persist-credentials: true
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
@@ -37,10 +34,10 @@ jobs:
           cd abbrv.jabref.org/journals
 
           # remove all lists without dot in them
-          # we use abbrevatiation lists containing dots in them only (to be consistent)
+          # we use abbreviation lists containing dots in them only (to be consistent)
           rm journal_abbreviations_entrez.csv
           rm journal_abbreviations_medicus.csv
-          rm journal_abbreviations_webofscience-dots.csv
+          rm journal_abbreviations_webofscience-dotless.csv
 
           # we currently do not have good support for BibTeX strings
           rm journal_abbreviations_ieee_strings.csv
@@ -50,14 +47,24 @@ jobs:
           cp * $GITHUB_WORKSPACE/build/journals/
 
           # ensure that the .java classes are the most recent ones
+          mkdir -p $GITHUB_WORKSPACE/buildSrc/src/copied/java/org/jabref/logic/journals
           cp $GITHUB_WORKSPACE/src/main/java/org/jabref/logic/journals/* $GITHUB_WORKSPACE/buildSrc/src/copied/java/org/jabref/logic/journals
 
           # create .mv file
           cd $GITHUB_WORKSPACE
           ./gradlew generateJournalAbbreviationList
       - uses: peter-evans/create-pull-request@v4
+        if: github.ref == 'refs/heads/main'
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           branch: update-journallist
           title: "[Bot] Update Journal abbrev list"
           commit-message: Update journal abbrev list
+      - name: Commit and push changes
+        uses: EndBug/add-and-commit@v9
+        if: github.ref != 'refs/heads/main'
+        with:
+          message: 'Update journal abbrev list'
+          committer_email: actions@github.com
+          fetch: false
+          push: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We changed database structure: in MySQL/MariaDB we renamed tables by adding a `JABREF_` prefix, and in PGSQL we moved tables in `jabref` schema. We added `VersionDBStructure` variable in `METADATA` table to indicate current version of structure, this variable is needed for automatic migration. [#9312](https://github.com/JabRef/jabref/issues/9312)
 - We moved some preferences options to a new tab in the preferences dialog. [#9442](https://github.com/JabRef/jabref/pull/9308)
+- We renamed "Medline abbrevation" to "dotless abbreviation". [#9504](https://github.com/JabRef/jabref/pull/9504)
+- We now have more "dots" in the offered journal abbrevations. [#9504](https://github.com/JabRef/jabref/pull/9504)
 
 
 
@@ -32,6 +34,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - In case a journal name of an IEEE journal is abbreviated, the "normal" abbreviation is used - and not the one of the IEEE BibTeX strings. [abbrv#91](https://github.com/JabRef/abbrv.jabref.org/issues/91)
 - We fixed an issue where the last opened libraries were not remembered when a new unsaved libray was open as well. [#9190](https://github.com/JabRef/jabref/issues/9190)
 - We fixed an issue where no context menu for the group "All entries" was present. [forum#3682](https://discourse.jabref.org/t/how-sort-groups-a-z-not-subgroups/3682)
+- We fixed an issue where extra curly braces in some fields would trigger an exception when selecting the entry or doing an integrity check [#9475](https://github.com/JabRef/jabref/issues/9475), [#9503](https://github.com/JabRef/jabref/issues/9503)
 - 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)
 
 ### Removed

diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/Abbreviation.java b/buildSrc/src/copied/java/org/jabref/logic/journals/Abbreviation.java
@@ -1,21 +1,34 @@
 package org.jabref.logic.journals;
 
+import java.io.Serializable;
 import java.util.Objects;
 
-public class Abbreviation implements Comparable<Abbreviation> {
+public class Abbreviation implements Comparable<Abbreviation>, Serializable {
 
-    private final String name;
+    private static final long serialVersionUID = 1;
+
+    private transient String name;
     private final String abbreviation;
+    private transient String dotlessAbbreviation;
     private final String shortestUniqueAbbreviation;
 
     public Abbreviation(String name, String abbreviation) {
         this(name, abbreviation, "");
     }
 
     public Abbreviation(String name, String abbreviation, String shortestUniqueAbbreviation) {
-        this.name = name;
-        this.abbreviation = abbreviation;
-        this.shortestUniqueAbbreviation = shortestUniqueAbbreviation.trim();
+        this(name,
+                abbreviation,
+                // "L. N." becomes "L  N ", we need to remove the double spaces inbetween
+                abbreviation.replace(".", " ").replace("  ", " ").trim(),
+                shortestUniqueAbbreviation.trim());
+    }
+
+    public Abbreviation(String name, String abbreviation, String dotlessAbbreviation, String shortestUniqueAbbreviation) {
+        this.name = name.intern();
+        this.abbreviation = abbreviation.intern();
+        this.dotlessAbbreviation = dotlessAbbreviation.intern();
+        this.shortestUniqueAbbreviation = shortestUniqueAbbreviation.trim().intern();
     }
 
     public String getName() {
@@ -34,8 +47,8 @@ public String getShortestUniqueAbbreviation() {
         return result;
     }
 
-    public String getMedlineAbbreviation() {
-        return getAbbreviation().replace(".", " ").replace("  ", " ").trim();
+    public String getDotlessAbbreviation() {
+        return this.dotlessAbbreviation;
     }
 
     @Override
@@ -46,23 +59,23 @@ public int compareTo(Abbreviation toCompare) {
     public String getNext(String current) {
         String currentTrimmed = current.trim();
 
-        if (getMedlineAbbreviation().equals(currentTrimmed)) {
+        if (getDotlessAbbreviation().equals(currentTrimmed)) {
             return getShortestUniqueAbbreviation().equals(getAbbreviation()) ? getName() : getShortestUniqueAbbreviation();
         } else if (getShortestUniqueAbbreviation().equals(currentTrimmed) && !getShortestUniqueAbbreviation().equals(getAbbreviation())) {
             return getName();
         } else if (getName().equals(currentTrimmed)) {
             return getAbbreviation();
         } else {
-            return getMedlineAbbreviation();
+            return getDotlessAbbreviation();
         }
     }
 
     @Override
     public String toString() {
-        return String.format("Abbreviation{name=%s, abbreviation=%s, medlineAbbreviation=%s, shortestUniqueAbbreviation=%s}",
+        return String.format("Abbreviation{name=%s, abbreviation=%s, dotlessAbbreviation=%s, shortestUniqueAbbreviation=%s}",
                 this.name,
                 this.abbreviation,
-                this.getMedlineAbbreviation(),
+                this.dotlessAbbreviation,
                 this.shortestUniqueAbbreviation);
     }
 

diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationLoader.java b/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationLoader.java
@@ -10,6 +10,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+/**
+ * <p>
+ *   This class loads abbreviations from a CSV file and stores them into a MV file
+ * </p>
+ * <p>
+ *   Abbreviations are available at <a href="https://github.com/JabRef/abbrv.jabref.org/">https://github.com/JabRef/abbrv.jabref.org/</a>.
+ * </p>
+ */
 public class JournalAbbreviationLoader {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(JournalAbbreviationLoader.class);
@@ -26,8 +34,8 @@ public static JournalAbbreviationRepository loadRepository(JournalAbbreviationPr
         // Initialize with built-in list
         try {
             Path tempDir = Files.createTempDirectory("jabref-journal");
-            Path tempJournalList = tempDir.resolve("journalList.mv");
-            Files.copy(JournalAbbreviationRepository.class.getResourceAsStream("/journals/journalList.mv"), tempJournalList);
+            Path tempJournalList = tempDir.resolve("journal-list.mv");
+            Files.copy(JournalAbbreviationRepository.class.getResourceAsStream("/journals/journal-list.mv"), tempJournalList);
             repository = new JournalAbbreviationRepository(tempJournalList);
             tempDir.toFile().deleteOnExit();
             tempJournalList.toFile().deleteOnExit();
@@ -39,12 +47,13 @@ public static JournalAbbreviationRepository loadRepository(JournalAbbreviationPr
         // Read external lists
         List<String> lists = journalAbbreviationPreferences.getExternalJournalLists();
         if (!(lists.isEmpty())) {
+            // reversing ensures that the latest lists overwrites the former one
             Collections.reverse(lists);
             for (String filename : lists) {
                 try {
                     repository.addCustomAbbreviations(readJournalListFromFile(Path.of(filename)));
                 } catch (IOException e) {
-                    LOGGER.error(String.format("Cannot read external journal list file %s", filename), e);
+                    LOGGER.error("Cannot read external journal list file {}", filename, e);
                 }
             }
         }