Fixing journal abbreviation roundtrip (#9453)

* checking for dot-less/medline abbreviations

* fixed regex

* fixed indentation

* Move code for checking dot-less abbreviations into separate method

* Add checks for dot-less abbreviations

* Add test case for dot-less abbreviations

* Update CHANGELOG.md

* Add new static class variable for Pattern

* Add checks for "?" journal names

* Add check requiring abbreviation be more than 2 words

CHANGELOG.md

@@ -95,6 +95,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where font size preferences did not apply correctly to preference dialog window and the menu bar. [#8386](https://github.com/JabRef/jabref/issues/8386) and [#9279](https://github.com/JabRef/jabref/issues/9279)
 - We fixed an issue that JabRef displayed the wrong group tree after loading. [koppor#637](https://github.com/koppor/jabref/issues/637)
 - We fixed an issue when using an unsafe character in the citation key, the auto-linking feature fails to link files. [#9267](https://github.com/JabRef/jabref/issues/9267)
+- We fixed an issue where a known journal's medline/dot-less abbreviation does not switch to the full name. [#9370](https://github.com/JabRef/jabref/issues/9370)
 
 ### Removed
 

src/main/java/org/jabref/logic/journals/JournalAbbreviationRepository.java

@@ -8,6 +8,7 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
 import org.h2.mvstore.MVMap;
@@ -17,6 +18,8 @@
  * A repository for all journal abbreviations, including add and find methods.
  */
 public class JournalAbbreviationRepository {
+    static final Pattern DOT = Pattern.compile("\\.");
+    static final Pattern QUESTION_MARK = Pattern.compile("\\?");
 
     private final MVMap<String, String> fullToAbbreviation;
     private final MVMap<String, String> abbreviationToFull;
@@ -49,14 +52,20 @@ private static boolean isMatchedAbbreviated(String name, Abbreviation abbreviati
      * Letters) or its abbreviated form (e.g. Phys. Rev. Lett.).
      */
     public boolean isKnownName(String journalName) {
+        // check for at least one "?"
+        if (QUESTION_MARK.matcher(journalName).find()) {
+            return false;
+        }
+
         String journal = journalName.trim().replaceAll(Matcher.quoteReplacement("\\&"), "&");
 
         boolean isKnown = customAbbreviations.stream().anyMatch(abbreviation -> isMatched(journal, abbreviation));
         if (isKnown) {
             return true;
         }
 
-        return fullToAbbreviation.containsKey(journal) || abbreviationToFull.containsKey(journal);
+        return fullToAbbreviation.containsKey(journal) || abbreviationToFull.containsKey(journal)
+                || findDottedAbbrFromDotless(journal).length() > 0;
     }
 
     /**
@@ -66,8 +75,40 @@ public boolean isKnownName(String journalName) {
     public boolean isAbbreviatedName(String journalName) {
         String journal = journalName.trim();
 
+        // journal abbreviation must be at least 2 words
+        boolean isMoreThanTwoWords = journalName.split(" ").length >= 2;
+
         return customAbbreviations.stream().anyMatch(abbreviation -> isMatchedAbbreviated(journal, abbreviation))
-                || abbreviationToFull.containsKey(journal);
+                || abbreviationToFull.containsKey(journal)
+                || (isMoreThanTwoWords && findDottedAbbrFromDotless(journal).length() > 0);
+    }
+
+    public String findDottedAbbrFromDotless(String journalName) {
+        // check for at least one "?"
+        if (QUESTION_MARK.matcher(journalName).find()) {
+            return "UNKNOWN";
+        }
+
+        String foundKey = "";
+
+        // check for a dot-less abbreviation
+        if (!DOT.matcher(journalName).find()) {
+            // use dot-less abbr to find full name using regex
+            String[] journalSplit = journalName.split(" ");
+
+            for (int i = 0; i < journalSplit.length; i++) {
+                String word = journalSplit[i] + "[\\.\\s]*";
+                journalSplit[i] = word;
+            }
+
+            String joined = String.join("", journalSplit);
+
+            foundKey = abbreviationToFull.keySet().stream()
+                                         .filter(s -> Pattern.compile(joined).matcher(s).find())
+                                         .collect(Collectors.joining());
+        }
+
+        return foundKey;
     }
 
     /**
@@ -87,7 +128,17 @@ public Optional<Abbreviation> get(String input) {
 
         return Optional.ofNullable(fullToAbbreviation.get(journal))
                        .map(abbreviation -> new Abbreviation(journal, abbreviation))
-                       .or(() -> Optional.ofNullable(abbreviationToFull.get(journal)).map(fullName -> new Abbreviation(fullName, journal)));
+                       .or(() -> {
+                           String abbr = "";
+
+                           // check for dot-less abbr
+                           if (isKnownName(journal) && isAbbreviatedName(journal)) {
+                               abbr = findDottedAbbrFromDotless(journal);
+                           }
+
+                           return Optional.ofNullable(abbreviationToFull.get(abbr.equals("") ? journal : abbr))
+                                          .map(fullName -> new Abbreviation(fullName, journal));
+                       });
     }
 
     public void addCustomAbbreviation(Abbreviation abbreviation) {

src/test/java/org/jabref/logic/journals/JournalAbbreviationRepositoryTest.java

@@ -252,4 +252,19 @@ void testUnabbreviateWithJournalExistsAndFJournalExists() {
                 .withField(StandardField.JOURNAL, "ACS Applied Materials & Interfaces");
         assertEquals(expectedAbbreviatedJournalEntry, abbreviatedJournalEntry);
     }
+
+    @Test
+    void testJournalDotlessAbbreviation() {
+        BibDatabase bibDatabase = new BibDatabase();
+        JournalAbbreviationRepository journalAbbreviationRepository = JournalAbbreviationLoader.loadBuiltInRepository();
+        UndoableUnabbreviator undoableUnabbreviator = new UndoableUnabbreviator(journalAbbreviationRepository);
+
+        BibEntry abbreviatedJournalEntry = new BibEntry(StandardEntryType.Article);
+        abbreviatedJournalEntry.setField(StandardField.JOURNAL, "ACS Appl Mater Interfaces");
+
+        undoableUnabbreviator.unabbreviate(bibDatabase, abbreviatedJournalEntry, StandardField.JOURNAL, new CompoundEdit());
+        BibEntry expectedAbbreviatedJournalEntry = new BibEntry(StandardEntryType.Article)
+                .withField(StandardField.JOURNAL, "ACS Applied Materials & Interfaces");
+        assertEquals(expectedAbbreviatedJournalEntry, abbreviatedJournalEntry);
+    }
 }