Add LWTA abbreviation support #12109

Thomas-Bridgart · 2024-10-27T08:24:09Z

(This is a slight remake of another pull request which I made from main by accident)
See issue koppor#215:

Currently I've written the code to read the .csv file containing all lwta abbreviations, and to abbreviate a journal name. I note the following problems with what I've written:

-- it doesn't work properly on some edge cases of lwta abbreviations (occasionally, the standard requires context clues -- e.g. distinguishing between 'real' (english) and 'real' (spanish), or how '&' should be removed if it means 'and', but not in abbreviations)

-- lwta abbreviations require the elimination of articles and prepositions (in most cases), which here I've only implemented by writing a (currently very in-exhaustive) list of such.

-- I'm a little unsure of the class structure I've written for the implementation

Furthermore, it will not quite be possible to write a fully correct unabbreviate method, as the abbreviation is not quite injective.

If the above problems are deal-breakers, then I won't bother continuing to write the frontend / mvstore code (hence why this incomplete pr exists).

Mandatory checks

I own the copyright of the code submitted and I licence it under the MIT license
Change in CHANGELOG.md described in a way that is understandable for the average user (if change is visible to the user)
Tests created for changes (if applicable)
Manually tested changed features in running JabRef (always required)
Screenshots added in PR description (for UI changes)
Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.

…arse file

…ed (e.g. turn international into int. instead of int.al)

… file paths)

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koppor · 2024-10-29T23:44:44Z

src/main/resources/ltwa_abb.csv is somewhere downloaded the net - koppor#215 (comment)

We MUST NOT include this file in the source code tree.

We need a gradle action downloading the file to build\resources\mainltwa_abb.csv. I think, hook into generateSources or smilar task.

koppor · 2024-10-29T23:46:12Z

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

@@ -22,6 +22,8 @@ public class AbbreviationParser {
    // Ensures ordering while preventing duplicates
    private final LinkedHashSet<Abbreviation> abbreviations = new LinkedHashSet<>();

+    private final LinkedHashSet<LwtaAbbreviation> lwtaAbbreviations = new LinkedHashSet<>();


Subclass the AbbreviationParser, because LWTA is a separate functionality (too little coupoling with other methods). someone will say that there should be composition over inheritance - not sure which method you really need of this class.

koppor · 2024-10-29T23:46:40Z

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

+                String name = csvRecord.size() > 0 ? csvRecord.get(0) : "";
+                String abbreviation = csvRecord.size() > 1 ? csvRecord.get(1) : "";
+
+                // Check name and abbreviation


Remove comment - this is clear from the statement.

koppor · 2024-10-29T23:48:05Z

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

+        if (string.endsWith("-")) {
+            string = string.substring(0, string.length() - 1);
+        }


Just use

string = org.jabref.model.strings.StringUtil.removeStringAtTheEnd(string, "-");

(replace by normal import - i just want tos show you the package)

koppor · 2024-10-29T23:49:29Z

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

+    private final boolean allowsPrefix;
+
+    enum Position {
+        ENDS_WORD, STARTS_WORD, IN_WORD, FULL_WORD


Sort more logically: full, starts, in, end

koppor · 2024-10-29T23:49:45Z

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

@@ -0,0 +1,41 @@
+package org.jabref.logic.journals;
+
+public class LwtaAbbreviation {


Refactor to record

koppor · 2024-10-29T23:51:24Z

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

+
+    private final Map<String, LwtaAbbreviation> lwtaToAbbreviationObject;
+
+    // incomplete list


What is that for an "incomplete" list. What should one do to add words? Either state that or remove the comment.

koppor · 2024-10-29T23:51:45Z

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

+    /**
+     * instantiates this class with a csv file
+     */


Remove comment - or replace it by an explenation of the @param file parameter

koppor · 2024-10-29T23:52:18Z

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

+
+public class LwtaAbbreviationRepository {
+
+    private final Map<String, LwtaAbbreviation> lwtaToAbbreviationObject;


Remove Object at the end. Nearly everything is an object in Java.

koppor · 2024-10-29T23:53:23Z

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

+    static final String[] JOURNAL_NAMES = new String[]{"international journal", "Journal of Medicine", "journal of medicine", "journal", "Physics & geobiology"};
+    static final String[] ABBREVIATED_NAMES = new String[]{"int. j.", "J. Medicine", "j. medicine", "journal", "Phys. geobiol."};
+
+    @Test
+    void abbreviateJournalNameTest() throws IOException {
+        Path path1 = Paths.get("src", "main", "resources", "ltwa_abb.csv");
+        LwtaAbbreviationRepository lwtaAbbreviationRepository = new LwtaAbbreviationRepository(path1);
+            for (int i = 0; i < JOURNAL_NAMES.length; i++) {
+                assertEquals(lwtaAbbreviationRepository.abbreviateJournalName(JOURNAL_NAMES[i]), ABBREVIATED_NAMES[i]);
+            }
+    }
+}


Convert to @ParameterizedTest.

Thomas-Bridgart added 8 commits October 27, 2024 12:57

Add lwta abbreviations and a method to abbreviate a journal name

40ae128

Add a csv file of lwta journal name abbreviations and add method to p…

1246973

…arse file

Add testing for lwta abbreviation method

463d8f4

fix lwta abbreviations to only allow suffixes/prefixes unless specifi…

d412e9b

…ed (e.g. turn international into int. instead of int.al)

warning clean up/comments for lwta abbreviation code

fbb5b6b

rewriteRun on ltwa abbreviation classes

809aa4d

Fix abbreviateJournalNameTest (use Path object to avoid using windows…

4aa2fa7

… file paths)

Merge branch 'JabRef:main' into lwta_abbreviation

42132bb

Thomas-Bridgart changed the title ~~Add Lwta abbreviation support~~ Add LWTA abbreviation support Oct 27, 2024

Thomas-Bridgart mentioned this pull request Oct 27, 2024

LWTA abbreviation support #12107

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Thomas-Bridgart marked this pull request as draft October 27, 2024 08:26

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Merge branch 'main' into lwta_abbreviation

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koppor requested changes Oct 29, 2024

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Add LWTA abbreviation support #12109

Add LWTA abbreviation support #12109

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koppor commented Oct 29, 2024

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koppor Oct 29, 2024

		@@ -0,0 +1,41 @@
		package org.jabref.logic.journals;

		public class LwtaAbbreviation {


		private final Map<String, LwtaAbbreviation> lwtaToAbbreviationObject;

		// incomplete list


		public class LwtaAbbreviationRepository {

		private final Map<String, LwtaAbbreviation> lwtaToAbbreviationObject;

Add LWTA abbreviation support #12109

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Thomas-Bridgart commented Oct 27, 2024

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