Refactor BibEntry deprecated method (JabRef#4554)

* Refactor BibEntry deprecated method * Fixed error * More on checkstyle fixing * Fixed checkstyle issues * Added custom entrytype for types not registered in the enumerator. * Added getTypeOrDefault method refactor code to use it and fix NPE problem * Fixing checkstyle rules * More on checkstyle * More on getType getTypeOrDefault replacement * Revert Article EntryType into Electronic * Added break line between different packages * Refactor BibtextEntryTypes.getTypeOrDefault method * Removed unused import * Removed extra new line, checkstyle error fixing
frasca80 · Dec 28, 2018 · 70b01a4 · 70b01a4
1 parent 78c901d
commit 70b01a4
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Showing 36 changed files with 120 additions and 89 deletions.
diff --git a/src/main/java/org/jabref/logic/importer/fileformat/BiblioscapeImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/BiblioscapeImporter.java
@@ -13,6 +13,7 @@
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 
 /**
@@ -255,7 +256,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                 if (!comments.isEmpty()) { // set comment if present
                     hm.put(FieldName.COMMENT, String.join(";", comments));
                 }
-                BibEntry b = new BibEntry(bibtexType);
+                BibEntry b = new BibEntry(BibtexEntryTypes.getTypeOrDefault(bibtexType));
                 b.setField(hm);
                 bibItems.add(b);
 

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java b/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
@@ -29,6 +29,7 @@
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.KeyCollisionException;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.BibtexString;
 import org.jabref.model.entry.CustomEntryType;
 import org.jabref.model.entry.EntryType;
@@ -504,7 +505,8 @@ private String parsePreamble() throws IOException {
     }
 
     private BibEntry parseEntry(String entryType) throws IOException {
-        BibEntry result = new BibEntry(entryType);
+        BibEntry result = new BibEntry(BibtexEntryTypes.getTypeOrDefault(entryType));
+
         skipWhitespace();
         consume('{', '(');
         int character = peek();

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/CopacImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/CopacImporter.java
@@ -11,6 +11,7 @@
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 
 /**
@@ -98,7 +99,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
 
             // Copac does not contain enough information on the type of the
             // document. A book is assumed.
-            BibEntry b = new BibEntry("book");
+            BibEntry b = new BibEntry(BibtexEntryTypes.BOOK);
 
             String[] lines = entry.split("\n");
 

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/EndnoteImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/EndnoteImporter.java
@@ -15,6 +15,7 @@
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.AuthorList;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 
 /**
@@ -253,7 +254,7 @@ else if ("P".equals(prefix)) {
                 hm.put(FieldName.PAGES, artnum);
             }
 
-            BibEntry b = new BibEntry(type);
+            BibEntry b = new BibEntry(BibtexEntryTypes.getTypeOrDefault(type));
             b.setField(hm);
             if (!b.getFieldNames().isEmpty()) {
                 bibitems.add(b);

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/GvkParser.java b/src/main/java/org/jabref/logic/importer/fileformat/GvkParser.java
@@ -12,6 +12,7 @@
 import org.jabref.logic.importer.ParseException;
 import org.jabref.logic.importer.Parser;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 
 import com.google.common.base.Strings;
@@ -360,7 +361,7 @@ private BibEntry parseEntry(Element e) {
          * dann @incollection annehmen, wenn weder ISBN noch
          * ZDB-ID vorhanden sind.
          */
-        BibEntry result = new BibEntry(entryType);
+        BibEntry result = new BibEntry(BibtexEntryTypes.getTypeOrDefault(entryType));
 
         // Zuordnung der Felder in Abhängigkeit vom Dokumenttyp
         if (author != null) {

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/InspecImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/InspecImporter.java
@@ -13,6 +13,7 @@
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.AuthorList;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 
 /**
@@ -120,7 +121,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                     }
                 }
             }
-            BibEntry b = new BibEntry(type);
+            BibEntry b = new BibEntry(BibtexEntryTypes.getTypeOrDefault(type));
             b.setField(h);
 
             bibitems.add(b);

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/IsiImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/IsiImporter.java
@@ -17,6 +17,7 @@
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.Month;
 
@@ -301,7 +302,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                 continue;
             }
 
-            BibEntry b = new BibEntry(Type);
+            BibEntry b = new BibEntry(BibtexEntryTypes.getTypeOrDefault(Type));
             // id assumes an existing database so don't
 
             // Remove empty fields:

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java
@@ -74,6 +74,7 @@
 import org.jabref.logic.importer.fileformat.medline.Text;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.strings.StringUtil;
 
@@ -262,7 +263,7 @@ private void parseBookArticle(PubmedBookArticle currentArticle, List<BibEntry> b
             putIfValueNotNull(fields, "pubstatus", bookData.getPublicationStatus());
         }
 
-        BibEntry entry = new BibEntry("article");
+        BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE);
         entry.setField(fields);
 
         bibItems.add(entry);
@@ -410,7 +411,7 @@ private void parseArticle(PubmedArticle article, List<BibEntry> bibItems) {
             }
         }
 
-        BibEntry entry = new BibEntry("article");
+        BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE);
         entry.setField(fields);
 
         bibItems.add(entry);

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java
@@ -16,6 +16,7 @@
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.AuthorList;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 
 /**
@@ -208,7 +209,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                 fields.put(FieldName.COMMENT, comment);
             }
 
-            BibEntry b = new BibEntry(type);
+            BibEntry b = new BibEntry(BibtexEntryTypes.getTypeOrDefault(type));
 
             // Remove empty fields:
             fields.entrySet().stream().filter(n -> n.getValue().trim().isEmpty()).forEach(fields::remove);

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/OvidImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/OvidImporter.java
@@ -14,6 +14,7 @@
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.AuthorList;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 
 /**
@@ -207,7 +208,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                 // Move the "chaptertitle" to just "title":
                 h.put(FieldName.TITLE, h.remove("chaptertitle"));
             }
-            BibEntry b = new BibEntry(entryType);
+            BibEntry b = new BibEntry(BibtexEntryTypes.getTypeOrDefault(entryType));
             b.setField(h);
 
             bibitems.add(b);

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java
@@ -16,6 +16,7 @@
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.AuthorList;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.Month;
 
@@ -265,7 +266,7 @@ else if ("AV".equals(tag)) {
 
             // create one here
             // type is set in the loop above
-            BibEntry entry = new BibEntry(type);
+            BibEntry entry = new BibEntry(BibtexEntryTypes.getTypeOrDefault(type));
             entry.setField(fields);
             // month has a special treatment as we use the separate method "setMonth" of BibEntry instead of directly setting the value
             month.ifPresent(entry::setMonth);

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/SilverPlatterImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/SilverPlatterImporter.java
@@ -14,6 +14,7 @@
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.entry.AuthorList;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 
 /**
@@ -180,7 +181,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
 
             }
 
-            BibEntry b = new BibEntry(type);
+            BibEntry b = new BibEntry(BibtexEntryTypes.getTypeOrDefault(type));
             // create one here
             b.setField(h);
 

diff --git a/src/main/java/org/jabref/logic/msbib/BibTeXConverter.java b/src/main/java/org/jabref/logic/msbib/BibTeXConverter.java
@@ -9,6 +9,7 @@
 import java.util.stream.Collectors;
 
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.Month;
 
@@ -29,7 +30,7 @@ public static BibEntry convert(MSBibEntry entry) {
         Map<String, String> fieldValues = new HashMap<>();
 
         String bibTexEntryType = MSBibMapping.getBiblatexEntryType(entry.getType());
-        result = new BibEntry(bibTexEntryType);
+        result = new BibEntry(BibtexEntryTypes.getTypeOrDefault(bibTexEntryType));
 
         // add String fields
         for (Map.Entry<String, String> field : entry.fields.entrySet()) {

diff --git a/src/main/java/org/jabref/logic/util/TestEntry.java b/src/main/java/org/jabref/logic/util/TestEntry.java
@@ -1,6 +1,7 @@
 package org.jabref.logic.util;
 
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
 
 public class TestEntry {
@@ -10,7 +11,7 @@ private TestEntry() {
 
     public static BibEntry getTestEntry() {
 
-        BibEntry entry = new BibEntry("article");
+        BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE);
         entry.setCiteKey("Smith2016");
         entry.setField(FieldName.AUTHOR, "Smith, Bill and Jones, Bob and Williams, Jeff");
         entry.setField(FieldName.EDITOR, "Taylor, Phil");

diff --git a/src/main/java/org/jabref/model/entry/BibEntry.java b/src/main/java/org/jabref/model/entry/BibEntry.java
@@ -111,7 +111,7 @@ private BibEntry(String id, String type) {
      * Constructs a new BibEntry. The internal ID is set to IdGenerator.next()
      */
     public BibEntry(EntryType type) {
-        this(type.getName());
+        this(IdGenerator.next(),type.getName());
     }
 
     public Optional<FieldChange> setMonth(Month parsedMonth) {
@@ -544,7 +544,7 @@ private boolean atLeastOnePresent(String[] fieldsToCheck, BibDatabase database)
      */
     @Override
     public Object clone() {
-        BibEntry clone = new BibEntry(type.getValue());
+        BibEntry clone = new BibEntry(IdGenerator.next(),type.getValue());
         clone.fields = FXCollections.observableMap(new ConcurrentHashMap<>(fields));
         return clone;
     }

diff --git a/src/main/java/org/jabref/model/entry/BibtexEntryTypes.java b/src/main/java/org/jabref/model/entry/BibtexEntryTypes.java
@@ -287,4 +287,8 @@ private BibtexEntryTypes() {
     public static Optional<EntryType> getType(String name) {
         return ALL.stream().filter(e -> e.getName().equalsIgnoreCase(name)).findFirst();
     }
+
+    public static EntryType getTypeOrDefault(String name) {
+        return getType(name).orElseGet(() -> new CustomEntryType(name, "required", "optional"));
+    }
 }
diff --git a/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java b/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java
@@ -10,6 +10,7 @@
 import org.jabref.logic.util.io.AutoLinkPreferences;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.metadata.FilePreferences;
 
@@ -30,7 +31,7 @@ public class AutoSetFileLinksUtilTest {
     private final AutoLinkPreferences autoLinkPrefs = new AutoLinkPreferences(false, "", true, ';');
     private final BibDatabaseContext databaseContext = mock(BibDatabaseContext.class);
     private final ExternalFileTypes externalFileTypes = mock(ExternalFileTypes.class);
-    private final BibEntry entry = new BibEntry("article");
+    private final BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE);
 
     @BeforeEach
     public void setUp(@TempDirectory.TempDir Path folder) throws Exception {

diff --git a/src/test/java/org/jabref/logic/TypedBibEntryTest.java b/src/test/java/org/jabref/logic/TypedBibEntryTest.java
@@ -3,6 +3,7 @@
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibtexEntryTypes;
+import org.jabref.model.entry.CustomEntryType;
 
 import org.junit.jupiter.api.Test;
 
@@ -14,7 +15,7 @@ public class TypedBibEntryTest {
 
     @Test
     public void hasAllRequiredFieldsFail() {
-        BibEntry e = new BibEntry(BibtexEntryTypes.ARTICLE.getName());
+        BibEntry e = new BibEntry(BibtexEntryTypes.ARTICLE);
         e.setField("author", "abc");
         e.setField("title", "abc");
         e.setField("journal", "abc");
@@ -25,7 +26,7 @@ public void hasAllRequiredFieldsFail() {
 
     @Test
     public void hasAllRequiredFields() {
-        BibEntry e = new BibEntry(BibtexEntryTypes.ARTICLE.getName());
+        BibEntry e = new BibEntry(BibtexEntryTypes.ARTICLE);
         e.setField("author", "abc");
         e.setField("title", "abc");
         e.setField("journal", "abc");
@@ -37,23 +38,23 @@ public void hasAllRequiredFields() {
 
     @Test
     public void hasAllRequiredFieldsForUnknownTypeReturnsTrue() {
-        BibEntry e = new BibEntry("articlllleeeee");
+        BibEntry e = new BibEntry(new CustomEntryType("articlllleeeee","required","optional"));
 
         TypedBibEntry typedEntry = new TypedBibEntry(e, BibDatabaseMode.BIBTEX);
         assertTrue(typedEntry.hasAllRequiredFields());
     }
 
     @Test
     public void getTypeForDisplayReturnsTypeName() {
-        BibEntry e = new BibEntry(BibtexEntryTypes.INPROCEEDINGS.getName());
+        BibEntry e = new BibEntry(BibtexEntryTypes.INPROCEEDINGS);
 
         TypedBibEntry typedEntry = new TypedBibEntry(e, BibDatabaseMode.BIBTEX);
         assertEquals("InProceedings", typedEntry.getTypeForDisplay());
     }
 
     @Test
     public void getTypeForDisplayForUnknownTypeCapitalizeFirstLetter() {
-        BibEntry e = new BibEntry("articlllleeeee");
+        BibEntry e = new BibEntry(new CustomEntryType("articlllleeeee","required","optional"));
 
         TypedBibEntry typedEntry = new TypedBibEntry(e, BibDatabaseMode.BIBTEX);
         assertEquals("Articlllleeeee", typedEntry.getTypeForDisplay());

diff --git a/src/test/java/org/jabref/logic/bibtex/BibEntryWriterTest.java b/src/test/java/org/jabref/logic/bibtex/BibEntryWriterTest.java
@@ -13,6 +13,7 @@
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BiblatexEntryTypes;
+import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
@@ -43,7 +44,7 @@ public void setUpWriter() {
     public void testSerialization() throws IOException {
         StringWriter stringWriter = new StringWriter();
 
-        BibEntry entry = new BibEntry("article");
+        BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE);
         //set a required field
         entry.setField("author", "Foo Bar");
         entry.setField("journal", "International Journal of Something");
@@ -405,7 +406,7 @@ public void addFieldWithLongerLength() throws IOException {
     public void doNotWriteEmptyFields() throws IOException {
         StringWriter stringWriter = new StringWriter();
 
-        BibEntry entry = new BibEntry("article");
+        BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE);
         entry.setField("author", "  ");
         entry.setField("note", "some note");
 
@@ -424,7 +425,7 @@ public void doNotWriteEmptyFields() throws IOException {
     public void trimFieldContents() throws IOException {
         StringWriter stringWriter = new StringWriter();
 
-        BibEntry entry = new BibEntry("article");
+        BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE);
         entry.setField("note", "        some note    \t");
 
         writer.write(entry, stringWriter, BibDatabaseMode.BIBTEX);
@@ -442,7 +443,7 @@ public void trimFieldContents() throws IOException {
     public void writeThrowsErrorIfFieldContainsUnbalancedBraces() {
         StringWriter stringWriter = new StringWriter();
 
-        BibEntry entry = new BibEntry("article");
+        BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE);
         entry.setField("note", "some text with unbalanced { braces");
 
         assertThrows(IOException.class, () -> writer.write(entry, stringWriter, BibDatabaseMode.BIBTEX));