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Refactor BibEntry deprecated method #4554

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merged 14 commits into from
Dec 28, 2018
Merged

Refactor BibEntry deprecated method #4554

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1632efd
Refactor BibEntry deprecated method
Dec 24, 2018
b281436
Fixed error
Dec 24, 2018
c13d9f5
More on checkstyle fixing
Dec 24, 2018
38248dd
Fixed checkstyle issues
Dec 24, 2018
2458fbb
Added custom entrytype for types not registered in the enumerator.
Dec 26, 2018
f6cfd28
Added getTypeOrDefault method refactor code to use it and fix NPE pro…
Dec 28, 2018
1d02074
Fixing checkstyle rules
Dec 28, 2018
80b2650
More on checkstyle
Dec 28, 2018
4e00355
More on getType getTypeOrDefault replacement
Dec 28, 2018
85ddbf5
Revert Article EntryType into Electronic
Dec 28, 2018
a5c092c
Added break line between different packages
Dec 28, 2018
46b4323
Refactor BibtextEntryTypes.getTypeOrDefault method
Dec 28, 2018
db0ddcb
Removed unused import
Dec 28, 2018
6233c6b
Removed extra new line, checkstyle error fixing
Dec 28, 2018
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3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/BiblioscapeImporter.java
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Expand Up @@ -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;

/**
Expand Down Expand Up @@ -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.getType(bibtexType).get());
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This may throw a NPE, because BibtexEntryTypes.getType(bibtexType) may return an empty optional. To handle such cases, one would need to add code similar to how you did it in BibtexParser. In order to reuse this code, I would propose to add a getTypeOrDefault method to BibtexEntryTypes.

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True

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Thanks. There are still a few other places where the new method should be used, this is also the reason why some of the unit tests fail at the moment.

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You're right. Fixed several tests all related with this NPE problem but some are failing. I switch to master and noticed that these are also failing on master so I believe these are non related.

b.setField(hm);
bibItems.add(b);

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3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
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Expand Up @@ -30,6 +30,7 @@
import org.jabref.model.database.KeyCollisionException;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibtexString;
import org.jabref.model.entry.BibtexEntryTypes;
import org.jabref.model.entry.CustomEntryType;
import org.jabref.model.entry.EntryType;
import org.jabref.model.entry.FieldName;
Expand Down Expand Up @@ -504,7 +505,7 @@ private String parsePreamble() throws IOException {
}

private BibEntry parseEntry(String entryType) throws IOException {
BibEntry result = new BibEntry(entryType);
BibEntry result = new BibEntry(BibtexEntryTypes.getType(entryType).get());
skipWhitespace();
consume('{', '(');
int character = peek();
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3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/CopacImporter.java
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Expand Up @@ -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;

/**
Expand Down Expand Up @@ -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");

Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/EndnoteImporter.java
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Expand Up @@ -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;

/**
Expand Down Expand Up @@ -253,7 +254,7 @@ else if ("P".equals(prefix)) {
hm.put(FieldName.PAGES, artnum);
}

BibEntry b = new BibEntry(type);
BibEntry b = new BibEntry(BibtexEntryTypes.getType(type).get());
b.setField(hm);
if (!b.getFieldNames().isEmpty()) {
bibitems.add(b);
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/GvkParser.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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.getType(entryType).get());

// Zuordnung der Felder in Abhängigkeit vom Dokumenttyp
if (author != null) {
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/InspecImporter.java
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Expand Up @@ -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;

/**
Expand Down Expand Up @@ -120,7 +121,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
}
}
}
BibEntry b = new BibEntry(type);
BibEntry b = new BibEntry(BibtexEntryTypes.getType(type).get());
b.setField(h);

bibitems.add(b);
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/IsiImporter.java
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Expand Up @@ -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;

Expand Down Expand Up @@ -301,7 +302,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
continue;
}

BibEntry b = new BibEntry(Type);
BibEntry b = new BibEntry(BibtexEntryTypes.getType(Type).get());
// id assumes an existing database so don't

// Remove empty fields:
Expand Down
5 changes: 3 additions & 2 deletions src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java
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Expand Up @@ -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;

Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -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);
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java
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Expand Up @@ -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;

/**
Expand Down Expand Up @@ -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.getType(type).get());

// Remove empty fields:
fields.entrySet().stream().filter(n -> n.getValue().trim().isEmpty()).forEach(fields::remove);
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/OvidImporter.java
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Expand Up @@ -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;

/**
Expand Down Expand Up @@ -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.getType(entryType).get());
b.setField(h);

bibitems.add(b);
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java
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Expand Up @@ -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;

Expand Down Expand Up @@ -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.getType(type).get());
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);
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/SilverPlatterImporter.java
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Expand Up @@ -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;

/**
Expand Down Expand Up @@ -180,7 +181,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {

}

BibEntry b = new BibEntry(type);
BibEntry b = new BibEntry(BibtexEntryTypes.getType(type).get());
// create one here
b.setField(h);

Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/msbib/BibTeXConverter.java
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Expand Up @@ -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;

Expand All @@ -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.getType(bibTexEntryType).get());

// add String fields
for (Map.Entry<String, String> field : entry.fields.entrySet()) {
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/logic/util/TestEntry.java
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@@ -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 {
Expand All @@ -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");
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/jabref/model/entry/BibEntry.java
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Expand Up @@ -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) {
Expand Down Expand Up @@ -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;
}
Expand Down
3 changes: 2 additions & 1 deletion src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java
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Expand Up @@ -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;

Expand All @@ -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 {
Expand Down
11 changes: 6 additions & 5 deletions src/test/java/org/jabref/logic/TypedBibEntryTest.java
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Expand Up @@ -4,6 +4,7 @@
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibtexEntryTypes;

import org.jabref.model.entry.CustomEntryType;
import org.junit.jupiter.api.Test;

import static org.junit.jupiter.api.Assertions.assertEquals;
Expand All @@ -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");
Expand All @@ -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");
Expand All @@ -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());
Expand Down
12 changes: 5 additions & 7 deletions src/test/java/org/jabref/logic/bibtex/BibEntryWriterTest.java
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Expand Up @@ -11,9 +11,7 @@
import org.jabref.logic.importer.fileformat.BibtexParser;
import org.jabref.logic.util.OS;
import org.jabref.model.database.BibDatabaseMode;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BiblatexEntryTypes;
import org.jabref.model.entry.LinkedFile;
import org.jabref.model.entry.*;
import org.jabref.model.util.DummyFileUpdateMonitor;
import org.jabref.model.util.FileUpdateMonitor;

Expand Down Expand Up @@ -43,7 +41,7 @@ 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");
Expand Down Expand Up @@ -405,7 +403,7 @@ 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");

Expand All @@ -424,7 +422,7 @@ 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);
Expand All @@ -442,7 +440,7 @@ 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));
Expand Down
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