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Fix citation key table #13151

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Merged
merged 6 commits into from
May 20, 2025
Merged

Fix citation key table #13151

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5b20613
Fix citation key table
koppor May 19, 2025
295c6fd
Use for-each instead of streams
koppor May 19, 2025
1518653
Fix table rendering
koppor May 19, 2025
1d7bd0c
Add sorting of entries by citation key (instead of number of fields)
koppor May 20, 2025
559f77a
Adapt test
koppor May 20, 2025
f1335ec
fix l10n
Siedlerchr May 20, 2025
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29 changes: 29 additions & 0 deletions jablib/src/main/java/org/jabref/logic/bibtex/comparator/BibEntryByCitationKeyComparator.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
package org.jabref.logic.bibtex.comparator;

import java.util.Comparator;

import org.jabref.model.entry.BibEntry;

public class BibEntryByCitationKeyComparator implements Comparator<BibEntry> {
@Override
public int compare(BibEntry e1, BibEntry e2) {
boolean e1HasCitationKey = e1.hasCitationKey();
boolean e2HasCitationKey = e2.hasCitationKey();

if (!e1HasCitationKey && !e2HasCitationKey) {
return 0;
}

if (e1HasCitationKey && !e2HasCitationKey) {
return -1;
}

if (!e1HasCitationKey && e2HasCitationKey) {
return 1;
}

assert e1HasCitationKey && e2HasCitationKey;
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Using assertions for control flow is not recommended as they can be disabled at runtime. Consider using a more robust method to ensure both entries have citation keys.


return e1.getCitationKey().get().compareTo(e2.getCitationKey().get());
}
}
30 changes: 30 additions & 0 deletions jablib/src/main/java/org/jabref/logic/bibtex/comparator/BibEntryByFieldsComparator.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
package org.jabref.logic.bibtex.comparator;

import java.util.Comparator;
import java.util.Iterator;

import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.Field;

/**
* Sorts entries by the number of fields and then by the field names.
*/
public class BibEntryByFieldsComparator implements Comparator<BibEntry> {
@Override
public int compare(BibEntry e1, BibEntry e2) {
int sizeComparison = e1.getFields().size() - e2.getFields().size();
if (sizeComparison != 0) {
return sizeComparison;
}
Iterator<String> it1 = e1.getFields().stream().map(Field::getName).sorted().iterator();
Iterator<String> it2 = e2.getFields().stream().map(Field::getName).sorted().iterator();
while (it1.hasNext() && it2.hasNext()) {
int fieldComparison = it1.next().compareTo(it2.next());
if (fieldComparison != 0) {
return fieldComparison;
}
}
assert !it1.hasNext() && !it2.hasNext();
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Using assertions for control flow is not recommended as they can be disabled at runtime, leading to unexpected behavior. Consider using a different approach to ensure iterators are exhausted.

return 0;
}
}
39 changes: 13 additions & 26 deletions jablib/src/main/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,14 @@
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.SequencedCollection;
import java.util.Set;

import org.jabref.logic.bibtex.comparator.BibEntryByCitationKeyComparator;
import org.jabref.logic.bibtex.comparator.BibEntryByFieldsComparator;
import org.jabref.logic.bibtex.comparator.FieldComparatorStack;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.Field;
import org.jabref.model.entry.types.EntryType;
Expand Down Expand Up @@ -55,38 +57,23 @@ public Result check(List<BibEntry> entries) {
return;
}

List<BibEntry> sortedEntries = entryTypeToEntriesMap
List<Comparator<BibEntry>> comparators = List.of(
new BibEntryByCitationKeyComparator(),
new BibEntryByFieldsComparator());
FieldComparatorStack<BibEntry> comparatorStack = new FieldComparatorStack<>(comparators);

List<BibEntry> differingEntries = entryTypeToEntriesMap
.get(entryType).stream()
.filter(entry -> !entry.getFields().equals(commonFields))
.sorted(getBibEntryComparator()).toList();
resultMap.put(entryType, new EntryTypeResult(uniqueFields, sortedEntries));
.sorted(comparatorStack)
.toList();

resultMap.put(entryType, new EntryTypeResult(uniqueFields, differingEntries));
});

return new Result(resultMap);
}

/**
* Sorts entries by the number of fields and then by the field names.
*/
private static Comparator<BibEntry> getBibEntryComparator() {
return (e1, e2) -> {
int sizeComparison = e1.getFields().size() - e2.getFields().size();
if (sizeComparison != 0) {
return sizeComparison;
}
Iterator<String> it1 = e1.getFields().stream().map(Field::getName).sorted().iterator();
Iterator<String> it2 = e2.getFields().stream().map(Field::getName).sorted().iterator();
while (it1.hasNext() && it2.hasNext()) {
int fieldComparison = it1.next().compareTo(it2.next());
if (fieldComparison != 0) {
return fieldComparison;
}
}
assert !it1.hasNext() && !it2.hasNext();
return 0;
};
}

private static void collectEntriesIntoMaps(List<BibEntry> entries, Map<EntryType, Set<Field>> entryTypeToFieldsInAnyEntryMap, Map<EntryType, Set<Field>> entryTypeToFieldsInAllEntriesMap, Map<EntryType, Set<BibEntry>> entryTypeToEntriesMap) {
entries.forEach(entry -> {
EntryType entryType = entry.getType();
Expand Down
54 changes: 26 additions & 28 deletions ...ava/org/jabref/logic/quality/consistency/BibliographyConsistencyCheckResultTxtWriter.java
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Expand Up @@ -3,6 +3,7 @@
import java.io.IOException;
import java.io.Writer;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import java.util.StringJoiner;
Expand Down Expand Up @@ -53,46 +54,43 @@ public void writeFindings() throws IOException {
super.writeFindings();

if (!isPorcelain) {
int widthSymbol = Localization.lang("Symbol").length();
int widthMeaning = Collections.max(List.of(
Localization.lang("Meaning").length(),
Localization.lang("required field is present").length(),
Localization.lang("optional field is present").length(),
Localization.lang("unknown field is present").length(),
Localization.lang("field is absent").length()
));

writer.write("\n");
writer.write("%s | %s\n".formatted(REQUIRED_FIELD_AT_ENTRY_TYPE_CELL_ENTRY, Localization.lang("required field is present")));
writer.write("%s | %s\n".formatted(OPTIONAL_FIELD_AT_ENTRY_TYPE_CELL_ENTRY, Localization.lang("optional field is present")));
writer.write("%s | %s\n".formatted(UNKNOWN_FIELD_AT_ENTRY_TYPE_CELL_ENTRY, Localization.lang("unknown field is present")));
writer.write("%s | %s\n".formatted(UNSET_FIELD_AT_ENTRY_TYPE_CELL_ENTRY, Localization.lang("field is absent")));
writer.write(("| %-" + widthSymbol + "s | %-" + widthMeaning + "s |\n").formatted(Localization.lang("Symbol"), Localization.lang("Meaning")));
writer.write(("| " + "-".repeat(widthSymbol) + " | " + "-".repeat(widthMeaning) + " |\n").formatted("--", "--"));
writer.write(("| %-" + widthSymbol + "s | %-" + widthMeaning + "s |\n").formatted(REQUIRED_FIELD_AT_ENTRY_TYPE_CELL_ENTRY, Localization.lang("required field is present")));
writer.write(("| %-" + widthSymbol + "s | %-" + widthMeaning + "s |\n").formatted(OPTIONAL_FIELD_AT_ENTRY_TYPE_CELL_ENTRY, Localization.lang("optional field is present")));
writer.write(("| %-" + widthSymbol + "s | %-" + widthMeaning + "s |\n").formatted(UNKNOWN_FIELD_AT_ENTRY_TYPE_CELL_ENTRY, Localization.lang("unknown field is present")));
writer.write(("| %-" + widthSymbol + "s | %-" + widthMeaning + "s |\n").formatted(UNSET_FIELD_AT_ENTRY_TYPE_CELL_ENTRY, Localization.lang("field is absent")));
}
}

private void initializeColumnWidths() {
columnWidths = new ArrayList<>(columnNames.size());

Integer max = getColumnWidthOfEntryTypes();
columnWidths.add(max);
int entryTypeWidth = "entry type".length();
int citationKeyWidth = "citation key".length();

max = getColumnWidthOfCitationKeys(max);
columnWidths.add(max);
for (var keysAndValue : result.entryTypeToResultMap().entrySet()) {
entryTypeWidth = Math.max(entryTypeWidth, keysAndValue.getKey().getDisplayName().length());
for (var entry : keysAndValue.getValue().sortedEntries()) {
citationKeyWidth = Math.max(citationKeyWidth, entry.getCitationKey().orElse("").length());
}
}

columnWidths.add(entryTypeWidth);
columnWidths.add(citationKeyWidth);
columnWidths.addAll(columnNames.stream().skip(2).map(String::length).toList());
}

private Integer getColumnWidthOfEntryTypes() {
int max = result.entryTypeToResultMap().keySet()
.stream()
.map(entryType -> entryType.getDisplayName().length())
.max(Integer::compareTo)
.get();
max = Math.max(max, "entry type".length());
return max;
}

private Integer getColumnWidthOfCitationKeys(Integer max) {
result.entryTypeToResultMap().values()
.stream()
.flatMap(entryTypeResult -> entryTypeResult.sortedEntries().stream())
.map(entry -> entry.getCitationKey().orElse("").length())
.max(Integer::compareTo)
.get();
return Math.max(max, "citation key".length());
}

@Override
protected void writeBibEntry(BibEntry bibEntry, String entryType, Set<Field> requiredFields, Set<Field> optionalFields) throws IOException {
List<String> theRecord = getFindingsAsList(bibEntry, entryType, requiredFields, optionalFields);
Expand Down
84 changes: 64 additions & 20 deletions ...org/jabref/logic/quality/consistency/BibliographyConsistencyCheckResultTxtWriterTest.java
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Expand Up @@ -50,10 +50,12 @@ void checkSimpleLibrary(@TempDir Path tempDir) throws IOException {
| Article | first | o | - |
| Article | second | - | ? |

x | required field is present
o | optional field is present
? | unknown field is present
- | field is absent
| Symbol | Meaning |
| ------ | ------------------------- |
| x | required field is present |
| o | optional field is present |
| ? | unknown field is present |
| - | field is absent |
""", Files.readString(txtFile).replace("\r\n", "\n"));
}

Expand Down Expand Up @@ -81,10 +83,45 @@ void checkDifferentOutputSymbols(@TempDir Path tempDir) throws IOException {
| ---------- | ------------ | ------ | ----- | ----- |
| Article | first | ? | o | x |

x | required field is present
o | optional field is present
? | unknown field is present
- | field is absent
| Symbol | Meaning |
| ------ | ------------------------- |
| x | required field is present |
| o | optional field is present |
| ? | unknown field is present |
| - | field is absent |
""", Files.readString(txtFile).replace("\r\n", "\n"));
}

@Test
void checkVeryLongCitationKey(@TempDir Path tempDir) throws IOException {
UnknownField customField = new UnknownField("custom");
BibEntry first = new BibEntry(StandardEntryType.Article, "first-very-long-key")
.withField(StandardField.AUTHOR, "Author One") // required
.withField(StandardField.TITLE, "Title") // required
.withField(StandardField.PAGES, "some pages") // optional
.withField(customField, "custom"); // unknown
BibEntry second = new BibEntry(StandardEntryType.Article, "second")
.withField(StandardField.AUTHOR, "Author One");
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(List.of(first, second));

Path txtFile = tempDir.resolve("checkDifferentOutputSymbols-result.txt");
try (Writer writer = new OutputStreamWriter(Files.newOutputStream(txtFile));
BibliographyConsistencyCheckResultTxtWriter BibliographyConsistencyCheckResultTxtWriter = new BibliographyConsistencyCheckResultTxtWriter(result, writer, false)) {
BibliographyConsistencyCheckResultTxtWriter.writeFindings();
}
assertEquals("""
Field Presence Consistency Check Result

| entry type | citation key | Custom | Pages | Title |
| ---------- | ------------------- | ------ | ----- | ----- |
| Article | first-very-long-key | ? | o | x |

| Symbol | Meaning |
| ------ | ------------------------- |
| x | required field is present |
| o | optional field is present |
| ? | unknown field is present |
| - | field is absent |
""", Files.readString(txtFile).replace("\r\n", "\n"));
}

Expand All @@ -106,11 +143,16 @@ void checkComplexLibrary(@TempDir Path tempDir) throws IOException {
.withField(StandardField.AUTHOR, "Author One")
.withField(StandardField.YEAR, "2024")
.withField(StandardField.PUBLISHER, "publisher");
// Entry added to check for alphabetical ordering of citation keys
BibEntry fifth = new BibEntry(StandardEntryType.InProceedings, "fifth")
.withField(StandardField.AUTHOR, "Author One")
.withField(StandardField.LOCATION, "location")
.withField(StandardField.YEAR, "2024");
BibEntry sixth = new BibEntry(StandardEntryType.InProceedings, "sixth")
.withField(StandardField.AUTHOR, "Author One")
.withField(StandardField.YEAR, "2024");

BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(List.of(first, second, third, fourth, fifth));
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(List.of(first, second, third, fourth, fifth, sixth));

Path txtFile = tempDir.resolve("checkSimpleLibrary-result.txt");
try (Writer writer = new OutputStreamWriter(Files.newOutputStream(txtFile));
Expand All @@ -120,17 +162,19 @@ void checkComplexLibrary(@TempDir Path tempDir) throws IOException {
assertEquals("""
Field Presence Consistency Check Result

| entry type | citation key | Location | Pages | Publisher |
| ------------- | ------------- | -------- | ----- | --------- |
| Article | first | - | o | - |
| Article | second | - | - | ? |
| InProceedings | fourth | - | - | o |
| InProceedings | third | ? | o | - |

x | required field is present
o | optional field is present
? | unknown field is present
- | field is absent
| entry type | citation key | Location | Pages | Publisher |
| ------------- | ------------ | -------- | ----- | --------- |
| Article | first | - | o | - |
| Article | second | - | - | ? |
| InProceedings | fourth | - | - | o |
| InProceedings | third | ? | o | - |

| Symbol | Meaning |
| ------ | ------------------------- |
| x | required field is present |
| o | optional field is present |
| ? | unknown field is present |
| - | field is absent |
""", Files.readString(txtFile).replace("\r\n", "\n"));
}

Expand Down