repo stringlengths 1 191 ⌀ | file stringlengths 23 351 | code stringlengths 0 5.32M | file_length int64 0 5.32M | avg_line_length float64 0 2.9k | max_line_length int64 0 288k | extension_type stringclasses 1
value |
|---|---|---|---|---|---|---|
null | jabref-main/src/main/java/org/jabref/logic/autosaveandbackup/AutosaveManager.java | package org.jabref.logic.autosaveandbackup;
import java.util.HashSet;
import java.util.Set;
import java.util.concurrent.ScheduledThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
import org.jabref.logic.util.CoarseChangeFilter;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.datab... | 3,954 | 35.962617 | 133 | java |
null | jabref-main/src/main/java/org/jabref/logic/autosaveandbackup/BackupManager.java | package org.jabref.logic.autosaveandbackup;
import java.io.IOException;
import java.io.Writer;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardCopyOption;
import java.nio.file.attribute.FileTime;
import java.... | 15,445 | 44.163743 | 178 | java |
null | jabref-main/src/main/java/org/jabref/logic/auxparser/AuxParser.java | package org.jabref.logic.auxparser;
import java.nio.file.Path;
public interface AuxParser {
/**
* Executes the parsing logic and returns a result containing all information and the generated BibDatabase.
*
* @param auxFile Path to the LaTeX AUX file
* @return an AuxParserResult containing the ... | 416 | 28.785714 | 112 | java |
null | jabref-main/src/main/java/org/jabref/logic/auxparser/AuxParserResult.java | package org.jabref.logic.auxparser;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.jabref.model.database.BibDatabase;
import org.jabref.model.entry.BibtexString;
public class AuxParserResult {
private final BibDatabase m... | 2,156 | 23.793103 | 87 | java |
null | jabref-main/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java | package org.jabref.logic.auxparser;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import java.util.regex.Matcher;
import java.util.rege... | 6,871 | 34.791667 | 132 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/BibEntryWriter.java | package org.jabref.logic.bibtex;
import java.io.IOException;
import java.io.StringWriter;
import java.util.Collection;
import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Optional;
import java.util.Set;
import java.util.SortedSet;
import java.util.Tre... | 8,266 | 39.925743 | 147 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/FieldContentFormatter.java | package org.jabref.logic.bibtex;
import java.util.HashSet;
import java.util.Objects;
import java.util.Set;
import java.util.regex.Pattern;
import org.jabref.model.entry.field.Field;
import org.jabref.model.entry.field.StandardField;
/**
* This class provides the reformatting needed when reading BibTeX fields format... | 2,006 | 34.210526 | 113 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/FieldPreferences.java | package org.jabref.logic.bibtex;
import java.util.Collection;
import java.util.List;
import javafx.beans.property.BooleanProperty;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import org.jabref.model.entry.field.Field;
public ... | 1,902 | 30.716667 | 153 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/FieldWriter.java | package org.jabref.logic.bibtex;
import org.jabref.model.entry.field.Field;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Converts JabRef's internal BibTeX representation of a BibTeX field to BibTeX text representation
*/
public class FieldWriter {
// See also ADR-0024
public static final... | 8,757 | 41.105769 | 192 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/FileFieldWriter.java | package org.jabref.logic.bibtex;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
import org.jabref.model.entry.LinkedFile;
public class FileFieldWriter {
private FileFieldWriter() {
}
public static String getStringRepresentation(List<Lin... | 2,112 | 29.185714 | 99 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/InvalidFieldValueException.java | package org.jabref.logic.bibtex;
/**
* @deprecated implement as {@link org.jabref.logic.integrity.IntegrityCheck} instead.
*/
@Deprecated
public class InvalidFieldValueException extends Exception {
public InvalidFieldValueException(String message) {
super(message);
}
}
| 290 | 21.384615 | 86 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/BibDatabaseDiff.java | package org.jabref.logic.bibtex.comparator;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import org.jabref.logic.database.DuplicateCheck;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.database.BibDatabaseMo... | 5,987 | 42.708029 | 135 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/BibEntryDiff.java | package org.jabref.logic.bibtex.comparator;
import org.jabref.model.entry.BibEntry;
public class BibEntryDiff {
private final BibEntry originalEntry;
private final BibEntry newEntry;
public BibEntryDiff(BibEntry originalEntry, BibEntry newEntry) {
this.originalEntry = originalEntry;
this.... | 495 | 21.545455 | 68 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/BibStringDiff.java | package org.jabref.logic.bibtex.comparator;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import org.jabref.model.database.BibDatabase;
import org.jabref.m... | 3,940 | 34.827273 | 112 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/BibtexStringComparator.java | package org.jabref.logic.bibtex.comparator;
import java.util.Comparator;
import java.util.Locale;
import org.jabref.model.entry.BibtexString;
public class BibtexStringComparator implements Comparator<BibtexString> {
private final boolean considerRefs;
/**
* @param considerRefs Indicates whether the st... | 1,833 | 28.111111 | 81 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/CrossRefEntryComparator.java | package org.jabref.logic.bibtex.comparator;
import java.util.Comparator;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.StandardField;
/**
* Compares Bibtex entries based on their 'crossref' fields. Entries including
* this field are deemed smaller than entries without this field. This... | 960 | 29.03125 | 78 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/EntryComparator.java | package org.jabref.logic.bibtex.comparator;
import java.util.Comparator;
import java.util.Locale;
import java.util.Objects;
import org.jabref.model.entry.AuthorList;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.Field;
import org.jabref.model.entry.field.FieldProperty;
import org.jabref.... | 5,519 | 38.428571 | 120 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/FieldComparator.java | package org.jabref.logic.bibtex.comparator;
import java.text.Collator;
import java.text.ParseException;
import java.text.RuleBasedCollator;
import java.util.Comparator;
import java.util.Locale;
import java.util.Optional;
import org.jabref.model.entry.AuthorList;
import org.jabref.model.entry.BibEntry;
import org.jabr... | 5,308 | 34.630872 | 115 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/FieldComparatorStack.java | package org.jabref.logic.bibtex.comparator;
import java.util.Comparator;
import java.util.List;
/**
* This class represents a list of comparators. The first Comparator takes precedence,
* and each time a Comparator returns 0, the next one is attempted. If all comparators
* return 0 the final result will be 0.
*/
... | 845 | 27.2 | 86 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/GroupDiff.java | package org.jabref.logic.bibtex.comparator;
import java.util.Optional;
import org.jabref.model.groups.GroupTreeNode;
import org.jabref.model.metadata.MetaData;
public class GroupDiff {
private final GroupTreeNode originalGroupRoot;
private final GroupTreeNode newGroupRoot;
GroupDiff(GroupTreeNode origin... | 1,339 | 32.5 | 120 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/IdComparator.java | package org.jabref.logic.bibtex.comparator;
import java.util.Comparator;
import org.jabref.model.entry.BibEntry;
/**
* Comparator for sorting BibEntry objects based on their ID. This
* can be used to sort entries back into the order they were created,
* provided the IDs given to entries are lexically monotonicall... | 525 | 26.684211 | 76 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/MetaDataDiff.java | package org.jabref.logic.bibtex.comparator;
import java.util.EnumSet;
import java.util.Objects;
import java.util.Optional;
import org.jabref.model.metadata.MetaData;
import org.jabref.preferences.PreferencesService;
public class MetaDataDiff {
public enum Difference {
PROTECTED,
GROUPS_ALTERED,
... | 3,780 | 37.191919 | 115 | java |
null | jabref-main/src/main/java/org/jabref/logic/bibtex/comparator/PreambleDiff.java | package org.jabref.logic.bibtex.comparator;
import java.util.Objects;
import java.util.Optional;
import org.jabref.model.database.BibDatabaseContext;
public class PreambleDiff {
private final String originalPreamble;
private final String newPreamble;
PreambleDiff(String originalPreamble, String newPrea... | 1,607 | 28.777778 | 120 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/BstEntry.java | package org.jabref.logic.bst;
import java.util.HashMap;
import java.util.Map;
import org.jabref.model.entry.BibEntry;
public class BstEntry {
public final BibEntry entry;
public final Map<String, String> localStrings = new HashMap<>();
public final Map<String, String> fields = new HashMap<>();
pu... | 452 | 19.590909 | 70 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/BstFunctions.java | package org.jabref.logic.bst;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
import java.util.Stack;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.jabref.logic.bst.util.BstCaseChanger;
import org.jabref.logic.bst.util.BstNameFormatter;
import org.jabref.logic.b... | 36,591 | 38.261803 | 155 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/BstPreviewLayout.java | package org.jabref.logic.bst;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.jabref.logic.cleanup.ConvertToBibtexCleanup;
import org.jabref.logic.formatter.bibtexfields.RemoveNewlinesFormatter;
import org.jabref.logic.l10n.Localization;
import org.jabref.logic.layout.format.L... | 3,498 | 38.314607 | 122 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/BstVM.java | package org.jabref.logic.bst;
import java.io.IOException;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Objects;
import java.util.Stack;
import org.jabref.model.database.BibDatabase;
import org.jabref.model.entry.BibEntry;
import org.antlr... | 4,031 | 34.06087 | 108 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/BstVMContext.java | package org.jabref.logic.bst;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Stack;
import org.jabref.model.database.BibDatabase;
public record BstVMContext(List<BstEntry> entries,
Map<String, St... | 842 | 35.652174 | 128 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/BstVMException.java | package org.jabref.logic.bst;
public class BstVMException extends RuntimeException {
public BstVMException(String string) {
super(string);
}
}
| 160 | 19.125 | 54 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/BstVMVisitor.java | package org.jabref.logic.bst;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.ListIterator;
import java.util.Map;
import org.jabref.logic.bibtex.FieldPreferences;
import org.jabref.logic.bibtex.FieldWriter;
import org.jabref.logic.bibtex.InvalidFieldValueException;
i... | 10,619 | 39.227273 | 135 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/util/BstCaseChanger.java | package org.jabref.logic.bst.util;
import java.util.Locale;
import java.util.Optional;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public final class BstCaseChanger {
private static final Logger LOGGER = LoggerFactory.getLogger(BstCaseChanger.class);
// stores whether the char before the curre... | 9,968 | 32.565657 | 148 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/util/BstNameFormatter.java | package org.jabref.logic.bst.util;
import java.util.Arrays;
import java.util.Locale;
import java.util.Optional;
import java.util.stream.Collectors;
import org.jabref.logic.bst.BstVMException;
import org.jabref.model.entry.Author;
import org.jabref.model.entry.AuthorList;
import org.slf4j.Logger;
import org.slf4j.Log... | 11,244 | 36.483333 | 151 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/util/BstPurifier.java | package org.jabref.logic.bst.util;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
*
* The |built_in| function {\.{purify\$}} pops the top (string) literal, removes
* nonalphanumeric characters except for |white_space| and |sep_char| characters
* (these get converted to a |space|) and removes certain... | 2,643 | 33.337662 | 88 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/util/BstTextPrefixer.java | package org.jabref.logic.bst.util;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* The |built_in| function {\.{text.prefix\$}} pops the top two literals (the
* integer literal |pop_lit1| and a string literal, in that order). It pushes
* the substring of the (at most) |pop_lit1| consecutive text char... | 2,461 | 33.194444 | 88 | java |
null | jabref-main/src/main/java/org/jabref/logic/bst/util/BstWidthCalculator.java | package org.jabref.logic.bst.util;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
*
* The |built_in| function {\.{purify\$}} pops the top (string) literal, removes
* nonalphanumeric characters except for |white_space| and |sep_char| characters
* (these get converted to a |space|) and removes certain... | 9,805 | 39.520661 | 100 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationkeypattern/AbstractCitationKeyPattern.java | package org.jabref.logic.citationkeypattern;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.stream.Collectors;
import org.jabref.model.entry.types.EntryType;
/**
* A... | 4,750 | 33.933824 | 120 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationkeypattern/BracketedPattern.java | package org.jabref.logic.citationkeypattern;
import java.math.BigInteger;
import java.text.Normalizer;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.EnumSet;
import java.util.List;
import java.util.Locale;
import java.util.Objects;
import java.util.Optional;
import... | 58,328 | 43.424219 | 154 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationkeypattern/CitationKeyGenerator.java | package org.jabref.logic.citationkeypattern;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.function.Function;
import java.util.regex.PatternSyntaxException;
import org.jabref.model.FieldChange;
import org.jabref.model.database.BibDatabase;
import... | 9,182 | 41.123853 | 159 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationkeypattern/CitationKeyPatternPreferences.java | package org.jabref.logic.citationkeypattern;
import javafx.beans.property.BooleanProperty;
import javafx.beans.property.ObjectProperty;
import javafx.beans.property.ReadOnlyObjectProperty;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.beans.property.SimpleObjectProperty;
import javafx.beans.propert... | 6,997 | 37.032609 | 101 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationkeypattern/DatabaseCitationKeyPattern.java | package org.jabref.logic.citationkeypattern;
import java.util.List;
import org.jabref.model.entry.types.EntryType;
public class DatabaseCitationKeyPattern extends AbstractCitationKeyPattern {
private final GlobalCitationKeyPattern globalCitationKeyPattern;
public DatabaseCitationKeyPattern(GlobalCitationKe... | 591 | 28.6 | 90 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationkeypattern/GlobalCitationKeyPattern.java | package org.jabref.logic.citationkeypattern;
import java.util.List;
import org.jabref.model.entry.types.EntryType;
public class GlobalCitationKeyPattern extends AbstractCitationKeyPattern {
public GlobalCitationKeyPattern(List<String> bibtexKeyPattern) {
defaultPattern = bibtexKeyPattern;
}
pub... | 585 | 25.636364 | 77 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationstyle/CSLAdapter.java | package org.jabref.logic.citationstyle;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibEntryTypesManager;
import de.undercouch.citeproc.... | 3,573 | 46.653333 | 257 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationstyle/CitationStyle.java | package org.jabref.logic.citationstyle;
import java.io.IOException;
import java.io.StringReader;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.NoSuchFileException;
import java.nio.file.Path;
impor... | 7,245 | 33.179245 | 118 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationstyle/CitationStyleCache.java | package org.jabref.logic.citationstyle;
import java.util.Objects;
import org.jabref.logic.preview.PreviewLayout;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.database.event.EntriesRemovedEvent;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.event.EntryChangedEven... | 2,567 | 32.789474 | 122 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationstyle/CitationStyleGenerator.java | package org.jabref.logic.citationstyle;
import java.io.IOException;
import java.util.Collections;
import java.util.List;
import org.jabref.logic.l10n.Localization;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibEntryTypesManager;
import o... | 4,093 | 50.175 | 207 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationstyle/CitationStyleOutputFormat.java | package org.jabref.logic.citationstyle;
import org.jabref.logic.util.OS;
public enum CitationStyleOutputFormat {
HTML("html", OS.NEWLINE + "<br>" + OS.NEWLINE),
TEXT("text", "");
private final String format;
private final String lineSeparator;
CitationStyleOutputFormat(String format, String lin... | 629 | 19.322581 | 68 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationstyle/CitationStylePreviewLayout.java | package org.jabref.logic.citationstyle;
import org.jabref.logic.preview.PreviewLayout;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibEntryTypesManager;
public class CitationStylePreviewLayout implements PreviewLayout {
private final C... | 1,259 | 30.5 | 160 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationstyle/JabRefItemDataProvider.java | package org.jabref.logic.citationstyle;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Locale;
import java.util.Optional;
import java.util.Set;
import org.jabref.logic.formatter.bibtexfields.RemoveNewlinesFormatter;
import org.jabref.lo... | 9,183 | 44.241379 | 570 | java |
null | jabref-main/src/main/java/org/jabref/logic/citationstyle/JabRefLocaleProvider.java | package org.jabref.logic.citationstyle;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.net.URL;
import java.util.HashMap;
import java.util.Map;
import de.undercouch.citeproc.LocaleProvider;
import de.undercouch.citeproc.helper.CSLUtils;
/**
* A {@link LocaleProvider} that loads locales... | 1,270 | 31.589744 | 105 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/CleanupJob.java | package org.jabref.logic.cleanup;
import java.util.List;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
@FunctionalInterface
public interface CleanupJob {
/**
* Cleanup the entry.
*/
List<FieldChange> cleanup(BibEntry entry);
}
| 280 | 16.5625 | 46 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/CleanupWorker.java | package org.jabref.logic.cleanup;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import org.jabref.logic.preferences.TimestampPreferences;
import org.jabref.model.FieldChange;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.entry.BibEntry;
import org.jabref.p... | 3,359 | 36.752809 | 138 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/ConvertToBiblatexCleanup.java | package org.jabref.logic.cleanup;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.Date;
import org.jabref.model.entry.EntryConverter;
import org.jabref.model.e... | 2,629 | 43.576271 | 106 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/ConvertToBibtexCleanup.java | package org.jabref.logic.cleanup;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.EntryConverter;
import org.jabref.model.entry.field.Field;
import org.jabref.model.entry.field.StandardF... | 2,066 | 38 | 135 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/DoiCleanup.java | package org.jabref.logic.cleanup;
import java.net.URLDecoder;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
import org.jabref.model.FieldChange;
import org.... | 2,949 | 36.820513 | 123 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/EprintCleanup.java | package org.jabref.logic.cleanup;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.Field;
import org.jabref.model.entry.field.StandardField;
import org... | 1,871 | 35 | 133 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/FieldFormatterCleanup.java | package org.jabref.logic.cleanup;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.event.EntriesEventSour... | 3,896 | 29.445313 | 98 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/FieldFormatterCleanups.java | package org.jabref.logic.cleanup;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.StringJoiner;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
imp... | 10,191 | 41.466667 | 140 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/FileLinksCleanup.java | package org.jabref.logic.cleanup;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import org.jabref.logic.bibtex.FileFieldWriter;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.LinkedFile;
import org.jabref.model.entry.field.S... | 1,327 | 34.891892 | 124 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/Formatter.java | package org.jabref.logic.cleanup;
/**
* The Formatter is used for a Filter design-pattern. Extending classes have to accept a String and returned a formatted
* version of it. Implementations have to reside in the logic package.
* <p>
* Example:
* <p>
* "John von Neumann" => "von Neumann, John"
*/
public abstrac... | 2,205 | 27.649351 | 120 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/ISSNCleanup.java | package org.jabref.logic.cleanup;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.StandardField;
import org.jabref.model.entry.identifier.ISSN;
public class ISSNCleanup imp... | 992 | 31.032258 | 104 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/MoveFieldCleanup.java | package org.jabref.logic.cleanup;
import java.util.List;
import java.util.Optional;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.Field;
import org.jabref.model.util.OptionalUtil;
/**
* Moves the content of one field to another field.
*/
public cla... | 956 | 28.90625 | 83 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/MoveFilesCleanup.java | package org.jabref.logic.cleanup;
import java.io.IOException;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import org.jabref.logic.externalfiles.LinkedFileHandler;
import org.jabref.model.FieldChange;
import org.jabref.model.database.BibDatabaseContext;
imp... | 1,897 | 32.298246 | 113 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/RelativePathsCleanup.java | package org.jabref.logic.cleanup;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import org.jabref.logic.util.io.FileUtil;
import org.jabref.model.FieldChange;
import org.jabref.model.database.BibDatabase... | 2,324 | 34.769231 | 121 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java | package org.jabref.logic.cleanup;
import java.io.IOException;
import java.nio.file.Path;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import org.jabref.logic.externalfiles.LinkedFileHandler;
import org.jabref.model.FieldChange;
import org.jabref.model.datab... | 2,142 | 33.015873 | 125 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/TimeStampToCreationDate.java | package org.jabref.logic.cleanup;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
import java.time.temporal.ChronoUnit;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import org.jabref.logic.preferences.TimestampPreferences;
impor... | 3,764 | 41.303371 | 155 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/TimeStampToModificationDate.java | package org.jabref.logic.cleanup;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
import java.time.temporal.ChronoUnit;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import org.jabref.logic.preferences.TimestampPreferences;
impor... | 3,784 | 41.52809 | 163 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/URLCleanup.java | package org.jabref.logic.cleanup;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.jabref.logic.formatter.bibtexfields.NormalizeDateFormatter;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.mod... | 5,087 | 44.026549 | 98 | java |
null | jabref-main/src/main/java/org/jabref/logic/cleanup/UpgradePdfPsToFileCleanup.java | package org.jabref.logic.cleanup;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.jabref.logic.bibtex.FileFieldWriter;
import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.Lin... | 2,197 | 35.032787 | 107 | java |
null | jabref-main/src/main/java/org/jabref/logic/crawler/Crawler.java | package org.jabref.logic.crawler;
import java.io.IOException;
import java.nio.file.Path;
import java.util.List;
import org.jabref.logic.exporter.SaveException;
import org.jabref.logic.git.SlrGitHandler;
import org.jabref.logic.importer.ParseException;
import org.jabref.model.entry.BibEntryTypesManager;
import org.jab... | 3,087 | 40.72973 | 118 | java |
null | jabref-main/src/main/java/org/jabref/logic/crawler/StudyCatalogToFetcherConverter.java | package org.jabref.logic.crawler;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
import org.jabref.logic.importer.ImportFormatPreferences;
import org.jabref.logic.importer.ImporterPreferences;
import org.jabref.logic.importer.SearchBasedFetcher;
import org.j... | 2,993 | 42.391304 | 137 | java |
null | jabref-main/src/main/java/org/jabref/logic/crawler/StudyFetcher.java | package org.jabref.logic.crawler;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import org.jabref.logic.importer.FetcherException;
import org.jabref.logic.importer.PagedSearchBasedFetcher;
import org.jabref.logic.importer.SearchBasedFetcher;
import or... | 3,389 | 40.851852 | 129 | java |
null | jabref-main/src/main/java/org/jabref/logic/crawler/StudyRepository.java | package org.jabref.logic.crawler;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.nio.charset.UnsupportedCharsetException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.time.LocalDateTime;
import java.time.temporal.ChronoUnit;
import java.util.List;
import java.ut... | 20,743 | 43.900433 | 189 | java |
null | jabref-main/src/main/java/org/jabref/logic/crawler/StudyYamlParser.java | package org.jabref.logic.crawler;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Path;
import org.jabref.model.study.Study;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
import com.fasterxml.... | 1,396 | 35.763158 | 122 | java |
null | jabref-main/src/main/java/org/jabref/logic/database/DatabaseMerger.java | package org.jabref.logic.database;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import org.jabref.model.database.BibDatabase;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.database.BibDatabaseModeDetection;
import org.jabref.model.entry.BibEntry;
... | 6,811 | 47.312057 | 160 | java |
null | jabref-main/src/main/java/org/jabref/logic/database/DuplicateCheck.java | package org.jabref.logic.database;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import org.jabref.logic.util.OS;
import org.... | 16,694 | 42.476563 | 144 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/AtomicFileOutputStream.java | package org.jabref.logic.exporter;
import java.io.FileOutputStream;
import java.io.FilterOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.nio.channels.FileLock;
import java.nio.channels.OverlappingFileLockException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.ni... | 10,254 | 36.702206 | 184 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/AtomicFileWriter.java | package org.jabref.logic.exporter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.nio.charset.Charset;
import java.nio.charset.CharsetEncoder;
import java.nio.file.Path;
import java.util.Collections;
import java.util.Set;
import java.util.TreeSet;
/**
* Writer that similar to the built-in... | 1,856 | 33.388889 | 116 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/BibDatabaseWriter.java | package org.jabref.logic.exporter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util... | 15,856 | 43.92068 | 151 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/BibWriter.java | package org.jabref.logic.exporter;
import java.io.IOException;
import java.io.Writer;
import org.jabref.model.strings.StringUtil;
/**
* Class to write to a .bib file. Used by {@link BibtexDatabaseWriter}
*/
public class BibWriter {
private final String newLineSeparator;
private final Writer writer;
p... | 1,958 | 25.835616 | 112 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/BibtexDatabaseWriter.java | package org.jabref.logic.exporter;
import java.io.IOException;
import java.io.Writer;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.util.Map;
import org.jabref.logic.bibtex.BibEntryWriter;
import org.jabref.logic.bibtex.FieldPreferences;
import org.jabref.logic.bibtex.FieldWri... | 6,233 | 37.720497 | 149 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/BlankLineBehaviour.java | package org.jabref.logic.exporter;
/**
* This enum represents the behaviour for blank lines in {@link TemplateExporter}
*/
public enum BlankLineBehaviour {
KEEP_BLANKS,
DELETE_BLANKS
}
| 196 | 18.7 | 81 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/EmbeddedBibFilePdfExporter.java | package org.jabref.logic.exporter;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.StringWriter;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.List;
import java.util... | 6,289 | 41.789116 | 150 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/Exporter.java | package org.jabref.logic.exporter;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import org.jabref.logic.journals.JournalAbbreviationRepository;
import org.jabref.logic.util.FileType;
import org.jabref.model.database.BibDatabase;... | 5,633 | 40.426471 | 197 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/ExporterFactory.java | package org.jabref.logic.exporter;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import org.jabref.logic.bibtex.FieldPreferences;
import org.jabref.logic.l10n.Localization;
import org.jabref.logic.layout.LayoutFormatterPreferences... | 5,603 | 61.966292 | 220 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/GroupSerializer.java | package org.jabref.logic.exporter;
import java.util.ArrayList;
import java.util.List;
import javafx.scene.paint.Color;
import org.jabref.logic.util.MetadataSerializationConfiguration;
import org.jabref.logic.util.io.FileUtil;
import org.jabref.model.groups.AbstractGroup;
import org.jabref.model.groups.AllEntriesGrou... | 10,095 | 54.472527 | 198 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/MSBibExporter.java | package org.jabref.logic.exporter;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.nio.file.Path;
import java.util.List;
import java.util.Objects;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import ja... | 2,138 | 35.254237 | 112 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java | package org.jabref.logic.exporter;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.StringJoiner;
import java.util.TreeMap;
import java.util.stream.Collectors;
import org.jabref.logic.citationkeypattern.AbstractCitationKe... | 8,573 | 48.848837 | 142 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/ModsExporter.java | package org.jabref.logic.exporter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.StringReader;
import java.io.StringWriter;
import java.math.BigInteger;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.List;
impor... | 21,413 | 43.987395 | 152 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/OOCalcDatabase.java | package org.jabref.logic.exporter;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.xml.parsers.DocumentBuilderFactory;
import org.jabref.logic.bibtex.comparator.FieldComparator;
import org.jabref.logic.bibtex.comparator.FieldComparat... | 6,224 | 39.686275 | 148 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/OpenDocumentRepresentation.java | package org.jabref.logic.exporter;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.jabref.logic.bibtex.comparator.FieldComparator;
import org.jabref.logic.bibtex.comparator.FieldComp... | 10,955 | 50.679245 | 152 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/OpenDocumentSpreadsheetCreator.java | package org.jabref.logic.exporter;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
impor... | 5,901 | 38.610738 | 119 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/OpenOfficeDocumentCreator.java | package org.jabref.logic.exporter;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
impor... | 5,193 | 38.648855 | 120 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/SaveConfiguration.java | package org.jabref.logic.exporter;
import org.jabref.model.metadata.SaveOrder;
public class SaveConfiguration {
// Encoding written at the top of the .bib file.
public static final String ENCODING_PREFIX = "Encoding: ";
private boolean reformatFile;
private SaveOrder saveOrder;
private boolean m... | 2,483 | 27.883721 | 113 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/SaveException.java | package org.jabref.logic.exporter;
import org.jabref.logic.l10n.Localization;
import org.jabref.model.entry.BibEntry;
/**
* Exception thrown if saving goes wrong. If caused by a specific
* entry, keeps track of which entry caused the problem.
*/
public class SaveException extends Exception {
public static fin... | 2,275 | 26.095238 | 100 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/TemplateExporter.java | package org.jabref.logic.exporter;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.Reader;
import java.net.URISyntaxException;
import java.net.URL;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;
import j... | 16,736 | 42.929134 | 132 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/XmpExporter.java | package org.jabref.logic.exporter;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import org.jabref.logic.util.StandardFileType;
import org.jabref.logic.xmp.XmpPreferences;
import org.jabref.logic.xmp.Xm... | 2,756 | 37.291667 | 121 | java |
null | jabref-main/src/main/java/org/jabref/logic/exporter/XmpPdfExporter.java | package org.jabref.logic.exporter;
import java.nio.file.Path;
import java.util.List;
import java.util.Objects;
import org.jabref.logic.l10n.Localization;
import org.jabref.logic.util.StandardFileType;
import org.jabref.logic.xmp.XmpPreferences;
import org.jabref.logic.xmp.XmpUtilWriter;
import org.jabref.model.databa... | 1,114 | 31.794118 | 115 | java |
null | jabref-main/src/main/java/org/jabref/logic/externalfiles/ExternalFilesContentImporter.java | package org.jabref.logic.externalfiles;
import java.io.IOException;
import java.nio.file.Path;
import org.jabref.logic.importer.ImportFormatPreferences;
import org.jabref.logic.importer.OpenDatabase;
import org.jabref.logic.importer.ParserResult;
import org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter;
i... | 1,119 | 34 | 113 | java |
null | jabref-main/src/main/java/org/jabref/logic/externalfiles/LinkedFileHandler.java | package org.jabref.logic.externalfiles;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardCopyOption;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Stream;
import org.jabref.logic.util.io.FileUtil;
impo... | 6,653 | 40.074074 | 166 | java |
null | jabref-main/src/main/java/org/jabref/logic/formatter/Formatters.java | package org.jabref.logic.formatter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.regex.Pattern;
import org.jabref.logic.cleanup.Formatter;
import org.jabref.logic.formatter.bibtexfields.CleanupUrlFormatter;
import org... | 5,206 | 41.680328 | 90 | java |
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