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Merge pull request #900 from JabRef/aux-dialog
Rework Aux dialog and logic
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| package net.sf.jabref.cli; | ||
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| import net.sf.jabref.logic.auxparser.AuxParser; | ||
| import net.sf.jabref.logic.auxparser.AuxParserResult; | ||
| import net.sf.jabref.model.database.BibDatabase; | ||
| import net.sf.jabref.logic.util.strings.StringUtil; | ||
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| public class AuxCommandLine { | ||
| private final String auxFile; | ||
| private final BibDatabase database; | ||
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| public AuxCommandLine(String auxFile, BibDatabase database) { | ||
| this.auxFile = StringUtil.getCorrectFileName(auxFile, "aux"); | ||
| this.database = database; | ||
| } | ||
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| public BibDatabase perform() { | ||
| BibDatabase subDatabase = null; | ||
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| if (!auxFile.isEmpty() && (database != null)) { | ||
| AuxParser auxParser = new AuxParser(auxFile, database); | ||
| AuxParserResult result = auxParser.parse(); | ||
| subDatabase = result.getGeneratedBibDatabase(); | ||
| // print statistics | ||
| System.out.println(result.getInformation(true)); | ||
| } | ||
| return subDatabase; | ||
| } | ||
| } |
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166 changes: 166 additions & 0 deletions
166
src/main/java/net/sf/jabref/logic/auxparser/AuxParser.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,166 @@ | ||
| package net.sf.jabref.logic.auxparser; | ||
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| import net.sf.jabref.model.database.BibDatabase; | ||
| import net.sf.jabref.model.entry.BibEntry; | ||
| import net.sf.jabref.model.entry.IdGenerator; | ||
| import org.apache.commons.logging.Log; | ||
| import org.apache.commons.logging.LogFactory; | ||
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| import java.io.*; | ||
| import java.nio.file.Path; | ||
| import java.util.*; | ||
| import java.util.regex.Matcher; | ||
| import java.util.regex.Pattern; | ||
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| /** | ||
| * LaTeX Aux to BibTeX Parser | ||
| * <p> | ||
| * Extracts a subset of BibTeX entries from a BibDatabase that are included in an aux file. | ||
| */ | ||
| public class AuxParser { | ||
| private static final Log LOGGER = LogFactory.getLog(AuxParser.class); | ||
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| private static final Pattern CITE_PATTERN = Pattern.compile("\\\\(citation|abx@aux@cite)\\{(.+)\\}"); | ||
| private static final Pattern INPUT_PATTERN = Pattern.compile("\\\\@input\\{(.+)\\}"); | ||
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| private final String auxFile; | ||
| private final BibDatabase masterDatabase; | ||
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| /** | ||
| * Generates a database based on the given aux file and BibTeX database | ||
| * | ||
| * @param auxFile Path to the LaTeX aux file | ||
| * @param database BibTeX database | ||
| */ | ||
| public AuxParser(String auxFile, BibDatabase database) { | ||
| this.auxFile = auxFile; | ||
| masterDatabase = database; | ||
| } | ||
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| /** | ||
| * Executes the parsing logic and returns a result containing all information and the generated BibDatabase. | ||
| * | ||
| * @return an AuxParserResult containing the generated BibDatabase and parsing statistics | ||
| */ | ||
| public AuxParserResult parse() { | ||
| return parseAuxFile(); | ||
| } | ||
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| /* | ||
| * Parses the aux file and extracts all bib keys. | ||
| * Also supports nested aux files (latex \\include). | ||
| * | ||
| * There exists no specification of the aux file. | ||
| * Every package, class or document can write to the aux file. | ||
| * The aux file consists of LaTeX macros and is read at the \begin{document} and again at the \end{document}. | ||
| * | ||
| * BibTeX citation: \citation{x,y,z} | ||
| * Biblatex citation: \abx@aux@cite{x,y,z} | ||
| * Nested aux files: \@input{x} | ||
| */ | ||
| private AuxParserResult parseAuxFile() { | ||
| AuxParserResult result = new AuxParserResult(masterDatabase); | ||
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| // nested aux files | ||
| List<String> fileList = new ArrayList<>(1); | ||
| fileList.add(auxFile); | ||
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| int fileIndex = 0; | ||
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| while (fileIndex < fileList.size()) { | ||
| String file = fileList.get(fileIndex); | ||
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| try (BufferedReader br = new BufferedReader(new FileReader(file))) { | ||
| String line; | ||
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| while ((line = br.readLine()) != null) { | ||
| Matcher citeMatch = CITE_PATTERN.matcher(line); | ||
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| while (citeMatch.find()) { | ||
| String keyString = citeMatch.group(2); | ||
| String[] keys = keyString.split(","); | ||
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| for (String key : keys) { | ||
| result.uniqueKeys.add(key.trim()); | ||
| } | ||
| } | ||
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| Matcher inputMatch = INPUT_PATTERN.matcher(line); | ||
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| while (inputMatch.find()) { | ||
| String inputString = inputMatch.group(1); | ||
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| String inputFile = inputString; | ||
| Path rootPath = new File(auxFile).toPath().getParent(); | ||
| if (rootPath != null) { | ||
| inputFile = rootPath.resolve(inputString).toString(); | ||
| } | ||
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| if (!fileList.contains(inputFile)) { | ||
| fileList.add(inputFile); | ||
| result.nestedAuxCount++; | ||
| } | ||
| } | ||
| } | ||
| } catch (FileNotFoundException e) { | ||
| LOGGER.info("Cannot locate input file", e); | ||
| } catch (IOException e) { | ||
| LOGGER.warn("Problem opening file", e); | ||
| } | ||
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| fileIndex++; | ||
| } | ||
| resolveTags(result); | ||
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| return result; | ||
| } | ||
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| /* | ||
| * Try to find an equivalent BibTeX entry inside the reference database for all keys inside the aux file. | ||
| */ | ||
| private void resolveTags(AuxParserResult result) { | ||
| for (String key : result.uniqueKeys) { | ||
| BibEntry entry = masterDatabase.getEntryByKey(key); | ||
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| if (entry == null) { | ||
| result.unresolvedKeys.add(key); | ||
| } else { | ||
| insertEntry(entry, result); | ||
| resolveCrossReferences(entry, result); | ||
| } | ||
| } | ||
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| // Copy database definitions | ||
| if (result.auxDatabase.getEntryCount() > 0) { | ||
| result.auxDatabase.copyPreamble(masterDatabase); | ||
| result.auxDatabase.copyStrings(masterDatabase); | ||
| } | ||
| } | ||
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| /* | ||
| * Resolves and adds CrossRef entries | ||
| */ | ||
| private void resolveCrossReferences(BibEntry entry, AuxParserResult result) { | ||
| entry.getFieldOptional("crossref").ifPresent(crossref -> { | ||
| if (!result.uniqueKeys.contains(crossref)) { | ||
| BibEntry refEntry = masterDatabase.getEntryByKey(crossref); | ||
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| if (refEntry == null) { | ||
| result.unresolvedKeys.add(crossref); | ||
| } else { | ||
| insertEntry(refEntry, result); | ||
| result.crossRefEntriesCount++; | ||
| } | ||
| } | ||
| }); | ||
| } | ||
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| /* | ||
| * Insert a clone of the given entry. The clone is given a new unique ID. | ||
| */ | ||
| private void insertEntry(BibEntry entry, AuxParserResult result) { | ||
| BibEntry clonedEntry = (BibEntry) entry.clone(); | ||
| clonedEntry.setId(IdGenerator.next()); | ||
| result.auxDatabase.insertEntry(clonedEntry); | ||
| } | ||
| } |
79 changes: 79 additions & 0 deletions
79
src/main/java/net/sf/jabref/logic/auxparser/AuxParserResult.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| package net.sf.jabref.logic.auxparser; | ||
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| import net.sf.jabref.logic.l10n.Localization; | ||
| import net.sf.jabref.model.database.BibDatabase; | ||
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| import java.util.ArrayList; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
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| public class AuxParserResult { | ||
| public final BibDatabase masterDatabase; | ||
| public final Set<String> uniqueKeys = new HashSet<>(); | ||
| public final List<String> unresolvedKeys = new ArrayList<>(); | ||
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| public BibDatabase auxDatabase = new BibDatabase(); | ||
| public int nestedAuxCount; | ||
| public int crossRefEntriesCount; | ||
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| public AuxParserResult(BibDatabase masterDatabase) { | ||
| this.masterDatabase = masterDatabase; | ||
| } | ||
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| public BibDatabase getGeneratedBibDatabase() { | ||
| return auxDatabase; | ||
| } | ||
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| public List<String> getUnresolvedKeys() { | ||
| return unresolvedKeys; | ||
| } | ||
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| public int getFoundKeysInAux() { | ||
| return uniqueKeys.size(); | ||
| } | ||
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| public int getResolvedKeysCount() { | ||
| return auxDatabase.getEntryCount() - crossRefEntriesCount; | ||
| } | ||
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| public int getUnresolvedKeysCount() { | ||
| return unresolvedKeys.size(); | ||
| } | ||
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| /** | ||
| * Query the number of extra entries pulled in due to crossrefs from other entries. | ||
| * | ||
| * @return The number of additional entries pulled in due to crossref | ||
| */ | ||
| public int getCrossRefEntriesCount() { | ||
| return crossRefEntriesCount; | ||
| } | ||
|
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| /** | ||
| * Prints parsing statistics | ||
| * | ||
| * @param includeMissingEntries | ||
| * @return | ||
| */ | ||
| public String getInformation(boolean includeMissingEntries) { | ||
| StringBuilder result = new StringBuilder(); | ||
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| result.append(Localization.lang("keys_in_database")).append(' ').append(masterDatabase.getEntryCount()).append('\n') | ||
| .append(Localization.lang("found_in_aux_file")).append(' ').append(getFoundKeysInAux()).append('\n') | ||
| .append(Localization.lang("resolved")).append(' ').append(getResolvedKeysCount()).append('\n') | ||
| .append(Localization.lang("not_found")).append(' ').append(getUnresolvedKeysCount()).append('\n') | ||
| .append(Localization.lang("crossreferenced entries included")).append(' ') | ||
| .append(getCrossRefEntriesCount()).append('\n'); | ||
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| if (includeMissingEntries && (getUnresolvedKeysCount() > 0)) { | ||
| for (String entry : unresolvedKeys) { | ||
| result.append(entry).append('\n'); | ||
| } | ||
| } | ||
| if (nestedAuxCount > 0) { | ||
| result.append(Localization.lang("nested_aux_files")).append(' ').append(nestedAuxCount); | ||
| } | ||
| return result.toString(); | ||
| } | ||
| } |
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