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Add Pseudonymization to CLI
- A new pseudonymize command has been created. - Test cases has been added. - The display of commands has been sorted for ease of use. - An entry has been added to CHANGELOG.md.
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‎CHANGELOG.md

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@@ -23,6 +23,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
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- We added an "Open example library" button to Welcome Tab. [#13014](https://github.com/JabRef/jabref/issues/13014)
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- We added automatic detection and selection of the identifier type (e.g., DOI, ISBN, arXiv) based on clipboard content when opening the "New Entry" dialog [#13111](https://github.com/JabRef/jabref/pull/13111)
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- We added support for import of a Refer/BibIX file format. [#13069](https://github.com/JabRef/jabref/issues/13069)
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- We added a new command (pseudonymize) to the anonymize the library. [#13109](https://github.com/JabRef/jabref/issues/13109)
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### Changed
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‎jabkit/src/main/java/org/jabref/cli/ArgumentProcessor.java

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@@ -39,15 +39,16 @@
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@Command(name = "jabkit",
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mixinStandardHelpOptions = true,
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subcommands = {
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GenerateCitationKeys.class,
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CheckConsistency.class,
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// CheckIntegrity.class,
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Fetch.class,
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Search.class,
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Convert.class,
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Fetch.class,
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GenerateBibFromAux.class,
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GenerateCitationKeys.class,
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Pdf.class,
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Preferences.class,
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Pdf.class
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Pseudonymize.class,
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Search.class
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})
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public class ArgumentProcessor implements Runnable {
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private static final Logger LOGGER = LoggerFactory.getLogger(ArgumentProcessor.class);

‎jabkit/src/main/java/org/jabref/cli/Pseudonymize.java

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package org.jabref.cli;
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import java.io.IOException;
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import java.nio.file.Path;
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import java.util.Objects;
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import java.util.Optional;
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import org.jabref.logic.importer.ParserResult;
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import org.jabref.logic.l10n.Localization;
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import org.jabref.logic.pseudonymization.Pseudonymization;
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import org.jabref.logic.pseudonymization.PseudonymizationResultCsvWriter;
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import org.jabref.model.database.BibDatabase;
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import org.jabref.model.database.BibDatabaseContext;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import picocli.CommandLine.Command;
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import picocli.CommandLine.Mixin;
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import picocli.CommandLine.Option;
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import picocli.CommandLine.Parameters;
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import picocli.CommandLine.ParentCommand;
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@Command(name = "pseudonymize", description = "Anonymize the library")
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public class Pseudonymize implements Runnable {
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private final static Logger LOGGER = LoggerFactory.getLogger(Pseudonymize.class);
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@ParentCommand
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private ArgumentProcessor argumentProcessor;
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@Mixin
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private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
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@Parameters(index = "0", description = "File to be anonymized")
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private String inputFile;
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@Option(names = {"--output"}, description = "Output file")
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private String outputFile;
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@Option(names = {"--key"}, description = "Output keys file")
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private String key;
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@Override
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public void run() {
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String fileName = getFileName(inputFile);
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String outputFileName = fileName + ".bib";
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String keyFileName = fileName + "_keys.csv";
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// todo: case- output file already exist !
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Optional<ParserResult> parserResult = ArgumentProcessor.importFile(
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inputFile,
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"bibtex",
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argumentProcessor.cliPreferences,
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sharedOptions.porcelain);
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if (parserResult.isEmpty()) {
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System.out.println(Localization.lang("Unable to open file '%0'.", inputFile));
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return;
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}
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if (parserResult.get().isInvalid()) {
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System.out.println(Localization.lang("Input file '%0' is invalid and could not be parsed.", inputFile));
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return;
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}
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System.out.println(Localization.lang("Anonymizing the library '%0' ...", fileName));
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Pseudonymization pseudonymization = new Pseudonymization();
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BibDatabaseContext databaseContext = parserResult.get().getDatabaseContext();
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Pseudonymization.Result result = pseudonymization.pseudonymizeLibrary(databaseContext);
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ArgumentProcessor.saveDatabase(
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argumentProcessor.cliPreferences,
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argumentProcessor.entryTypesManager,
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new BibDatabase(result.bibDatabaseContext().getEntries()),
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Path.of(Objects.requireNonNullElse(outputFile, outputFileName)));
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try {
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Path keysPath = Path.of(Objects.requireNonNullElse(key, keyFileName));
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System.out.println(Localization.lang("Saving") + ": " + keysPath);
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PseudonymizationResultCsvWriter.writeValuesMappingAsCsv(keysPath, result);
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} catch (IOException ex) {
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System.err.println(Localization.lang("Unable to save keys: %0", ex.getMessage()));
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LOGGER.error("Unable to save keys of anonymized library");
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}
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}
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public static String getFileName(String inputFile) {
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String fileName = Path.of(inputFile).getFileName().toString();
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int dotIndex = fileName.lastIndexOf('.');
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String suffix = "_pseudo";
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if (dotIndex != -1) {
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return fileName.substring(0, dotIndex) + suffix;
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} else {
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return fileName + suffix;
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}
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}
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}

‎jabkit/src/test/java/org/jabref/cli/ArgumentProcessorTest.java

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@@ -169,4 +169,23 @@ void checkConsistencyPorcelain() throws URISyntaxException {
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System.setOut(System.out);
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}
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@Test
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void performPseudonymize(@TempDir Path tempDir) throws URISyntaxException {
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Path path = Path.of(Objects.requireNonNull(ArgumentProcessorTest.class.getResource("Chocolate.bib")).toURI());
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String inputFile = path.toAbsolutePath().toString();
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Path fileOutput = tempDir.resolve("Choco_pseudo.bib").toAbsolutePath();
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Path keyOutput = tempDir.resolve("Choco_pseudo_keys.csv").toAbsolutePath();
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List<String> args = List.of(
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"pseudonymize", inputFile,
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"--output", fileOutput.toString(),
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"--key", keyOutput.toString());
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commandLine.execute(args.toArray(String[]::new));
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assertTrue(Files.exists(fileOutput));
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assertTrue(Files.exists(keyOutput));
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}
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}

‎jabkit/src/test/resources/org/jabref/cli/Chocolate.bib

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@Article{Corti_2009,
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author = {Corti, Roberto and Flammer, Andreas J. and Hollenberg, Norman K. and Lüscher, Thomas F.},
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date = {2009-03},
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journaltitle = {Circulation},
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title = {Cocoa and Cardiovascular Health},
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doi = {10.1161/circulationaha.108.827022},
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issn = {1524-4539},
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number = {10},
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pages = {1433--1441},
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volume = {119},
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file = {:DownloadedViaJabRef/Corti et al. (2009-03) Cocoa Cardiovascular Health.pdf:PDF},
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publisher = {Ovid Technologies (Wolters Kluwer Health)},
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}
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@Article{Cooper_2007,
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author = {Cooper, Karen A. and Donovan, Jennifer L. and Waterhouse, Andrew L. and Williamson, Gary},
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date = {2007-08},
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journaltitle = {British Journal of Nutrition},
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title = {Cocoa and health: a decade of research},
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doi = {10.1017/s0007114507795296},
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issn = {1475-2662},
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number = {1},
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pages = {1--11},
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volume = {99},
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file = {:DownloadedViaJabRef/Cooper et al. (2007-08) Cocoa health_ decade.pdf:PDF},
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publisher = {Cambridge University Press (CUP)},
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}
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@Article{Ding_2006,
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author = {Ding, Eric L and Hutfless, Susan M and Ding, Xin and Girotra, Saket},
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date = {2006-01},
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journaltitle = {Nutrition &amp; Metabolism},
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title = {Chocolate and Prevention of Cardiovascular Disease: A Systematic Review},
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doi = {10.1186/1743-7075-3-2},
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issn = {1743-7075},
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number = {1},
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volume = {3},
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file = {:DownloadedViaJabRef/Ding et al. (2006-01) Chocolate Prevention Cardiovascular.pdf:PDF},
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publisher = {Springer Science and Business Media LLC},
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}
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@Article{Keen_2001,
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author = {Keen, Carl L.},
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date = {2001-10},
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journaltitle = {Journal of the American College of Nutrition},
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title = {Chocolate: Food as Medicine/Medicine as Food},
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doi = {10.1080/07315724.2001.10719181},
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issn = {1541-1087},
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number = {sup5},
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pages = {436S--439S},
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volume = {20},
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publisher = {Informa UK Limited},
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}
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@Article{Katz_2011,
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author = {Katz, David L. and Doughty, Kim and Ali, Ather},
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date = {2011-11},
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journaltitle = {Antioxidants &amp; Redox Signaling},
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title = {Cocoa and Chocolate in Human Health and Disease},
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doi = {10.1089/ars.2010.3697},
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issn = {1557-7716},
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number = {10},
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pages = {2779--2811},
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volume = {15},
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file = {:DownloadedViaJabRef/Katz et al. (2011-11) Cocoa Chocolate Human.pdf:PDF},
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publisher = {Mary Ann Liebert Inc},
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readstatus = {skimmed},
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}
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@Article{Parker_2006,
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author = {Parker, Gordon and Parker, Isabella and Brotchie, Heather},
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date = {2006-06},
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journaltitle = {Journal of Affective Disorders},
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title = {Mood state effects of chocolate},
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doi = {10.1016/j.jad.2006.02.007},
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issn = {0165-0327},
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number = {2–3},
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pages = {149--159},
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volume = {92},
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groups = {Used},
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publisher = {Elsevier BV},
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readstatus = {read},
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}
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@Article{Scholey_2013,
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author = {Scholey, Andrew and Owen, Lauren},
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date = {2013-10},
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journaltitle = {Nutrition Reviews},
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title = {Effects of chocolate on cognitive function and mood: a systematic review},
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doi = {10.1111/nure.12065},
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issn = {0029-6643},
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number = {10},
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pages = {665--681},
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volume = {71},
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file = {:Used/Scholey & Owen (2013-10) Effects chocolate cognitive.pdf:PDF},
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groups = {Used},
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publisher = {Oxford University Press (OUP)},
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readstatus = {read},
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}
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@Article{Tan_2021,
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author = {Tan, Terence Yew Chin and Lim, Xin Yi and Yeo, Julie Hsiao Hui and Lee, Shaun Wen Huey and Lai, Nai Ming},
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date = {2021-08},
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journaltitle = {Nutrients},
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title = {The Health Effects of Chocolate and Cocoa: A Systematic Review},
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doi = {10.3390/nu13092909},
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issn = {2072-6643},
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number = {9},
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pages = {2909},
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volume = {13},
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file = {:DownloadedViaJabRef/Tan et al. (2021-08) Health Effects Chocolate.pdf:PDF},
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publisher = {MDPI AG},
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readstatus = {skimmed},
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}
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@Article{Macht_2007,
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author = {Macht, Michael and Mueller, Jochen},
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date = {2007-11},
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journaltitle = {Appetite},
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title = {Immediate effects of chocolate on experimentally induced mood states},
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doi = {10.1016/j.appet.2007.05.004},
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issn = {0195-6663},
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number = {3},
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pages = {667--674},
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volume = {49},
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groups = {Used},
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publisher = {Elsevier BV},
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readstatus = {read},
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}
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@Article{Tokede_2011,
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author = {Tokede, O A and Gaziano, J M and Djoussé, L},
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date = {2011-05},
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journaltitle = {European Journal of Clinical Nutrition},
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title = {Effects of cocoa products/dark chocolate on serum lipids: a meta-analysis},
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doi = {10.1038/ejcn.2011.64},
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issn = {1476-5640},
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number = {8},
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pages = {879--886},
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volume = {65},
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publisher = {Springer Science and Business Media LLC},
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}
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@Article{Garcia_2018,
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author = {Garcia, Jose P and Santana, Adrian and Baruqui, Diego Lugo and Suraci, Nicholas},
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date = {2018-12},
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journaltitle = {Reviews in Cardiovascular Medicine},
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title = {The Cardiovascular effects of chocolate.},
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doi = {10.31083/j.rcm.2018.04.3187},
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issn = {2153-8174},
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number = {4},
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volume = {19},
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publisher = {IMR Press},
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}
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@Article{Hooper_2012,
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author = {Hooper, Lee and Kay, Colin and Abdelhamid, Asmaa and Kroon, Paul A and Cohn, Jeffrey S and Rimm, Eric B and Cassidy, Aedín},
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date = {2012-03},
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journaltitle = {The American Journal of Clinical Nutrition},
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title = {Effects of chocolate, cocoa, and flavan-3-ols on cardiovascular health: a systematic review and meta-analysis of randomized trials},
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doi = {10.3945/ajcn.111.023457},
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issn = {0002-9165},
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number = {3},
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pages = {740--751},
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volume = {95},
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publisher = {Elsevier BV},
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readstatus = {skimmed},
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}
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@Article{Di_Renzo_2012,
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author = {Di Renzo, Gian Carlo and Brillo, Eleonora and Romanelli, Maila and Porcaro, Giuseppina and Capanna, Federica and Kanninen, Tomi T and Gerli, Sandro and Clerici, Graziano},
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date = {2012-06},
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journaltitle = {The Journal of Maternal-Fetal &amp; Neonatal Medicine},
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title = {Potential effects of chocolate on human pregnancy: a randomized controlled trial},
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doi = {10.3109/14767058.2012.683085},
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issn = {1476-4954},
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number = {10},
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pages = {1860--1867},
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volume = {25},
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groups = {Used},
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publisher = {Informa UK Limited},
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readstatus = {read},
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}
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@Article{Richard_2017,
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author = {Richard, Anna and Meule, Adrian and Friese, Malte and Blechert, Jens},
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date = {2017-09},
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journaltitle = {Frontiers in Psychology},
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title = {Effects of Chocolate Deprivation on Implicit and Explicit Evaluation of Chocolate in High and Low Trait Chocolate Cravers},
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doi = {10.3389/fpsyg.2017.01591},
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issn = {1664-1078},
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volume = {8},
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groups = {Used},
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publisher = {Frontiers Media SA},
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readstatus = {read},
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}
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@Article{Fulton_1969,
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author = {Fulton, James E., Jr. and Plewig, Gerd and Kligman, Albert M.},
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date = {1969-12},
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journaltitle = {JAMA: The Journal of the American Medical Association},
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title = {{Effect of Chocolate on Acne Vulgaris}},
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doi = {10.1001/jama.1969.03160370055011},
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eprint = {https://jamanetwork.com/journals/jama/articlepdf/350738/jama\_210\_11\_011.pdf},
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issn = {0098-7484},
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number = {11},
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pages = {2071-2074},
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url = {https://doi.org/10.1001/jama.1969.03160370055011},
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volume = {210},
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publisher = {American Medical Association (AMA)},
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}
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@Comment{jabref-meta: databaseType:biblatex;}
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@Comment{jabref-meta: grouping:
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0 AllEntriesGroup:;
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1 SearchGroup:Entries without a group\;0\;groups !=~ .+\;0\;1\;1\;\;\;\;;
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1 SearchGroup:Entries without a linked file\;0\;file !=~ .+\;0\;1\;1\;\;\;\;;
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1 StaticGroup:Paywalled\;0\;1\;\;\;\;;
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1 SearchGroup:To read\;0\;groups !=~ .+ and readstatus !=~ .+\;0\;1\;1\;0x008080ff\;\;\;;
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1 KeywordGroup:Skimmed\;0\;readstatus\;skimmed\;0\;0\;1\;0xffff00ff\;\;\;;
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1 KeywordGroup:Read\;0\;readstatus\;read\;0\;0\;0\;0x00ff00ff\;\;\;;
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1 StaticGroup:Used\;0\;1\;0x0000ffff\;\;\;;
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}
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@Comment{jabref-meta: groups-search-syntax-version:6.0-alpha_1}

‎jablib/src/main/java/module-info.java

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exports org.jabref.logic.shared.event;
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exports org.jabref.logic.crawler;
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exports org.jabref.logic.git;
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exports org.jabref.logic.pseudonymization;
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requires javafx.base;
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requires javafx.graphics;

‎jablib/src/main/resources/l10n/JabRef_en.properties

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Unable\ to\ open\ file\ '%0'.=Unable to open file '%0'.
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Unknown\ export\ format\ '%0'.=Unknown export format '%0'.
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Updating\ PDF\ metadata.=Updating PDF metadata.
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Anonymizing\ the\ library\ '%0'\ ...=Anonymizing the library '%0' ...
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Unable\ to\ save\ keys\:\ %0=Unable to save keys: %0

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