Add Pseudonymization to CLI

.jbang/JabKitLauncher.java

@@ -15,6 +15,7 @@
 //SOURCES ../jabkit/src/main/java/org/jabref/cli/Pdf.java
 //SOURCES ../jabkit/src/main/java/org/jabref/cli/PdfUpdate.java
 //SOURCES ../jabkit/src/main/java/org/jabref/cli/Preferences.java
+//SOURCES ../jabkit/src/main/java/org/jabref/cli/Pseudonymize.java
 //SOURCES ../jabkit/src/main/java/org/jabref/cli/Search.java
 //SOURCES ../jabkit/src/main/java/org/jabref/JabKit.java
 //FILES tinylog.properties=../jabkit/src/main/resources/tinylog.properties

CHANGELOG.md

@@ -24,6 +24,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added an "Open example library" button to Welcome Tab. [#13014](https://github.com/JabRef/jabref/issues/13014)
 - 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)
 - We added support for import of a Refer/BibIX file format. [#13069](https://github.com/JabRef/jabref/issues/13069)
+- We added a new `jabkit` command `pseudonymize` to pseudonymize the library. [#13109](https://github.com/JabRef/jabref/issues/13109)
 - We added functionality to focus running instance when trying to start a second instance. [#13129](https://github.com/JabRef/jabref/issues/13129)
 
 ### Changed

jabkit/build.gradle.kts

@@ -57,6 +57,8 @@ dependencies {
 
     implementation("org.apache.lucene:lucene-queryparser:${luceneVersion}")
 
+    implementation("io.github.adr:e-adr:2.0.0-SNAPSHOT")
+
     testImplementation(project(":test-support"))
     testImplementation("org.mockito:mockito-core:5.18.0") {
         exclude(group = "net.bytebuddy", module = "byte-buddy")

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

@@ -20,5 +20,10 @@
     requires org.tinylog.api;
     requires org.tinylog.api.slf4j;
     requires org.tinylog.impl;
+
     requires java.xml;
+
+    // region: other libraries (alphabetically)
+    requires io.github.adr;
+    // endregion
 }

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

@@ -24,6 +24,7 @@
 import org.jabref.logic.os.OS;
 import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.util.BuildInfo;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -38,16 +39,18 @@
 
 @Command(name = "jabkit",
         mixinStandardHelpOptions = true,
+        // sorted alphabetically
         subcommands = {
-                GenerateCitationKeys.class,
                 CheckConsistency.class,
 //                CheckIntegrity.class,
-                Fetch.class,
-                Search.class,
                 Convert.class,
+                Fetch.class,
                 GenerateBibFromAux.class,
+                GenerateCitationKeys.class,
+                Pdf.class,
                 Preferences.class,
-                Pdf.class
+                Pseudonymize.class,
+                Search.class
         })
 public class ArgumentProcessor implements Runnable {
     private static final Logger LOGGER = LoggerFactory.getLogger(ArgumentProcessor.class);
@@ -150,8 +153,17 @@ protected static void saveDatabase(CliPreferences cliPreferences,
                                        BibEntryTypesManager entryTypesManager,
                                        BibDatabase newBase,
                                        Path outputFile) {
+        saveDatabaseContext(cliPreferences, entryTypesManager, new BibDatabaseContext(newBase), outputFile);
+    }
+
+    protected static void saveDatabaseContext(CliPreferences cliPreferences,
+                                       BibEntryTypesManager entryTypesManager,
+                                       BibDatabaseContext bibDatabaseContext,
+                                       Path outputFile) {
         try {
-            System.out.println(Localization.lang("Saving") + ": " + outputFile);
+            if (!FileUtil.isBibFile(outputFile)) {
+                System.err.println(Localization.lang("Invalid output file type provided."));
+            }
             try (AtomicFileWriter fileWriter = new AtomicFileWriter(outputFile, StandardCharsets.UTF_8)) {
                 BibWriter bibWriter = new BibWriter(fileWriter, OS.NEWLINE);
                 SelfContainedSaveConfiguration saveConfiguration = (SelfContainedSaveConfiguration) new SelfContainedSaveConfiguration()
@@ -162,13 +174,14 @@ protected static void saveDatabase(CliPreferences cliPreferences,
                         cliPreferences.getFieldPreferences(),
                         cliPreferences.getCitationKeyPatternPreferences(),
                         entryTypesManager);
-                databaseWriter.saveDatabase(new BibDatabaseContext(newBase));
+                databaseWriter.saveDatabase(bibDatabaseContext);
 
                 // Show just a warning message if encoding did not work for all characters:
                 if (fileWriter.hasEncodingProblems()) {
                     System.err.println(Localization.lang("Warning") + ": "
                             + Localization.lang("UTF-8 could not be used to encode the following characters: %0", fileWriter.getEncodingProblems()));
                 }
+                System.out.println(Localization.lang("Saved %0.", outputFile));
             }
         } catch (IOException ex) {
             System.err.println(Localization.lang("Could not save file.") + "\n" + ex.getLocalizedMessage());

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

@@ -0,0 +1,118 @@
+package org.jabref.cli;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Optional;
+
+import org.jabref.logic.importer.ParserResult;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.pseudonymization.Pseudonymization;
+import org.jabref.logic.pseudonymization.PseudonymizationResultCsvWriter;
+import org.jabref.logic.util.io.FileUtil;
+import org.jabref.model.database.BibDatabaseContext;
+
+import io.github.adr.linked.ADR;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Mixin;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.ParentCommand;
+
+@Command(name = "pseudonymize", description = "Perform pseudonymization of the library")
+public class Pseudonymize implements Runnable {
+    private final static Logger LOGGER = LoggerFactory.getLogger(Pseudonymize.class);
+    private static final String PSEUDO_SUFFIX = ".pseudo";
+    private static final String BIB_EXTENSION = ".bib";
+    private static final String CSV_EXTENSION = ".csv";
+
+    @ParentCommand
+    private ArgumentProcessor argumentProcessor;
+
+    @Mixin
+    private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
+
+    @ADR(45)
+    @Option(names = {"--input"}, description = "BibTeX file to be pseudonymized", required = true)
+    private String inputFile;
+
+    @Option(names = {"--output"}, description = "Output pseudo-bib file")
+    private String outputFile;
+
+    @Option(names = {"--key"}, description = "Output pseudo-keys file")
+    private String keyFile;
+
+    @Option(names = {"-f", "--force"}, description = "Overwrite output file(s) if any exist(s)")
+    private boolean force;
+
+    @Override
+    public void run() {
+        Path inputPath = Path.of(inputFile);
+        String fileName = FileUtil.getBaseName(inputFile);
+        Path pseudoBibPath = resolveOutputPath(outputFile, inputPath, fileName + PSEUDO_SUFFIX + BIB_EXTENSION);
+        Path pseudoKeyPath = resolveOutputPath(keyFile, inputPath, fileName + PSEUDO_SUFFIX + CSV_EXTENSION);
+
+        Optional<ParserResult> parserResult = ArgumentProcessor.importFile(
+                inputFile,
+                "bibtex",
+                argumentProcessor.cliPreferences,
+                sharedOptions.porcelain);
+
+        if (parserResult.isEmpty()) {
+            System.out.println(Localization.lang("Unable to open file '%0'.", inputFile));
+            return;
+        }
+
+        if (parserResult.get().isInvalid()) {
+            System.out.println(Localization.lang("Input file '%0' is invalid and could not be parsed.", inputFile));
+            return;
+        }
+
+        System.out.println(Localization.lang("Pseudonymizing library '%0'...", fileName));
+        Pseudonymization pseudonymization = new Pseudonymization();
+        BibDatabaseContext databaseContext = parserResult.get().getDatabaseContext();
+        Pseudonymization.Result result = pseudonymization.pseudonymizeLibrary(databaseContext);
+
+        if (!fileOverwriteCheck(pseudoBibPath)) {
+            return;
+        }
+
+        ArgumentProcessor.saveDatabaseContext(
+                argumentProcessor.cliPreferences,
+                argumentProcessor.entryTypesManager,
+                result.bibDatabaseContext(),
+                pseudoBibPath);
+
+        if (!fileOverwriteCheck(pseudoKeyPath)) {
+            return;
+        }
+
+        try {
+            PseudonymizationResultCsvWriter.writeValuesMappingAsCsv(pseudoKeyPath, result);
+            System.out.println(Localization.lang("Saved %0.", pseudoKeyPath));
+        } catch (IOException ex) {
+            LOGGER.error("Unable to save keys for pseudonymized library", ex);
+        }
+    }
+
+    private Path resolveOutputPath(String customPath, Path inputPath, String defaultFileName) {
+        return customPath != null ? Path.of(customPath) : inputPath.getParent().resolve(defaultFileName);
+    }
+
+    private boolean fileOverwriteCheck(Path filePath) {
+        if (!Files.exists(filePath)) {
+            return true;
+        }
+
+        String fileName = filePath.getFileName().toString();
+
+        if (!force) {
+            System.out.println(Localization.lang("File '%0' already exists. Use -f or --force to overwrite.", fileName));
+            return false;
+        }
+
+        System.out.println(Localization.lang("File '%0' already exists. Overwriting.", fileName));
+        return true;
+    }
+}

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

@@ -103,6 +103,7 @@
     exports org.jabref.logic.shared.event;
     exports org.jabref.logic.crawler;
     exports org.jabref.logic.git;
+    exports org.jabref.logic.pseudonymization;
 
     requires java.base;
 

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

@@ -2946,3 +2946,8 @@ The\ following\ providers\ are\ available\:=The following providers are availabl
 Unable\ to\ open\ file\ '%0'.=Unable to open file '%0'.
 Unknown\ export\ format\ '%0'.=Unknown export format '%0'.
 Updating\ PDF\ metadata.=Updating PDF metadata.
+File\ '%0'\ already\ exists.\ Overwriting.=File '%0' already exists. Overwriting.
+File\ '%0'\ already\ exists.\ Use\ -f\ or\ --force\ to\ overwrite.=File '%0' already exists. Use -f or --force to overwrite.
+Pseudonymizing\ library\ '%0'...=Pseudonymizing library '%0'...
+Invalid\ output\ file\ type\ provided.=Invalid output file type provided.
+Saved\ %0.=Saved %0.