Feat: Add integrity check to cli

docs/requirements/cli.md

@@ -0,0 +1,14 @@
+---
+parent: Requirements
+---
+# CLI
+
+## Unified `--input` option across all commands
+`req~jabkit.cli.input-flag~1`
+
+All `jabkit` commands that need a file input must have the `--input` option to specify the input file.
+See [ADR 45](../decisions/0045-use-input-flag-always-for-input-files.md) for more details.
+
+Needs: impl
+
+<!-- markdownlint-disable-file MD022 -->

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

@@ -33,6 +33,7 @@ class CheckConsistency implements Callable<Integer> {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
+    // [impl->req~jabkit.cli.input-flag~1]
     @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
     private Path inputFile;
 

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

@@ -28,7 +28,6 @@
 import static picocli.CommandLine.Command;
 import static picocli.CommandLine.Mixin;
 import static picocli.CommandLine.Option;
-import static picocli.CommandLine.Parameters;
 
 @Command(name = "check-integrity", description = "Check integrity of the database.")
 class CheckIntegrity implements Callable<Integer> {
@@ -41,12 +40,14 @@ class CheckIntegrity implements Callable<Integer> {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Parameters(converter = CygWinPathConverter.class, description = "BibTeX file to check", arity = "1")
+    // [impl->req~jabkit.cli.input-flag~1]
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
     private Path inputFile;
 
     @Option(names = {"--output-format"}, description = "Output format: errorformat, txt or csv", defaultValue = "errorformat")
     private String outputFormat;
 
+    // in BibTeX it could be preferences.getEntryEditorPreferences().shouldAllowIntegerEditionBibtex()
     @Option(names = {"--allow-integer-edition"}, description = "Allows Integer edition: true or false", defaultValue = "true")
     private boolean allowIntegerEdition = true;
 

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

@@ -37,6 +37,7 @@ public class Convert implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
+    // [impl->req~jabkit.cli.input-flag~1]
     @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input file", required = true)
     private Path inputFile;
 

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

@@ -5,6 +5,7 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.auxparser.AuxParser;
 import org.jabref.logic.auxparser.AuxParserResult;
 import org.jabref.logic.auxparser.AuxParserStatisticsProvider;
@@ -35,8 +36,9 @@ class GenerateBibFromAux implements Runnable {
     @Option(names = "--aux", required = true)
     private Path auxFile;
 
-    @Option(names = "--input", required = true)
-    private String inputFile;
+    // [impl->req~jabkit.cli.input-flag~1]
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
+    private Path inputFile;
 
     @Option(names = "--output")
     private Path outputFile;

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

@@ -4,6 +4,7 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
@@ -28,8 +29,9 @@ public class GenerateCitationKeys implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Option(names = "--input", description = "The input .bib file.", required = true)
-    private String inputFile;
+    // [impl->req~jabkit.cli.input-flag~1]
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
+    private Path inputFile;
 
     @Option(names = "--output", description = "The output .bib file.")
     private Path outputFile;

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

@@ -9,6 +9,7 @@
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.bibtex.FieldPreferences;
 import org.jabref.logic.exporter.EmbeddedBibFilePdfExporter;
@@ -49,8 +50,9 @@ class PdfUpdate implements Runnable {
     @Option(names = {"-k", "--citation-key"}, description = "Citation keys", required = true)
     private List<String> citationKeys = List.of(); // ToDo: check dedault value
 
-    @Option(names = "--input", description = "Input file", required = true)
-    private Path inputFile; // Local files only
+    // [impl->req~jabkit.cli.input-flag~1]
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
+    private Path inputFile;
 
     @Option(names = "--input-format", description = "Input format of the file", required = true)
     private String inputFormat = "*";

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

@@ -47,6 +47,7 @@ class Search implements Runnable {
     @Option(names = {"--query"}, description = "Search query", required = true)
     private String query;
 
+    // [impl->req~jabkit.cli.input-flag~1]
     @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
     private Path inputFile;
 

jablib/src/main/java/org/jabref/logic/importer/ParserResult.java

@@ -163,8 +163,6 @@ public Map<BibEntry, Range> getArticleRanges() {
     }
 
     public record Range(int startLine, int startColumn, int endLine, int endColumn) {
-        public static Range getNullRange() {
-            return new Range(0, 0, 0, 0);
-        }
+        public static final Range NULL_RANGE = new Range(0, 0, 0, 0);
     }
 }

jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java

@@ -106,6 +106,7 @@ public class BibtexParser implements Parser {
     private int line = 1;
     private int column = 1;
     // Stores the last read column of the highest column number encountered on any line so far.
+    // The intended data structure is Stack, but it is not used because Java code style checkers complain.
     // In basic JDK data structures, there is no size-limited stack. We did not want to include Apache Commons Collections only for "CircularFifoBuffer"
     private final Deque<Integer> highestColumns = new ArrayDeque<>();
 

jablib/src/main/java/org/jabref/logic/integrity/IntegrityCheckResultErrorFormatWriter.java

@@ -14,7 +14,7 @@
 public class IntegrityCheckResultErrorFormatWriter extends IntegrityCheckResultWriter {
 
     private final ParserResult parserResult;
-    private Path inputFile;
+    private final Path inputFile;
 
     public IntegrityCheckResultErrorFormatWriter(Writer writer, List<IntegrityMessage> messages, ParserResult parserResult, Path inputFile) {
         super(writer, messages);
@@ -26,9 +26,9 @@ public IntegrityCheckResultErrorFormatWriter(Writer writer, List<IntegrityMessag
     public void writeFindings() throws IOException {
         for (IntegrityMessage message : messages) {
             Map<Field, ParserResult.Range> fieldRangeMap = parserResult.getFieldRanges().getOrDefault(message.entry(), new HashMap<>());
-            ParserResult.Range fieldRange = fieldRangeMap.getOrDefault(message.field(), fieldRangeMap.getOrDefault(InternalField.KEY_FIELD, parserResult.getArticleRanges().getOrDefault(message.entry(), ParserResult.Range.getNullRange())));
+            ParserResult.Range fieldRange = fieldRangeMap.getOrDefault(message.field(), fieldRangeMap.getOrDefault(InternalField.KEY_FIELD, parserResult.getArticleRanges().getOrDefault(message.entry(), ParserResult.Range.NULL_RANGE)));
 
-            System.out.printf("%s:%d:%d: %s\n".formatted(
+            writer.write("%s:%d:%d: %s\n".formatted(
                     inputFile,
                     fieldRange.startLine(),
                     fieldRange.startColumn(),

jablib/src/main/java/org/jabref/logic/integrity/IntegrityCheckResultTxtWriter.java

@@ -12,9 +12,13 @@ public IntegrityCheckResultTxtWriter(Writer writer, List<IntegrityMessage> messa
 
     @Override
     public void writeFindings() throws IOException {
-        messages.forEach(System.out::println);
+        for (IntegrityMessage message : messages) {
+            writer.write(message.toString());
+            writer.write(System.lineSeparator());
+        }
     }
 
     @Override
-    public void close() throws IOException { }
+    public void close() throws IOException {
+    }
 }