feat: move data changelog exporter to java from node

Author: whaleyr

src/main/java/org/cpicpgx/DataArtifactArchive.java

@@ -1,6 +1,7 @@
 package org.cpicpgx;
 
 import org.apache.commons.cli.*;
+import org.checkerframework.checker.units.qual.C;
 import org.cpicpgx.exporter.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -71,6 +72,7 @@ private void write() throws IOException {
     exporters.add(new TestAlertExporter());
     exporters.add(new PairsExporter());
     exporters.add(new AlleleSummaryExporter());
+    exporters.add(new ChangelogExporter());
 
     exporters.forEach(e -> {
       Path dirPath = getDirectoryPath(e.getFileType().name().toLowerCase());

src/main/java/org/cpicpgx/exporter/ChangelogExporter.java

@@ -0,0 +1,50 @@
+package org.cpicpgx.exporter;
+
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVPrinter;
+import org.cpicpgx.db.ConnectionFactory;
+import org.cpicpgx.model.FileType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.FileWriter;
+import java.lang.invoke.MethodHandles;
+import java.nio.file.Path;
+import java.sql.Connection;
+import java.sql.ResultSet;
+
+public class ChangelogExporter extends BaseExporter {
+    private static final Logger sf_logger = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+    private static final String FILE_NAME = "data.tsv";
+    private static final String SQL_STMT = "select date as \"Date of Change\", type as \"Type of Data\", entityname as \"Subject\", note as \"Note of Change\" from change_log_view order by date desc, type, entityname, note";
+
+    public static void main(String[] args) {
+        ChangelogExporter exporter = new ChangelogExporter();
+        try {
+            exporter.parseArgs(args);
+            exporter.export();
+        } catch (Exception e) {
+            sf_logger.error("Error exporting changelog", e);
+        }
+    }
+
+    @Override
+    public FileType getFileType() {
+        return FileType.CHANGELOG;
+    }
+
+    @Override
+    public void export() throws Exception {
+        Path filePath = this.directory.resolve(FILE_NAME);
+        try (
+                FileWriter fileWriter = new FileWriter(filePath.toFile());
+                Connection conn = ConnectionFactory.newConnection();
+                ResultSet rs = conn.prepareStatement(SQL_STMT).executeQuery();
+                CSVPrinter printer = CSVFormat.TDF.builder()
+                        .setHeader(rs)
+                        .build().print(fileWriter)
+        ) {
+            printer.printRecords(rs);
+        }
+    }
+}

src/main/java/org/cpicpgx/model/FileType.java

@@ -10,6 +10,7 @@ public enum FileType {
   ALLELE_DEFINITION,
   ALLELE_FUNCTION_REFERENCE,
   ALLELE_SUMMARY,
+  CHANGELOG,
   DIPLOTYPE_PHENOTYPE,
   DRUG_RESOURCE,
   DRUG_REVIEW,