Implement plugin to fixup biom migration for VDI

Model/src/main/java/org/gusdb/wdk/model/fix/table/edaanalysis/plugins/BiomVdiMigrationFixer.java

@@ -0,0 +1,78 @@
+package org.gusdb.wdk.model.fix.table.edaanalysis.plugins;
+
+import org.apache.log4j.Logger;
+import org.gusdb.wdk.model.WdkModel;
+import org.gusdb.wdk.model.fix.table.TableRowInterfaces;
+import org.gusdb.wdk.model.fix.table.edaanalysis.AbstractAnalysisUpdater;
+import org.gusdb.wdk.model.fix.table.edaanalysis.AnalysisRow;
+import org.json.JSONObject;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Pattern;
+import java.util.stream.Collectors;
+
+public class BiomVdiMigrationFixer extends AbstractAnalysisUpdater {
+  private static final Logger LOG = Logger.getLogger(BiomVdiMigrationFixer.class);
+  private static final Pattern VAR_ID_PATTERN = Pattern.compile("variableId\":\\s*\"([a-zA-Z0-9\\._-]+)");
+
+  private Map<String, String> fixedUpMapping;
+
+  @Override
+  public void configure(WdkModel wdkModel, List<String> additionalArgs) throws Exception {
+    this.fixedUpMapping = readFixedUpMapping(Path.of(additionalArgs.get(0)));
+    this._writeToDb = additionalArgs.size() == 2 && additionalArgs.get(1).equals("-write");
+  }
+
+  @Override
+  public boolean isPerformTableBackup() {
+    return _writeToDb;
+  }
+
+  @Override
+  public TableRowInterfaces.RowResult<AnalysisRow> processRecord(AnalysisRow nextRow) throws Exception {
+    if (!nextRow.getDatasetId().startsWith("EDAUD")) {
+      new TableRowInterfaces.RowResult<>(nextRow)
+          .setShouldWrite(false);
+    }
+    String descriptor = nextRow.getDescriptor().toString();
+    LOG.info("Analysis descriptor before migration: " + descriptor);
+
+    // Find all variable IDs.
+    final Set<String> currentVarIds = VAR_ID_PATTERN.matcher(descriptor).results()
+        .map(match -> match.group(1))
+        .collect(Collectors.toSet());
+
+    // Replace all variable IDs with value converted from legacy variable ID.
+    for (String currentVarId: currentVarIds) {
+      descriptor = descriptor.replaceAll(currentVarId, fixupId(currentVarId));
+    }
+
+    // Create a copy with just the dataset ID updated to VDI counterpart.
+    nextRow.setDescriptor(new JSONObject(descriptor));
+
+    LOG.info("Analysis descriptor after migration: " + descriptor);
+
+    return new TableRowInterfaces.RowResult<>(nextRow)
+        .setShouldWrite(_writeToDb);
+  }
+
+  private Map<String, String> readFixedUpMapping(Path mappingFile) throws IOException {
+    return Files.readAllLines(mappingFile).stream()
+        .map(line -> line.split(","))
+        .collect(Collectors.toMap(tokens -> tokens[0], tokens -> tokens[1]));
+  }
+
+  private String fixupId(String currentVarId) {
+    return this.fixedUpMapping.getOrDefault(currentVarId, currentVarId);
+  }
+
+  @Override
+  public void dumpStatistics() {
+
+  }
+}