Write measurement ID into provenance file

qbicsoftware · Apr 16, 2024 · 7b00866 · 7b00866
1 parent 2c2e892
commit 7b00866
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diff --git a/src/main/java/life/qbic/data/processing/Provenance.java b/src/main/java/life/qbic/data/processing/Provenance.java
@@ -39,6 +39,9 @@ public class Provenance {
   @JsonProperty("user")
   public String userWorkDirectoryPath;
 
+  @JsonProperty("measurementId")
+  public String qbicMeasurementID;
+
   /**
    * A list of ordered processing folder stops the dataset has traversed and passed successfully.
    * <p>

diff --git a/src/main/java/life/qbic/data/processing/evaluation/EvaluationRequest.java b/src/main/java/life/qbic/data/processing/evaluation/EvaluationRequest.java
@@ -2,6 +2,7 @@
 
 import static org.apache.logging.log4j.LogManager.getLogger;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
@@ -149,6 +150,14 @@ private void evaluateDirectory(File taskDir) {
     Matcher matcher = measurementIdPattern.matcher(dataset.getName());
     var measurementIdResult = matcher.results().map(MatchResult::group).findFirst();
     if (measurementIdResult.isPresent()) {
+      provenance.qbicMeasurementID = measurementIdResult.get();
+      provenance.addToHistory(taskDir.getAbsolutePath());
+      try {
+        updateProvenanceFile(provenanceSearch.get(), provenance);
+      } catch (IOException e) {
+        LOG.error("Could not update provenance file: %s".formatted(taskDir.getAbsolutePath()), e);
+        moveToSystemIntervention(taskDir, e.getMessage());
+      }
       moveToTargetDir(taskDir);
       try {
         createMarkerFile(targetDirectory, taskDir.getName());
@@ -166,6 +175,11 @@ private void evaluateDirectory(File taskDir) {
     moveBackToOrigin(taskDir, provenance, errorMessage.toString());
   }
 
+  private void updateProvenanceFile(File provenanceFile, Provenance provenance) throws IOException {
+    var mapper = new ObjectMapper();
+    mapper.writerWithDefaultPrettyPrinter().writeValue(provenanceFile, provenance);
+  }
+
   private boolean createMarkerFile(Path targetDirectory, String name) throws IOException {
     Path markerFileName = Paths.get(".MARKER_is_finished_" + name);
     return targetDirectory.resolve(markerFileName).toFile().createNewFile();