cleanup unused code

src/main/java/life/qbic/io/PetabParser.java

@@ -2,7 +2,6 @@
 
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileOutputStream;
 import java.io.FileReader;
 import java.io.IOException;
 import java.nio.charset.Charset;
@@ -12,7 +11,6 @@
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
 import java.util.Objects;
 import life.qbic.model.petab.PetabMetadata;
 
@@ -84,31 +82,4 @@ private File findYaml(File directory) {
     return null;
   }
 
-  /**
-   * adds key-value pairs to the bottom of a petab.yaml found below the provided path
-   *
-   * @param outputPath the path of the PEtab
-   * @param properties map of properties to add
-   */
-  public void addParameters(String outputPath, Map<String, String> properties) {
-
-    File directory = new File(outputPath);
-
-    File yaml = findYaml(directory);
-    if (yaml != null) {
-      FileOutputStream fos = null;
-      try {
-        fos = new FileOutputStream(yaml.getPath(), true);
-        for (Map.Entry<String, String> entry : properties.entrySet()) {
-          String line = entry.getKey() + ": " + entry.getValue() + "\n";
-          fos.write(line.getBytes());
-        }
-        fos.close();
-      } catch (IOException e) {
-        throw new RuntimeException(e);
-      }
-    }
-  }
-
-
 }

src/main/java/life/qbic/io/commandline/DownloadPetabCommand.java

@@ -54,7 +54,6 @@ public void run() {
         System.out.println("Could not add dataset identifier.");
         throw new RuntimeException(e);
       }
-      //parser.addParameters(outputPath, result.getProperties()); //TODO: might be used in the future
       System.out.println("Done");
     }
 

src/main/java/life/qbic/io/commandline/UploadPetabResultCommand.java

@@ -58,7 +58,8 @@ public void run() {
       }
       System.out.println();
       System.out.println("Reference datasets found, uploading dataset...");
-      System.out.println();//TODO copy and remove source references
+      System.out.println();
+      //TODO copy and remove source references here
       DataSetPermId result = openbis.registerDataset(Path.of(dataPath), experimentID, parents);
       System.out.printf("Dataset %s was successfully created%n", result.getPermId());
     }