Update CLI options default values and add new options

Author: oshando

swan-pipeline/src/main/java/de/fraunhofer/iem/swan/cli/CliRunner.java

@@ -2,6 +2,7 @@
 
 import picocli.CommandLine;
 
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.concurrent.Callable;
@@ -11,16 +12,19 @@
 public class CliRunner implements Callable<Integer> {
 
     @CommandLine.Option(names = {"-test", "--test-data"}, description = {"Path of test JARs or class files"})
-    private String testDataDir = "/input/test-data";
+    private String testDataDir = "";
 
     @CommandLine.Option(names = {"-train", "--train-data"}, description = {"Path of training JARs or class files"})
-    private String trainDataDir = "/input/train-data";
+    private String trainDataDir = "";
 
     @CommandLine.Option(names = {"-d", "--dataset"}, description = {"Path to JSON dataset file"})
-    private String datasetJson = "/input/dataset/swan-dataset.json";
+    private String datasetJson = "/dataset/swan-dataset.json";
+
+    @CommandLine.Option(names = {"-in", "--train-instances"}, description = {"Path to ARFF files that contain training instances"})
+    private List<String> instancesArff = new ArrayList<>();
 
     @CommandLine.Option(names = {"-o", "--output"}, description = {"Directory to save output files"})
-    private String outputDir = "/swan-output";
+    private String outputDir = "";
 
     @CommandLine.Option(names = {"-f", "--feature"}, description = {"Select one or more feature sets: all, code, doc-auto or doc-manual"})
     private List<String> featureSet =  Collections.singletonList("code");
@@ -52,9 +56,7 @@ public class CliRunner implements Callable<Integer> {
     @CommandLine.Option(names = {"-pt", "--prediction-threshold"}, description = {"Threshold for predicting categories"})
     private double predictionThreshold = 0.5;
 
-
-    @Override
-    public Integer call() throws Exception {
+    public SwanOptions initializeOptions(){
 
         SwanOptions options = new SwanOptions(testDataDir,
                 trainDataDir,
@@ -70,7 +72,14 @@ public Integer call() throws Exception {
                 split,
                 phase);
         options.setPredictionThreshold(predictionThreshold);
+        options.setInstances(instancesArff);
+
+        return options;
+    }
+
+    @Override
+    public Integer call() throws Exception {
 
-        return new SwanCli().run(options);
+        return new SwanCli().run(initializeOptions());
     }
 }

swan-pipeline/src/main/java/de/fraunhofer/iem/swan/cli/SwanCli.java

@@ -4,7 +4,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.List;
 import java.util.concurrent.CancellationException;
 
 /**
@@ -13,39 +15,44 @@
 public class SwanCli {
 
     private static final Logger logger = LoggerFactory.getLogger(SwanCli.class);
+    private SwanPipeline swanPipeline;
 
     public Integer run(SwanOptions options) throws Exception {
 
         FileUtility fileUtility = new FileUtility();
 
-        if (options.getDatasetJson().contentEquals("/input/dataset/swan-dataset.json")) {
+        if (options.getDatasetJson().contentEquals("/dataset/swan-dataset.json")) {
             options.setDatasetJson(fileUtility.getResourceFile(options.getDatasetJson()).getAbsolutePath());
         }
 
-        if (options.getTrainDataDir().contentEquals("/input/train-data")) {
-            options.setTrainDataDir(fileUtility.getResourceDirectory("/input/train-data").getAbsolutePath());
-        }
-
-        if (options.getTestDataDir().contentEquals("/input/test-data")) {
-            options.setTestDataDir(fileUtility.getResourceDirectory("/input/test-data").getAbsolutePath());
-        }
-
-        if(options.getSrmClasses().contains("all")){
+        if (options.getSrmClasses().contains("all")) {
             options.setSrmClasses(Arrays.asList("source", "sink", "sanitizer", "authentication"));
         }
 
-        if(options.getCweClasses().contains("all")){
+        if (options.getCweClasses().contains("all")) {
             options.setCweClasses(Arrays.asList("cwe078", "cwe079", "cwe089", "cwe306", "cwe601", "cwe862", "cwe863"));
         }
 
-        if(options.getFeatureSet().contains("all")){
+        if (options.getFeatureSet().contains("all")) {
             options.setFeatureSet(Arrays.asList("code", "doc-manual", "doc-auto"));
         }
 
+        if (options.getInstances().isEmpty()) {
+
+            List<String> instances = new ArrayList<>();
+
+            for (String feature : options.getFeatureSet()){
+                String filepath = "/dataset/" + options.getToolkit() + "-" + feature + "-instances.arff";
+                instances.add(fileUtility.getResourceFile(filepath).getAbsolutePath());
+            }
+
+            options.setInstances(instances);
+        }
+
         logger.info("SWAN options: {}", options);
 
         try {
-            SwanPipeline swanPipeline = new SwanPipeline(options);
+            swanPipeline = new SwanPipeline(options);
             swanPipeline.run();
 
             return 0;
@@ -60,4 +67,8 @@ public Integer run(SwanOptions options) throws Exception {
             fileUtility.dispose();
         }
     }
+
+    public SwanPipeline getSwanPipeline() {
+        return swanPipeline;
+    }
 }

swan-pipeline/src/main/java/de/fraunhofer/iem/swan/cli/SwanOptions.java

@@ -24,6 +24,7 @@ public class SwanOptions {
     private double trainTestSplit;
     private String phase;
     private double predictionThreshold;
+    private List<String> instancesArff;
 
     public SwanOptions(String testDataDir, String trainDataDir, String datasetJson, String outputDir,
                        List<String> featureSet, String toolkit, List<String> srmClasses,
@@ -177,12 +178,21 @@ public void setPredictionThreshold(double predictionThreshold) {
         this.predictionThreshold = predictionThreshold;
     }
 
+    public List<String> getInstances() {
+        return instancesArff;
+    }
+
+    public void setInstances(List<String> instancesArff) {
+        this.instancesArff = instancesArff;
+    }
+
     @Override
     public String toString() {
         return "SwanOptions{" +
                 "testData='" + testDataDir + '\'' +
                 ", trainData='" + trainDataDir + '\'' +
                 ", datasetJson='" + datasetJson + '\'' +
+                ", instances='" + instancesArff + '\'' +
                 ", outputDir='" + outputDir + '\'' +
                 ", featureSet='" + featureSet + '\'' +
                 ", learningMode='" + toolkit + '\'' +