Rename toolkit command line option

oshando · oshando · commit c54207e1050a · 2022-01-17T12:25:22.000+01:00
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/cli/CliRunner.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/cli/CliRunner.java
@@ -25,8 +25,8 @@ public class CliRunner implements Callable<Integer> {
     @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");
 
-    @CommandLine.Option(names = {"-l", "--learning"}, description = {"Learning modes: meka, weka, ml-plan"})
-    private String learningMode = "meka";
+    @CommandLine.Option(names = {"-t", "--toolkit"}, description = {"ML toolkit: meka, weka, ml-plan"})
+    private String toolkit = "meka";
 
     @CommandLine.Option(names = {"-s", "--srm"}, description = {"SRM: all, source, sink, sanitizer, authentication, relevant"})
     private List<String> srmClasses = Collections.singletonList("all");
@@ -61,7 +61,7 @@ public Integer call() throws Exception {
                 datasetJson,
                 outputDir,
                 featureSet,
-                learningMode,
+                toolkit,
                 srmClasses,
                 cweClasses,
                 exportArffData,
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/cli/SwanOptions.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/cli/SwanOptions.java
@@ -15,7 +15,7 @@ public class SwanOptions {
     private String datasetJson;
     private String outputDir;
     private List<String> featureSet;
-    private String learningMode;
+    private String toolkit;
     private List<String> srmClasses;
     private List<String> cweClasses;
     private boolean exportArffData;
@@ -26,15 +26,15 @@ public class SwanOptions {
     private double predictionThreshold;
 
     public SwanOptions(String testDataDir, String trainDataDir, String datasetJson, String outputDir,
-                       List<String> featureSet, String learningMode, List<String> srmClasses,
+                       List<String> featureSet, String toolkit, List<String> srmClasses,
                        List<String> cweClasses, boolean exportArffData, boolean isDocumented,
                        int iterations, double trainTestSplit, String phase) {
         this.testDataDir = testDataDir;
         this.trainDataDir = trainDataDir;
         this.datasetJson = datasetJson;
         this.outputDir = outputDir;
         this.featureSet = featureSet;
-        this.learningMode = learningMode;
+        this.toolkit = toolkit;
         this.srmClasses = srmClasses;
         this.cweClasses = cweClasses;
         this.exportArffData = exportArffData;
@@ -45,14 +45,14 @@ public SwanOptions(String testDataDir, String trainDataDir, String datasetJson,
     }
 
     public SwanOptions(String testDataDir, String trainDataDir, String datasetJson, String outputDir,
-                       List<String> featureSet, String learningMode, List<String> srmClasses, List<String> cweClasses,
+                       List<String> featureSet, String toolkit, List<String> srmClasses, List<String> cweClasses,
                        boolean exportArffData, boolean isDocumented, int iterations, double trainTestSplit) {
         this.testDataDir = testDataDir;
         this.trainDataDir = trainDataDir;
         this.datasetJson = datasetJson;
         this.outputDir = outputDir;
         this.featureSet = featureSet;
-        this.learningMode = learningMode;
+        this.toolkit = toolkit;
         this.srmClasses = srmClasses;
         this.cweClasses = cweClasses;
         this.exportArffData = exportArffData;
@@ -101,12 +101,12 @@ public void setFeatureSet(List<String> featureSet) {
         this.featureSet = featureSet;
     }
 
-    public String getLearningMode() {
-        return learningMode;
+    public String getToolkit() {
+        return toolkit;
     }
 
-    public void setLearningMode(String learningMode) {
-        this.learningMode = learningMode;
+    public void setToolkit(String toolkit) {
+        this.toolkit = toolkit;
     }
 
     public List<String> getSrmClasses() {
@@ -185,7 +185,7 @@ public String toString() {
                 ", datasetJson='" + datasetJson + '\'' +
                 ", outputDir='" + outputDir + '\'' +
                 ", featureSet='" + featureSet + '\'' +
-                ", learningMode='" + learningMode + '\'' +
+                ", learningMode='" + toolkit + '\'' +
                 ", srmClasses=" + srmClasses +
                 ", cweClasses=" + cweClasses +
                 ", exportArffData=" + exportArffData +
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/features/FeatureSet.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/features/FeatureSet.java
@@ -29,7 +29,7 @@ abstract class FeatureSet {
     protected SourceFileLoader testData;
     protected DocFeatureHandler docFeatureHandler;
     protected HashMap<String, Instances> instances;
-    protected ModelEvaluator.Mode mode;
+    protected ModelEvaluator.Toolkit toolkit;
 
     /**
      * Available feature sets:
@@ -58,12 +58,12 @@ public static FeatureSet.Type getValue(String value) {
         }
     }
 
-    public FeatureSet(SrmList trainData, SourceFileLoader testData, SwanOptions options, ModelEvaluator.Mode mode) {
+    public FeatureSet(SrmList trainData, SourceFileLoader testData, SwanOptions options, ModelEvaluator.Toolkit toolkit) {
         this.instanceMap = new HashMap<>();
         this.options = options;
         this.trainData = trainData;
         this.testData = testData;
-        this.mode = mode;
+        this.toolkit = toolkit;
         instances = new HashMap<>();
     }
 
@@ -232,7 +232,7 @@ public ArrayList<Instance> getCodeInstances(Instances instances, Set<Method> met
             for (Category cat : categories) {
                 if (cat.isAuthentication() && !method.getAuthSrm().isEmpty()) {
 
-                    if (mode == ModelEvaluator.Mode.MEKA)
+                    if (toolkit == ModelEvaluator.Toolkit.MEKA)
                         inst.setValue(instances.attribute(cat.getId()), "1");
                     else {
                         for (Category auth : method.getAuthSrm()) {
@@ -302,7 +302,7 @@ public ArrayList<Instance> getDocInstances(Instances instances, Set<Method> meth
                 inst.setDataset(instances);
                 isNewInstance = true;
 
-                switch (mode) {
+                switch (toolkit) {
                     case MEKA:
                         for (Category cat : categories) {
                             if (method.getAllCategories().contains(cat) || (cat.isAuthentication() && !method.getAuthSrm().isEmpty())) {
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/features/FeatureSetSelector.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/features/FeatureSetSelector.java
@@ -9,7 +9,7 @@ public class FeatureSetSelector {
 
     public IFeatureSet select(SrmList trainData, SourceFileLoader testData, SwanOptions options) {
 
-        switch (ModelEvaluator.Mode.valueOf(options.getLearningMode().toUpperCase())) {
+        switch (ModelEvaluator.Toolkit.valueOf(options.getToolkit().toUpperCase())) {
 
             case MEKA:
                 MekaFeatureSet mekaFeatureSet = new MekaFeatureSet(trainData, testData, options);
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/features/MekaFeatureSet.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/features/MekaFeatureSet.java
@@ -17,7 +17,7 @@
 public class MekaFeatureSet extends FeatureSet implements IFeatureSet {
 
     public MekaFeatureSet(SrmList trainData, SourceFileLoader testData, SwanOptions options) {
-        super(trainData, testData, options, ModelEvaluator.Mode.MEKA);
+        super(trainData, testData, options, ModelEvaluator.Toolkit.MEKA);
     }
 
     /**
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/features/WekaFeatureSet.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/features/WekaFeatureSet.java
@@ -19,7 +19,7 @@
 public class WekaFeatureSet extends FeatureSet implements IFeatureSet {
 
     public WekaFeatureSet(SrmList trainData, SourceFileLoader testData, SwanOptions options) {
-        super(trainData, testData, options, ModelEvaluator.Mode.WEKA);
+        super(trainData, testData, options, ModelEvaluator.Toolkit.WEKA);
     }
 
     /**
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/model/ModelEvaluator.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/model/ModelEvaluator.java
@@ -5,9 +5,9 @@
 import de.fraunhofer.iem.swan.features.IFeatureSet;
 import de.fraunhofer.iem.swan.features.MekaFeatureSet;
 import de.fraunhofer.iem.swan.features.WekaFeatureSet;
-import de.fraunhofer.iem.swan.model.engine.MLPlan;
-import de.fraunhofer.iem.swan.model.engine.Meka;
-import de.fraunhofer.iem.swan.model.engine.Weka;
+import de.fraunhofer.iem.swan.model.toolkit.MLPlan;
+import de.fraunhofer.iem.swan.model.toolkit.Meka;
+import de.fraunhofer.iem.swan.model.toolkit.Weka;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import java.util.Set;
@@ -20,7 +20,7 @@
  */
 public class ModelEvaluator {
 
-    public enum Mode {
+    public enum Toolkit {
         WEKA,
         MEKA,
         MLPLAN
@@ -49,7 +49,7 @@ public ModelEvaluator(IFeatureSet features, SwanOptions options, Set<Method> met
      */
     public void trainModel() {
 
-        switch (Mode.valueOf(options.getLearningMode().toUpperCase())) {
+        switch (Toolkit.valueOf(options.getToolkit().toUpperCase())) {
 
             case MEKA:
                 logger.info("Evaluating model with MEKA");
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/model/toolkit/MLPlan.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/model/toolkit/MLPlan.java
@@ -1,4 +1,4 @@
-package de.fraunhofer.iem.swan.model.engine;
+package de.fraunhofer.iem.swan.model.toolkit;
 
 import ai.libs.jaicore.ml.classification.loss.dataset.EClassificationPerformanceMeasure;
 import ai.libs.jaicore.ml.core.dataset.schema.attribute.IntBasedCategoricalAttribute;
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/model/toolkit/Meka.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/model/toolkit/Meka.java
@@ -1,4 +1,4 @@
-package de.fraunhofer.iem.swan.model.engine;
+package de.fraunhofer.iem.swan.model.toolkit;
 
 import de.fraunhofer.iem.swan.cli.SwanOptions;
 import de.fraunhofer.iem.swan.data.Category;
diff --git a/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/model/toolkit/Weka.java b/swan-pipeline/src/main/java/de/fraunhofer/iem/swan/model/toolkit/Weka.java
@@ -1,4 +1,4 @@
-package de.fraunhofer.iem.swan.model.engine;
+package de.fraunhofer.iem.swan.model.toolkit;
 
 import de.fraunhofer.iem.swan.cli.SwanOptions;
 import de.fraunhofer.iem.swan.features.WekaFeatureSet;

Original file line number	Diff line number	Diff line change
`@@ -17,7 +17,7 @@`
`17`	`17`	`public class MekaFeatureSet extends FeatureSet implements IFeatureSet {`
`18`	`18`
`19`	`19`	`public MekaFeatureSet(SrmList trainData, SourceFileLoader testData, SwanOptions options) {`
`20`		`- super(trainData, testData, options, ModelEvaluator.Mode.MEKA);`
	`20`	`+ super(trainData, testData, options, ModelEvaluator.Toolkit.MEKA);`
`21`	`21`	`}`
`22`	`22`
`23`	`23`	`/**`
Original file line number	Diff line number	Diff line change
`@@ -19,7 +19,7 @@`
`19`	`19`	`public class WekaFeatureSet extends FeatureSet implements IFeatureSet {`
`20`	`20`
`21`	`21`	`public WekaFeatureSet(SrmList trainData, SourceFileLoader testData, SwanOptions options) {`
`22`		`- super(trainData, testData, options, ModelEvaluator.Mode.WEKA);`
	`22`	`+ super(trainData, testData, options, ModelEvaluator.Toolkit.WEKA);`
`23`	`23`	`}`
`24`	`24`
`25`	`25`	`/**`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-package de.fraunhofer.iem.swan.model.engine;`
	`1`	`+package de.fraunhofer.iem.swan.model.toolkit;`
`2`	`2`
`3`	`3`	`import ai.libs.jaicore.ml.classification.loss.dataset.EClassificationPerformanceMeasure;`
`4`	`4`	`import ai.libs.jaicore.ml.core.dataset.schema.attribute.IntBasedCategoricalAttribute;`