Replace System.out/err.println with logging in analysis and test code

core/com.ibm.wala.cast.python.test/source/com/ibm/wala/cast/python/test/TestCalls.java

@@ -170,10 +170,10 @@ public Void performAnalysis(PropagationCallGraphBuilder builder) throws CancelEx
   public void testCalls8()
       throws ClassHierarchyException, IllegalArgumentException, CancelException, IOException {
     CallGraph CG = process("calls8.py");
-    System.err.println(CG);
+    LOGGER.info("Call graph for calls8.py: " + CG);
     CG.forEach(
         (n) -> {
-          System.err.println(n.getIR());
+          LOGGER.fine("Node IR: " + n.getIR());
         });
     // verifyGraphAssertions(CG, assertionsCalls6);
   }

core/com.ibm.wala.cast.python.test/source/com/ibm/wala/cast/python/test/TestClasses.java

@@ -6,10 +6,13 @@
 import com.ibm.wala.ipa.cha.ClassHierarchyException;
 import com.ibm.wala.util.CancelException;
 import java.io.IOException;
+import java.util.logging.Logger;
 import org.junit.Test;
 
 public class TestClasses extends TestJythonCallGraphShape {
 
+  private static final Logger LOGGER = Logger.getLogger(TestClasses.class.getName());
+
   protected static final Object[][] assertionsClasses1 =
       new Object[][] {
         new Object[] {ROOT, new String[] {"script classes1.py"}},
@@ -114,7 +117,7 @@ public void testClasses3()
     SSAPropagationCallGraphBuilder builder =
         (SSAPropagationCallGraphBuilder) engine.defaultCallGraphBuilder();
     CallGraph CG = builder.makeCallGraph(builder.getOptions());
-    System.err.println(CG);
+    LOGGER.info("Call graph for classes3.py: " + CG);
     verifyGraphAssertions(CG, assertionsClasses3);
   }
 }

core/com.ibm.wala.cast.python.test/source/com/ibm/wala/cast/python/test/TestSource.java

@@ -4,17 +4,20 @@
 import com.ibm.wala.ipa.cha.ClassHierarchyException;
 import com.ibm.wala.util.CancelException;
 import java.io.IOException;
+import java.util.logging.Logger;
 import org.junit.Test;
 
 public class TestSource extends TestJythonCallGraphShape {
 
+  private static final Logger LOGGER = Logger.getLogger(TestSource.class.getName());
+
   @Test
   public void testSource1()
       throws ClassHierarchyException, IllegalArgumentException, CancelException, IOException {
     CallGraph CG = process("src1.py");
     CG.forEach(
         (n) -> {
-          System.err.println(n.getIR());
+          LOGGER.fine("Node IR: " + n.getIR());
         });
     // verifyGraphAssertions(CG, assertionsCalls1);
   }

core/com.ibm.wala.cast.python/source/com/ibm/wala/cast/python/client/PythonTurtlePandasMergeAnalysis.java

@@ -54,10 +54,14 @@
 import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
+import java.util.logging.Logger;
 import org.json.JSONObject;
 
 public class PythonTurtlePandasMergeAnalysis extends PythonTurtleAnalysisEngine {
 
+  private static final Logger LOGGER =
+      Logger.getLogger(PythonTurtlePandasMergeAnalysis.class.getName());
+
   class DataFrameState {
     private final String fileName;
     private final String sheetName;
@@ -261,7 +265,7 @@ public IntSet getTargets(int d1) {
               ValueState vs = domain.getMappedObject(d1);
               if (AccessPath.isRootedAtLocal(ref, vs.fst)) {
                 ValueState nvs = vs.assign(colName == null ? "*" : colName);
-                System.err.println("found " + nvs);
+                LOGGER.fine("Found value state: " + nvs);
                 if (!domain.hasMappedIndex(nvs)) {
                   domain.add(nvs);
                 }
@@ -278,7 +282,7 @@ public IntSet getTargets(int d1) {
                 if (!domain.hasMappedIndex(nvs)) {
                   domain.add(nvs);
                 }
-                System.err.println("found " + nvs);
+                LOGGER.fine("Found value state: " + nvs);
                 return IntSetUtil.make(new int[] {d1, domain.getMappedIndex(nvs)});
               } else {
                 return IntSetUtil.make(new int[] {d1});
@@ -316,7 +320,7 @@ public IntSet getTargets(int d1) {
                           flow.snd);
                   if (!domain.hasMappedIndex(adapt)) {
                     int idx = domain.add(adapt);
-                    System.err.println(adapt + " is " + idx);
+                    LOGGER.fine("Added adapted value state: " + adapt + " with index " + idx);
                   }
                   result.add(domain.getMappedIndex(adapt));
                 }
@@ -481,30 +485,31 @@ public int compare(
       for (BasicBlockInContext<IExplodedBasicBlock> bbic : stmts) {
         if (bbic.getLastInstruction() != null) {
           if (bbic.getMethod() != currentMethod) {
-            System.err.println("method " + currentMethod);
+            LOGGER.info("Processing method: " + currentMethod);
             currentMethod = bbic.getMethod();
           }
-          System.err.println(
-              bbic.getLastInstruction().toString(bbic.getNode().getIR().getSymbolTable()));
+          LOGGER.info(
+              "Instruction: "
+                  + bbic.getLastInstruction().toString(bbic.getNode().getIR().getSymbolTable()));
           result
               .getResult(bbic)
               .foreach(
                   (i) -> {
-                    System.err.println(domain.getMappedObject(i));
+                    LOGGER.fine("Domain mapped object: " + domain.getMappedObject(i));
                   });
         }
       }
 
       for (BasicBlockInContext<IExplodedBasicBlock> bbic : stmts) {
         SSAInstruction inst = bbic.getLastInstruction();
         if (merges.containsKey(inst)) {
-          System.err.println(merges.get(inst));
+          LOGGER.info("Merge instruction: " + merges.get(inst));
           result
               .getResult(bbic)
               .foreach(
                   (i) -> {
                     ValueState val = domain.getMappedObject(i);
-                    System.err.println(val);
+                    LOGGER.fine("Value state: " + val);
                   });
         }
       }

core/com.ibm.wala.cast.python/source/com/ibm/wala/cast/python/client/PythonTurtleSKLearnClassifierAnalysis.java

@@ -45,9 +45,13 @@
 import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
+import java.util.logging.Logger;
 
 public class PythonTurtleSKLearnClassifierAnalysis extends PythonTurtleAnalysisEngine {
 
+  private static final Logger LOGGER =
+      Logger.getLogger(PythonTurtleSKLearnClassifierAnalysis.class.getName());
+
   private enum State {
     FRESH,
     FIT
@@ -147,7 +151,7 @@ public LabeledGraph<TurtlePath, EdgeType> performAnalysis(PropagationCallGraphBu
 
     objs.forEach(
         (tp) -> {
-          System.out.println(" " + tp.position() + " " + tp.value());
+          LOGGER.info("Tensor position and value: " + tp.position() + " " + tp.value());
         });
 
     ISupergraph<BasicBlockInContext<IExplodedBasicBlock>, CGNode> supergraph =
@@ -217,7 +221,7 @@ public IntSet getTargets(int d1) {
                   ClassifierState adapt = new ClassifierState(dest.getNode(), i + 1, flow.state);
                   if (!domain.hasMappedIndex(adapt)) {
                     int idx = domain.add(adapt);
-                    System.err.println(adapt + " is " + idx);
+                    LOGGER.fine("Added classifier state: " + adapt + " with index " + idx);
                   }
                   result.add(domain.getMappedIndex(adapt));
                 }
@@ -260,7 +264,8 @@ public IntSet getTargets(int d1) {
                                 new ClassifierState(dest.getNode(), pyCall.getDef(0), flow.state);
                             if (!domain.hasMappedIndex(adapt)) {
                               int i = domain.add(adapt);
-                              System.err.println(adapt + " is " + i);
+                              LOGGER.fine(
+                                  "Added return classifier state: " + adapt + " with index " + i);
                             }
                             result.add(domain.getMappedIndex(adapt));
                           }
@@ -568,7 +573,7 @@ Iterable<FactPair> trace(
                         (n) -> {
                           ClassifierState s = domain.getMappedObject(n);
                           if (s.vn == vn && s.node == bbic.getNode()) {
-                            System.err.println(
+                            LOGGER.info(
                                 ((AstMethod) bbic.getMethod())
                                         .debugInfo()
                                         .getInstructionPosition(inst.iIndex())
@@ -587,7 +592,7 @@ Iterable<FactPair> trace(
                                                     fp.fst.getLastInstructionIndex()));
                                       }
                                     });
-                            System.err.println(trace);
+                            LOGGER.info("Trace positions: " + trace);
                           }
                         });
               }

core/com.ibm.wala.cast.python/source/com/ibm/wala/cast/python/ipa/callgraph/PythonSSAPropagationCallGraphBuilder.java

@@ -667,8 +667,8 @@ private InstanceKey toTrampolineIfNeeded(InstanceKey ik, InstanceKey container)
               .isSubclassOf(
                   ik.getConcreteType(),
                   getClassHierarchy().lookupClass(PythonTypes.LambdaMethod))) {
-        System.err.println(ik.getConcreteType().getName().toString());
-        System.err.println(container.getConcreteType().getName().toString());
+        logger.fine("Instance key concrete type: " + ik.getConcreteType().getName().toString());
+        logger.fine("Container concrete type: " + container.getConcreteType().getName().toString());
         TypeReference trampolineClassRef =
             PythonInstanceMethodTrampoline.findOrCreate(
                 ik.getConcreteType().getReference(), getClassHierarchy());

core/com.ibm.wala.cast.python/source/com/ibm/wala/cast/python/ir/PythonCAstToIRTranslator.java

@@ -665,7 +665,7 @@ protected void leaveVar(CAstNode n, WalkContext c, CAstVisitor<WalkContext> visi
     assert nm != null : "cannot find var for " + CAstPrinter.print(n, context.getSourceMap());
 
     if ("0".equals(nm)) {
-      System.err.println("got here");
+      LOGGER.fine("got here");
     }
 
     if (isGlobalVar(nm)) {
@@ -1202,7 +1202,7 @@ protected boolean doVisit(CAstNode n, WalkContext context, CAstVisitor<WalkConte
       int numOfChildren = n.getChildCount();
       for (int i = 0; i < numOfChildren; i++) {
         String val = (String) n.getChild(i).getChild(0).getValue();
-        System.out.println("Hey " + val);
+        LOGGER.fine("Processing global declaration: " + val);
         addGlobal(context.currentScope(), val);
       }
       return true;

jep/com.ibm.wala.cast.python.cpython/source/com/ibm/wala/cast/python/parquet/ParquetPythonReader.java

@@ -240,6 +240,6 @@ public static void main(String... args) throws IOException, ClassHierarchyExcept
               code.add((SourceModule) f);
             });
     IClassHierarchy cha = CPythonAstToCAstTranslator.load(code);
-    System.err.println(cha);
+    LOGGER.info("Class hierarchy: " + cha);
   }
 }

jython/com.ibm.wala.cast.python.jython/source/com/ibm/wala/cast/python/loader/Python2Loader.java

@@ -32,9 +32,13 @@
 import java.io.IOException;
 import java.util.Collections;
 import java.util.List;
+import java.util.logging.Logger;
 import org.python.core.PyObject;
 
 public class Python2Loader extends PythonLoader {
+
+  private static final Logger LOGGER = Logger.getLogger(Python2Loader.class.getName());
+
   public Python2Loader(IClassHierarchy cha, IClassLoader parent) {
     super(cha, parent, Collections.emptyList());
   }
@@ -97,7 +101,15 @@ protected Object eval(CAstOperator op, Object lhs, Object rhs) {
                   PyObject x =
                       Python2Interpreter.getInterp().eval(lhs + " " + op.getValue() + " " + rhs);
                   if (x.isNumberType()) {
-                    System.err.println(lhs + " " + op.getValue() + " " + rhs + " -> " + x.asInt());
+                    LOGGER.fine(
+                        "Expression evaluation: "
+                            + lhs
+                            + " "
+                            + op.getValue()
+                            + " "
+                            + rhs
+                            + " -> "
+                            + x.asInt());
                     return x.asInt();
                   }
                 } catch (Exception e) {

jython/com.ibm.wala.cast.python.jython/source/com/ibm/wala/cast/python/parser/PythonParser.java

@@ -55,6 +55,7 @@
 import java.util.LinkedList;
 import java.util.Map;
 import java.util.function.Supplier;
+import java.util.logging.Logger;
 import org.python.antlr.PythonTree;
 import org.python.antlr.ast.Assert;
 import org.python.antlr.ast.Assign;
@@ -125,6 +126,8 @@
 
 public abstract class PythonParser<T> extends AbstractParser implements TranslatorToCAst {
 
+  private static final Logger LOGGER = Logger.getLogger(PythonParser.class.getName());
+
   private static boolean COMPREHENSION_IR = true;
 
   private CAstType codeBody =
@@ -508,8 +511,9 @@ public CAstNode visitClassDef(ClassDef arg0) throws Exception {
             public Collection<CAstType> getSupertypes() {
               Collection<CAstType> supertypes = HashSetFactory.make();
               for (expr e : arg0.getInternalBases()) {
-                System.out.println(
-                    arg0.getInternalName()
+                LOGGER.fine(
+                    "Class inheritance: "
+                        + arg0.getInternalName()
                         + " "
                         + arg0.getType()
                         + " extends "
@@ -1966,7 +1970,7 @@ public String getMsg() {
   }
 
   public void print(PyObject ast) {
-    System.err.println(ast.getClass());
+    LOGGER.fine("AST class: " + ast.getClass());
   }
 
   /**

jython/com.ibm.wala.cast.python.jython3/source/com/ibm/wala/cast/python/client/PytestAnalysisEngine.java

@@ -22,9 +22,12 @@
 import com.ibm.wala.util.intset.OrdinalSet;
 import java.io.File;
 import java.util.List;
+import java.util.logging.Logger;
 
 public class PytestAnalysisEngine<T> extends PythonAnalysisEngine<T> {
 
+  private static final Logger LOGGER = Logger.getLogger(PytestAnalysisEngine.class.getName());
+
   private class PytestTargetSelector implements MethodTargetSelector {
     private final MethodTargetSelector base;
 
@@ -35,7 +38,7 @@ private PytestTargetSelector(MethodTargetSelector base) {
     @Override
     public IMethod getCalleeTarget(CGNode caller, CallSiteReference site, IClass receiver) {
       if (site.getDeclaredTarget().getDeclaringClass().equals(PytestLoader.pytestType)) {
-        System.err.println("pytest call site " + site + " " + receiver);
+        LOGGER.fine("Pytest call site: " + site + " " + receiver);
         PointerKeyFactory pkf = builder.getPointerKeyFactory();
         for (SSAAbstractInvokeInstruction inst : caller.getIR().getCalls(site)) {
           PointerKey test = pkf.getPointerKeyForLocal(caller, inst.getUse(0));
@@ -56,19 +59,19 @@ public IMethod getCalleeTarget(CGNode caller, CallSiteReference site, IClass rec
                             PointerKey names = pkf.getPointerKeyForInstanceField(p, ns);
                             OrdinalSet<InstanceKey> namesObjs =
                                 builder.getPointerAnalysis().getPointsToSet(names);
-                            System.err.println("names: " + namesObjs);
+                            LOGGER.fine("Parameter names: " + namesObjs);
 
                             IField vs =
                                 p.getConcreteType()
                                     .getField(Atom.findOrCreateUnicodeAtom("values"));
                             PointerKey values = pkf.getPointerKeyForInstanceField(p, vs);
                             OrdinalSet<InstanceKey> valsObjs =
                                 builder.getPointerAnalysis().getPointsToSet(values);
-                            System.err.println("values: " + valsObjs);
+                            LOGGER.fine("Parameter values: " + valsObjs);
                           });
                 }
               });
-          System.err.println(test + " " + testObjs);
+          LOGGER.fine("Test pointer key and objects: " + test + " " + testObjs);
         }
       }
       return base.getCalleeTarget(caller, site, receiver);

jython/com.ibm.wala.cast.python.jython3/source/com/ibm/wala/cast/python/loader/PytestLoader.java

@@ -27,9 +27,12 @@
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
+import java.util.logging.Logger;
 
 public class PytestLoader extends Python3Loader {
 
+  private static final Logger LOGGER = Logger.getLogger(PytestLoader.class.getName());
+
   public static final TypeReference pytestType =
       TypeReference.findOrCreate(PythonTypes.pythonLoader, "LPytest");
 
@@ -148,6 +151,6 @@ private void handlePytest(WalkContext context, CAstEntity fn, int function) {
   @Override
   protected void finishTranslation() {
     super.finishTranslation();
-    System.err.println("xxsymbol " + testParams);
+    LOGGER.fine("Test parameters: " + testParams);
   }
 }

jython/com.ibm.wala.cast.python.jython3/source/com/ibm/wala/cast/python/parser/PythonParser.java

@@ -2058,7 +2058,7 @@ public CAstNode visitTryExcept(TryExcept arg0) throws Exception {
       CAstVisitor child = new CAstVisitor(catches, parser);
       CAstNode block = child.block(arg0.getInternalBody());
 
-      System.err.println("catches: " + handlers);
+      LOGGER.fine("Exception handlers: " + handlers);
 
       return Ast.makeNode(
           CAstNode.TRY,
@@ -2496,7 +2496,7 @@ public String getMsg() {
   }
 
   public void print(PyObject ast) {
-    System.err.println(ast.getClass());
+    LOGGER.fine("AST class: " + ast.getClass());
   }
 
   /**