add support for configuration file (#41)

* init commit Ghidrathon configuration

* adding default configuration file

* adding comments and unit tests

data/GhidrathonConfig.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<GHIDRATHON_CONFIG>
+    <ARRAY NAME="JAVA_EXCLUDE_LIBS" TYPE="string">
+        <A VALUE="pdb" />
+    </ARRAY>
+    <ARRAY NAME="PYTHON_SHARED_MODULES" TYPE="string">
+        <A VALUE="numpy" />
+    </ARRAY>
+    <ARRAY NAME="PYTHON_INCLUDE_PATHS" TYPE="string">
+    </ARRAY>
+</GHIDRATHON_CONFIG>
+

data/python/tests/test_cpython.py

@@ -0,0 +1,26 @@
+# Copyright (C) 2022 Mandiant, Inc. All Rights Reserved.
+# Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at: [package root]/LICENSE.txt
+# Unless required by applicable law or agreed to in writing, software distributed under the License
+#  is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and limitations under the License.
+
+"""Unit tests to verify CPython modules
+
+Note: you must run these tests from the Ghidra script manager or headless mode
+"""
+
+import unittest
+import warnings
+
+
+class TestCPython(unittest.TestCase):
+    def test_numpy(self):
+        try:
+            import numpy
+
+            a = numpy.array(["cat", "dog"])
+        except ImportError:
+            warnings.warn("numpy module is not installed - ignoring test")
+            pass

data/python/tests/test_jepbridge.py

@@ -21,6 +21,12 @@ def assertIsJavaObject(self, o):
         if not (o is None or isinstance(o, Object)):
             raise AssertionError("Object %s is not valid" % str(o))
 
+    def assertIsNotJavaObject(self, o):
+        from java.lang import Object
+
+        if isinstance(o, Object):
+            raise AssertionError("Object %s is not valid" % str(o))
+
     def test_type_instance(self):
         # see Jep: https://github.com/ninia/jep/blob/15e36a7ba54eb7d8f7ffd85f16675fa4fd54eb1d/src/test/python/test_import.py#L54-L65
         from java.lang import Object
@@ -46,3 +52,8 @@ def test_ghidra_script_variables(self):
 
     def test_ghidra_script_methods(self):
         self.assertIsInstance(getGhidraVersion(), str)
+
+    def test_java_excluded_packages(self):
+        import pdb
+
+        self.assertIsNotJavaObject(pdb)

src/main/java/ghidrathon/GhidrathonClassEnquirer.java

@@ -0,0 +1,50 @@
+// Copyright (C) 2022 Mandiant, Inc. All Rights Reserved.
+// Licensed under the Apache License, Version 2.0 (the "License");
+//  you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at: [package root]/LICENSE.txt
+// Unless required by applicable law or agreed to in writing, software distributed under the License
+//  is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and limitations under the License.
+
+package ghidrathon;
+
+import java.util.List;
+import java.util.ArrayList;
+
+import jep.ClassList;
+import jep.ClassEnquirer;
+
+/**
+ * Implements Jep ClassEnquirer used to handle Java imports from Python - specifically we
+ * use this class to handle naming conflicts, e.g. pdb
+ */
+public class GhidrathonClassEnquirer implements ClassEnquirer {
+
+	private final List<String> javaExcludeLibs = new ArrayList<String>();
+	private final ClassEnquirer classList = ClassList.getInstance();
+
+	public void addJavaExcludeLib(String name) {
+		javaExcludeLibs.add(name);
+	}
+
+	public void addJavaExcludeLibs(List<String> names) {
+		javaExcludeLibs.addAll(names);
+	}
+
+	public boolean isJavaPackage(String name) {
+		if (javaExcludeLibs.contains(name)) {
+			return false;
+		}
+
+		return classList.isJavaPackage(name);
+	}
+
+	public String[] getClassNames(String name) {
+		return classList.getClassNames(name);
+	}
+
+	public String[] getSubPackages(String name) {
+		return classList.getSubPackages(name);
+	}
+
+}

src/main/java/ghidrathon/GhidrathonConfig.java

@@ -0,0 +1,85 @@
+// Copyright (C) 2022 Mandiant, Inc. All Rights Reserved.
+// Licensed under the Apache License, Version 2.0 (the "License");
+//  you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at: [package root]/LICENSE.txt
+// Unless required by applicable law or agreed to in writing, software distributed under the License
+//  is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and limitations under the License.
+
+package ghidrathon;
+
+import java.util.List;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Collections;
+
+/**
+ * Ghidrathon's configuration class
+ *
+ * Stores
+ *   - stdout and stderr
+ *   - Python modules to handle as shared modules - relevant to CPython modules
+ *   - Java package names to exclude from Python imports
+ *   - Python include paths to add to Python interpreter environment
+ */
+public class GhidrathonConfig {
+
+	private final List<String> javaExcludeLibs = new ArrayList<String>();
+	private final List<String> pyIncludePaths = new ArrayList<String>();
+	private final List<String> pySharedModules = new ArrayList<String>();
+
+	private PrintWriter out = null;
+	private PrintWriter err = null;
+
+	public void addStdOut(PrintWriter out) {
+		this.out = out;
+	}
+
+	public void addStdErr(PrintWriter err) {
+		this.err = err;
+	}
+
+	public PrintWriter getStdOut() {
+		return out;
+	}
+
+	public PrintWriter getStdErr() {
+		return err;
+	}
+
+	public void addPythonSharedModule(String name) {
+		pySharedModules.add(name);
+	}
+
+	public void addPythonSharedModules(List<String> names) {
+		pySharedModules.addAll(names);
+	}
+
+	public Iterable<String> getPythonSharedModules() {
+		return Collections.unmodifiableList(pySharedModules);
+	}
+
+	public void addJavaExcludeLib(String name) {
+		javaExcludeLibs.add(name);
+	}
+
+	public void addJavaExcludeLibs(List<String> names) {
+		javaExcludeLibs.addAll(names);
+	}
+
+	public Iterable<String> getJavaExcludeLibs() {
+		return Collections.unmodifiableList(javaExcludeLibs);
+	}
+
+	public void addPythonIncludePath(String path) {
+		pyIncludePaths.add(path);
+	}
+
+	public void addPythonIncludePaths(List<String> paths) {
+		pyIncludePaths.addAll(paths);
+	}
+
+	public Iterable<String> getPythonIncludePaths() {
+		return Collections.unmodifiableList(pyIncludePaths);
+	}
+}

src/main/java/ghidrathon/GhidrathonConsoleInputThread.java

@@ -8,37 +8,44 @@
 
 package ghidrathon;
 
-import java.io.BufferedReader;
 import java.io.File;
+import java.io.PrintWriter;
 import java.io.IOException;
+import java.io.BufferedReader;
 import java.io.InputStreamReader;
-import java.io.PrintWriter;
 import java.util.concurrent.atomic.AtomicBoolean;
 
 import generic.jar.ResourceFile;
-import ghidra.app.plugin.core.interpreter.InterpreterConsole;
-import ghidra.app.script.GhidraState;
+
 import ghidra.util.Msg;
+import ghidra.app.script.GhidraState;
+import ghidra.app.plugin.core.interpreter.InterpreterConsole;
+
+import ghidrathon.GhidrathonUtils;
+import ghidrathon.GhidrathonConfig;
 import ghidrathon.interpreter.GhidrathonInterpreter;
 
 public class GhidrathonConsoleInputThread extends Thread {
 
 	private static int generationCount = 0;
+
 	private GhidrathonPlugin plugin = null;
 	private InterpreterConsole console = null;
-	private AtomicBoolean shouldContinue = new AtomicBoolean(true);
 	private GhidrathonInterpreter python = null;
-	private PrintWriter err = null;
-	private PrintWriter out = null;
+
+	private AtomicBoolean shouldContinue = new AtomicBoolean(true);
+	private GhidrathonConfig config = GhidrathonUtils.getDefaultGhidrathonConfig();
 
 	GhidrathonConsoleInputThread(GhidrathonPlugin plugin) {
 
 		super("Ghidrathon console input thread (generation " + ++generationCount + ")");
 
 		this.plugin = plugin;
 		this.console = plugin.getConsole();
-		this.err = console.getErrWriter();
-		this.out = console.getOutWriter();
+
+		// init Ghidrathon configuration
+		config.addStdErr(console.getErrWriter());
+		config.addStdOut(console.getOutWriter());
 
 	}
 
@@ -56,7 +63,7 @@ public void run() {
 
 		try {
 
-			python = GhidrathonInterpreter.get(out, err);
+			python = GhidrathonInterpreter.get(config);
 
 			python.printWelcome();
 
@@ -66,7 +73,7 @@ public void run() {
 				python.close();
 			}
 
-			e.printStackTrace(err);
+			e.printStackTrace(config.getStdErr());
 			return;
 
 		}
@@ -95,7 +102,6 @@ public void run() {
 					continue;
 				}
 
-
 				boolean moreInputWanted = evalPython(line);
 
 				this.plugin.flushConsole();

src/main/java/ghidrathon/GhidrathonScript.java

@@ -20,6 +20,8 @@
 import ghidra.framework.plugintool.PluginTool;
 import ghidra.app.script.GhidraScriptProvider;
 
+import ghidrathon.GhidrathonUtils;
+import ghidrathon.GhidrathonConfig;
 import ghidrathon.interpreter.GhidrathonInterpreter;
 
 public class GhidrathonScript extends GhidraScript {
@@ -28,24 +30,26 @@ public class GhidrathonScript extends GhidraScript {
 	protected void run() {
 
 		GhidrathonInterpreter python = null;
-
-		final PrintWriter out = getStdOut();
-		final PrintWriter err = getStdErr();
+		GhidrathonConfig config = GhidrathonUtils.getDefaultGhidrathonConfig();
+
+		// init Ghidrathon configuration
+		config.addStdOut(getStdOut());
+		config.addStdErr(getStdErr());
 
 		try {
 
-			python = GhidrathonInterpreter.get(out, err);
+			python = GhidrathonInterpreter.get(config);
 
 			// run Python script from Python interpreter
 			python.runScript(getSourceFile(), this);
 
 			// flush stdout and stderr to ensure all is printed to console window
-			err.flush();
-			out.flush();
+			config.getStdErr().flush();
+			config.getStdOut().flush();
 
 		} catch (RuntimeException e) {
 
-			e.printStackTrace(err);
+			e.printStackTrace(config.getStdErr());
 
 		} finally {
 
@@ -68,13 +72,14 @@ protected void run() {
 	public void runScript(String name, GhidraState scriptState) {
 
 		GhidrathonInterpreter python = null;
-
-		final PrintWriter out = getStdOut();
-		final PrintWriter err = getStdErr();
+		GhidrathonConfig config = GhidrathonUtils.getDefaultGhidrathonConfig();
+
+		config.addStdOut(getStdOut());
+		config.addStdErr(getStdErr());
 
 		try {
 
-			python = GhidrathonInterpreter.get(out, err);
+			python = GhidrathonInterpreter.get(config);
 
 			ResourceFile source = GhidraScriptUtil.findScriptByName(name);
 			if (source == null) {
@@ -109,7 +114,7 @@ public void runScript(String name, GhidraState scriptState) {
 
 		} catch (Exception e) {
 
-			e.printStackTrace(err);
+			e.printStackTrace(config.getStdErr());
 
 		} finally {