From 1a8ec9e809639a8b11e5ba675f4939f8884b6f29 Mon Sep 17 00:00:00 2001
From: katherine-hough <32645020+katherine-hough@users.noreply.github.com>
Date: Sun, 26 Nov 2023 13:10:48 -0500
Subject: [PATCH] * Started working on Jar driver
---
Phosphor/pom.xml | 36 ++-----
.../columbia/cs/psl/phosphor/OptionsUtil.java | 88 -----------------
.../cs/psl/phosphor/PhosphorOption.java | 95 +++++++++++++++----
.../src/main/resources/META-INF/MANIFEST.MF | 5 -
.../swe/phosphor/instrument/Instrumenter.java | 46 ++++-----
.../instrument/PhosphorInstrumentation.java | 23 ++++-
.../instrument/PhosphorInstrumenter.java | 25 +++--
pom.xml | 2 +-
8 files changed, 144 insertions(+), 176 deletions(-)
delete mode 100644 Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/OptionsUtil.java
delete mode 100644 Phosphor/src/main/resources/META-INF/MANIFEST.MF
diff --git a/Phosphor/pom.xml b/Phosphor/pom.xml
index 9d0ef5706..db28b1a93 100644
--- a/Phosphor/pom.xml
+++ b/Phosphor/pom.xml
@@ -17,37 +17,19 @@
maven-jar-plugin
- src/main/resources/META-INF/MANIFEST.MF
+
+
+ edu.columbia.cs.psl.phosphor.Java8PreMain
+
+ true
+
-
- java/
- sun/
-
+ true
-
- org.apache.maven.plugins
- maven-javadoc-plugin
- 3.1.1
-
- none
- true
- 8
- sun.*:java.*
-
-
-
- attach-javadoc
-
- jar
-
-
-
-
org.codehaus.mojo
exec-maven-plugin
- 1.6.0
generate-stubs
@@ -95,7 +77,8 @@
- edu/columbia/cs/psl/phosphor/org/objectweb/asm/tree/FrameNode.class
+
+ edu/columbia/cs/psl/phosphor/org/objectweb/asm/tree/FrameNode.class
@@ -109,6 +92,7 @@
+ true
true
true
diff --git a/Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/OptionsUtil.java b/Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/OptionsUtil.java
deleted file mode 100644
index 0bd356470..000000000
--- a/Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/OptionsUtil.java
+++ /dev/null
@@ -1,88 +0,0 @@
-package edu.columbia.cs.psl.phosphor;
-
-import edu.columbia.cs.psl.phosphor.struct.SinglyLinkedList;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.Options;
-
-import java.util.*;
-
-public class OptionsUtil {
- /**
- * Creates a standardized copy of the specified properties where each Phosphor option without an argument is mapped
- * to either true or not present in the properties, each Phosphor option with an argument is either mapped to a
- * non-null, non-empty string or not present in properties, and no other keys are present in the properties.
- *
- * @param properties properties to be standardized
- * @return a standardized copy of properties
- */
- private static Properties standardize(Properties properties) {
- Properties result = new Properties();
- Map phosphorOptionMap = createOptionMap();
- for (String key : properties.stringPropertyNames()) {
- String value = properties.getProperty(key);
- if (phosphorOptionMap.containsKey(key)) {
- Option option = phosphorOptionMap.get(key);
- if (option.hasArg() && value != null && !value.isEmpty()) {
- result.setProperty(option.getOpt(), value);
- } else if (!option.hasArg() && (value == null || value.isEmpty() || "true".equalsIgnoreCase(value))) {
- result.setProperty(option.getOpt(), "true");
- }
- } else {
- throw new IllegalArgumentException("Unknown option: " + key);
- }
- }
- return result;
- }
-
- /**
- * @return a mapping from the names of configuration options available in Phosphor to an instance of
- * org.apache.commons.cli.Option that represents that configuration option
- */
- private static Map createOptionMap() {
- Map map = new HashMap<>();
- Options options = PhosphorOption.createOptions(false);
- for (Option option : options.getOptions()) {
- map.put(option.getOpt(), option);
- if (option.hasLongOpt()) {
- map.put(option.getLongOpt(), option);
- }
- }
- return map;
- }
-
- public static String[] createPhosphorMainArguments(Properties properties) {
- properties = standardize(properties);
- SinglyLinkedList arguments = new SinglyLinkedList<>();
- Set propNames = properties.stringPropertyNames();
- for (String propName : propNames) {
- arguments.addLast("-" + propName);
- if (!"true".equals(properties.getProperty(propName))) {
- arguments.addLast(properties.getProperty(propName));
- }
- }
- arguments.addLast("temp/");
- arguments.addLast("temp2/");
- return arguments.toArray(new String[0]);
- }
-
- public static Set> getConfigurationClasses(Properties properties) {
- Set> classes = new HashSet<>();
- Options options = PhosphorOption.createOptions(false);
- for (Option option : options.getOptions()) {
- if (option.getType().equals(Class.class)) {
- String key = option.getOpt();
- if (properties.containsKey(key)) {
- try {
- Class clazz = Class.forName(properties.getProperty(key));
- classes.add(clazz);
- } catch (ReflectiveOperationException e) {
- String message =
- String.format("Failed to create %s class: %s", key, properties.getProperty(key));
- throw new IllegalArgumentException(message, e);
- }
- }
- }
- }
- return classes;
- }
-}
diff --git a/Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/PhosphorOption.java b/Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/PhosphorOption.java
index 3087b1809..522fd76fa 100644
--- a/Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/PhosphorOption.java
+++ b/Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/PhosphorOption.java
@@ -7,9 +7,10 @@
import org.apache.commons.cli.*;
import org.objectweb.asm.ClassVisitor;
+import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
-import java.util.EnumMap;
+import java.util.*;
public enum PhosphorOption {
@@ -369,42 +370,94 @@ public static Options createOptions(boolean forRuntimeInst) {
}
}
}
- for(OptionGroup group : groupMap.values()) {
+ for (OptionGroup group : groupMap.values()) {
options.addOptionGroup(group);
}
return options;
}
- public static CommandLine configure(boolean forRuntimeInst, String[] args) {
- CommandLineParser parser = new DefaultParser();
- Options options = createOptions(forRuntimeInst);
+ public static CommandLine configure(boolean isRuntime, String[] args) {
+ String commandSynopsis = "java -jar phosphor.jar [OPTIONS] ";
+ Options options = createOptions(isRuntime);
CommandLine line;
try {
- line = parser.parse(options, args);
- } catch(org.apache.commons.cli.ParseException exp) {
- if(forRuntimeInst) {
- System.err.println(exp.getMessage());
+ line = new DefaultParser().parse(options, args);
+ } catch (ParseException e) {
+ if (isRuntime) {
+ System.err.println(e.getMessage());
return null;
}
- HelpFormatter formatter = new HelpFormatter();
- formatter.printHelp("java -jar phosphor.jar [OPTIONS] [input] [output]", options);
- System.err.println(exp.getMessage());
- if(exp.getMessage().contains("-multiTaint")) {
- System.err.println("Note: the -multiTaint option has been removed, and is now enabled by default (int tags no longer exist)");
- }
- return null;
+ new HelpFormatter().printHelp(commandSynopsis, options);
+ throw new IllegalArgumentException(e);
}
- if(!forRuntimeInst && (line.hasOption("help") || line.getArgs().length != 2)) {
- HelpFormatter formatter = new HelpFormatter();
- formatter.printHelp("java -jar phosphor.jar [OPTIONS] [input] [output]", options);
+ if (!isRuntime && line.hasOption("help")) {
+ new HelpFormatter().printHelp(commandSynopsis, options);
return null;
}
- for(PhosphorOption phosphorOption : values()) {
- phosphorOption.configure(forRuntimeInst, line.hasOption(phosphorOption.optionName), line);
+ if (!isRuntime && line.getArgs().length != 2) {
+ new HelpFormatter().printHelp(commandSynopsis, options);
+ throw new IllegalArgumentException("Missing command line arguments");
+ }
+ for (PhosphorOption phosphorOption : values()) {
+ phosphorOption.configure(isRuntime, line.hasOption(phosphorOption.optionName), line);
}
return line;
}
+ public static Set> getClassOptionValues(CommandLine line) {
+ // This method should not be called from instrumented JVMs.
+ // Therefore, the use of JCL classes is acceptable.
+ Set> classes = new HashSet<>();
+ for (Option option : line.getOptions()) {
+ if (option.getType().equals(Class.class)) {
+ if (line.hasOption(option.getOpt())) {
+ try {
+ classes.add((Class) line.getParsedOptionValue(option.getOpt()));
+ } catch (ParseException e) {
+ throw new IllegalArgumentException(
+ "Failed to process " + option.getOpt() + ": " + line.getOptionValue(option.getOpt()));
+ }
+ }
+ }
+ }
+ return classes;
+ }
+
+ public static CommandLine configure(Properties properties, File source, File destination) {
+ // This method should not be called from instrumented JVMs.
+ // Therefore, the use of JCL classes is acceptable.
+ List arguments = new LinkedList<>();
+ for (String key : properties.stringPropertyNames()) {
+ String value = properties.getProperty(key);
+ if (value == null || value.isEmpty() || value.equals("true")) {
+ arguments.add("-" + key);
+ } else if (!value.equals("false")) {
+ arguments.add("-" + key);
+ arguments.add(value);
+ }
+ }
+ arguments.add(source.getAbsolutePath());
+ arguments.add(destination.getAbsolutePath());
+ return configure(false, arguments.toArray(new String[0]));
+ }
+
+ public static Properties toProperties(CommandLine line) {
+ // This method should not be called from instrumented JVMs.
+ // Therefore, the use of JCL classes is acceptable.
+ Properties properties = new Properties();
+ for (Option option : line.getOptions()) {
+ String key = option.getOpt();
+ if (line.hasOption(key)) {
+ String value = line.getOptionValue(key);
+ if (value == null) {
+ value = "true";
+ }
+ properties.put(key, value);
+ }
+ }
+ return properties;
+ }
+
private enum PhosphorOptionGroup {
GENERAL, CONTROL_PROPAGATION
}
diff --git a/Phosphor/src/main/resources/META-INF/MANIFEST.MF b/Phosphor/src/main/resources/META-INF/MANIFEST.MF
deleted file mode 100644
index f8fd3bc8e..000000000
--- a/Phosphor/src/main/resources/META-INF/MANIFEST.MF
+++ /dev/null
@@ -1,5 +0,0 @@
-Manifest-Version: 1.0
-Created-By: 1.6.0_06 (Sun Microsystems Inc.)
-Main-Class: edu.columbia.cs.psl.phosphor.Instrumenter
-Premain-Class: edu.columbia.cs.psl.phosphor.Java8PreMain
-Can-Retransform-Classes: true
diff --git a/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/Instrumenter.java b/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/Instrumenter.java
index 87e645525..cb7158a3e 100644
--- a/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/Instrumenter.java
+++ b/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/Instrumenter.java
@@ -27,14 +27,14 @@ public Instrumenter(Instrumentation instrumentation, boolean verbose) {
this.verbose = verbose;
}
- public void process(File source, File target) throws IOException, InterruptedException, ExecutionException {
+ public void process(File source, File destination) throws IOException, InterruptedException, ExecutionException {
if (!source.exists()) {
throw new IllegalArgumentException("Source file not found: " + source);
} else if (!source.isDirectory() && !isClass(source.getName()) && !isArchive(source.getName())) {
throw new IllegalArgumentException("Unknown source file type: " + source);
}
Queue> futures = new LinkedList<>();
- processFile(futures, source, target);
+ processFile(futures, source, destination);
while (!futures.isEmpty()) {
futures.poll().get();
}
@@ -51,9 +51,9 @@ public void process(File source, File target) throws IOException, InterruptedExc
}
}
- private void instrumentClass(File source, File target) {
+ private void instrumentClass(File source, File destination) {
try (InputStream input = Files.newInputStream(source.toPath());
- OutputStream output = Files.newOutputStream(target.toPath())) {
+ OutputStream output = Files.newOutputStream(destination.toPath())) {
instrumentClass(InstrumentUtil.readAllBytes(input), output);
} catch (Throwable t) {
errors.add(t);
@@ -69,27 +69,27 @@ private void instrumentClass(byte[] classFileBuffer, OutputStream output) throws
}
}
- private void processFile(Collection> futures, File source, File target)
+ private void processFile(Collection> futures, File source, File destination)
throws IOException, InterruptedException {
if (source.isDirectory()) {
- InstrumentUtil.ensureDirectory(target);
+ InstrumentUtil.ensureDirectory(destination);
for (File child : Objects.requireNonNull(source.listFiles())) {
- processFile(futures, child, new File(target, child.getName()));
+ processFile(futures, child, new File(destination, child.getName()));
}
} else if (isClass(source.getName())) {
- futures.add(executor.submit(() -> instrumentClass(source, target), null));
+ futures.add(executor.submit(() -> instrumentClass(source, destination), null));
} else if (isArchive(source.getName())) {
- processZip(Files.newInputStream(source.toPath()), Files.newOutputStream(target.toPath()));
+ processZip(Files.newInputStream(source.toPath()), Files.newOutputStream(destination.toPath()));
} else {
- if (copy(source, target)) {
- if (source.canExecute() && !target.setExecutable(true)) {
- errors.add(new IOException("Failed to set execute permission for: " + target));
+ if (copy(source, destination)) {
+ if (source.canExecute() && !destination.setExecutable(true)) {
+ errors.add(new IOException("Failed to set execute permission for: " + destination));
}
- if (source.canRead() && !target.setReadable(true)) {
- errors.add(new IOException("Failed to set read permission for: " + target));
+ if (source.canRead() && !destination.setReadable(true)) {
+ errors.add(new IOException("Failed to set read permission for: " + destination));
}
- if (source.canWrite() && !target.setWritable(true)) {
- errors.add(new IOException("Failed to set write permission for: " + target));
+ if (source.canWrite() && !destination.setWritable(true)) {
+ errors.add(new IOException("Failed to set write permission for: " + destination));
}
}
}
@@ -144,9 +144,9 @@ private void writeZipResults(OutputStream out, List> futures)
}
}
- private boolean copy(File source, File target) {
+ private boolean copy(File source, File destination) {
try (InputStream in = Files.newInputStream(source.toPath());
- OutputStream out = Files.newOutputStream(target.toPath())) {
+ OutputStream out = Files.newOutputStream(destination.toPath())) {
InstrumentUtil.copy(in, out);
return true;
} catch (IOException e) {
@@ -193,14 +193,14 @@ public ZipResult(ZipEntry entry, byte[] buffer) throws IOException, InterruptedE
public static long instrument(
File source,
- File target,
+ File destination,
Properties options,
Instrumentation instrumentation,
boolean verbose,
String modules)
throws IOException {
- if (target.exists()) {
- throw new IllegalArgumentException("Target location for instrumentation already exists.");
+ if (destination.exists()) {
+ throw new IllegalArgumentException("Destination location for instrumentation already exists.");
}
if (!source.exists()) {
throw new IllegalArgumentException("Source location not found: " + source);
@@ -208,9 +208,9 @@ public static long instrument(
long startTime = System.currentTimeMillis();
try {
if (InstrumentUtil.isModularJvm(source)) {
- JLinkInvoker.invoke(source, target, instrumentation, options, modules);
+ JLinkInvoker.invoke(source, destination, instrumentation, options, modules);
} else {
- new Instrumenter(instrumentation, verbose).process(source, target);
+ new Instrumenter(instrumentation, verbose).process(source, destination);
}
return System.currentTimeMillis() - startTime;
} catch (IOException | InterruptedException | ExecutionException e) {
diff --git a/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/PhosphorInstrumentation.java b/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/PhosphorInstrumentation.java
index e7b0de35b..6494fe1e2 100644
--- a/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/PhosphorInstrumentation.java
+++ b/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/PhosphorInstrumentation.java
@@ -1,7 +1,11 @@
package edu.gmu.swe.phosphor.instrument;
-import edu.columbia.cs.psl.phosphor.*;
+import edu.columbia.cs.psl.phosphor.Configuration;
+import edu.columbia.cs.psl.phosphor.PhosphorOption;
+import edu.columbia.cs.psl.phosphor.PhosphorPatcher;
+import edu.columbia.cs.psl.phosphor.PreMain;
import edu.columbia.cs.psl.phosphor.instrumenter.TaintTrackingClassVisitor;
+import edu.columbia.cs.psl.phosphor.org.apache.commons.cli.CommandLine;
import java.io.File;
import java.io.IOException;
@@ -25,16 +29,25 @@ public class PhosphorInstrumentation implements Instrumentation {
@Override
public void configure(File source, Properties options) throws IOException {
- options.put("java8", String.valueOf(!InstrumentUtil.isModularJvm(source)));
- String[] arguments = OptionsUtil.createPhosphorMainArguments(options);
+ options.remove("help");
+ CommandLine line = PhosphorOption.configure(options, source, new File("temp/"));
+ assert line != null;
+ initialize(line);
+ }
+
+ public void initialize(CommandLine line) throws IOException {
+ File source = new File(line.getArgs()[0]);
+ Set> configurationClasses = PhosphorOption.getClassOptionValues(line);
+ if (InstrumentUtil.isJavaHome(source)) {
+ Configuration.IS_JAVA_8 = !InstrumentUtil.isModularJvm(source);
+ }
setUpClassLoader(source);
- PhosphorOption.configure(false, arguments);
Configuration.init();
TaintTrackingClassVisitor.IS_RUNTIME_INST = false;
transformer = new PreMain.PCLoggingTransformer();
classPathElements = new HashSet<>();
classPathElements.add(InstrumentUtil.getClassPathElement(PreMain.class));
- OptionsUtil.getConfigurationClasses(options).stream()
+ configurationClasses.stream()
.map(InstrumentUtil::getClassPathElement)
.forEach(classPathElements::add);
}
diff --git a/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/PhosphorInstrumenter.java b/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/PhosphorInstrumenter.java
index 1f4715bc7..d59e92dc0 100644
--- a/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/PhosphorInstrumenter.java
+++ b/phosphor-instrument-jigsaw/src/main/java/edu/gmu/swe/phosphor/instrument/PhosphorInstrumenter.java
@@ -1,5 +1,9 @@
package edu.gmu.swe.phosphor.instrument;
+import edu.columbia.cs.psl.phosphor.Configuration;
+import edu.columbia.cs.psl.phosphor.PhosphorOption;
+import edu.columbia.cs.psl.phosphor.org.apache.commons.cli.CommandLine;
+
import java.io.File;
import java.io.IOException;
@@ -9,13 +13,20 @@ private PhosphorInstrumenter() {
}
public static void main(String[] args) throws IOException {
- // TODO
+ PhosphorInstrumentation instrumentation = new PhosphorInstrumentation();
+ CommandLine line = PhosphorOption.configure(false, args);
+ if(line == null) {
+ // The "help" option was specified
+ return;
+ }
File source = new File(args[0]);
- File target = new File(args[1]);
- boolean verbose = Boolean.parseBoolean(args[2]);
- String modules = args[3];
- System.out.printf("Instrumenting %s to %s%n", source, target);
- long elapsedTime = Instrumenter.instrument(source, target, null, null, verbose, modules);
- System.out.printf("Finished generation after %dms%n", elapsedTime);
+ File destination = new File(args[1]);
+ instrumentation.initialize(line);
+ boolean verbose = !Configuration.QUIET_MODE;
+ String modules = line.hasOption("jvmModules") ? line.getOptionValue("jvmModules") : "ALL-MODULE-PATH";
+ System.out.printf("Instrumenting %s to %s%n", source, destination);
+ long elapsedTime = Instrumenter.instrument(source, destination, PhosphorOption.toProperties(line),
+ instrumentation, verbose, modules);
+ System.out.printf("Finished instrumentation after %dms%n", elapsedTime);
}
}
diff --git a/pom.xml b/pom.xml
index d0b6e72e4..15275c612 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,7 +8,7 @@
MIT License
- http://www.opensource.org/licenses/mit-license.php
+ https://www.opensource.org/licenses/mit-license.php
repo