Add unit tests and fix issues

java/ql/src/semmle/code/java/dataflow/ExternalFlow.qll

@@ -71,6 +71,7 @@ private import internal.DataFlowPrivate
 private module Frameworks {
   private import semmle.code.java.frameworks.ApacheHttp
   private import semmle.code.java.frameworks.apache.Lang
+  private import semmle.code.java.frameworks.guava.Guava
 }
 
 private predicate sourceModelCsv(string row) {

java/ql/src/semmle/code/java/frameworks/guava/Guava.qll

@@ -6,3 +6,4 @@ import java
 import StringUtils
 import Collections
 import Preconditions
+import IO

java/ql/src/semmle/code/java/frameworks/guava/IO.qll

@@ -14,7 +14,17 @@ private class GuavaIoCsv extends SummaryModelCsv {
         "com.google.common.io;BaseEncoding;true;decodingSource;(CharSource);;Argument[0];ReturnValue;taint",
         "com.google.common.io;BaseEncoding;true;encode;(byte[]);;Argument[0];ReturnValue;taint",
         "com.google.common.io;BaseEncoding;true;encode;(byte[],int,int);;Argument[0];ReturnValue;taint",
-        "com.google.common.io;ByteSource;true;asCharSource;(Charset);;Argument[0];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;withSeparator;(String,int);;Argument[0];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;decode;(CharSequence);;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;decodingStream;(Reader);;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;decodingSource;(CharSource);;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;encode;(byte[]);;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;upperCase;();;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;lowerCase;();;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;withPadChar;(char);;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;omitPadding;();;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;BaseEncoding;true;encode;(byte[],int,int);;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;ByteSource;true;asCharSource;(Charset);;Argument[-1];ReturnValue;taint",
         "com.google.common.io;ByteSource;true;concat;;;Argument[0];ReturnValue;taint",
         "com.google.common.io;ByteSource;true;openStream;();;Argument[-1];ReturnValue;taint",
         "com.google.common.io;ByteSource;true;openBufferedStream;();;Argument[-1];ReturnValue;taint",
@@ -22,15 +32,16 @@ private class GuavaIoCsv extends SummaryModelCsv {
         "com.google.common.io;ByteSource;true;slice;(long,long);;Argument[-1];ReturnValue;taint",
         "com.google.common.io;ByteSource;true;wrap;(byte[]);;Argument[0];ReturnValue;taint",
         "com.google.common.io;ByteStreams;false;copy;(InputStream,OutputStream);;Argument[0];Argument[1];taint",
+        "com.google.common.io;ByteStreams;false;copy;(ReadablyByteChannel,WritableByteChannel);;Argument[0];Argument[1];taint",
         "com.google.common.io;ByteStreams;false;limit;(InputStream,long);;Argument[0];ReturnValue;taint",
         "com.google.common.io;ByteStreams;false;newDataInput;(byte[]);;Argument[0];ReturnValue;taint",
         "com.google.common.io;ByteStreams;false;newDataInput;(byte[],int);;Argument[0];ReturnValue;taint",
         "com.google.common.io;ByteStreams;false;newDataInput;(ByteArrayInputStream);;Argument[0];ReturnValue;taint",
-        "com.google.common.io;ByteStreams;false;read;(InputStream,byte[],int,int);;Argument[0];Argument[-1];taint",
+        "com.google.common.io;ByteStreams;false;read;(InputStream,byte[],int,int);;Argument[0];Argument[1];taint",
         "com.google.common.io;ByteStreams;false;readFully;(InputStream,byte[]);;Argument[0];Argument[1];taint",
         "com.google.common.io;ByteStreams;false;readFully;(InputStream,byte[],int,int);;Argument[0];Argument[1];taint",
         "com.google.common.io;ByteStreams;false;toByteArray;(InputStream);;Argument[0];ReturnValue;taint",
-        "com.google.common.io;CharSource;true;asByteSource;(Charset);;Argument[0];ReturnValue;taint",
+        "com.google.common.io;CharSource;true;asByteSource;(Charset);;Argument[-1];ReturnValue;taint",
         "com.google.common.io;CharSource;true;concat;;;Argument[0];ReturnValue;taint",
         "com.google.common.io;CharSource;true;copyTo;(Appendable);;Argument[-1];Argument[0];taint",
         "com.google.common.io;CharSource;true;openStream;();;Argument[-1];ReturnValue;taint",
@@ -38,9 +49,10 @@ private class GuavaIoCsv extends SummaryModelCsv {
         "com.google.common.io;CharSource;true;read;();;Argument[-1];ReturnValue;taint",
         "com.google.common.io;CharSource;true;readFirstLine;();;Argument[-1];ReturnValue;taint",
         "com.google.common.io;CharSource;true;readLines;();;Argument[-1];ReturnValue;taint",
+        "com.google.common.io;CharSource;true;lines;();;Argument[-1];ReturnValue;taint",
         "com.google.common.io;CharSource;true;wrap;(CharSequence);;Argument[0];ReturnValue;taint",
         "com.google.common.io;CharStreams;false;copy;(Readable,Appendable);;Argument[0];Argument[1];taint",
-        "com.google.common.io;CharStreams;false;readLines;(Readable);;Argument[0];Argument[-1];taint",
+        "com.google.common.io;CharStreams;false;readLines;(Readable);;Argument[0];ReturnValue;taint",
         "com.google.common.io;CharStreams;false;toString;(Readable);;Argument[0];ReturnValue;taint",
         "com.google.common.io;Closer;true;register;;;Argument[0];ReturnValue;value",
         "com.google.common.io;Files;false;getFileExtension;(String);;Argument[0];ReturnValue;taint",
@@ -48,8 +60,8 @@ private class GuavaIoCsv extends SummaryModelCsv {
         "com.google.common.io;Files;false;simplifyPath;(String);;Argument[0];ReturnValue;taint",
         "com.google.common.io;MoreFiles;false;getFileExtension;(Path);;Argument[0];ReturnValue;taint",
         "com.google.common.io;MoreFiles;false;getNameWithoutExtension;(Path);;Argument[0];ReturnValue;taint",
-        "com.google.common.io;LineReader;false;LineReader;(Reader);;Argument[0];ReturnValue;taint",
-        "com.google.common.io;LineReader;false;readLine;();;Argument[-1];ReturnValue;taint"
+        "com.google.common.io;LineReader;false;LineReader;(Readable);;Argument[0];ReturnValue;taint",
+        "com.google.common.io;LineReader;true;readLine;();;Argument[-1];ReturnValue;taint"
       ]
   }
 }

java/ql/test/library-tests/frameworks/guava/TestCollect.java

@@ -72,7 +72,7 @@ class TestCollect {
         sink(t1.remove("r", "c")); // $numTaintFlow=1
 
         t3.row("r").put("c", x);
-        sink(t3);  // MISSING:$numTaintFlow=1
+        sink(t3);  // $ MISSING:numTaintFlow=1
     }
 
     void test4(Multimap<String, String> m1, Multimap<String, String> m2, Multimap<String, String> m3, 
@@ -94,7 +94,7 @@ class TestCollect {
         }
 
         m5.asMap().get("k").add(x);
-        sink(m5);  // MISSING:$numTaintFlow=1
+        sink(m5);  // $ MISSING:numTaintFlow=1
     }
 
     void test5(Comparator<String> comp, SortedSet<String> sorS, SortedMap<String, String> sorM) {

java/ql/test/library-tests/frameworks/guava/TestIO.java

@@ -0,0 +1,116 @@
+package com.google.common.io;
+
+import com.google.common.collect.ImmutableList;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.lang.StringBuffer;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.Closeable;
+import java.nio.file.Path;
+import java.io.IOException;
+
+class TestIO {
+    Object taint() { return null; }
+    String staint(){ return (String) taint(); }
+    byte[] btaint() { return (byte[]) taint(); }
+    InputStream itaint() { return (InputStream) taint(); }
+    Reader rtaint() { return new InputStreamReader(itaint()); }
+    Path ptaint() { return (Path) taint(); }
+
+    void sink(Object o) {}
+
+    void test1() {
+        BaseEncoding enc = BaseEncoding.base64();
+        sink(enc.decode(staint())); // $numTaintFlow=1
+        sink(enc.encode(btaint())); // $numTaintFlow=1
+        sink(enc.encode(btaint(), 0, 42)); // $numTaintFlow=1
+        sink(enc.decodingStream(rtaint())); // $numTaintFlow=1
+        sink(enc.decodingSource(CharSource.wrap(staint()))); // $numTaintFlow=1
+        sink(enc.withSeparator(staint(), 10).omitPadding().lowerCase().decode("abc")); // $numTaintFlow=1
+    }
+
+    void test2() throws IOException {
+        ByteSource b = ByteSource.wrap(btaint());
+        sink(b.openStream()); // $numTaintFlow=1
+        sink(b.openBufferedStream()); // $numTaintFlow=1
+        sink(b.asCharSource(null)); // $numTaintFlow=1
+        sink(b.slice(42,1337)); // $numTaintFlow=1
+        sink(b.read()); // $numTaintFlow=1
+        sink(ByteSource.concat(ByteSource.empty(), ByteSource.empty(), b)); // $numTaintFlow=1
+        sink(ByteSource.concat(ImmutableList.of(ByteSource.empty(), ByteSource.empty(), b))); // $numTaintFlow=1
+        sink(b.read(new MyByteProcessor())); // $ MISSING:numTaintFlow=1
+
+        CharSource c = CharSource.wrap(staint());
+        sink(c.openStream()); // $numTaintFlow=1
+        sink(c.openBufferedStream()); // $numTaintFlow=1
+        sink(c.asByteSource(null)); // $numTaintFlow=1
+        sink(c.readFirstLine()); // $numTaintFlow=1
+        sink(c.readLines()); // $numTaintFlow=1
+        sink(c.read()); // $numTaintFlow=1
+        sink(c.lines()); // $numTaintFlow=1
+        sink(CharSource.concat(CharSource.empty(), CharSource.empty(), c)); // $numTaintFlow=1
+        sink(CharSource.concat(ImmutableList.of(CharSource.empty(), CharSource.empty(), c))); // $numTaintFlow=1
+        sink(c.readLines(new MyLineProcessor())); // $ MISSING:numTaintFlow=1
+        c.forEachLine(l -> sink(l)); // $ MISSING:numTaintFlow=1
+        StringBuffer buf = new StringBuffer();
+        c.copyTo(buf);
+        sink(buf); // $numTaintFlow=1
+    }
+
+    class MyByteProcessor implements ByteProcessor<Object> {
+        byte[] buf;
+        public Object getResult() { return buf; }
+        public boolean processBytes(byte[] b, int off, int len)  { this.buf = b; return false; }
+    }
+
+    class MyLineProcessor implements LineProcessor<String> {
+        String s = "";
+        public String getResult() { return s; }
+        public boolean processLine(String l)  { this.s += l; return true; }
+    }
+
+    void test3() throws IOException {
+        sink(ByteStreams.limit(itaint(), 1337)); // $numTaintFlow=1
+        sink(ByteStreams.newDataInput(btaint())); // $numTaintFlow=1
+        sink(ByteStreams.newDataInput(btaint(), 0)); // $numTaintFlow=1
+        sink(ByteStreams.newDataInput(btaint())); // $numTaintFlow=1
+        sink(ByteStreams.newDataInput(btaint()).readLine()); // $ MISSING:numTaintFlow=1
+        sink(ByteStreams.newDataInput(new ByteArrayInputStream(btaint()))); // $numTaintFlow=1
+        byte[] b1 = null, b2 = null, b3 = null;
+        ByteStreams.read(itaint(), b1, 0, 42);
+        sink(b1); // $numTaintFlow=1
+        ByteStreams.readFully(itaint(), b2);
+        sink(b2); // $numTaintFlow=1
+        ByteStreams.readFully(itaint(), b3, 0, 42);
+        sink(b3); // $numTaintFlow=1
+        sink(ByteStreams.readBytes(itaint(), new MyByteProcessor())); // $ MISSING:numTaintFlow=1
+        sink(ByteStreams.toByteArray(itaint())); // $numTaintFlow=1
+
+        StringBuffer buf = new StringBuffer();
+        CharStreams.copy(rtaint(), buf);
+        sink(buf); // $numTaintFlow=1
+        sink(CharStreams.readLines(rtaint())); // $numTaintFlow=1
+        sink(CharStreams.readLines(rtaint(), new MyLineProcessor())); // $ MISSING:numTaintFlow=1
+        sink(CharStreams.toString(rtaint())); // $numTaintFlow=1
+    }
+
+    void test4() throws IOException {
+        sink(Closer.create().register((Closeable) taint())); // $numTaintFlow=1
+        sink(new LineReader(rtaint()).readLine()); // $numTaintFlow=1
+        sink(Files.simplifyPath(staint())); // $numTaintFlow=1
+        sink(Files.getFileExtension(staint())); // $numTaintFlow=1
+        sink(Files.getNameWithoutExtension(staint())); // $numTaintFlow=1
+        sink(MoreFiles.getFileExtension(ptaint())); // $numTaintFlow=1
+        sink(MoreFiles.getNameWithoutExtension(ptaint())); // $numTaintFlow=1
+    }
+
+    void test6() throws IOException {
+        sink(new CountingInputStream(itaint())); // $numTaintFlow=1
+        byte[] buf = null;
+        new CountingInputStream(itaint()).read(buf, 0, 42); 
+        sink(buf); // $numTaintFlow=1
+        sink(new LittleEndianDataInputStream(itaint())); // $numTaintFlow=1
+        sink(new LittleEndianDataInputStream(itaint()).readUTF()); // $ MISSING:numTaintFlow=1
+    }
+}

java/ql/test/stubs/guava-30.0/com/google/common/io/CountingInputStream.java

@@ -0,0 +1,52 @@
+/*
+ * Copyright (C) 2007 The Guava Authors
+ *
+ * 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
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * 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 com.google.common.io;
+import java.io.FilterInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+public final class CountingInputStream extends FilterInputStream {
+  public CountingInputStream(InputStream in) {
+    super(in);
+  }
+
+  public long getCount() {
+    return 0;
+  }
+
+  @Override
+  public int read() throws IOException {
+    return 0;
+  }
+
+  @Override
+  public int read(byte[] b, int off, int len) throws IOException {
+    return 0;
+  }
+
+  @Override
+  public long skip(long n) throws IOException {
+    return 0;
+  }
+
+  @Override
+  public synchronized void mark(int readlimit) {
+  }
+
+  @Override
+  public synchronized void reset() throws IOException {
+  }
+
+}

java/ql/test/stubs/guava-30.0/com/google/common/io/LittleEndianDataInputStream.java

@@ -0,0 +1,99 @@
+/*
+ * Copyright (C) 2007 The Guava Authors
+ *
+ * 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
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * 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 com.google.common.io;
+import java.io.DataInput;
+import java.io.FilterInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+public final class LittleEndianDataInputStream extends FilterInputStream implements DataInput {
+  public LittleEndianDataInputStream(InputStream in) {
+    super(in);
+  }
+
+  @Override
+  public String readLine() {
+    return null;
+  }
+
+  @Override
+  public void readFully(byte[] b) throws IOException {
+  }
+
+  @Override
+  public void readFully(byte[] b, int off, int len) throws IOException {
+  }
+
+  @Override
+  public int skipBytes(int n) throws IOException {
+    return 0;
+  }
+
+  @Override
+  public int readUnsignedByte() throws IOException {
+    return 0;
+  }
+
+  @Override
+  public int readUnsignedShort() throws IOException {
+    return 0;
+  }
+
+  @Override
+  public int readInt() throws IOException {
+    return 0;
+  }
+
+  @Override
+  public long readLong() throws IOException {
+    return 0;
+  }
+
+  @Override
+  public float readFloat() throws IOException {
+    return 0;
+  }
+
+  @Override
+  public double readDouble() throws IOException {
+    return 0;
+  }
+
+  @Override
+  public String readUTF() throws IOException {
+    return null;
+  }
+
+  @Override
+  public short readShort() throws IOException {
+    return 0;
+  }
+
+  @Override
+  public char readChar() throws IOException {
+    return '0';
+  }
+
+  @Override
+  public byte readByte() throws IOException {
+    return 0;
+  }
+
+  @Override
+  public boolean readBoolean() throws IOException {
+    return false;
+  }
+
+}