Merge pull request #415 from apache/refactoring/409-Update-dependencies

Issue #409: Update dependencies

.github/workflows/codeql.yml

@@ -71,7 +71,7 @@ jobs:
       run: echo "CACHE_DATE=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
 
     - name: Build with Maven
-      run: mvn --no-transfer-progress -B clean verify --file pom.xml
+      run: mvn --no-transfer-progress -B -DskipTests clean verify --file pom.xml
 
     - name: Perform CodeQL Analysis
       uses: github/codeql-action/analyze@v3

jVinci/src/main/java/org/apache/vinci/transport/BaseServerRunnable.java

@@ -37,7 +37,7 @@ public class BaseServerRunnable implements Runnable {
 
   private BaseServer parent;
 
-  private static final ThreadLocal THREAD_LOCAL_SOCKET = new ThreadLocal();
+  private static final ThreadLocal<Socket> THREAD_LOCAL_SOCKET = new ThreadLocal<>();
 
   /**
    * Allows anyone in the calling chain of the 'run' method to get access to the socket being used
@@ -46,7 +46,7 @@ public class BaseServerRunnable implements Runnable {
    * @return -
    */
   public static Socket getSocket() {
-    return (Socket) THREAD_LOCAL_SOCKET.get();
+    return THREAD_LOCAL_SOCKET.get();
   }
 
   /**
@@ -104,7 +104,7 @@ public void run() {
     } catch (Throwable e) {
       Debug.reportException(e);
     } finally {
-      THREAD_LOCAL_SOCKET.set(null);
+      THREAD_LOCAL_SOCKET.remove();
       try {
         socket.close();
       } catch (IOException f) {

jVinci/src/main/java/org/apache/vinci/transport/XTalkTransporter.java

@@ -63,13 +63,12 @@ public class XTalkTransporter implements FrameTransporter {
   public KeyValuePair fromStream(InputStream is, Frame f) throws IOException, EOFException {
     char[] cbuffer = new char[128];
     byte[] buffer = new byte[128];
-    int marker = is.read();
-    if (marker == -1) {
-      throw new EOFException();
-    }
+    var marker = readByte(is);
+
     if ((byte) marker != DOCUMENT_MARKER) {
       throw new IOException("Expected document marker: " + (char) marker);
     }
+
     return fromStreamWork(is, f, buffer, cbuffer);
   }
 
@@ -93,15 +92,15 @@ public KeyValuePair fromStreamWork(InputStream is, Frame f) throws IOException {
 
   public KeyValuePair fromStreamWork(InputStream is, Frame f, byte[] buffer, char[] cbuffer)
           throws IOException {
-    int version = is.read();
-    if ((byte) version != VERSION_CODE) {
+    var version = readByte(is);
+    if (version != VERSION_CODE) {
       throw new IOException(
               "Xtalk version code doesn't match " + (int) VERSION_CODE + ": " + version);
     }
     int top_field_count = readInt(is);
     // Skip over intro PI's.
-    int marker;
-    while ((marker = is.read()) == PI_MARKER) {
+    byte marker;
+    while ((marker = readByte(is)) == PI_MARKER) {
       ignorePI(is);
       top_field_count--;
     }
@@ -112,7 +111,7 @@ public KeyValuePair fromStreamWork(InputStream is, Frame f, byte[] buffer, char[
     top_field_count--;
     // Skip over trailing PI's
     while (top_field_count > 0) {
-      marker = is.read();
+      marker = readByte(is);
       if ((byte) marker != 'p') {
         throw new IOException("Expected pi marker: " + (char) marker);
       }
@@ -187,12 +186,12 @@ public KeyValuePair consumeRootChildren(InputStream is, Frame f, byte[] buffer,
     int field_count = readInt(is);
     KeyValuePair return_me = null;
     if (field_count != 0) {
-      int marker = is.read();
+      var marker = readByte(is);
       if ((byte) marker == ELEMENT_MARKER) {
         return_me = consumeRootElement(is, f, buffer, cbuffer);
         field_count--;
         if (field_count > 0) {
-          marker = is.read();
+          marker = readByte(is);
         } else {
           return return_me;
         }
@@ -238,7 +237,7 @@ public KeyValuePair consumeRootElement(InputStream is, Frame f, byte[] buffer, c
         // it is of a different type.
       }
     } else {
-      int sub_marker = is.read();
+      var sub_marker = readByte(is);
       if (sub_field_count == 1 && (byte) sub_marker == STRING_MARKER) {
         value = consumeLeaf(is, f);
         if (tag_name.startsWith(TransportConstants.VINCI_NAMESPACE)) {
@@ -301,7 +300,7 @@ public void consumeChildren(InputStream is, Frame f, int field_count, int marker
           if (sub_field_count == 0) {
             value = f.createSubFrame(tag_name, sub_field_count);
           } else {
-            int sub_marker = is.read();
+            var sub_marker = readByte(is);
             if (sub_field_count == 1 && (byte) sub_marker == STRING_MARKER) {
               value = consumeLeaf(is, f);
             } else {
@@ -319,7 +318,7 @@ public void consumeChildren(InputStream is, Frame f, int field_count, int marker
       }
       field_count--;
       if (field_count > 0) {
-        marker = is.read();
+        marker = readByte(is);
       }
     }
   }
@@ -671,4 +670,17 @@ public void attributesToBin(OutputStream os, Attributes attributes, byte[] workb
     }
   }
 
-} // class
+  private static byte readByte(InputStream aIs) throws IOException {
+    int byteAsInt = aIs.read();
+
+    if (byteAsInt == -1) {
+      throw new EOFException("Unexpected end of stream");
+    }
+
+    if (byteAsInt < Byte.MIN_VALUE || byteAsInt > Byte.MAX_VALUE) {
+      throw new IOException("Illegal byte value [" + byteAsInt + "]");
+    }
+
+    return (byte) byteAsInt;
+  }
+}

jVinci/src/main/java/org/apache/vinci/transport/document/XTalkToSAX.java

@@ -96,7 +96,7 @@ public void resizeBuffers(int toSize) {
    * the document. Use bufferSize() and resizeBuffers to manage memory in applications where very
    * large strings may be encountered and the same object is used to parse many incoming documents.
    * 
-   * @param is
+   * @param aIs
    *          -
    * @param handler
    *          -
@@ -108,19 +108,17 @@ public void resizeBuffers(int toSize) {
    * @pre handler != null
    * @pre is != null
    */
-  public void parse(InputStream is, ContentHandler handler) throws IOException, SAXException {
-    this.is = is;
+  public void parse(InputStream aIs, ContentHandler handler) throws IOException, SAXException {
+    this.is = aIs;
     this.handler = handler;
     try {
-      int marker = is.read();
-      if (marker == -1) {
-        throw new EOFException();
-      }
+      var marker = readByte(aIs);
+
       if ((byte) marker != XTalkTransporter.DOCUMENT_MARKER) {
         throw new IOException("Expected document marker: " + (char) marker);
       }
-      int version = is.read();
-      if ((byte) version != XTalkTransporter.VERSION_CODE) {
+      var version = readByte(aIs);
+      if (version != XTalkTransporter.VERSION_CODE) {
         throw new IOException("Xtalk version code doesn't match "
                 + (int) XTalkTransporter.VERSION_CODE + ": " + version);
       }
@@ -129,19 +127,20 @@ public void parse(InputStream is, ContentHandler handler) throws IOException, SA
       handler.endDocument();
     } finally {
       // nullify refs to allow GC
-      is = null;
+      aIs = null;
       handler = null;
     }
   }
 
   private void doTopLevelParse() throws IOException, SAXException {
     int top_field_count = XTalkTransporter.readInt(is);
     // Skip over intro PI's.
-    int marker;
+    byte marker;
     if (top_field_count < 1) {
       throw new IOException("No top level element.");
     }
-    while ((marker = is.read()) == XTalkTransporter.PI_MARKER) {
+
+    while ((marker = readByte(is)) == XTalkTransporter.PI_MARKER) {
       String target = consumeString();
       String data = consumeString();
       handler.processingInstruction(target, data);
@@ -157,7 +156,7 @@ private void doTopLevelParse() throws IOException, SAXException {
     top_field_count--;
     // Handle trailing PI's
     while (top_field_count > 0) {
-      if (is.read() != XTalkTransporter.PI_MARKER) {
+      if (readByte(is) != XTalkTransporter.PI_MARKER) {
         throw new IOException("Expected PI marker.");
       }
       doProcessingInstruction();
@@ -198,8 +197,8 @@ private void doElement() throws IOException, SAXException {
     handler.startElement("", tagName, tagName, workAttributes);
     int field_count = XTalkTransporter.readInt(is);
     for (int i = 0; i < field_count; i++) {
-      int marker = is.read();
-      switch ((byte) marker) {
+      var marker = readByte(is);
+      switch (marker) {
         case XTalkTransporter.PI_MARKER:
           doProcessingInstruction();
           break;
@@ -220,4 +219,17 @@ private void doElement() throws IOException, SAXException {
     handler.endElement(null, null, tagName);
   }
 
+  private static byte readByte(InputStream aIs) throws IOException {
+    int byteAsInt = aIs.read();
+
+    if (byteAsInt == -1) {
+      throw new EOFException("Unexpected end of stream");
+    }
+
+    if (byteAsInt < Byte.MIN_VALUE || byteAsInt > Byte.MAX_VALUE) {
+      throw new IOException("Illegal byte value [" + byteAsInt + "]");
+    }
+
+    return (byte) byteAsInt;
+  }
 }

uimafit-core/pom.xml

@@ -80,13 +80,14 @@
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>org.springframework</groupId>
-      <artifactId>spring-test</artifactId>
+      <groupId>org.slf4j</groupId>
+      <artifactId>slf4j-simple</artifactId>
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>org.slf4j</groupId>
-      <artifactId>slf4j-simple</artifactId>
+      <groupId>com.github.h-thurow</groupId>
+      <artifactId>simple-jndi</artifactId>
+      <version>0.24.0</version>
       <scope>test</scope>
     </dependency>
   </dependencies>
@@ -172,7 +173,8 @@
               <configuration>
                 <excludes combine.children="append">
                   <!-- These test files are unreasonable to bear a license header -->
-                  <exclude>src/test/resources/log4j.properties</exclude>
+                  <exclude>src/test/resources/jndi.properties</exclude>
+                  <exclude>src/test/resources/jndi/DO-NOT-DELETE</exclude>
                   <!-- Plain documentation -->
                   <exclude>README*</exclude>
                   <!-- Release files -->
@@ -204,6 +206,16 @@
             </execution>
           </executions>
         </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-dependency-plugin</artifactId>
+          <configuration>
+            <ignoredDependencies combine.children="append">
+              <!-- Used via reflection -->
+              <ignoredDependency>com.github.h-thurow:simple-jndi</ignoredDependency>
+            </ignoredDependencies>
+          </configuration>
+        </plugin>
       </plugins>
     </pluginManagement>
   </build>

uimafit-core/src/main/java/org/apache/uima/fit/factory/locator/JndiResourceLocator.java

@@ -31,7 +31,11 @@
 
 /**
  * Locate an object via JNDI.
+ * 
+ * @deprecated To be removed without replacement
+ * @forRemoval 4.0.0
  */
+@Deprecated
 public class JndiResourceLocator extends Resource_ImplBase implements ExternalResourceLocator {
   /**
    * The name of the JNDI resource to look up.
@@ -60,6 +64,7 @@ public boolean initialize(ResourceSpecifier aSpecifier, Map aAdditionalParams)
     return true;
   }
 
+  @Override
   public Object getResource() {
     return resource;
   }