Merge pull request #801 from lesserwhirls/jdom-5

[5.x]: Set setExpandEntities to false on SAXBuilder

Author: haileyajohnson

bufr/src/main/java/ucar/nc2/iosp/bufr/tables/BufrTables.java

@@ -808,6 +808,7 @@ private static void readBmetTableB(InputStream ios, TableB b) throws IOException
     org.jdom2.Document doc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       doc = builder.build(ios);
     } catch (JDOMException e) {
       throw new IOException(e.getMessage());

bufr/src/main/java/ucar/nc2/iosp/bufr/tables/CodeFlagTables.java

@@ -100,6 +100,7 @@ static void init(Map<Short, CodeFlagTables> table) {
     String filename = BufrTables.RESOURCE_PATH + CodeFlagFilename;
     try (InputStream is = CodeFlagTables.class.getResourceAsStream(filename)) {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       org.jdom2.Document tdoc = builder.build(is);
       org.jdom2.Element root = tdoc.getRootElement();
 

bufr/src/main/java/ucar/nc2/iosp/bufr/tables/TableA.java

@@ -39,6 +39,7 @@ private static void init() {
 
       HashMap<Integer, String> map = new HashMap<>(100);
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       org.jdom2.Document tdoc = builder.build(is);
       org.jdom2.Element root = tdoc.getRootElement();
 

bufr/src/main/java/ucar/nc2/iosp/bufr/tables/WmoXmlReader.java

@@ -178,6 +178,7 @@ static void readWmoXmlTableB(InputStream ios, TableB b) throws IOException {
     org.jdom2.Document doc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       doc = builder.build(ios);
     } catch (JDOMException e) {
       throw new IOException(e.getMessage());
@@ -394,6 +395,7 @@ static void readWmoXmlTableD(InputStream ios, TableD tableD) throws IOException
     org.jdom2.Document doc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       doc = builder.build(ios);
     } catch (JDOMException e) {
       throw new IOException(e.getMessage());

bufr/src/test/java/ucar/nc2/iosp/bufr/tables/CodeTableGen.java

@@ -99,6 +99,7 @@ static public void prettyPrint() throws IOException {
     org.jdom2.Document doc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       doc = builder.build("C:/docs/bufr/wmo/Code-FlagTables-11-2007.xml");
 
       Format pretty = Format.getPrettyFormat();
@@ -169,6 +170,7 @@ static public void passOne() throws IOException {
     org.jdom2.Document orgDoc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       orgDoc = builder.build(orgXml);
 
       org.jdom2.Document tdoc = new org.jdom2.Document();
@@ -250,6 +252,7 @@ static public void passTwo() throws IOException {
     org.jdom2.Document tdoc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       tdoc = builder.build(trans1);
 
       org.jdom2.Document ndoc = new org.jdom2.Document();
@@ -335,6 +338,7 @@ static public void passThree() throws IOException {
     org.jdom2.Document tdoc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       tdoc = builder.build(trans2);
 
       /*

bufr/src/test/java/ucar/nc2/iosp/bufr/tables/CompareTableB.java

@@ -50,6 +50,7 @@ public void readBmt() throws IOException {
     org.jdom2.Document doc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       doc = builder.build(bmt);
       Element root = doc.getRootElement();
       int count = makeBmtTable(root.getChildren("featureCatalogue"));

bufr/src/test/java/ucar/nc2/iosp/bufr/tables/CompareTableD.java

@@ -41,6 +41,7 @@ public void readBmt() throws IOException {
     org.jdom2.Document doc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       doc = builder.build(bmt);
       Element root = doc.getRootElement();
       int count = makeBmtTable(root.getChildren("featureCatalogue"));
@@ -185,6 +186,7 @@ public void readTable() throws IOException {
     org.jdom2.Document doc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       doc = builder.build(robbxml);
       Element root = doc.getRootElement();
       int count = makeTable(root.getChildren("sequence"));

bufr/src/test/java/ucar/nc2/iosp/bufr/tables/WmoTableDVariations.java

@@ -69,6 +69,7 @@ private static void tableDVariations(String tableLocation, Formatter out, Missin
     Document doc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       doc = builder.build(ios);
     } catch (JDOMException e) {
       throw new IOException(e.getMessage());

cdm-test/src/test/java/thredds/featurecollection/TestFeatureCollectionConfig.java

@@ -110,6 +110,7 @@ public void testFeatureCollectionReader() throws IOException, JDOMException {
     File configFile = new File(TestDir.cdmUnitTestDir + "tds/config/fnmoc.xml");
     org.jdom2.Document doc;
     SAXBuilder builder = new SAXBuilder();
+    builder.setExpandEntities(false);
     doc = builder.build(configFile);
 
     XMLOutputter xmlOut = new XMLOutputter();

cdm-test/src/timing/java/ucar/nc2/util/xml/TimeJdomReading.java

@@ -19,6 +19,7 @@ public class TimeJdomReading {
     org.jdom2.Document doc;
     try {
       SAXBuilder builder = new SAXBuilder();
+      builder.setExpandEntities(false);
       doc = builder.build(filename);
     } catch (JDOMException e) {
       throw new IOException(e.getMessage());