Test 4.4.4

CMakeLists.txt

@@ -69,7 +69,7 @@ endif()
 #-----------------------------------------------------------------------------
 set (API_VERSION_MAJOR 4)
 set (API_VERSION_MINOR 4)
-set (API_VERSION_PATCH 3)
+set (API_VERSION_PATCH 4)
 set (API_VERSION "${API_VERSION_MAJOR}.${API_VERSION_MINOR}.${API_VERSION_PATCH}")
 set (ABI_CURRENT 1)
 set (ABI_REVISION 0)
@@ -224,10 +224,10 @@ find_package(LibXml2)
 #find_package(PythonInterp)
 
 #Find the java runtime and sdk
-#if(ENABLE_JAVA_BINDINGS)
-#    find_package(Java 1.6)
-#    find_package(JNI)
-#endif()
+if(ENABLE_JAVA)
+    find_package(Java 1.6)
+    find_package(JNI)
+endif()
 
 
 find_library(PTHREAD pthread)

Docker.ubuntu

@@ -0,0 +1,14 @@
+# Docker file for an ubuntu image for testing NAPI with an up-to-date distro
+FROM ubuntu:20.04
+
+RUN apt update && apt-get install -y \
+    gcc \
+    g++ \
+    gfortran \
+    libhdf5-dev \
+    libmxml-dev \
+    cmake \
+    default-jdk 
+
+
+CMD /bin/bash

applications/NXtranslate/text_xml/xml_retriever_dom.cpp

@@ -1,4 +1,6 @@
 #include <iostream>
+#define LIBXML_LEGACY_ENABLED
+#include <libxml/SAX.h>
 #include <libxml/parser.h>
 #include <libxml/parserInternals.h>
 #include <stdexcept>

applications/NXtranslate/xml_parser.cpp

@@ -1,3 +1,5 @@
+#define LIBXML_LEGACY_ENABLED
+#include <libxml/SAX.h>
 #include <libxml/parser.h>
 #include <libxml/parserInternals.h>
 #include <iostream>

applications/nxingest/nxingest_main.cpp

@@ -43,7 +43,7 @@
     whitespace_cb(mxml_node_t *node,        /* I - Element node */
         	  int         where)        /* I - Open or close tag? */
 {
-	if (strncmp(node->value.element.name, "?xml", 4) == 0)
+	if (strncmp(mxmlGetElement(node), "?xml", 4) == 0)
 		return(NULL);
 	if (where == MXML_WS_BEFORE_OPEN )
 		return ("\n");
@@ -112,11 +112,11 @@ int main (int argc, char *argv[])
 		outFp = fopen(outputFl, "w");
 		if( outFp == 0 ) throw log.set("main", "Can't open the output file!", outputFl, "", NXING_ERR_CANT_OPEN_OUTPUT);
 
-		if(inTree->type == MXML_ELEMENT  && (strncmp(inTree->value.element.name, "?xml", 4) == 0)){	
-			outTree = mxmlNewElement(MXML_NO_PARENT,  inTree->value.element.name);
+		if(mxmlGetType(inTree) == MXML_ELEMENT  && (strncmp(mxmlGetElement(inTree), "?xml", 4) == 0)){
+			outTree = mxmlNewElement(MXML_NO_PARENT,  mxmlGetElement(inTree));
 		}
 
-		log.set("main", "Output Created, first tag added!", inTree->value.element.name).printLevel(NXING_LOG_DEBUG);
+		log.set("main", "Output Created, first tag added!", mxmlGetElement(inTree)).printLevel(NXING_LOG_DEBUG);
 		//
 
 		// Open the neXus file.

applications/nxingest/nxingest_parse.cpp

@@ -73,27 +73,32 @@ mxml_node_t *parseXml(mxml_node_t *inNode, mxml_node_t *topNode, mxml_node_t **o
 
 	int type_descent = MXML_DESCEND;		
 	const char 		*type;
+	const char 		*attName;
+	const char 		*attValue;
 
 	while( (inNode = mxmlWalkNext(inNode, topNode, type_descent)) != NULL )
 	{
 		inNextNode = inNode; // Get the last inNode to pass back to the calling function
-		if(inNode->type == MXML_ELEMENT)
+		if(mxmlGetType(inNode) == MXML_ELEMENT)
 		{
 			type_descent = MXML_DESCEND;
 
 			type = mxmlElementGetAttr(inNode, "type");
 			if(type != 0) 
 			{	
-				log.set("parseXml", "Found element : ", inNode->value.element.name).printLevel(NXING_LOG_DEBUG);
+				log.set("parseXml", "Found element : ", mxmlGetElement(inNode)).printLevel(NXING_LOG_DEBUG);
 				if(strcmp(type, "tbl") == 0 ) // Simple table.
 				{
-					log.set("parseXml", "Get new table", inNode->value.element.name).printLevel(NXING_LOG_DEBUG);
-					outNextNode = mxmlNewElement(*outNode, inNode->value.element.name );
+					log.set("parseXml", "Get new table", mxmlGetElement(inNode)).printLevel(NXING_LOG_DEBUG);
+					outNextNode = mxmlNewElement(*outNode, mxmlGetElement(inNode) );
 					// add the attributes of the input node : 
-					if(inNode->value.element.num_attrs > 1)
-						for(int i = 0; i< inNode->value.element.num_attrs; i++)
-							if(strcmp(inNode->value.element.attrs[i].name, "type") != 0)
-								mxmlElementSetAttr(outNextNode, inNode->value.element.attrs[i].name, inNode->value.element.attrs[i].value);
+					if(mxmlElementGetAttrCount(inNode) > 1)
+						for(int i = 0; i< mxmlElementGetAttrCount(inNode); i++) {
+
+							attValue = mxmlElementGetAttrByIndex(inNode, i, &attName);
+							if(strcmp(attName, "type") != 0)
+								mxmlElementSetAttr(outNextNode, attName, attValue);
+						}
 					inNode = parseXml(inNode, inNode, &outNextNode, nx);
 				} 
 				else if(strcmp(type, "user_tbl") == 0 )	// User table. There may be several user. Need to loop over the different NXusers.
@@ -103,50 +108,52 @@ mxml_node_t *parseXml(mxml_node_t *inNode, mxml_node_t *topNode, mxml_node_t **o
 					do{
 						userInNode = inNode;
 
-						log.set("parseXml", type, "Start", inNode->value.element.name).printLevel(NXING_LOG_DEBUG);
-						outNextNode = mxmlNewElement(*userOutNode, userInNode->value.element.name );
-						if(userInNode->value.element.num_attrs > 1)
-							for(int i = 0; i< userInNode->value.element.num_attrs; i++)
-								if(strcmp(userInNode->value.element.attrs[i].name, "type") != 0)
-									mxmlElementSetAttr(outNextNode, userInNode->value.element.attrs[i].name, userInNode->value.element.attrs[i].value);
+						log.set("parseXml", type, "Start", mxmlGetElement(inNode)).printLevel(NXING_LOG_DEBUG);
+						outNextNode = mxmlNewElement(*userOutNode, mxmlGetElement(userInNode) );
+						if(mxmlElementGetAttrCount(userInNode) > 1)
+							for(int i = 0; i< mxmlElementGetAttrCount(userInNode); i++) {
+								attValue = mxmlElementGetAttrByIndex(userInNode, i, &attName);
+								if(strcmp(attName, "type") != 0)
+									mxmlElementSetAttr(outNextNode, attName, attValue);
+							}
 
-						log.set("parseXml", type, "Element added",userInNode->value.element.name).printLevel(NXING_LOG_DEBUG);
+						log.set("parseXml", type, "Element added",mxmlGetElement(userInNode)).printLevel(NXING_LOG_DEBUG);
 						parseXml(userInNode, topNode, &outNextNode, nx);
-						log.set("parseXml", type, "Parsed", inNode->value.element.name).printLevel(NXING_LOG_DEBUG);
+						log.set("parseXml", type, "Parsed", mxmlGetElement(inNode)).printLevel(NXING_LOG_DEBUG);
 
 					}while(nx.nextUser() != -1); 
 					inNode = mxmlWalkNext(inNode, topNode, MXML_NO_DESCEND); 
 				}
 				else if(strcmp(type, "keyword_tag") == 0 ) // simple Tag record
 				{
-					log.set("parseXml", type, "Read",inNode->value.element.name).printLevel(NXING_LOG_DEBUG);
+					log.set("parseXml", type, "Read",mxmlGetElement(inNode)).printLevel(NXING_LOG_DEBUG);
 					inNode = readKeyword(inNode, outNode, nx);
 					type_descent = MXML_NO_DESCEND;
 				}
 				else if(strcmp(type, "tag") == 0 ) // simple Tag record
 				{
-					log.set("parseXml", type, "Read",inNode->value.element.name).printLevel(NXING_LOG_DEBUG);
+					log.set("parseXml", type, "Read",mxmlGetElement(inNode)).printLevel(NXING_LOG_DEBUG);
 					inNode = readRecord(inNode, outNode, nx);
 					type_descent = MXML_NO_DESCEND;
 				}
 				else if(strcmp(type, "param_str") == 0 ) // Parameter with a string value
 				{
-					log.set("parseXml", type, "Read", inNode->value.element.name).printLevel(NXING_LOG_DEBUG);
+					log.set("parseXml", type, "Read", mxmlGetElement(inNode)).printLevel(NXING_LOG_DEBUG);
 					inNode = readParam(inNode, outNode, nx, STR);
 					type_descent = MXML_NO_DESCEND;
 				}
 				else if(strcmp(type, "param_num") == 0 ) // Parameter with a numeric value
 				{
-					log.set("parseXml", type, "Read",inNode->value.element.name).printLevel(NXING_LOG_DEBUG);
+					log.set("parseXml", type, "Read",mxmlGetElement(inNode)).printLevel(NXING_LOG_DEBUG);
 					inNode = readParam(inNode, outNode, nx, NUM);
 					type_descent = MXML_NO_DESCEND;
 
 				}
 			}
 		}
-		if(inNode->type == MXML_TEXT && strlen(inNode->value.text.string) > 0)
+		if(mxmlGetType(inNode) == MXML_TEXT && strlen(mxmlGetText(inNode, NULL)) > 0)
 		{
-			log.set("parseXml", "Unexpected text (may be comments)", inNode->value.text.string).printLevel(NXING_LOG_DEBUG);
+			log.set("parseXml", "Unexpected text (may be comments)", mxmlGetText(inNode, NULL)).printLevel(NXING_LOG_DEBUG);
 		}
 	}
 	return (inNextNode);
@@ -174,15 +181,15 @@ mxml_node_t * readRecord(mxml_node_t *inNode, mxml_node_t **outNode, NxClass nx)
 	// 
 	while( (inNode = mxmlWalkNext(inNode, topNode, MXML_DESCEND)) != NULL )
 	{
-		if(inNode->type == MXML_ELEMENT)
+		if(mxmlGetType(inNode) == MXML_ELEMENT)
 		{
-			if(strcmp(inNode->value.element.name, "icat_name") == 0) 
+			if(strcmp(mxmlGetElement(inNode), "icat_name") == 0)
 			{				
 				log.set("readRecord", "ICAT name",mxmlGetItem(inNode, name)).printLevel(NXING_LOG_DEBUG);
 				mxmlGetItem(inNode, name);
 				log.set("readRecord", "ICAT name",name).printLevel(NXING_LOG_DEBUG);
 			} 
-			else if(strcmp(inNode->value.element.name, "value") == 0) 
+			else if(strcmp(mxmlGetElement(inNode), "value") == 0)
 			{
 				getValue(inNode, nx, value);
 			}
@@ -209,19 +216,19 @@ mxml_node_t * readKeyword(mxml_node_t *inNode, mxml_node_t **outNode, NxClass nx
 	char keys[] = " ,;";
 
 	// 
-	strcpy(keywordStr , inNode->value.element.name);
+	strcpy(keywordStr , mxmlGetElement(inNode));
 
 	while( (inNode = mxmlWalkNext(inNode, topNode, MXML_DESCEND)) != NULL )
 	{
-		if(inNode->type == MXML_ELEMENT)
+		if(mxmlGetType(inNode) == MXML_ELEMENT)
 		{
-			if(strcmp(inNode->value.element.name, "icat_name") == 0) 
+			if(strcmp(mxmlGetElement(inNode), "icat_name") == 0)
 			{				
 				log.set("readRecord", "ICAT name",mxmlGetItem(inNode, name)).printLevel(NXING_LOG_DEBUG);
 				mxmlGetItem(inNode, name);
 				log.set("readRecord", "ICAT name",name).printLevel(NXING_LOG_DEBUG);
 			} 
-			else if(strcmp(inNode->value.element.name, "value") == 0) 
+			else if(strcmp(mxmlGetElement(inNode), "value") == 0)
 			{
 				getValue(inNode, nx, value);
 			}
@@ -289,29 +296,29 @@ mxml_node_t * readParam(mxml_node_t *inNode, mxml_node_t **outNode, NxClass nx,
 
 	while( (inNode = mxmlWalkNext(inNode, topNode, MXML_DESCEND)) != NULL )
 	{
-		if(inNode->type == MXML_ELEMENT)
+		if(mxmlGetType(inNode) == MXML_ELEMENT)
 		{
-			if(strcmp(inNode->value.element.name, "icat_name") == 0) 
+			if(strcmp(mxmlGetElement(inNode), "icat_name") == 0)
 			{				
 				log.set("readParam", "ICAT name", mxmlGetItem(inNode, str)).printLevel(NXING_LOG_DEBUG);
 				buff = mxmlGetItem(inNode, str);					
 				if(buff != 0) name = buff;
 				else name = "";			} 
-			else if(strcmp(inNode->value.element.name, "value") == 0) 
+			else if(strcmp(mxmlGetElement(inNode), "value") == 0)
 			{
 				log.set("readParam", "Value ", mxmlGetItem(inNode, str)).printLevel(NXING_LOG_DEBUG);
 				buff = getValue(inNode, nx, str);
 				if(buff != 0) value = buff;
 				else value = "";
 			}
-			else if(strcmp(inNode->value.element.name, "units") == 0) 
+			else if(strcmp(mxmlGetElement(inNode), "units") == 0)
 			{
 				log.set("readParam", "Units", mxmlGetItem(inNode, str)).printLevel(NXING_LOG_DEBUG);
 				buff = getValue(inNode, nx, str);
 				if(buff != 0) units = buff;
 				else units = "";
 			} 
-			else if(strcmp(inNode->value.element.name, "description") == 0) 
+			else if(strcmp(mxmlGetElement(inNode), "description") == 0)
 			{
 				log.set("readParam", "Description", mxmlGetItem(inNode, str)).printLevel(NXING_LOG_DEBUG);
 				buff = getValue(inNode, nx, str);

applications/nxingest/nxingest_utils.cpp

@@ -74,9 +74,9 @@ char* mxmlGetItem(mxml_node_t *node, char* str){
 	topNode = node;	
 
 	strcpy(str, "");
-	while( (node = mxmlWalkNext(node, topNode, MXML_DESCEND)) != NULL  && node->type == MXML_TEXT)
+	while( (node = mxmlWalkNext(node, topNode, MXML_DESCEND)) != NULL  && mxmlGetType(node) == MXML_TEXT)
 	{
-		strcat(str, node->value.text.string);
+		strcat(str, mxmlGetText(node, NULL));
 		strcat(str, " ");
 	}
 	while(strlen(str) > 0 && str[strlen(str)-1] == ' ')
@@ -89,9 +89,9 @@ char* mxmlGetItem(mxml_node_t *node){
 	topNode = node;	
 	while( (node = mxmlWalkNext(node, topNode, MXML_DESCEND)) != NULL )
 	{
-		if(node->type == MXML_TEXT && strlen(node->value.text.string) > 0)
+		if(mxmlGetType(node) == MXML_TEXT && strlen(mxmlGetText(node, NULL)) > 0)
 		{
-			return node->value.text.string; 
+			return strdup(mxmlGetText(node, NULL));
 		}
 	}
 	return 0;

bindings/CMakeLists.txt

@@ -44,9 +44,9 @@ if(ENABLE_FORTRAN90)
 endif()
 
 #add_subdirectory (idl)
-#if (NOT(Java_JAVAC_EXECUTABLE MATCHES NOTFOUND))
-#    add_subdirectory (java)
-#endif ()
+if (NOT(Java_JAVAC_EXECUTABLE MATCHES NOTFOUND))
+    add_subdirectory (java)
+endif ()
 #add_subdirectory (matlab)
 #if (PYTHONINTERP_FOUND)
 #    add_subdirectory (python)

bindings/cpp/NeXusFile.cpp

@@ -1242,7 +1242,7 @@ void File::getAttr(const std::string& name, std::vector<std::string>& array) {
   }
 
   // get attrInfo
-  char attr_name[name.size()+1];
+  char * attr_name = new char[name.size()+1];
   strcpy(attr_name, name.c_str());
 
   int type;
@@ -1273,6 +1273,7 @@ void File::getAttr(const std::string& name, std::vector<std::string>& array) {
     end = data.find(sep, start);
   }
   array.push_back(data.substr(start));
+  delete [] attr_name;
 }
 
 vector<AttrInfo> File::getAttrInfos() {

bindings/java/CMakeLists.txt

@@ -50,20 +50,20 @@ if(DEFINED Java_JAVAC_EXECUTABLE)
              ${PROJECT_SOURCE_DIR}/bindings/java/org/nexusformat/NexusFile.java 
              ${JAVA_TEST})
 
-         SET(JAVA_CLASSES ${PROJECT_BINARY_DIR}/bindings/java/ncsa/hdf/hdflib/HDFException.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/ncsa/hdf/hdflib/HDFJavaException.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/ncsa/hdf/hdflib/HDFNotImplementedException.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/ncsa/hdf/hdflib/HDFConstants.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/ncsa/hdf/hdflib/HDFArray.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/ncsa/hdf/hdflib/HDFNativeData.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/org/nexusformat/NexusException.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/org/nexusformat/NXlink.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/org/nexusformat/NeXusFileInterface.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/org/nexusformat/AttributeEntry.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/org/nexusformat/NexusFile.class 
-             ${PROJECT_BINARY_DIR}/bindings/java/TestJapi.class)
-
-        SET(EXTRA_CLASSES ${PROJECT_BINARY_DIR}/bindings/java/ncsa/hdf/hdflib/ArrayDescriptor.class)
+         SET(JAVA_CLASSES ncsa/hdf/hdflib/HDFException.class
+             ncsa/hdf/hdflib/HDFJavaException.class
+             ncsa/hdf/hdflib/HDFNotImplementedException.class
+             ncsa/hdf/hdflib/HDFConstants.class
+             ncsa/hdf/hdflib/HDFArray.class
+             ncsa/hdf/hdflib/HDFNativeData.class
+             org/nexusformat/NexusException.class
+             org/nexusformat/NXlink.class
+             org/nexusformat/NeXusFileInterface.class
+             org/nexusformat/AttributeEntry.class
+             org/nexusformat/NexusFile.class
+             TestJapi.class)
+
+        SET(EXTRA_CLASSES ncsa/hdf/hdflib/ArrayDescriptor.class)
 
         SET(JNI_HEADER native/org_nexusformat_NexusFile.h)
 
@@ -90,15 +90,15 @@ if(DEFINED Java_JAVAC_EXECUTABLE)
         ADD_CUSTOM_COMMAND( 
             OUTPUT    ${JAR_ARCHIVE}
             COMMAND   ${Java_JAR_EXECUTABLE}
-            ARGS      cvf ${JAR_ARCHIVE} ${JAVA_CLASSES} ${EXTRA_CLASSES}
+            ARGS      cvf ${JAR_ARCHIVE} -C ${PROJECT_BINARY_DIR}/bindings/java/ ${JAVA_CLASSES} ${EXTRA_CLASSES}
             DEPENDS   ${EXTRA_CLASSES}
             COMMENT   "Build JAR File"
         )
 
         ADD_CUSTOM_COMMAND( 
             OUTPUT    ${JNI_HEADER}
-            COMMAND   ${Java_JAVAH_EXECUTABLE}
-            ARGS      -jni -d native -classpath . org.nexusformat.NexusFile
+            COMMAND   ${Java_JAVAC_EXECUTABLE}
+            ARGS      -h native ${PROJECT_SOURCE_DIR}/bindings/java/org/nexusformat/NexusFile.java
             DEPENDS   ${JAR_ARCHIVE}
             COMMENT   "Build JNI Header"
         )
@@ -113,7 +113,7 @@ if(DEFINED Java_JAVAC_EXECUTABLE)
         )
 
         ADD_CUSTOM_TARGET(NexusJavaBuild ALL echo
-           DEPENDS   ${JAR_ARCHIVE}
+           DEPENDS   ${JAR_ARCHIVE} ${JNI_HEADER}
         )
 
         ADD_CUSTOM_TARGET(NexusJavadocBuild ALL echo

bindings/java/ncsa/hdf/hdflib/HDFNativeData.java

@@ -120,10 +120,8 @@ public Object byteToNumber( byte[] barray, Object obj)
      *
      *  @param dataType  the type of the iamge data
      *  @param datasize  the size of the image data array
-     *  @returns         an array of 'datasize' numbers of 'dataType
+     *  @return         an array of 'datasize' numbers of 'dataType
      *
-     *  @see ncsa.hdf.hdfobject.HDFGR 
-     *  @see ncsa.hdf.hdfobject.HDFSDS
      */
 public static Object defineDataObject(int dataType, int datasize)
     {