Xml from file

examples/c++/setAnnotation.cpp

@@ -11,29 +11,6 @@
 using namespace std;
 LIBSBML_CPP_NAMESPACE_USE
 
-XMLNode* parseAnnotation(const std::string& annotationFile)
-{
-	// read file into memory
-	FILE* file = fopen(annotationFile.c_str(), "r");
-	fseek(file, 0, SEEK_END);
-	long length = ftell(file);
-
-	fseek(file, 0, SEEK_SET);
-	char* data = new char[length + 1];
-
-	// fill data with zeros
-	memset(data, 0, length + 1);
-
-	fread(data, 1, length, file);
-	fclose(file);
-	data[length] = '\0';
-
-	// parse the string
-	XMLNode* xmlnode = XMLNode::convertStringToXMLNode(data);
-	delete[] data;
-	return xmlnode;
-}
-
 bool setAnnotation(const std::string& sbmlFile, const std::string& metaId,
 	const std::string& annotationFile, const std::string& outputFile)
 {
@@ -52,7 +29,7 @@ bool setAnnotation(const std::string& sbmlFile, const std::string& metaId,
 		return false;
 	}
 
-	XMLNode* annotation = parseAnnotation(annotationFile);
+	XMLNode* annotation = XMLNode::readXMLNodeFromFile(annotationFile);
 	if (!annotation)
 	{
 		cerr << "the annotation could not be parsed from file: " << annotationFile << "." << std::endl;

src/sbml/xml/ExpatParser.cpp

@@ -375,14 +375,6 @@ ExpatParser::parseNext ()
     return false;
   }
 
-  // catch whether an xml declaration has been found
-  // Expat does not report a missing xml declaration
-  if (!mHandler.hasXMLDeclaration())
-  {
-    reportError(MissingXMLDecl, "", 1, 1);
-    return false;
-  }
-
   if ( !error() && done )
   {
     mHandler.endDocument();

src/sbml/xml/XMLNode.cpp

@@ -48,6 +48,7 @@
 #include <sbml/xml/XMLInputStream.h>
 #include <sbml/xml/XMLOutputStream.h>
 #include <sbml/xml/XMLConstructorException.h>
+#include <sbml/xml/XMLErrorLog.h>
 /** @endcond */
 
 #include <sbml/xml/XMLNode.h>
@@ -675,28 +676,17 @@ XMLNode*
 XMLNode::readXMLNodeFromFile(const std::string& filename)
 {
   XMLNode * xmlnode = NULL;
-  if (util_file_exists(filename.c_str()))
+  if (!util_file_exists(filename.c_str()))
   {
-    // read file into memory
-    FILE* file = fopen(filename.c_str(), "r");
-    fseek(file, 0, SEEK_END);
-    long length = ftell(file);
-
-    fseek(file, 0, SEEK_SET);
-    char* data = new char[length + 1];
-
-    // fill data with zeros
-    memset(data, 0, length + 1);
+    return xmlnode;
+  }
+  XMLErrorLog * log = new XMLErrorLog();
 
-    fread(data, 1, length, file);
-    fclose(file);
-    data[length] = '\0';
+  XMLInputStream stream(filename.c_str(), true, "", log);
+  if (!stream.peek().isStart())
+    return NULL;
 
-    // parse the string
-    xmlnode = XMLNode::convertStringToXMLNode(data);
-    delete[] data;
-  }
-  return xmlnode;
+  return new XMLNode(stream);
 }
 
 /** @cond doxygenLibsbmlInternal */

src/sbml/xml/XMLNode.h

@@ -527,6 +527,32 @@ class LIBLAX_EXTERN XMLNode : public XMLToken
   static XMLNode* convertStringToXMLNode(const std::string& xmlstr,
                                          const XMLNamespaces* xmlns = NULL);
 
+
+  /**
+  * Returns an XMLNode which is readfrom a file containing XML
+  * content.
+  *
+  * The XML namespace must be defined using argument @p xmlns if the
+  * corresponding XML namespace attribute is not part of the file of the
+  * first argument.
+  *
+  * @param filename string name of file to be read to a XML node.
+  * @param xmlns XMLNamespaces the namespaces to set (default value is @c NULL).
+  *
+  * @note The caller owns the returned XMLNode and is reponsible for
+  * deleting it.  The returned XMLNode object is a dummy root (container)
+  * XMLNode if the top-level element in the given XML string is NOT
+  * <code>&lt;html&gt;</code>, <code>&lt;body&gt;</code>,
+  * <code>&lt;annotation&gt;</code>, or <code>&lt;notes&gt;</code>.  In
+  * the dummy root node, each top-level element in the given XML string is
+  * contained as a child XMLNode. XMLToken::isEOF() can be used to
+  * identify if the returned XMLNode object is a dummy node.
+  *
+  * @return a XMLNode which is read from file @p filename.  If the
+  * conversion failed, this method returns @c NULL.
+  *
+  * @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif@~
+  */
   static XMLNode* readXMLNodeFromFile(const std::string& filename);
 
 

src/sbml/xml/XercesParser.cpp

@@ -694,12 +694,6 @@ XercesParser::parseNext ()
     result = false;
   }
 
-  if (! static_cast <XercesReader *> (mReader) ->hasXMLDeclaration())
-  {
-    reportError(MissingXMLDecl, "", 1, 1);
-    return false;
-  }
-
   return result;
 }
 

src/sbml/xml/test/TestRunner.c

@@ -39,14 +39,19 @@
  * and also available online as http://sbml.org/software/libsbml/license.html
  * ---------------------------------------------------------------------- -->*/
 
-#include <string.h>
 #include <check.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <sbml/common/extern.h>
+#include <sbml/util/memory.h>
 
 #ifdef LIBSBML_USE_VLD
   #include <vld.h>
 #endif
 
 #if defined(__cplusplus)
+LIBSBML_CPP_NAMESPACE_USE
 CK_CPPSTART
 #endif
 
@@ -66,10 +71,48 @@ Suite *create_suite_XMLOutputStream (void);
 Suite *create_suite_XMLAttributes_C (void);
 Suite *create_suite_XMLExceptions (void);
 
+/**
+ * Global.
+ *
+ * Declared extern in TestAnnotation suite.
+ */
+char *TestDataDirectory;
+
+
+/**
+ * Sets TestDataDirectory for the the TestAnnotation suite.
+ *
+ * For Automake's distcheck target to work properly, TestDataDirectory must
+ * begin with the value of the environment variable SRCDIR.
+ */
+void
+setTestDataDirectory (void)
+{
+  char *srcdir = getenv("srcdir");
+  size_t  length  = (srcdir == NULL) ? 0 : strlen(srcdir);
+
+
+  /**
+   * strlen("/test-data/") = 11 + 1 (for NULL) = 12
+   */
+  TestDataDirectory = (char *) safe_calloc( length + 12, sizeof(char) );
+
+  if (srcdir != NULL)
+  {
+    strcpy(TestDataDirectory, srcdir);
+    strcat(TestDataDirectory, "/");
+  }
+
+  strcat(TestDataDirectory, "test-data/");
+}
+
+
 int
 main (int argc, char* argv[]) 
 { 
   int num_failed = 0;
+  setTestDataDirectory();
+//  SRunner *runner = srunner_create(create_suite_XMLNode());
   SRunner *runner = srunner_create(create_suite_XMLAttributes());
   srunner_add_suite(runner, create_suite_CopyAndClone());
 
@@ -97,6 +140,8 @@ main (int argc, char* argv[])
 
   srunner_free(runner);
 
+  free(TestDataDirectory);
+
   return num_failed;
 }
 

src/sbml/xml/test/TestXMLNode.cpp

@@ -51,6 +51,21 @@ LIBSBML_CPP_NAMESPACE_USE
 
 CK_CPPSTART
 
+extern char *TestDataDirectory;
+
+static bool
+equals(const char* expected, const char* actual)
+{
+  if (!strcmp(expected, actual)) return true;
+
+  printf("\nStrings are not equal:\n");
+  printf("Expected:\n[%s]\n", expected);
+  printf("Actual:\n[%s]\n", actual);
+
+  return false;
+}
+
+
 START_TEST (test_XMLNode_getIndex)
 {
 	const char* xmlstr = "<annotation>\n"
@@ -1640,6 +1655,97 @@ END_TEST
 //END_TEST
 //
 
+
+START_TEST(test_read_from_file)
+{
+  char *filename = safe_strcat(TestDataDirectory, "just_annotation.xml");
+  XMLNode *node = XMLNode::readXMLNodeFromFile(filename);
+
+  fail_unless(node != NULL);
+
+  fail_unless(node->getNumChildren() == 1);
+
+  const XMLNode_t* rdf = XMLNode_getChild(node, 0);
+
+  fail_unless(!strcmp(XMLNode_getName(rdf), "RDF"));
+  fail_unless(!strcmp(XMLNode_getPrefix(rdf), "rdf"));
+  fail_unless(!strcmp(XMLNode_getURI(rdf), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+  fail_unless(XMLNode_getNumChildren(rdf) == 1);
+
+  const XMLNode_t* desc = XMLNode_getChild(rdf, 0);
+
+  fail_unless(!strcmp(XMLNode_getName(desc), "Description"));
+  fail_unless(!strcmp(XMLNode_getPrefix(desc), "rdf"));
+  fail_unless(!strcmp(XMLNode_getURI(desc), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+  fail_unless(XMLNode_getNumChildren(desc) == 1);
+
+  const XMLNode_t * is1 = XMLNode_getChild(desc, 0);
+  fail_unless(!strcmp(XMLNode_getName(is1), "is"));
+  fail_unless(!strcmp(XMLNode_getPrefix(is1), "bqbiol"));
+  fail_unless(XMLNode_getNumChildren(is1) == 1);
+
+  const XMLNode_t * Bag = XMLNode_getChild(is1, 0);
+  fail_unless(!strcmp(XMLNode_getName(Bag), "Bag"));
+  fail_unless(!strcmp(XMLNode_getPrefix(Bag), "rdf"));
+  fail_unless(!strcmp(XMLNode_getURI(Bag), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+  fail_unless(XMLNode_getNumChildren(Bag) == 4);
+
+  const XMLNode_t * li = XMLNode_getChild(Bag, 0);
+  fail_unless(!strcmp(XMLNode_getName(li), "li"));
+  fail_unless(!strcmp(XMLNode_getPrefix(li), "rdf"));
+  fail_unless(!strcmp(XMLNode_getURI(li), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+  fail_unless(li->getAttrValue(0) == "http://identifiers.org/chebi/CHEBI:59789");
+  fail_unless(XMLNode_getNumChildren(li) == 0);
+
+  const XMLNode_t * hasProp1 = XMLNode_getChild(Bag, 1);
+  fail_unless(!strcmp(XMLNode_getName(hasProp1), "hasProperty"));
+  fail_unless(!strcmp(XMLNode_getPrefix(hasProp1), "bqbiol"));
+  fail_unless(XMLNode_getNumChildren(hasProp1) == 1);
+
+  const XMLNode_t * Bag1 = XMLNode_getChild(hasProp1, 0);
+  fail_unless(!strcmp(XMLNode_getName(Bag1), "Bag"));
+  fail_unless(!strcmp(XMLNode_getPrefix(Bag1), "rdf"));
+  fail_unless(!strcmp(XMLNode_getURI(Bag1), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+  fail_unless(XMLNode_getNumChildren(Bag1) == 1);
+
+  const XMLNode_t * li_Bag1 = XMLNode_getChild(Bag1, 0);
+  fail_unless(!strcmp(XMLNode_getName(li_Bag1), "li"));
+  fail_unless(!strcmp(XMLNode_getPrefix(li_Bag1), "rdf"));
+  fail_unless(!strcmp(XMLNode_getURI(li_Bag1), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+  fail_unless(XMLNode_getNumChildren(li_Bag1) == 0);
+
+
+  const XMLNode_t * li2 = XMLNode_getChild(Bag, 2);
+  fail_unless(!strcmp(XMLNode_getName(li2), "li"));
+  fail_unless(!strcmp(XMLNode_getPrefix(li2), "rdf"));
+  fail_unless(!strcmp(XMLNode_getURI(li2), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
+  fail_unless(XMLNode_getNumChildren(li2) == 0);
+
+  free(filename);
+  delete(node);
+}
+END_TEST
+
+START_TEST(test_read_from_file2)
+{
+  const char * expected = "<thing>\n"
+    "  <child att=\"yes\"/>\n"
+    "</thing>";
+
+  char *filename = safe_strcat(TestDataDirectory, "random.xml");
+  XMLNode *node = XMLNode::readXMLNodeFromFile(filename);
+
+  fail_unless(node != NULL);
+
+  std::string random = XMLNode::convertXMLNodeToString(node);
+
+  fail_unless(equals(expected, random.c_str()));
+
+  safe_free(filename);
+  delete(node);
+}
+END_TEST
+
 Suite *
 create_suite_XMLNode (void)
 {
@@ -1665,6 +1771,9 @@ create_suite_XMLNode (void)
   tcase_add_test( tcase, test_XMLNode_namespace_set_clear );
   tcase_add_test( tcase, test_XMLNode_attribute_add_remove);
   tcase_add_test( tcase, test_XMLNode_attribute_set_clear);
+  tcase_add_test( tcase, test_read_from_file);
+  tcase_add_test(tcase, test_read_from_file2);
+
   suite_add_tcase(suite, tcase);
 
   return suite;

src/sbml/xml/test/test-data/just_annotation.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<annotation>
+    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vcard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+      <rdf:Description rdf:about="#metaid_0000036">
+        <bqbiol:is>
+          <rdf:Bag>
+            <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:59789"/>
+            <bqbiol:hasProperty>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/>
+              </rdf:Bag>
+            </bqbiol:hasProperty>
+            <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15414"/>
+            <bqbiol:hasProperty>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://amas/match_score/by_name/1.0"/>
+              </rdf:Bag>
+            </bqbiol:hasProperty>
+          </rdf:Bag>
+        </bqbiol:is>
+      </rdf:Description>
+    </rdf:RDF>
+  </annotation>

src/sbml/xml/test/test-data/random.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<thing>
+  <child att="yes"/>
+</thing>