Issue 296 setannotation

examples/c++/CMakeLists.txt

@@ -73,6 +73,7 @@ foreach(example
     translateL3Math
     unsetAnnotation
     unsetNotes
+    setAnnotation
     validateSBML
 
 )

examples/c++/setAnnotation.cpp

@@ -0,0 +1,114 @@
+/**
+ * Example, reading an SBML file containing an element with provided 
+ * meta id, reading a raw annoation from a file, and adding it to the 
+ * element. 
+ * 
+ */
+
+#include <iostream>
+#include <sbml/SBMLTypes.h>
+
+using namespace std;
+
+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)
+{
+	auto *document = readSBML(sbmlFile.c_str());
+	if (document->getNumErrors(LIBSBML_SEV_ERROR) > 0)
+	{
+		cerr << "Encountered the following SBML errors:" << std::endl;
+		document->printErrors();
+		return false;
+	}
+
+	auto* element = document->getElementByMetaId(metaId);
+	if (!element)
+	{
+		cerr << "No element with meta id " << metaId << " found." << std::endl;
+		return false;
+	}
+
+	auto annotation = parseAnnotation(annotationFile);
+	if (!annotation)
+	{
+		cerr << "the annotation could not be parsed from file: " << annotationFile << "." << std::endl;
+		return false;
+	}
+	auto annotationString = annotation->toXMLString();
+	element->setAnnotation(annotation, false);
+
+	// at this point we'd expect the annotation to be set precisely to what it was 
+	// in the file.
+
+
+	auto resultingAnnotation = element->getAnnotationString();
+
+	if (annotationString != resultingAnnotation)
+	{
+		cerr << "Annotation was not set correctly." << std::endl;
+		return false;
+	}
+
+	// write document to output file
+	writeSBMLToFile(document, outputFile.c_str());
+
+	delete document;
+
+	return true;
+}
+
+int main(int argc, char* argv[])
+{
+	std::string sbmlFile;
+	std::string metaId;
+	std::string annotationFile;
+	std::string outputFile;
+
+	if (argc != 5)
+	{
+		cout << endl
+				 << "  usage: setAnnotaion <input-filename> <element-meta-id> <annotation-file> <output-file>" << endl
+				 << "  Adds controlled vocabulary term to a species"          << endl
+				 << endl;
+		return 1;
+
+
+		//sbmlFile = "bm190.xml";
+		//annotationFile = "annotation.xml";
+		//metaId = "metaid_0000036";
+		//outputFile = "bm190_out.xml";
+
+	}
+	else
+	{
+		sbmlFile = argv[1];
+		metaId = argv[2];
+		annotationFile = argv[3];
+		outputFile = argv[4];
+	}
+
+	setAnnotation(sbmlFile, metaId, annotationFile, outputFile);
+}

src/sbml/SBase.cpp

@@ -1249,11 +1249,23 @@ SBase::setIdAttribute (const std::string& sid)
   }
 }
 
+int
+SBase::setAnnotation(const XMLNode* annotation)
+{
+  return SBase::setAnnotation(annotation, true);
+}
+
+int
+SBase::setAnnotation(const std::string& annotation)
+{
+  return SBase::setAnnotation(annotation, true);
+}
+
 /*
  * Sets the annotation of this SBML object to a copy of annotation.
  */
 int
-SBase::setAnnotation (const XMLNode* annotation)
+SBase::setAnnotation (const XMLNode* annotation, bool parseRdf)
 {
   //
   // (*NOTICE*)
@@ -1274,7 +1286,7 @@ SBase::setAnnotation (const XMLNode* annotation)
     delete mAnnotation;
 
     // the annotation is an rdf annotation but the object has no metaid
-    if (RDFAnnotationParser::hasRDFAnnotation(annotation) == true
+    if (parseRdf && RDFAnnotationParser::hasRDFAnnotation(annotation) == true
       && (RDFAnnotationParser::hasCVTermRDFAnnotation(annotation) == true
       || RDFAnnotationParser::hasHistoryRDFAnnotation(annotation) == true)
       && isSetMetaId() == false)
@@ -1342,7 +1354,7 @@ SBase::setAnnotation (const XMLNode* annotation)
   }
 
 
-  if(mAnnotation != NULL
+  if(parseRdf && mAnnotation != NULL
         && RDFAnnotationParser::hasCVTermRDFAnnotation(mAnnotation))
   {
     // parse mAnnotation (if any) and set mCVTerms
@@ -1351,7 +1363,7 @@ SBase::setAnnotation (const XMLNode* annotation)
     mCVTermsChanged = true;
   }
 
-  if(getLevel() > 2 && mAnnotation != NULL
+  if(parseRdf && getLevel() > 2 && mAnnotation != NULL
      && RDFAnnotationParser::hasHistoryRDFAnnotation(mAnnotation))
   {
     // parse mAnnotation (if any) and set mHistory
@@ -1371,7 +1383,7 @@ SBase::setAnnotation (const XMLNode* annotation)
  * Sets the annotation (by string) of this SBML object to a copy of annotation.
  */
 int
-SBase::setAnnotation (const std::string& annotation)
+SBase::setAnnotation (const std::string& annotation, bool parseRdf)
 {
 
   int success = LIBSBML_OPERATION_FAILED;
@@ -1404,7 +1416,7 @@ SBase::setAnnotation (const std::string& annotation)
 
   if(annt_xmln != NULL)
   {
-    success = setAnnotation(annt_xmln);
+    success = setAnnotation(annt_xmln, parseRdf);
     delete annt_xmln;
   }
   return success;
@@ -4272,13 +4284,21 @@ SBase::getSBMLNamespaces() const
  */
 char*
 SBase::toSBML ()
+{  
+  return safe_strdup( toSBMLString().c_str() );
+}
+
+/*
+ * @return the partial SBML that describes this SBML object.
+ */
+std::string SBase::toSBMLString()
 {
-  ostringstream    os;
-  XMLOutputStream  stream(os, "UTF-8", false);
+	ostringstream    os;
+	XMLOutputStream  stream(os, "UTF-8", false);
 
-  write(stream);
+	write(stream);
 
-  return safe_strdup( os.str().c_str() );
+  return os.str();
 }
 
 

src/sbml/SBase.h

@@ -1229,6 +1229,54 @@ class LIBSBML_EXTERN SBase
    * @see unsetAnnotation()
    */
   virtual int setAnnotation (const XMLNode* annotation);
+
+  /**
+   * Sets the value of the "annotation" subelement of this SBML object.
+   *
+   * The content of @p annotation is copied, and any previous content of
+   * this object's "annotation" subelement is deleted.
+   *
+   * Whereas the SBase "notes" subelement is a container for content to be
+   * shown directly to humans, the "annotation" element is a container for
+   * optional software-generated content @em not meant to be shown to
+   * humans.  Every object derived from SBase can have its own value for
+   * "annotation".  The element's content type is <a target="_blank"
+   * href="http://www.w3.org/TR/2004/REC-xml-20040204/#elemdecls">XML type
+   * "any"</a>, allowing essentially arbitrary well-formed XML data
+   * content.
+   *
+   * SBML places a few restrictions on the organization of the content of
+   * annotations; these are intended to help software tools read and write
+   * the data as well as help reduce conflicts between annotations added by
+   * different tools.  Please see the SBML specifications for more details.
+   *
+   * Call this method will result in any existing content of the
+   * "annotation" subelement to be discarded.  Unless you have taken steps
+   * to first copy and reconstitute any existing annotations into the @p
+   * annotation that is about to be assigned, it is likely that performing
+   * such wholesale replacement is unfriendly towards other software
+   * applications whose annotations are discarded.  An alternative may be
+   * to use SBase::appendAnnotation(const XMLNode* annotation) or
+   * SBase::appendAnnotation(const std::string& annotation).
+   *
+   * @param annotation an XML structure that is to be used as the new content
+   * of the "annotation" subelement of this object.
+   *
+	 * @param parseRdf if true, the annotation will be parsed for RDF content.
+	 * This should only be set, if the RDF follows the subset described in the
+	 * SBML specification.
+	 *
+   * @copydetails doc_returns_one_success_code
+   * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+   *
+   * @see getAnnotationString()
+   * @see isSetAnnotation()
+   * @see setAnnotation(const std::string& annotation)
+   * @see appendAnnotation(const XMLNode* annotation)
+   * @see appendAnnotation(const std::string& annotation)
+   * @see unsetAnnotation()
+   */
+  virtual int setAnnotation(const XMLNode* annotation, bool parseRdf);
 
 
   /**
@@ -1262,6 +1310,55 @@ class LIBSBML_EXTERN SBase
    *
    * @param annotation an XML string that is to be used as the content
    * of the "annotation" subelement of this object.
+	 *
+   * @copydetails doc_returns_success_code
+   * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+   * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+   *
+   * @see getAnnotationString()
+   * @see isSetAnnotation()
+   * @see setAnnotation(const XMLNode* annotation)
+   * @see appendAnnotation(const XMLNode* annotation)
+   * @see appendAnnotation(const std::string& annotation)
+   * @see unsetAnnotation()
+   */
+  virtual int setAnnotation(const std::string& annotation);
+
+  /**
+   * Sets the value of the "annotation" subelement of this SBML object.
+   *
+   * The content of @p annotation is copied, and any previous content of
+   * this object's "annotation" subelement is deleted.
+   *
+   * Whereas the SBase "notes" subelement is a container for content to be
+   * shown directly to humans, the "annotation" element is a container for
+   * optional software-generated content @em not meant to be shown to
+   * humans.  Every object derived from SBase can have its own value for
+   * "annotation".  The element's content type is <a target="_blank"
+   * href="http://www.w3.org/TR/2004/REC-xml-20040204/#elemdecls">XML type
+   * "any"</a>, allowing essentially arbitrary well-formed XML data
+   * content.
+   *
+   * SBML places a few restrictions on the organization of the content of
+   * annotations; these are intended to help software tools read and write
+   * the data as well as help reduce conflicts between annotations added by
+   * different tools.  Please see the SBML specifications for more details.
+   *
+   * Call this method will result in any existing content of the
+   * "annotation" subelement to be discarded.  Unless you have taken steps
+   * to first copy and reconstitute any existing annotations into the @p
+   * annotation that is about to be assigned, it is likely that performing
+   * such wholesale replacement is unfriendly towards other software
+   * applications whose annotations are discarded.  An alternative may be
+   * to use SBase::appendAnnotation(const XMLNode* annotation) or
+   * SBase::appendAnnotation(const std::string& annotation).
+   *
+   * @param annotation an XML string that is to be used as the content
+   * of the "annotation" subelement of this object.
+   * 
+   * @param parseRdf if true, the annotation will be parsed for RDF content.
+   * This should only be set, if the RDF follows the subset described in the 
+   * SBML specification.
    *
    * @copydetails doc_returns_success_code
    * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
@@ -1274,7 +1371,7 @@ class LIBSBML_EXTERN SBase
    * @see appendAnnotation(const std::string& annotation)
    * @see unsetAnnotation()
    */
-  virtual int setAnnotation (const std::string& annotation);
+  virtual int setAnnotation (const std::string& annotation, bool parseRdf);
 
 
   /**
@@ -2313,7 +2410,9 @@ s.setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></b
 
   /**
    * Returns a string consisting of a partial SBML corresponding to just
-   * this object.
+   * this object. 
+   * 
+   * The string is owned by the caller and has to be freed manualy. 
    * 
    * @return the partial SBML that describes this SBML object.
    *
@@ -2323,6 +2422,18 @@ s.setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></b
    */
   char* toSBML();
 
+  /**
+   * Returns a string consisting of a partial SBML corresponding to just
+   * this object.
+   *
+   * @return the partial SBML that describes this SBML object.
+   *
+   * @warning <span class="warning">This is primarily provided for testing
+   * and debugging purposes.  It may be removed in a future version of
+   * libSBML.</span>
+   */
+  std::string toSBMLString();
+
 
   /**
    * Returns this element as an XMLNode.