static int saveSBOLDocument(const char* filename) {
int invalid = 0;
if (!isValidSBOL(OUTPUT)) {
invalid = 1;
printf("WARNING: %s is not valid SBOL. Saving anyway.\n", filename);
}
int written = xmlSaveFile(filename, OUTPUT);
return (int) invalid || written == -1;
}
void readDocument(Document* destination, char* filename) {
DESTINATION = destination;
// parse
safeXmlInitParser();
DOCUMENT = xmlParseFile(filename);
if (!DOCUMENT) {
printf("Error reading %s\n", filename);
return;
}
// validate
if (!isValidSBOL(DOCUMENT)) {
printf("%s is not a valid SBOL document.\n", filename);
return;
}
// create XPath context
CONTEXT = xmlXPathNewContext(DOCUMENT);
xmlXPathRegisterNs(CONTEXT, (const xmlChar*)NSPREFIX_SBOL, (const xmlChar*)NSURL_SBOL);
xmlXPathRegisterNs(CONTEXT, (const xmlChar*)NSPREFIX_RDF, (const xmlChar*)NSURL_RDF);
#define GLOBAL_XPATH BAD_CAST "//" NSPREFIX_SBOL ":"
// create all the SBOLObjects
processNodes(readDNASequenceContent, GLOBAL_XPATH NODENAME_DNASEQUENCE);
processNodes(readSequenceAnnotationContent, GLOBAL_XPATH NODENAME_SEQUENCEANNOTATION);
processNodes(readDNAComponentContent, GLOBAL_XPATH NODENAME_DNACOMPONENT);
processNodes(readCollectionContent, GLOBAL_XPATH NODENAME_COLLECTION);
// link them together with pointers
processNodes(readSequenceAnnotationReferences, GLOBAL_XPATH NODENAME_SEQUENCEANNOTATION);
processNodes(readDNAComponentReferences, GLOBAL_XPATH NODENAME_DNACOMPONENT);
processNodes(readCollectionReferences, GLOBAL_XPATH NODENAME_COLLECTION);
#undef GLOBAL_XPATH
// clean up
xmlXPathFreeContext(CONTEXT);
xmlFreeDoc(DOCUMENT);
DESTINATION = NULL;
xmlCleanupParser();
}
