public static void main(String[] args) throws Exception {
URIFactoryMemory factory = URIFactoryMemory.getSingleton();
G graph = new GraphMemory(factory.getURI("http://mesh"));
GraphLoader_MESH_XML loader = new GraphLoader_MESH_XML();
loader.populate(new GDataConf(GFormat.MESH_XML, "/data/mesh/desc2013.xml"), graph);
URI dna_barcoding = factory.getURI("http://D058893");
System.out.println(graph);
System.out.println(graph.containsVertex(dna_barcoding));
}
/**
* Apply the given action to the graph.
*
* @param action the action to perform
* @param g the graph on which the action must be performed
* @throws SLIB_Ex_Critic
*/
public static void applyAction(GAction action, G g) throws SLIB_Ex_Critic {
applyAction(URIFactoryMemory.getSingleton(), action, g);
}
/**
* MeSH Loader. This class permits to load the MeSH trees into a Directed Acyclic Graph
* http://www.nlm.nih.gov/mesh/trees.html
*
* <p>The loader was designed for the 2013 XML version of the MeSH, coherency with prior or older
* version hasn't been tested.
*
* @author Sébastien Harispe <*****@*****.**>
*/
public class GraphLoader_MESH_XML implements GraphLoader {
Logger logger = LoggerFactory.getLogger(this.getClass());
Map<String, MeshConcept> idToConcepts = new HashMap<String, MeshConcept>();
Set<MeshConcept> concepts = new HashSet<MeshConcept>();
G graph;
URIFactory factory = URIFactoryMemory.getSingleton();
int conceptIgnored = 0;
/** */
public static final String ARG_PREFIX = "prefix";
String default_namespace;
/**
* Return parent ID i.e. giving C10.228.140.300.275.500 will return C10.228.140.300.275
*
* @return a String associated to the parent ID.
*/
private String getParentId(String id) {
String[] data = id.split("\\.");
String idParent = null;
for (int i = data.length - 2; i >= 0; i--) {
if (idParent == null) {
idParent = data[i];
} else {
idParent = data[i] + "." + idParent;
}
}
return idParent;
}
void addConcept(MeshConcept concept) {
if (!concept.treeNumberList.isEmpty()) {
for (String s : concept.treeNumberList) {
idToConcepts.put(s, concept);
}
concepts.add(concept);
} else {
logger.info(
"Warning: no tree number associated to " + concept.descriptorUI + " concept ignored...");
conceptIgnored++;
}
}
@Override
public void populate(GDataConf conf, G g) throws SLIB_Exception {
this.graph = g;
default_namespace = (String) conf.getParameter(ARG_PREFIX);
if (default_namespace == null) {
default_namespace = graph.getURI().getNamespace();
}
try {
logger.info("-------------------------------------");
logger.info("Loading Mesh XML");
logger.info("-------------------------------------");
idToConcepts = new HashMap<String, MeshConcept>();
SAXParserFactory parserfactory = SAXParserFactory.newInstance();
SAXParser saxParser;
saxParser = parserfactory.newSAXParser();
saxParser.parse(conf.getLoc(), new MeshXMLHandler(this));
logger.info(
"Number of descriptor loaded " + concepts.size() + " (ignored " + conceptIgnored + ")");
logger.info("Loading relationships ");
// Create universal root if required
URI universalRoot = OWL.THING;
if (!graph.containsVertex(universalRoot)) {
graph.addV(universalRoot);
}
// create relationships and roots of each tree
for (Entry<String, MeshConcept> e : idToConcepts.entrySet()) {
MeshConcept c = e.getValue();
URI vConcept = getOrCreateVertex(c.descriptorUI);
for (String treeNumber : c.treeNumberList) {
String parentId = getParentId(treeNumber);
if (parentId != null) {
MeshConcept parent = idToConcepts.get(parentId);
if (parent == null) {
throw new SLIB_Ex_Critic(
"Cannot locate parent identified by TreeNumber "
+ treeNumber
+ "\nError occured processing\n"
+ c);
} else {
// System.out.println("\t" + parentId + "\t" + parent.descriptorUI);
URI vParent = getOrCreateVertex(parent.descriptorUI);
E edge = new Edge(vConcept, RDFS.SUBCLASSOF, vParent);
g.addE(edge);
}
} else {
/* Those vertices are the inner roots of each trees,
* i.e. Psychiatry and Psychology [F] tree has for inner roots:
* - Behavior and Behavior Mechanisms [F01]
* - Psychological Phenomena and Processes [F02]
* - Mental Disorders [F03]
* - Behavioral Disciplines and Activities [F04]
* A vertex has already been created for each inner root (e.g. F01, F02, F03, F04)
* , we therefore create a vertex for the tree root (e.g. F).
* Finally all the tree roots are rooted by a global root which do not
* correspond to a concept specified into the mesh.
*
* More information about MeSH trees at http://www.nlm.nih.gov/mesh/trees.html
*/
// we link the tree inner root to the root tree
char localNameTreeRoot = treeNumber.charAt(0); // id of the tree root
URI rootTree = getOrCreateVertex(localNameTreeRoot + ""); // e.g. F
E treeInnerRootToTreeRoot = new Edge(vConcept, RDFS.SUBCLASSOF, rootTree);
g.addE(treeInnerRootToTreeRoot);
// logger.debug("Creating Edge : " + treeInnerRootToTreeRoot);
// we link the tree root to the universal root
E treeRootToUniversalRoot = new Edge(rootTree, RDFS.SUBCLASSOF, universalRoot);
g.addE(treeRootToUniversalRoot);
// logger.debug("Creating Edge : " + treeRootToUniversalRoot);
}
}
}
} catch (IOException ex) {
throw new SLIB_Ex_Critic(ex.getMessage());
} catch (ParserConfigurationException ex) {
throw new SLIB_Ex_Critic(ex.getMessage());
} catch (SAXException ex) {
throw new SLIB_Ex_Critic(ex.getMessage());
} catch (SLIB_Ex_Critic ex) {
throw new SLIB_Ex_Critic(ex.getMessage());
}
logger.info("MESH loader - process performed");
logger.info("-------------------------------------");
}
private URI getOrCreateVertex(String descriptorUI) {
String uriConceptAsString = default_namespace + descriptorUI;
URI uriConcept = factory.getURI(uriConceptAsString);
if (!graph.containsVertex(uriConcept)) {
graph.addV(uriConcept);
}
return uriConcept;
}
public static void main(String[] args) throws Exception {
URIFactoryMemory factory = URIFactoryMemory.getSingleton();
G graph = new GraphMemory(factory.getURI("http://mesh"));
GraphLoader_MESH_XML loader = new GraphLoader_MESH_XML();
loader.populate(new GDataConf(GFormat.MESH_XML, "/data/mesh/desc2013.xml"), graph);
URI dna_barcoding = factory.getURI("http://D058893");
System.out.println(graph);
System.out.println(graph.containsVertex(dna_barcoding));
}
}
