/**
* Example the conclusions graph for introduction of restrictions which require a comprehension
* rewrite and declare new (anon) classes for those restrictions.
*/
public void comprehensionAxioms(Model premises, Model conclusions) {
// Comprehend all restriction declarations and note them in a map
Map<Resource, Resource> comprehension = new HashMap<>();
StmtIterator ri = conclusions.listStatements(null, RDF.type, OWL.Restriction);
while (ri.hasNext()) {
Resource restriction = ri.nextStatement().getSubject();
StmtIterator pi = restriction.listProperties(OWL.onProperty);
while (pi.hasNext()) {
Resource prop = (Resource) pi.nextStatement().getObject();
StmtIterator vi = restriction.listProperties();
while (vi.hasNext()) {
Statement rs = vi.nextStatement();
if (!rs.getPredicate().equals(OWL.onProperty)) {
// Have a restriction on(prop) of type rs in the conclusions
// So assert a premise that such a restriction could exisit
Resource comp =
premises
.createResource()
.addProperty(RDF.type, OWL.Restriction)
.addProperty(OWL.onProperty, prop)
.addProperty(rs.getPredicate(), rs.getObject());
comprehension.put(restriction, comp);
}
}
}
}
// Comprehend any intersectionOf lists. Introduce anon class which has the form
// of the intersection expression.
// Rewrite queries of the form (X intersectionOf Y) to the form
// (X equivalentClass ?CC) (?CC intersectionOf Y)
StmtIterator ii = conclusions.listStatements(null, OWL.intersectionOf, (RDFNode) null);
List<Statement> intersections = new ArrayList<>();
while (ii.hasNext()) {
intersections.add(ii.nextStatement());
}
for (Statement is : intersections) {
// Declare in the premises that such an intersection exists
Resource comp =
premises
.createResource()
.addProperty(RDF.type, OWL.Class)
.addProperty(
OWL.intersectionOf, mapList(premises, (Resource) is.getObject(), comprehension));
// Rewrite the conclusions to be a test for equivalence between the class being
// queried and the comprehended interesection
conclusions.remove(is);
conclusions.add(is.getSubject(), OWL.equivalentClass, comp);
}
// Comprehend any oneOf lists
StmtIterator io = conclusions.listStatements(null, OWL.oneOf, (RDFNode) null);
while (io.hasNext()) {
Statement s = io.nextStatement();
Resource comp = premises.createResource().addProperty(OWL.oneOf, s.getObject());
}
}
public static String RenderTemplatePage(Bindings b, String templateName) throws IOException {
MediaType mt = MediaType.TEXT_HTML;
Resource config = model.createResource("eh:/root");
Mode prefixMode = Mode.PreferPrefixes;
ShortnameService sns = new StandardShortnameService();
List<Resource> noResults = CollectionUtils.list(root.inModel(model));
Graph resultGraph = graphModel.getGraph();
resultGraph.getPrefixMapping().setNsPrefix("api", API.NS);
resultGraph.add(Triple.create(root.asNode(), API.items.asNode(), RDF.nil.asNode()));
APIResultSet rs = new APIResultSet(resultGraph, noResults, true, true, "details", View.ALL);
VelocityRenderer vr = new VelocityRenderer(mt, null, config, prefixMode, sns);
VelocityRendering vx = new VelocityRendering(b, rs, vr);
VelocityEngine ve = vx.createVelocityEngine();
VelocityContext vc = vx.createVelocityContext(b);
ByteArrayOutputStream bos = new ByteArrayOutputStream();
Writer w = new OutputStreamWriter(bos, "UTF-8");
Template t = ve.getTemplate(templateName);
t.merge(vc, w);
w.close();
return bos.toString();
}
/**
* Helper. Adds to the target model a translation of the given RDF list with each element replaced
* according to the map.
*/
private Resource mapList(Model target, Resource list, Map<Resource, Resource> map) {
if (list.equals(RDF.nil)) {
return RDF.nil;
} else {
Resource head = (Resource) list.getRequiredProperty(RDF.first).getObject();
Resource rest = (Resource) list.getRequiredProperty(RDF.rest).getObject();
Resource mapElt = target.createResource();
Resource mapHead = map.get(head);
if (mapHead == null) mapHead = head;
mapElt.addProperty(RDF.first, mapHead);
mapElt.addProperty(RDF.rest, mapList(target, rest, map));
return mapElt;
}
}
/** Initialize the result model. */
public void initResults() {
testResults = ModelFactory.createDefaultModel();
jena2 = testResults.createResource(BASE_RESULTS_URI + "#jena2");
jena2.addProperty(
RDFS.comment,
testResults.createLiteral(
"<a xmlns=\"http://www.w3.org/1999/xhtml\" href=\"http://jena.sourceforce.net/\">Jena2</a> includes a rule-based inference engine for RDF processing, "
+ "supporting both forward and backward chaining rules. Its OWL rule set is designed to provide sound "
+ "but not complete instance resasoning for that fragment of OWL/Full limited to the OWL/lite vocabulary. In"
+ "particular it does not support unionOf/complementOf.",
true));
jena2.addProperty(RDFS.label, "Jena2");
testResults.setNsPrefix("results", OWLResults.NS);
}
/** Run a single test of any sort, performing any appropriate logging and error reporting. */
public void runTest(Resource test) {
System.out.println("Running " + test);
boolean success = false;
boolean fail = false;
try {
success = doRunTest(test);
} catch (Exception e) {
fail = true;
System.out.print("\nException: " + e);
e.printStackTrace();
}
testCount++;
if (success) {
System.out.print((testCount % 40 == 0) ? ".\n" : ".");
System.out.flush();
passCount++;
} else {
System.out.println("\nFAIL: " + test);
}
Resource resultType = null;
if (fail) {
resultType = OWLResults.FailingRun;
} else {
if (test.hasProperty(RDF.type, OWLTest.NegativeEntailmentTest)
|| test.hasProperty(RDF.type, OWLTest.ConsistencyTest)) {
resultType = success ? OWLResults.PassingRun : OWLResults.FailingRun;
} else {
resultType = success ? OWLResults.PassingRun : OWLResults.IncompleteRun;
}
}
// log to the rdf result format
Resource result =
testResults
.createResource()
.addProperty(RDF.type, OWLResults.TestRun)
.addProperty(RDF.type, resultType)
.addProperty(OWLResults.test, test)
.addProperty(OWLResults.system, jena2);
}
/**
* agINFRA Social visualization components aux. tool
*
* @param args
* @throws FileNotFoundException
*/
public static void main(String[] args) throws FileNotFoundException {
System.out.println("Hello");
// PARAMS
if (args.length != 5) {
System.out.println(
"Proper Arguments are: [Dataset files full path] [URL store] [URI graph base] [Destination directory] [commit to 4store]");
System.out.println(
"Example: java -jar xxxxx.jar /home/carlos/Desktop/agINFRA-workflow/workflow/loms/bioe/ http://localhost:81 http://laclo.laflor /home/carlos/Desktop/agINFRA-workflow/workflow/loms/bioerdf/ false");
System.exit(0);
}
String dspath = args[0];
String urlStore = args[1];
String uriGraph = args[2];
String destination = args[3];
String commit4store_arg = args[4];
/*String dspath = "/home/carlos/workspace/WebAPI/ds/";
String urlStore = "http://4store.ipb.ac.rs:81";
String uriGraph = "http://aginfra.eu";
String localCouchdbProxy = "localhost";
String commit4store_arg = "no";*/
boolean commit4store = false;
if (commit4store_arg.equals("commit")) commit4store = true;
String output = "0"; // valor de retorno
String status = "ERROR";
String errorDescription = "";
String tmpMetadataFile = "";
// check if type is valid
boolean bContinuar = true;
// StorageService service;
ArrayList<KeyValue> keyValues = new ArrayList<KeyValue>();
HashMap fileDatasetMap = new HashMap();
/*
//Fetch and download IPB metadata sets.
//CouchDB via PHP local proxy
//http://agro.ipb.ac.rs/agcouchdb/_design/datasets/_view/list?limit=10
//http://localhost/ag_couch_proxy/proxy-IPB-datasets.php
try{
System.out.println("Connecting IPB CouchDB...");
String url = "http://"+localCouchdbProxy+"/ag_couch_proxy/proxy-IPB-datasets.php?dspath="+dspath;
WebResource webResource = Client.create().resource(url);
//System.out.println(url);
ClientResponse response = webResource.accept(MediaType.APPLICATION_JSON,MediaType.TEXT_HTML,MediaType.WILDCARD).get(ClientResponse.class);
if (response.getStatus() != 200) {
throw new RuntimeException("Failed : HTTP error code : " + response.getStatus());
}
//String response_str = response.getEntity(String.class); //I don't know why this does not work when running in shell
String response_str = getStringFromInputStream(response.getEntityInputStream());
//System.out.println(response_str); //debug
System.out.println("Finished IPB call");
System.out.println("Reading Dataset Map...");
//READ CSV
//create BufferedReader to read csv file
StringTokenizer st = null;
int lineNumber = 0, tokenNumber = 0;
//read comma separated file line by line
Scanner scanner = new Scanner(response_str);
while (scanner.hasNextLine())
{
lineNumber++;
String strLine = scanner.nextLine();
//break comma separated line using ","
st = new StringTokenizer(strLine, ",");
String datasetFile = "";
String datasetName = "";
while(st.hasMoreTokens())
{
//display csv values
tokenNumber++;
//System.out.println("Line # " + lineNumber +", Token # " + tokenNumber + ", Token : "+ st.nextToken());
if(tokenNumber == 1)
datasetFile = st.nextToken();
if(tokenNumber == 2)
datasetName = st.nextToken();
}
fileDatasetMap.put(datasetFile,datasetName);
//reset token number
tokenNumber = 0;
}
System.out.println("Finished Map reading");
} catch (Exception e) {
e.printStackTrace();
}
*/
/*
//foreach dataset.tar.gz **
//Iterate
File root = new File("ds/");
Collection files = FileUtils.listFiles(root, null, false);
//mini db processed files
ArrayList processed = new ArrayList();
try {
BufferedReader br = new BufferedReader(new FileReader("processed.txt"));
String line;
while((line = br.readLine()) != null) {
processed.add(line);
}
} catch (IOException e) {
e.printStackTrace();
}
System.out.println("Iterating all downloaded datasets tgz files...");
int dsCount = 0;
for (Iterator iterator = files.iterator(); iterator.hasNext();) {
File dsFile = (File) iterator.next();
String inputDataset = dsFile.getAbsolutePath();
dsCount = dsCount + 1;
System.out.println(" Processing "+dsCount+":"+inputDataset); //debug
//po5i: mini db processed files
if(processed.contains(inputDataset)){
System.out.println(" >>Already processed... skipping... ");
continue;
}
else
{
processed.add(inputDataset);
try {
FileWriter fileWritter = new FileWriter("processed.txt",true);
BufferedWriter bufferWritter = new BufferedWriter(fileWritter);
bufferWritter.write(inputDataset+"\n");
bufferWritter.close();
} catch (IOException e) {
e.printStackTrace();
}
}
//Set the GraphID
String graphID = (String) fileDatasetMap.get(dsFile.getName());
System.out.println(" Graph:: "+graphID);
//Uncompress the dataset and iterate throughout the files
try {
FileInputStream fin = new FileInputStream(inputDataset);
BufferedInputStream in = new BufferedInputStream(fin);
FileOutputStream out = new FileOutputStream("ds/archive.tar");
GzipCompressorInputStream gzIn;
gzIn = new GzipCompressorInputStream(in);
final byte[] buffer = new byte[1024];
int n = 0;
while (-1 != (n = gzIn.read(buffer))) {
out.write(buffer, 0, n);
}
out.close();
gzIn.close();
//read the tar
File input = new File("ds/archive.tar"); //getFile("ds/archive.tar");
InputStream is = new FileInputStream(input);
ArchiveInputStream in1 = new ArchiveStreamFactory().createArchiveInputStream("tar", is);
TarArchiveEntry entry = (TarArchiveEntry)in1.getNextEntry();
while (entry != null) {// create a file with the same name as the tarEntry
File destPath = new File("ds/extract/" + entry.getName());
if (entry.isDirectory()) {
destPath.mkdirs();
} else {
destPath.createNewFile();
OutputStream out1 = new FileOutputStream(destPath);
IOUtils.copy(in1, out1);
out1.close();
}
entry = (TarArchiveEntry)in1.getNextEntry();
}
in1.close();
} catch (Exception e) {
e.printStackTrace();
}*/
// Iterate on extracted files
try {
File root1 = new File(dspath);
Collection files1 = FileUtils.listFiles(root1, null, true);
// new File(dspath+"../rdf").mkdir();
for (Iterator iterator1 = files1.iterator(); iterator1.hasNext(); ) {
File lomFile = (File) iterator1.next();
String inputFile = lomFile.getAbsolutePath();
// System.out.println(" Processing:"+inputFile); //debug
if (bContinuar) {
// save metadata stream in a local file
tmpMetadataFile = inputFile;
String valid = "1";
// valid = XMLValidator.validate(tmpMetadataFile,
// StorageService.getXSDFile(storageType));
boolean hasSource = false;
if (tmpMetadataFile.length() > 0) {
// TODO: metadata validation
// valid = "1";
if (valid.equalsIgnoreCase("1")) {
// generate id for the new material
// output = graphID;
// save metatada in rdf
// obtain key-value pairs
try {
LOMParser.parseToKeyValue(tmpMetadataFile);
if (!LOMParser.keyValues.isEmpty()) {
keyValues = LOMParser.keyValues;
}
} catch (MalformedURLException e1) {
e1.printStackTrace();
} catch (IOException e1) {
e1.printStackTrace();
}
if (!keyValues.isEmpty()) {
int canSave = 1;
if (canSave > 0) {
// 4store
// save to rdf this triple (slow)
// HandleGraph graph = new HandleGraph(urlStore,uriGraph);
// result = graph.AppendTriple(graphID, keyValues);
// 4store
// prepare RDF file (better)
try {
// HELP: http://www.roseindia.net/tutorials/rdf/generateRDF.shtml
Model model = ModelFactory.createDefaultModel();
for (KeyValue kv : keyValues) {
String s = uriGraph + "/" + lomFile.getName();
// String p = URLEncoder.encode(kv.getKey(),"UTF-8");
String p = kv.getKey().replaceAll("[^\\w\\s\\.]", "_");
String v = kv.getValue();
// obtener el autor del CDATA en variable v
if (v.contains("CDATA")) {
v = v.replace("<![CDATA[", "");
v = v.replace("]]>", "");
VCardEngine vcardEngine = new VCardEngine();
VCard vcard = vcardEngine.parse(v);
if (vcard.hasFN()) v = vcard.getFN().getFormattedName();
else if (vcard.hasN()) v = vcard.getN().getFamilyName();
else {
// format string it can be parsed.
StringBuffer sb;
sb = new StringBuffer(v);
sb.insert(v.indexOf("VERSION:"), "\n");
v = sb.toString();
sb = new StringBuffer(v);
sb.insert(v.indexOf(" FN:") + 1, "\n");
v = sb.toString();
sb = new StringBuffer(v);
sb.insert(v.indexOf(" N:") + 1, "\n");
v = sb.toString();
sb = new StringBuffer(v);
sb.insert(v.indexOf("ORG:"), "\n");
v = sb.toString();
sb = new StringBuffer(v);
sb.insert(v.indexOf("EMAIL:"), "\n");
v = sb.toString();
sb = new StringBuffer(v);
sb.insert(v.indexOf("END:"), "\n");
v = sb.toString();
vcard = vcardEngine.parse(v);
if (vcard.hasFN()) v = vcard.getFN().getFormattedName();
else if (vcard.hasN()) v = vcard.getN().getFamilyName();
else {
System.out.println(" ~ ~ Problem with:::" + v);
System.out.println(" ~ ~ When Processing:" + inputFile); // debug
}
// System.out.println(" ~ author is: "+v);
}
}
// System.out.println("p: "+p+"\t\t\t v: "+v);
Property lom_prop = model.createProperty("http://ltsc.ieee.org/xsd/LOM#" + p);
Resource node = model.createResource(s).addProperty(lom_prop, v);
}
FileOutputStream fop = null;
File rdfFile =
new File(destination + lomFile.getName().replace(".xml", ".rdf"));
fop = new FileOutputStream(rdfFile);
// model.write(System.out);
model.write(fop);
// 4store
if (commit4store) {
HandleGraph graph = new HandleGraph(urlStore, uriGraph);
int result = graph.AppendGraph(rdfFile.getAbsolutePath()); // returns 0-1
}
} catch (Exception e) {
e.printStackTrace();
}
// break; //debug
}
output = "1";
} else {
output = "0";
errorDescription = "Could not handle metadata to key-value";
}
} else {
errorDescription = "XML Validation:" + valid;
}
} else {
errorDescription = "Could not handle metadata file";
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
/*//break; //debug
//Borrar todo lo de ds/extract/, rdf y el archive.tar para liberar espacio
try {
FileUtils.deleteDirectory(new File("ds/extract/"));
FileUtils.deleteDirectory(new File("ds/rdf/"));
FileUtils.deleteQuietly(new File("ds/archive.tar"));
} catch (IOException e) {
e.printStackTrace();
}
}
*/
// prepare response
if (output.contentEquals("0")) status = "ERROR: " + errorDescription;
else status = "OK";
System.out.println(status);
}