/** Test successful search for a Platform in Turtle */
@Test
public void testSearchTurtle() throws Exception {
final String[] searchTypes = {"http://purl.org/podd/ns/poddScience#Platform"}; // ,
// OWL.THING.stringValue()
// };
final MediaType requestMediaType = MediaType.APPLICATION_RDF_TURTLE;
final Model resultModel =
this.internalTestSearchRdf("Scan", searchTypes, requestMediaType, null);
Assert.assertEquals("Not the expected number of results", 5, resultModel.size());
System.out.println(resultModel.toString());
Assert.assertEquals(
"Expected Platform CabScan not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("CabScan")).size());
Assert.assertEquals(
"Expected Platform PlantScan not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("PlantScan")).size());
}
/** Test successful search for a FOR Codes in RDF/XML */
@Test
public void testSearchRdfForWildtTypeAssertion() throws Exception {
final String[] searchTypes = {"http://purl.org/podd/ns/poddScience#WildTypeAssertion"};
final MediaType requestMediaType = MediaType.APPLICATION_RDF_XML;
final Model resultModel = this.internalTestSearchRdf("", searchTypes, requestMediaType, null);
// verify:
Assert.assertEquals("Not the expected number of results", 4, resultModel.size());
Assert.assertEquals(
"Expected Assertion 'Yes' not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("Yes")).size());
Assert.assertEquals(
"Expected Assertion 'Unknown' not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("Unknown")).size());
Assert.assertEquals(
"Expected Assertion 'Not Applicable' not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("Not Applicable")).size());
}
/** Test a search in RDF/XML, with no "searchTypes" specified. */
@Test
public void testSearchRdfWithoutSearchTypes() throws Exception {
final String[] searchTypes = {}; // EVERYTHING in the search space is
// compared
final MediaType requestMediaType = MediaType.APPLICATION_RDF_XML;
final Model resultModel = this.internalTestSearchRdf("e", searchTypes, requestMediaType, null);
// verify:
Assert.assertEquals("Not the expected number of results", 224, resultModel.size());
Assert.assertEquals(
"dcTerms not found",
1,
resultModel
.filter(null, null, PODD.VF.createLiteral("The PODD Ontology for Dublin Core Terms"))
.size());
Assert.assertEquals(
"The PODD Ontology for Dublin Core Terms not found",
1,
resultModel
.filter(null, null, PODD.VF.createLiteral("The PODD Ontology for Dublin Core Terms"))
.size());
}
/**
* Test successful search for a Platform in RDF/XML including owl:Thing in the list to verify that
* it doesn't expand the search space, as the search types must all match. Ie, it is not the case
* that if "any" types match the search will succeed.
*/
@Test
public void testSearchRdfForPlatformsWithOWLThing() throws Exception {
final String[] searchTypes = {
"http://purl.org/podd/ns/poddScience#Platform", OWL.THING.stringValue()
};
final MediaType requestMediaType = MediaType.APPLICATION_RDF_XML;
final Model resultModel = this.internalTestSearchRdf("me", searchTypes, requestMediaType, null);
// verify:
Assert.assertEquals("Not the expected number of results", 9, resultModel.size());
Assert.assertEquals(
"Expected Platform SPAD Meter not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("SPAD Meter")).size());
Assert.assertEquals(
"Expected Platform Pyrometer not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("Pyrometer")).size());
Assert.assertEquals(
"Expected Platform SC1 Porometer not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("SC1 Porometer")).size());
}
/** Test successful search for PoddScience:Sex values in RDF/XML */
@Test
public void testSearchRdfForSex() throws Exception {
// prepare: add an artifact
final InferredOWLOntologyID testArtifact =
this.loadTestArtifact(
TestConstants.TEST_ARTIFACT_20130206, MediaType.APPLICATION_RDF_TURTLE);
final String[] searchTypes = {"http://purl.org/podd/ns/poddScience#Sex"};
final MediaType requestMediaType = MediaType.APPLICATION_RDF_XML;
final Model resultModel =
this.internalTestSearchRdf(
"", searchTypes, requestMediaType, testArtifact.getOntologyIRI().toString());
Assert.assertEquals("Not the expected number of results", 5, resultModel.size());
Assert.assertEquals(
"Value Hermaphrodite not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("Hermaphrodite")).size());
Assert.assertEquals(
"Value Male not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("Male")).size());
}
public VocabBuilder(String filename, RDFFormat format) throws IOException, RDFParseException {
Path file = Paths.get(filename);
if (!Files.exists(file)) throw new FileNotFoundException(filename);
if (format == null) {
format = Rio.getParserFormatForFileName(filename);
log.trace("detected input format from filename {}: {}", filename, format);
}
try (final InputStream inputStream = Files.newInputStream(file)) {
log.trace("Loading input file");
model = Rio.parse(inputStream, "", format);
}
// import
Set<Resource> owlOntologies = model.filter(null, RDF.TYPE, OWL.ONTOLOGY).subjects();
if (!owlOntologies.isEmpty()) {
setPrefix(owlOntologies.iterator().next().stringValue());
}
}
/** Test successful search for a custom Platform in RDF/XML */
@Test
public void testSearchRdfForCustomPlatforms() throws Exception {
// prepare:
final InferredOWLOntologyID testArtifact =
this.loadTestArtifact(
TestConstants.TEST_ARTIFACT_20130206, MediaType.APPLICATION_RDF_TURTLE);
final String[] searchTypes = {"http://purl.org/podd/ns/poddScience#Platform"};
final MediaType requestMediaType = MediaType.APPLICATION_RDF_XML;
final Model resultModel =
this.internalTestSearchRdf(
"lat", searchTypes, requestMediaType, testArtifact.getOntologyIRI().toString());
// verify:
Assert.assertEquals("Not the expected number of results", 1, resultModel.size());
Assert.assertEquals(
"Expected Platform 1 not found",
1,
resultModel.filter(null, null, PODD.VF.createLiteral("Platform 1")).size());
}
/** Test successful search for a PODD Project in RDF/XML */
@Test
public void testSearchRdfForProjects() throws Exception {
// prepare:
final InferredOWLOntologyID testArtifact =
this.loadTestArtifact(
TestConstants.TEST_ARTIFACT_20130206, MediaType.APPLICATION_RDF_TURTLE);
final String[] searchTypes = {"http://purl.org/podd/ns/poddScience#Project"};
final MediaType requestMediaType = MediaType.APPLICATION_RDF_XML;
final Model resultModel =
this.internalTestSearchRdf(
"Cot", searchTypes, requestMediaType, testArtifact.getOntologyIRI().toString());
// verify:
Assert.assertEquals("Not the expected number of results", 1, resultModel.size());
Assert.assertTrue(
"Expected Project not found",
resultModel
.filter(null, RDFS.LABEL, null)
.objectString()
.contains("Cotton Leaf Morphology"));
}
@Test
public void testPostRdfBasic() throws Exception {
// prepare: add an artifact
final InferredOWLOntologyID testArtifact =
this.loadTestArtifact(
TestConstants.TEST_ARTIFACT_20130206, MediaType.APPLICATION_RDF_TURTLE);
final ClientResource searchClientResource =
new ClientResource(this.getUrl(PoddWebConstants.PATH_SEARCH));
try {
searchClientResource.addQueryParameter(
PoddWebConstants.KEY_ARTIFACT_IDENTIFIER, testArtifact.getOntologyIRI().toString());
// prepare: the test input
final String[] objectUris = {
"http://purl.org/podd/basic-1-20130206/object:2966",
"http://purl.org/podd/basic-2-20130206/artifact:1#Demo-Genotype",
"http://purl.org/podd/basic-2-20130206/artifact:1#SqueekeeMaterial",
"http://purl.org/podd/ns/poddScience#WildType_NotApplicable",
"http://purl.org/podd/ns/poddPlant#DeltaTporometer-63",
"http://purl.org/podd/ns/poddBase#DisplayType_LongText"
};
final String[] expectedLabels = {
"Project#2012-0006_ Cotton Leaf Morphology",
"Demo genotype",
"Squeekee material",
"Not Applicable",
"Delta-T porometer",
null
};
final Model testModel = new LinkedHashModel();
for (final String s : objectUris) {
testModel.add(PODD.VF.createURI(s), RDFS.LABEL, PODD.VF.createLiteral("?blank"));
}
final RDFFormat inputFormat = RDFFormat.RDFXML;
final MediaType inputMediaType = MediaType.valueOf(inputFormat.getDefaultMIMEType());
// build input representation
final ByteArrayOutputStream output = new ByteArrayOutputStream(8096);
Rio.write(testModel, output, inputFormat);
final Representation input = new StringRepresentation(output.toString(), inputMediaType);
// invoke service
final Representation results =
this.doTestAuthenticatedRequest(
searchClientResource,
Method.POST,
input,
inputMediaType,
Status.SUCCESS_OK,
AbstractResourceImplTest.WITH_ADMIN);
// verify: response
final Model resultModel = this.assertRdf(results, RDFFormat.RDFXML, 5);
// verify: each URI has the expected label
for (int i = 0; i < objectUris.length; i++) {
final String objectString =
resultModel.filter(PODD.VF.createURI(objectUris[i]), RDFS.LABEL, null).objectString();
Assert.assertEquals("Not the expected label", expectedLabels[i], objectString);
}
} finally {
this.releaseClient(searchClientResource);
}
}
public void generate(String className, PrintWriter out)
throws IOException, GraphUtilException, GenerationException {
// be sure to have at least the uri constants generated
if (stringGeneration == null && uriGeneration == null) {
uriGeneration = GenerationSetting.createDefault(caseFormat, "", "");
// throw new GenerationException("no generation settings present, please set explicitly");
}
log.trace("classname: {}", className);
if (StringUtils.isBlank(name)) {
name = className;
}
if (StringUtils.isBlank(prefix)) {
throw new GenerationException("could not detect prefix, please set explicitly");
} else {
log.debug("prefix: {}", prefix);
}
Pattern pattern = Pattern.compile(Pattern.quote(getPrefix()) + "(.+)");
ConcurrentMap<String, URI> splitUris = new ConcurrentHashMap<>();
for (Resource nextSubject : model.subjects()) {
if (nextSubject instanceof URI) {
Matcher matcher = pattern.matcher(nextSubject.stringValue());
if (matcher.find()) {
String k = matcher.group(1);
URI putIfAbsent = splitUris.putIfAbsent(k, (URI) nextSubject);
if (putIfAbsent != null) {
log.warn(
"Conflicting keys found: uri={} key={} existing={}",
nextSubject.stringValue(),
k,
putIfAbsent);
}
}
}
}
// print
// package is optional
if (StringUtils.isNotBlank(packageName)) {
out.printf("package %s;%n%n", getPackageName());
}
// imports
out.println("import org.openrdf.model.URI;");
out.println("import org.openrdf.model.ValueFactory;");
out.println("import org.openrdf.model.impl.ValueFactoryImpl;");
out.println();
final URI pfx = new URIImpl(prefix);
Literal oTitle =
getFirstExistingObjectLiteral(model, pfx, getPreferredLanguage(), LABEL_PROPERTIES);
Literal oDescr =
getFirstExistingObjectLiteral(model, pfx, getPreferredLanguage(), COMMENT_PROPERTIES);
Set<Value> oSeeAlso = model.filter(pfx, RDFS.SEEALSO, null).objects();
// class JavaDoc
out.println("/**");
if (oTitle != null) {
out.printf(
" * %s.%n",
WordUtils.wrap(oTitle.getLabel().replaceAll("\\s+", " "), 70, "\n * ", false));
out.println(" * <p>");
}
if (oDescr != null) {
out.printf(
" * %s.%n",
WordUtils.wrap(oDescr.getLabel().replaceAll("\\s+", " "), 70, "\n * ", false));
out.println(" * <p>");
}
out.printf(" * Namespace %s.%n", name);
out.printf(" * Prefix: {@code <%s>}%n", prefix);
if (!oSeeAlso.isEmpty()) {
out.println(" *");
for (Value s : oSeeAlso) {
if (s instanceof URI) {
out.printf(" * @see <a href=\"%s\">%s</a>%n", s.stringValue(), s.stringValue());
}
}
}
out.println(" */");
// class Definition
out.printf("public class %s {%n", className);
out.println();
// constants
out.printf(getIndent(1) + "/** {@code %s} **/%n", prefix);
out.printf(getIndent(1) + "public static final String NAMESPACE = \"%s\";%n", prefix);
out.println();
out.printf(getIndent(1) + "/** {@code %s} **/%n", name.toLowerCase());
out.printf(getIndent(1) + "public static final String PREFIX = \"%s\";%n", name.toLowerCase());
out.println();
List<String> keys = new ArrayList<>();
keys.addAll(splitUris.keySet());
Collections.sort(keys, String.CASE_INSENSITIVE_ORDER);
// do the string constant generation (if set)
if (stringGeneration != null) {
for (String key : keys) {
final Literal comment =
getFirstExistingObjectLiteral(
model, splitUris.get(key), getPreferredLanguage(), COMMENT_PROPERTIES);
final Literal label =
getFirstExistingObjectLiteral(
model, splitUris.get(key), getPreferredLanguage(), LABEL_PROPERTIES);
out.println(getIndent(1) + "/**");
if (label != null) {
out.printf(getIndent(1) + " * %s%n", label.getLabel());
out.println(getIndent(1) + " * <p>");
}
out.printf(getIndent(1) + " * {@code %s}.%n", splitUris.get(key).stringValue());
if (comment != null) {
out.println(getIndent(1) + " * <p>");
out.printf(
getIndent(1) + " * %s%n",
WordUtils.wrap(
comment.getLabel().replaceAll("\\s+", " "),
70,
"\n" + getIndent(1) + " * ",
false));
}
out.println(getIndent(1) + " *");
out.printf(getIndent(1) + " * @see <a href=\"%s\">%s</a>%n", splitUris.get(key), key);
out.println(getIndent(1) + " */");
final String nextKey =
cleanKey(
// NOTE: CONSTANT PREFIX and constant SUFFIX are NOT part of caseFormatting
String.format(
"%s%s%s",
StringUtils.defaultString(stringGeneration.getConstantPrefix()),
doCaseFormatting(key, stringGeneration.getCaseFormat()),
StringUtils.defaultString(stringGeneration.getConstantSuffix())));
checkField(className, nextKey);
out.printf(
getIndent(1) + "public static final String %s = %s.NAMESPACE + \"%s\";%n",
nextKey,
className,
key);
out.println();
}
}
// do the entire uri constant generation
if (uriGeneration != null) {
for (String key : keys) {
Literal comment =
getFirstExistingObjectLiteral(
model, splitUris.get(key), getPreferredLanguage(), COMMENT_PROPERTIES);
Literal label =
getFirstExistingObjectLiteral(
model, splitUris.get(key), getPreferredLanguage(), LABEL_PROPERTIES);
out.println(getIndent(1) + "/**");
if (label != null) {
out.printf(getIndent(1) + " * %s%n", label.getLabel());
out.println(getIndent(1) + " * <p>");
}
out.printf(getIndent(1) + " * {@code %s}.%n", splitUris.get(key).stringValue());
if (comment != null) {
out.println(getIndent(1) + " * <p>");
out.printf(
getIndent(1) + " * %s%n",
WordUtils.wrap(
comment.getLabel().replaceAll("\\s+", " "),
70,
"\n" + getIndent(1) + " * ",
false));
}
out.println(getIndent(1) + " *");
out.printf(getIndent(1) + " * @see <a href=\"%s\">%s</a>%n", splitUris.get(key), key);
out.println(getIndent(1) + " */");
final String nextKey =
cleanKey(
// NOTE: CONSTANT PREFIX and constant SUFFIX are NOT part of caseFormatting
String.format(
"%s%s%s",
StringUtils.defaultString(uriGeneration.getConstantPrefix()),
doCaseFormatting(key, uriGeneration.getCaseFormat()),
StringUtils.defaultString(uriGeneration.getConstantSuffix())));
// String nextKey = cleanKey(doCaseFormatting(key, uriGeneration.getCaseFormat()));
checkField(className, nextKey);
out.printf(getIndent(1) + "public static final URI %s;%n", nextKey);
out.println();
}
// static init
out.println(getIndent(1) + "static {");
out.printf(getIndent(2) + "ValueFactory factory = ValueFactoryImpl.getInstance();%n");
out.println();
for (String key : keys) {
final String nextKey =
cleanKey(
// NOTE: CONSTANT PREFIX and constant SUFFIX are NOT part of caseFormatting
String.format(
"%s%s%s",
StringUtils.defaultString(uriGeneration.getConstantPrefix()),
doCaseFormatting(key, uriGeneration.getCaseFormat()),
StringUtils.defaultString(uriGeneration.getConstantSuffix())));
out.printf(
getIndent(2) + "%s = factory.createURI(%s.NAMESPACE, \"%s\");%n",
nextKey,
className,
key);
}
out.println(getIndent(1) + "}");
out.println();
}
// private contructor to avoid instances
out.printf(getIndent(1) + "private %s() {%n", className);
out.println(getIndent(2) + "//static access only");
out.println(getIndent(1) + "}");
out.println();
// class end
out.println("}");
out.flush();
}