Revision 8763
Added by ben leinfelder about 10 years ago
| DatapackageSummarizer.java | ||
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import com.hp.hpl.jena.rdf.model.Property; |
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import com.hp.hpl.jena.rdf.model.Resource; |
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import com.hp.hpl.jena.tdb.TDBFactory; |
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import com.hp.hpl.jena.util.iterator.ExtendedIterator; |
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import edu.ucsb.nceas.metacat.DBUtil; |
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import edu.ucsb.nceas.metacat.DocumentImpl; |
| ... | ... | |
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public static String OBOE_SBC = "OBOE-SBC"; |
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// package visibility for testing only |
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boolean randomize = false; |
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public void indexEphemeralAnnotation(Identifier metadataPid) throws Exception {
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// generate an annotation for the metadata given |
| ... | ... | |
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// read the annotation into the triplestore |
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InputStream source = IOUtils.toInputStream(rdfContent, "UTF-8"); |
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String name = "http://annotation";
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String name = "http://annotation/" + metadataPid.getValue();
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boolean loaded = dataset.containsNamedModel(name); |
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if (loaded) {
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dataset.removeNamedModel(name); |
| ... | ... | |
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Map<String, List<Object>> fields = new HashMap<String, List<Object>>(); |
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// TODO: look up the query to use (support multiple like in the indexing project) |
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String q = null; |
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q = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " |
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List<String> queries = new ArrayList<String>(); |
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queries.add("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
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+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " |
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+ "PREFIX owl: <http://www.w3.org/2002/07/owl#> " |
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+ "PREFIX oboe-core: <http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#> " |
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+ "PREFIX oa: <http://www.w3.org/ns/oa#> " |
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+ "PREFIX dcterms: <http://purl.org/dc/terms/> " |
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+ "SELECT ?standard_sm ?id " |
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+ "SELECT ?standard_sm ?pid "
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+ "FROM <$GRAPH_NAME> " |
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+ "WHERE { "
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+ " ?measurement rdf:type oboe-core:Measurement . " |
| ... | ... | |
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+ " ?annotation oa:hasBody ?measurement . " |
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+ " ?annotation oa:hasTarget ?target . " |
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+ " ?target oa:hasSource ?metadata . " |
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+ " ?metadata dcterms:identifier ?id . " |
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+ "}"; |
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q = q.replaceAll("\\$GRAPH_NAME", name);
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Query query = QueryFactory.create(q); |
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QueryExecution qexec = QueryExecutionFactory.create(query, dataset); |
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ResultSet results = qexec.execSelect(); |
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while (results.hasNext()) {
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QuerySolution solution = results.next(); |
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System.out.println(solution.toString()); |
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+ " ?metadata dcterms:identifier ?pid . " |
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+ "}"); |
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queries.add("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
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+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " |
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+ "PREFIX owl: <http://www.w3.org/2002/07/owl#> " |
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+ "PREFIX oboe-core: <http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#> " |
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+ "PREFIX oa: <http://www.w3.org/ns/oa#> " |
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+ "PREFIX dcterms: <http://purl.org/dc/terms/> " |
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+ "SELECT ?characteristic_sm ?pid " |
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+ "FROM <$GRAPH_NAME>" |
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+ "WHERE { "
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+ " ?measurement rdf:type oboe-core:Measurement . " |
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+ " ?measurement rdf:type ?restriction . " |
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+ " ?restriction owl:onProperty oboe-core:ofCharacteristic . " |
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+ " ?restriction owl:allValuesFrom ?characteristic . " |
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+ " ?characteristic rdfs:subClassOf+ ?characteristic_sm . " |
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+ " ?characteristic_sm rdfs:subClassOf oboe-core:Characteristic . " |
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+ " ?annotation oa:hasBody ?measurement . " |
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+ " ?annotation oa:hasTarget ?target . " |
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+ " ?target oa:hasSource ?metadata . " |
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+ " ?metadata dcterms:identifier ?pid . " |
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+ "}"); |
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for (String q: queries) {
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q = q.replaceAll("\\$GRAPH_NAME", name);
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Query query = QueryFactory.create(q); |
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QueryExecution qexec = QueryExecutionFactory.create(query, dataset); |
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ResultSet results = qexec.execSelect(); |
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// find the index document we are trying to augment with the annotation |
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if (solution.contains("id")) {
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String id = solution.getLiteral("id").getString();
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if (!id.equals(metadataPid.getValue())) {
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// skip any solution that does not annotate the given pid |
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continue; |
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} |
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while (results.hasNext()) {
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QuerySolution solution = results.next(); |
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System.out.println(solution.toString()); |
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}
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// loop through the solution variables, add an index value for each
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Iterator<String> varNameIter = solution.varNames();
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while (varNameIter.hasNext()) {
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String key = varNameIter.next();
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if (key.equals("id")) {
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// don't include the id
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continue; |
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// find the index document we are trying to augment with the annotation
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if (solution.contains("pid")) {
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String id = solution.getLiteral("pid").getString();
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if (!id.equals(metadataPid.getValue())) {
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// skip any solution that does not annotate the given pid
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continue;
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}
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} |
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String value = solution.get(key).toString(); |
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List<Object> values = fields.get(key); |
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if (values == null) {
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values = new ArrayList<Object>(); |
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// loop through the solution variables, add an index value for each |
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Iterator<String> varNameIter = solution.varNames(); |
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while (varNameIter.hasNext()) {
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String key = varNameIter.next(); |
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if (key.equals("pid")) {
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// don't include the id |
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continue; |
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} |
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String value = solution.get(key).toString(); |
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List<Object> values = fields.get(key); |
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if (values == null) {
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values = new ArrayList<Object>(); |
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} |
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values.add(value); |
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fields.put(key, values); |
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} |
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values.add(value); |
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fields.put(key, values); |
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} |
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}
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}
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// clean up the triple store |
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TDBFactory.release(dataset); |
| ... | ... | |
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private Resource lookupStandard(OntClass standardClass, Attribute attribute) {
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// what's our unit? |
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String unit = attribute.getUnit().toLowerCase(); |
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/* |
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boolean found = false; |
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List<String> tokens = Arrays.asList(unit.split(" "));
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boolean found = false; |
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ExtendedIterator iter = standardClass.listSubClasses(false); |
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if (randomize) {
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List subclasses = iter.toList(); |
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int size = subclasses.size(); |
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Long index = new Long(Math.round(Math.floor((Math.random() * (size-1))))); |
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OntClass subclass = (OntClass) subclasses.get( index.intValue() ); |
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return subclass; |
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} |
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while (iter.hasNext()) {
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OntClass subclass = (OntClass) iter.next(); |
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String subclassName = subclass.getLocalName().toLowerCase(); |
| ... | ... | |
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return subclass; |
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} |
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} |
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*/ |
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// try to look it up if we got this far |
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return BioPortalService.lookupAnnotationClass(standardClass, unit, OBOE_SBC); |
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} |
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private Resource lookupCharacteristic(OntClass characteristicClass, Attribute attribute) {
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// what's our label?
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// what are we looking for?
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String label = attribute.getLabel().toLowerCase(); |
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List<String> tokens = Arrays.asList(label.split(" "));
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String definition = attribute.getDefinition(); |
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String text = label + " " + definition; |
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/* |
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// find something that matches |
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boolean found = false; |
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// find something that matches
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List<String> tokens = Arrays.asList(label.split(" "));
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ExtendedIterator iter = characteristicClass.listSubClasses(); |
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if (randomize) {
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List subclasses = iter.toList(); |
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int size = subclasses.size(); |
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Long index = new Long(Math.round(Math.floor((Math.random() * (size-1))))); |
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OntClass subclass = (OntClass) subclasses.get( index.intValue() ); |
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return subclass; |
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} |
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while (iter.hasNext()) {
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OntClass subclass = (OntClass) iter.next(); |
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String subclassName = subclass.getLocalName().toLowerCase(); |
| ... | ... | |
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return subclass; |
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} |
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} |
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*/ |
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// try to look it up if we got this far
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return BioPortalService.lookupAnnotationClass(characteristicClass, attribute.getDefinition(), OBOE_SBC);
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// try to look it up from the service
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return BioPortalService.lookupAnnotationClass(characteristicClass, text, OBOE_SBC);
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} |
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|
Also available in: Unified diff
simplify lookup for classes and orcid. remove the "random" annotation code branches -- just too confusing to look at those bogus classes especially now that we have "real" generated annotations.