Revision 8692
Added by ben leinfelder over 10 years ago
| metacat-index/src/main/resources/application-context-annotation.xml | ||
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<beans xmlns="http://www.springframework.org/schema/beans" |
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" |
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xmlns:p="http://www.springframework.org/schema/p" |
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xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd"> |
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<bean id="rdfXmlSubprocessor" class="edu.ucsb.nceas.metacat.index.annotation.RdfXmlSubprocessor"> |
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<property name="matchDocument" |
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value="/d100:systemMetadata/formatId[text()='http://www.w3.org/TR/rdf-syntax-grammar']" /> |
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<property name="fieldList"> |
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<list> |
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<ref bean="annotation.measurement" /> |
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</list> |
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</property> |
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</bean> |
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<bean id="annotation.measurement" class="edu.ucsb.nceas.metacat.index.annotation.SparqlField"> |
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<constructor-arg name="name" value="measurement_sm" /> |
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<constructor-arg name="query"> |
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<value> |
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<![CDATA[ |
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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 ao: <http://purl.org/ao/> |
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PREFIX dcterms: <http://purl.org/dc/terms/> |
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PREFIX pav: <http://purl.org/pav/> |
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PREFIX foaf: <http://xmlns.com/foaf/0.1/> |
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SELECT ?measurement_sm ?pid |
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FROM <$GRAPH_NAME> |
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WHERE {
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?measurement_sm rdf:type oboe-core:Measurement . |
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?measurement_sm 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+ ?allChar . |
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?allChar rdfs:subClassOf oboe-core:Characteristic . |
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OPTIONAL {
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?measurement_sm rdf:type ?restriction2 . |
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?restriction2 owl:onProperty oboe-core:usesStandard . |
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?restriction2 owl:allValuesFrom ?standard . |
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} |
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?annotation ao:context ?measurement_sm . |
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?annotation ao:annotatesResource ?metadata . |
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?metadata dcterms:identifier ?pid . |
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?annotation pav:createdBy ?person . |
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?person foaf:name ?name . |
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?annotation pav:createdOn ?date . |
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} |
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]]> |
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</value> |
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</constructor-arg> |
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<!--property name="multivalue" value="false" /--> |
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</bean> |
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</beans> |
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| metacat-index/src/test/java/edu/ucsb/nceas/metacat/index/SolrIndexIT.java | ||
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private String annotation_id = "http://doi.org/annotation.1.1"; |
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private static final String ANNOTATION_SYSTEM_META_FILE_PATH = "src/test/resources/annotation-system-meta-example.xml"; |
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private static final String ANNOTATION_FILE_PATH = "src/test/resources/annotation-example.rdf";; |
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private static final String AO_FILE_PATH = "src/test/resources/ao-example.rdf";; |
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private static final String OA_FILE_PATH = "src/test/resources/oa-example.rdf";; |
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private SolrIndex solrIndex = null; |
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@Before |
| ... | ... | |
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} |
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/** |
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* Test building index for annotation. |
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* Test building index for annotation using OpenAnnotation.
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*/ |
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@Test |
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public void testAnnotation() throws Exception {
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public void testOpenAnnotation() throws Exception {
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SystemMetadata systemMetadata = TypeMarshaller.unmarshalTypeFromFile(SystemMetadata.class, SYSTEMMETAFILEPATH); |
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InputStream emlInputStream = new FileInputStream(new File(EMLFILEPATH)); |
| ... | ... | |
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// augment with the dynamic field |
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SystemMetadata annotationSystemMetadata = TypeMarshaller.unmarshalTypeFromFile(SystemMetadata.class, ANNOTATION_SYSTEM_META_FILE_PATH); |
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InputStream annotationInputStream = new FileInputStream(new File(ANNOTATION_FILE_PATH));
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InputStream annotationInputStream = new FileInputStream(new File(OA_FILE_PATH));
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Identifier annotationPid = new Identifier(); |
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annotationPid.setValue(annotation_id); |
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solrIndex.update(annotationPid, annotationSystemMetadata, annotationInputStream); |
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String annotationResult = doQuery(solrIndex.getSolrServer()); |
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assertTrue(annotationResult.contains("measurement_sm"));
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assertTrue(annotationResult.contains("characteristic_sm"));
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} |
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| metacat-index/src/main/java/edu/ucsb/nceas/metacat/index/annotation/RdfXmlSubprocessor.java | ||
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solrDoc = documentsToIndex.get(id); |
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if (solrDoc == null) {
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solrDoc = new SolrDoc(); |
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solrDoc.addField(new SolrElementField(SolrElementField.FIELD_ID, id)); |
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documentsToIndex.put(id, solrDoc); |
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} |
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} |
| ... | ... | |
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} |
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// add the pending |
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for (SolrElementField field: pendingDoc.getFieldList()) {
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if (field.getName().equals(SolrElementField.FIELD_ID) && mergedDoc.hasField(SolrElementField.FIELD_ID)) {
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continue; |
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} |
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mergedDoc.addField(field); |
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} |
| ... | ... | |
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* Get the SolrDoc for the specified id |
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*/ |
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public static SolrDoc getSolrDoc(String id) throws SolrServerException, MalformedURLException, UnsupportedType, NotFound, ParserConfigurationException, IOException, SAXException {
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SolrDoc doc = new SolrDoc();
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SolrDoc doc = null;
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if (solrServer != null) {
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String query = QUERY + "\"" + id + "\""; |
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SolrParams solrParams = SolrRequestParsers.parseQueryString(query); |
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QueryResponse qr = solrServer.query(solrParams); |
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SolrDocument orig = qr.getResults().get(0); |
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IndexSchema indexSchema = SolrQueryServiceController.getInstance().getSchema(); |
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for (String fieldName : orig.getFieldNames()) {
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// don't transfer the copyTo fields, otherwise there are errors |
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if (indexSchema.isCopyFieldTarget(indexSchema.getField(fieldName))) {
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continue; |
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} |
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for (Object value : orig.getFieldValues(fieldName)) {
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String stringValue = value.toString(); |
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// special handling for dates in ISO 8601 |
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if (value instanceof Date) {
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stringValue = DateTimeMarshaller.serializeDateToUTC((Date) value); |
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SolrDateConverter converter = new SolrDateConverter(); |
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stringValue = converter.convert(stringValue); |
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if (!qr.getResults().isEmpty()) {
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doc = new SolrDoc(); |
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SolrDocument orig = qr.getResults().get(0); |
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IndexSchema indexSchema = SolrQueryServiceController.getInstance().getSchema(); |
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for (String fieldName : orig.getFieldNames()) {
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// don't transfer the copyTo fields, otherwise there are errors |
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if (indexSchema.isCopyFieldTarget(indexSchema.getField(fieldName))) {
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continue; |
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} |
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SolrElementField field = new SolrElementField(fieldName, stringValue); |
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log.debug("Adding field: " + fieldName);
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doc.addField(field); |
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for (Object value : orig.getFieldValues(fieldName)) {
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String stringValue = value.toString(); |
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// special handling for dates in ISO 8601 |
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if (value instanceof Date) {
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stringValue = DateTimeMarshaller.serializeDateToUTC((Date) value); |
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SolrDateConverter converter = new SolrDateConverter(); |
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stringValue = converter.convert(stringValue); |
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} |
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SolrElementField field = new SolrElementField(fieldName, stringValue); |
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log.debug("Adding field: " + fieldName);
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doc.addField(field); |
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} |
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} |
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} |
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| metacat-index/src/main/resources/application-context-ao.xml | ||
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<beans xmlns="http://www.springframework.org/schema/beans" |
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" |
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xmlns:p="http://www.springframework.org/schema/p" |
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xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd"> |
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<bean id="rdfXmlSubprocessor" class="edu.ucsb.nceas.metacat.index.annotation.RdfXmlSubprocessor"> |
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<property name="matchDocument" |
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value="/d100:systemMetadata/formatId[text()='http://www.w3.org/TR/rdf-syntax-grammar']" /> |
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<property name="fieldList"> |
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<list> |
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<ref bean="annotation.measurement" /> |
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</list> |
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</property> |
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</bean> |
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<bean id="annotation.measurement" class="edu.ucsb.nceas.metacat.index.annotation.SparqlField"> |
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<constructor-arg name="name" value="measurement_sm" /> |
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<constructor-arg name="query"> |
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<value> |
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<![CDATA[ |
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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 ao: <http://purl.org/ao/> |
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PREFIX dcterms: <http://purl.org/dc/terms/> |
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PREFIX pav: <http://purl.org/pav/> |
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PREFIX foaf: <http://xmlns.com/foaf/0.1/> |
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SELECT ?measurement_sm ?pid |
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FROM <$GRAPH_NAME> |
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WHERE {
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?measurement_sm rdf:type oboe-core:Measurement . |
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?measurement_sm 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+ ?allChar . |
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?allChar rdfs:subClassOf oboe-core:Characteristic . |
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OPTIONAL {
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?measurement_sm rdf:type ?restriction2 . |
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?restriction2 owl:onProperty oboe-core:usesStandard . |
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?restriction2 owl:allValuesFrom ?standard . |
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} |
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?annotation ao:context ?measurement_sm . |
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?annotation ao:annotatesResource ?metadata . |
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?metadata dcterms:identifier ?pid . |
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?annotation pav:createdBy ?person . |
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?person foaf:name ?name . |
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?annotation pav:createdOn ?date . |
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} |
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]]> |
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</value> |
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</constructor-arg> |
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<!--property name="multivalue" value="false" /--> |
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</bean> |
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</beans> |
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| metacat-index/src/main/resources/application-context-oa.xml | ||
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<beans xmlns="http://www.springframework.org/schema/beans" |
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" |
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xmlns:p="http://www.springframework.org/schema/p" |
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xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd"> |
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<bean id="rdfXmlSubprocessor" class="edu.ucsb.nceas.metacat.index.annotation.RdfXmlSubprocessor"> |
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<property name="matchDocument" |
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value="/d100:systemMetadata/formatId[text()='http://www.w3.org/TR/rdf-syntax-grammar']" /> |
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<property name="fieldList"> |
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<list> |
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<ref bean="annotation.measurement" /> |
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</list> |
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</property> |
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</bean> |
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<bean id="annotation.measurement" class="edu.ucsb.nceas.metacat.index.annotation.SparqlField"> |
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<constructor-arg name="name" value="characteristic_sm" /> |
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<constructor-arg name="query"> |
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<value> |
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<![CDATA[ |
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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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PREFIX pav: <http://purl.org/pav/> |
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PREFIX foaf: <http://xmlns.com/foaf/0.1/> |
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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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OPTIONAL {
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?measurement rdf:type ?restriction2 . |
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?restriction2 owl:onProperty oboe-core:usesStandard . |
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?restriction2 owl:allValuesFrom ?standard . |
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} |
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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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?annotation oa:annotatedBy ?person . |
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?person foaf:name ?name . |
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} |
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]]> |
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</value> |
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</constructor-arg> |
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<!--property name="multivalue" value="false" /--> |
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</bean> |
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</beans> |
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| metacat-index/src/main/resources/index-processor-context.xml | ||
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| 27 | 27 |
<import resource="application-context-resource-map.xml" /> |
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<import resource="application-context-systemmeta100.xml" /> |
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<import resource="application-context-annotation.xml" /> |
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<import resource="application-context-oa.xml" /> |
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<!-- <import resource="application-context-ao.xml" /> --> |
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<bean id="dateConverter" class="org.dataone.cn.indexer.convert.SolrDateConverter" /> |
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<bean id="fgdcDateConverter" class="org.dataone.cn.indexer.convert.FgdcDateConverter"/> |
Also available in: Unified diff
switch to the OpenAnnotation (OA) model for annotating datapackages with measurements/characteristics (semtools)