Revision 9420
Added by ben leinfelder over 8 years ago
| metacat-index/src/main/java/edu/ucsb/nceas/metacat/index/annotation/MetacatAnnotatorSubprocessor.java | ||
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package edu.ucsb.nceas.metacat.index.annotation; |
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import java.io.IOException; |
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import java.io.InputStream; |
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import java.util.Iterator; |
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import java.util.List; |
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import java.util.Map; |
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import javax.xml.xpath.XPathExpressionException; |
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import org.apache.commons.codec.EncoderException; |
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import org.apache.commons.logging.Log; |
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import org.apache.commons.logging.LogFactory; |
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import org.dataone.cn.indexer.annotation.AnnotatorSubprocessor; |
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import org.dataone.cn.indexer.solrhttp.SolrDoc; |
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import org.dataone.cn.indexer.solrhttp.SolrElementField; |
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import edu.ucsb.nceas.metacat.index.resourcemap.ResourceMapSubprocessor; |
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public class MetacatAnnotatorSubprocessor extends AnnotatorSubprocessor {
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private static Log log = LogFactory.getLog(AnnotatorSubprocessor.class); |
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@Override |
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public Map<String, SolrDoc> processDocument(String annotationId, Map<String, SolrDoc> docs, |
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InputStream is) throws Exception {
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// check for annotations, and add them if found |
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SolrDoc annotations = parseAnnotation(is); |
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if (annotations != null) {
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String referencedPid = annotations.getIdentifier(); |
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SolrDoc referencedDoc = docs.get(referencedPid); |
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// make sure we have a reference for the document we annotating |
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if (referencedDoc == null) {
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try {
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referencedDoc = ResourceMapSubprocessor.getSolrDoc(referencedPid); |
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} catch (Exception e) {
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log.error("Unable to retrieve solr document: " + referencedPid
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+ ". Exception attempting to communicate with solr server.", e); |
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} |
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if (referencedDoc == null) {
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referencedDoc = new SolrDoc(); |
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} |
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docs.put(referencedPid, referencedDoc); |
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} |
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// make sure we say we annotate the object |
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SolrDoc annotationDoc = docs.get(annotationId); |
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if (annotationDoc != null) {
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annotationDoc.addField(new SolrElementField(FIELD_ANNOTATES, referencedPid)); |
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} |
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// add the annotations to the referenced document |
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Iterator<SolrElementField> annotationIter = annotations.getFieldList().iterator(); |
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while (annotationIter.hasNext()) {
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SolrElementField annotation = annotationIter.next(); |
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if (!this.getFieldsToMerge().contains(annotation.getName())) {
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log.debug("SKIPPING field (not in fieldsToMerge): " + annotation.getName());
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continue; |
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} |
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referencedDoc.addField(annotation); |
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log.debug("ADDING annotation to " + referencedPid + ": " + annotation.getName()
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+ "=" + annotation.getValue()); |
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} |
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} else {
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log.warn("Annotations were not found when parsing: " + annotationId);
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} |
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// return the collection that we have augmented |
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return docs; |
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} |
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/** |
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* Merge updates with existing solr documents |
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* |
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* @param indexDocument |
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* @return |
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* @throws IOException |
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* @throws EncoderException |
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* @throws XPathExpressionException |
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*/ |
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public SolrDoc mergeWithIndexedDocument(SolrDoc indexDocument) throws IOException, |
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EncoderException, XPathExpressionException {
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return mergeWithIndexedDocument(indexDocument, getFieldsToMerge()); |
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} |
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/** |
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* Inspired by SubprocessorUtility method, but works with embedded solr server |
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* @param indexDocument |
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* @param fieldsToMerge |
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* @return |
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* @throws IOException |
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* @throws EncoderException |
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* @throws XPathExpressionException |
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*/ |
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private SolrDoc mergeWithIndexedDocument(SolrDoc indexDocument, List<String> fieldsToMerge) |
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throws IOException, EncoderException, XPathExpressionException {
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log.debug("about to merge indexed document with new doc to insert for pid: "
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+ indexDocument.getIdentifier()); |
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SolrDoc solrDoc = null; |
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try {
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solrDoc = ResourceMapSubprocessor.getSolrDoc(indexDocument.getIdentifier()); |
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} catch (Exception e) {
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log.error("Could not retrieve existing index document: " + indexDocument.getIdentifier(), e);
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} |
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if (solrDoc != null) {
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log.debug("found existing doc to merge for pid: " + indexDocument.getIdentifier());
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for (SolrElementField field : solrDoc.getFieldList()) {
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if (fieldsToMerge.contains(field.getName()) |
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&& !indexDocument.hasFieldWithValue(field.getName(), field.getValue())) {
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indexDocument.addField(field); |
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log.debug("merging field: " + field.getName() + " with value: "
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+ field.getValue()); |
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} |
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} |
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} |
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return indexDocument; |
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} |
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} |
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| metacat-index/src/main/resources/application-context-annotator.xml | ||
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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="annotatorSubprocessor" class="org.dataone.cn.indexer.annotation.AnnotatorSubprocessor">
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<bean id="annotatorSubprocessor" class="edu.ucsb.nceas.metacat.index.annotation.MetacatAnnotatorSubprocessor">
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<!-- match annotation documents --> |
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<property name="matchDocuments"> |
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<property name="fieldList"> |
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<list> |
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<ref bean="annotation.expansion" /> |
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<ref bean="annotation.bioportal.expansion" /> |
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<ref bean="annotation.esor.expansion" /> |
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</list> |
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</property> |
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<property name="fieldsToMerge"> |
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<list> |
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<value>sem_annotation</value> |
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<value>sem_annotation_bioportal_sm</value> |
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<value>sem_annotation_esor_sm</value> |
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<value>sem_annotates</value> |
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<value>sem_annotated_by</value> |
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</list> |
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</property> |
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</property> |
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<property name="ontologyList"> |
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<list> |
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<value>http://purl.org/spar/datacite/</value> |
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<value>http://purl.org/dc/terms/</value> |
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<value>http://www.w3.org/2006/time</value> |
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<value>http://purl.dataone.org/ontologies/observation/d1-ECSO.owl</value> |
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<value>http://purl.dataone.org/ontologies/provenance/ProvONE/v1/owl/provone.owl</value> |
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<value>http://purl.obolibrary.org/obo/envo.owl</value> |
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<value>http://purl.obolibrary.org/obo/chebi.owl</value> |
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</list> |
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</property> |
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</bean> |
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<bean id="annotation.expansion" class="org.dataone.cn.indexer.annotation.SparqlField"> |
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PREFIX owl: <http://www.w3.org/2002/07/owl#> |
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SELECT ?sem_annotation |
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FROM <$GRAPH_NAME> |
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WHERE {
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<$CONCEPT_URI> rdfs:subClassOf+ ?sem_annotation . |
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} |
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</constructor-arg> |
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<!--property name="multivalue" value="false" /--> |
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</bean> |
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<!-- bioportal-based annotation --> |
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<bean id="annotation.bioportal.expansion" class="org.dataone.cn.indexer.annotation.SparqlField"> |
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<constructor-arg name="name" value="sem_annotation_bioportal_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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SELECT ?sem_annotation_bioportal_sm |
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WHERE {
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<$CONCEPT_URI> rdfs:subClassOf+ ?sem_annotation_bioportal_sm . |
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} |
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]]> |
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</value> |
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</constructor-arg> |
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</bean> |
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<bean id="annotation.bioportal.raw" class="org.dataone.cn.indexer.annotation.SparqlField"> |
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<constructor-arg name="name" value="sem_annotation_bioportal_raw_sm" /> |
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<constructor-arg name="query"> |
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<value> |
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<![CDATA[ |
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> |
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> |
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PREFIX owl: <http://www.w3.org/2002/07/owl#> |
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SELECT ?sem_annotation_bioportal_raw_sm |
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WHERE {
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<$CONCEPT_URI> rdf:about ?sem_annotation_bioportal_raw_sm . |
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} |
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]]> |
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</value> |
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</constructor-arg> |
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</bean> |
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<!-- esor-based annotation --> |
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<bean id="annotation.esor.expansion" class="org.dataone.cn.indexer.annotation.SparqlField"> |
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<constructor-arg name="name" value="sem_annotation_esor_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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SELECT ?sem_annotation_esor_sm |
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WHERE {
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<$CONCEPT_URI> rdfs:subClassOf+ ?sem_annotation_esor_sm . |
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} |
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]]> |
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</value> |
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</constructor-arg> |
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</bean> |
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<bean id="annotation.esor.raw" class="org.dataone.cn.indexer.annotation.SparqlField"> |
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<constructor-arg name="name" value="sem_annotation_esor_raw_sm" /> |
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<constructor-arg name="query"> |
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<value> |
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<![CDATA[ |
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> |
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> |
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PREFIX owl: <http://www.w3.org/2002/07/owl#> |
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SELECT ?sem_annotation_esor_raw_sm |
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WHERE {
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<$CONCEPT_URI> rdf:about ?sem_annotation_esor_raw_sm . |
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} |
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]]> |
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</value> |
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</constructor-arg> |
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</bean> |
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</beans> |
Also available in: Unified diff
subclass AnnotatorSubprocessor for use in metacat-index (uses embedded solr server and solrj for retrieving/merging existing documents).