mirror of
https://github.com/hapifhir/hapi-fhir.git
synced 2025-03-09 14:33:32 +00:00
Fulltext searching works
This commit is contained in:
jamesagnew
parent
23b35661ea
commit
3fc7a16735
@ -110,7 +110,7 @@ public class OperationParameter implements IParameter {
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myMax = 1;
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}
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myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType);
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myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType) || String.class.equals(myParameterType);
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/*
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* The parameter can be of type string for validation methods - This is a bit
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@ -173,6 +173,12 @@ public class OperationParameter implements IParameter {
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DateRangeParam dateRangeParam = new DateRangeParam();
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dateRangeParam.setValuesAsQueryTokens(parameters);
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matchingParamValues.add(dateRangeParam);
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} else if (String.class.isAssignableFrom(myParameterType)) {
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for (String next : paramValues) {
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matchingParamValues.add(next);
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}
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} else {
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for (String nextValue : paramValues) {
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FhirContext ctx = theRequest.getServer().getFhirContext();
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@ -78,7 +78,6 @@
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<dependency>
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<groupId>org.javassist</groupId>
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<artifactId>javassist</artifactId>
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<version>3.20.0-GA</version>
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</dependency>
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<dependency>
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@ -239,6 +238,14 @@
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<groupId>org.hibernate</groupId>
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<artifactId>hibernate-search-orm</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.lucene</groupId>
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<artifactId>lucene-highlighter</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.lucene</groupId>
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<artifactId>lucene-analyzers-phonetic</artifactId>
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</dependency>
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<!-- Misc -->
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<dependency>
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@ -31,6 +31,7 @@ import java.util.Comparator;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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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 java.util.Set;
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@ -1189,6 +1190,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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return translateForcedIdToPid(theId, myEntityManager);
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}
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public static void validateResourceType(BaseHasResource theEntity, String theResourceName) {
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if (!theResourceName.equals(theEntity.getResourceType())) {
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throw new ResourceNotFoundException("Resource with ID " + theEntity.getIdDt().getIdPart() + " exists but it is not of type " + theResourceName + ", found resource of type " + theEntity.getResourceType());
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}
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}
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static Long translateForcedIdToPid(IIdType theId, EntityManager entityManager) {
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if (isValidPid(theId)) {
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return theId.getIdPartAsLong();
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@ -1271,9 +1278,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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if (theEntity.isParamsCoordsPopulated()) {
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paramsCoords.addAll(theEntity.getParamsCoords());
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}
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Collection<ResourceLink> resourceLinks = new ArrayList<ResourceLink>();
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Collection<ResourceLink> existingResourceLinks = new ArrayList<ResourceLink>();
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if (theEntity.isHasLinks()) {
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resourceLinks.addAll(theEntity.getResourceLinks());
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existingResourceLinks.addAll(theEntity.getResourceLinks());
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}
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Set<ResourceIndexedSearchParamString> stringParams = null;
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@ -1326,6 +1333,19 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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}
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links = extractResourceLinks(theEntity, theResource);
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/*
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* If the existing resource already has links and those match links we still want,
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* use them instead of removing them and re adding them
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*/
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for (Iterator<ResourceLink> existingLinkIter = existingResourceLinks.iterator(); existingLinkIter.hasNext(); ) {
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ResourceLink nextExisting = existingLinkIter.next();
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if (links.remove(nextExisting)) {
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existingLinkIter.remove();
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links.add(nextExisting);
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}
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}
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populateResourceIntoEntity(theResource, theEntity);
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theEntity.setUpdated(theUpdateTime);
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@ -1431,7 +1451,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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}
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// Store resource links
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for (ResourceLink next : resourceLinks) {
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for (ResourceLink next : existingResourceLinks) {
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myEntityManager.remove(next);
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}
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for (ResourceLink next : links) {
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@ -1045,9 +1045,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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}
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private void validateResourceType(BaseHasResource entity) {
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if (!myResourceName.equals(entity.getResourceType())) {
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throw new ResourceNotFoundException("Resource with ID " + entity.getIdDt().getIdPart() + " exists but it is not of type " + myResourceName + ", found resource of type " + entity.getResourceType());
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}
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validateResourceType(entity, myResourceName);
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}
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private void validateResourceTypeAndThrowIllegalArgumentException(IIdType theId) {
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@ -23,7 +23,9 @@ package ca.uhn.fhir.jpa.dao;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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@ -32,23 +34,37 @@ import javax.persistence.PersistenceContext;
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import javax.persistence.PersistenceContextType;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.Validate;
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import org.apache.commons.lang3.builder.HashCodeBuilder;
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import org.apache.lucene.analysis.Analyzer;
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import org.apache.lucene.analysis.TokenStream;
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import org.apache.lucene.analysis.core.KeywordAnalyzer;
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import org.apache.lucene.search.Query;
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import org.apache.lucene.search.highlight.Formatter;
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import org.apache.lucene.search.highlight.Highlighter;
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import org.apache.lucene.search.highlight.QueryScorer;
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import org.apache.lucene.search.highlight.Scorer;
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import org.apache.lucene.search.highlight.SimpleHTMLFormatter;
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import org.apache.lucene.search.highlight.TokenGroup;
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import org.hibernate.search.jpa.FullTextEntityManager;
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import org.hibernate.search.jpa.FullTextQuery;
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import org.hibernate.search.query.dsl.BooleanJunction;
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import org.hibernate.search.query.dsl.QueryBuilder;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.transaction.annotation.Transactional;
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import ca.uhn.fhir.context.FhirContext;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Sets;
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import ca.uhn.fhir.jpa.dao.FhirSearchDao.MySuggestionFormatter;
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import ca.uhn.fhir.jpa.entity.ResourceTable;
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import ca.uhn.fhir.model.api.IQueryParameterType;
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import ca.uhn.fhir.model.dstu.resource.BaseResource;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.server.Constants;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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public class FhirSearchDao extends BaseHapiFhirDao<IBaseResource> implements ISearchDao {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSearchDao.class);
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@ -56,61 +72,6 @@ public class FhirSearchDao extends BaseHapiFhirDao<IBaseResource> implements ISe
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@PersistenceContext(type = PersistenceContextType.TRANSACTION)
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private EntityManager myEntityManager;
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@Transactional()
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@Override
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public List<Long> search(String theResourceName, SearchParameterMap theParams) {
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return doSearch(theResourceName, theParams, null);
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}
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private List<Long> doSearch(String theResourceName, SearchParameterMap theParams, Long theReferencingPid) {
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FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
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QueryBuilder qb = em
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.getSearchFactory()
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.buildQueryBuilder()
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.forEntity(ResourceTable.class).get();
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BooleanJunction<?> bool = qb.bool();
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List<List<? extends IQueryParameterType>> contentAndTerms = theParams.remove(Constants.PARAM_CONTENT);
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addTextSearch(qb, bool, contentAndTerms, "myContentText");
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List<List<? extends IQueryParameterType>> textAndTerms = theParams.remove(Constants.PARAM_TEXT);
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addTextSearch(qb, bool, textAndTerms, "myNarrativeText");
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if (theReferencingPid != null) {
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bool.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(theReferencingPid).createQuery());
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}
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if (bool.isEmpty()) {
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return null;
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}
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if (isNotBlank(theResourceName)) {
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bool.must(qb.keyword().onField("myResourceType").matching(theResourceName).createQuery());
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}
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Query luceneQuery = bool.createQuery();
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// wrap Lucene query in a javax.persistence.Query
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FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, ResourceTable.class);
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jpaQuery.setProjection("myId");
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// execute search
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List<?> result = jpaQuery.getResultList();
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ArrayList<Long> retVal = new ArrayList<Long>();
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for (Object object : result) {
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Object[] nextArray = (Object[]) object;
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Long next = (Long)nextArray[0];
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if (next != null) {
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retVal.add(next);
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}
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}
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return retVal;
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}
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private void addTextSearch(QueryBuilder qb, BooleanJunction<?> bool, List<List<? extends IQueryParameterType>> contentAndTerms, String field) {
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if (contentAndTerms == null) {
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return;
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@ -131,9 +92,55 @@ public class FhirSearchDao extends BaseHapiFhirDao<IBaseResource> implements ISe
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}
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}
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private List<Long> doSearch(String theResourceName, SearchParameterMap theParams, Long theReferencingPid) {
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FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
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QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(ResourceTable.class).get();
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BooleanJunction<?> bool = qb.bool();
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List<List<? extends IQueryParameterType>> contentAndTerms = theParams.remove(Constants.PARAM_CONTENT);
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addTextSearch(qb, bool, contentAndTerms, "myContentText");
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List<List<? extends IQueryParameterType>> textAndTerms = theParams.remove(Constants.PARAM_TEXT);
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addTextSearch(qb, bool, textAndTerms, "myNarrativeText");
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if (theReferencingPid != null) {
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bool.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(theReferencingPid).createQuery());
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}
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if (bool.isEmpty()) {
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return null;
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}
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if (isNotBlank(theResourceName)) {
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bool.must(qb.keyword().onField("myResourceType").matching(theResourceName).createQuery());
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}
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Query luceneQuery = bool.createQuery();
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// wrap Lucene query in a javax.persistence.Query
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FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, ResourceTable.class);
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jpaQuery.setProjection("myId");
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// execute search
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List<?> result = jpaQuery.getResultList();
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ArrayList<Long> retVal = new ArrayList<Long>();
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for (Object object : result) {
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Object[] nextArray = (Object[]) object;
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Long next = (Long) nextArray[0];
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if (next != null) {
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retVal.add(next);
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}
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}
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return retVal;
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}
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@Override
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public List<Long> everything(String theResourceName, SearchParameterMap theParams) {
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Long pid = null;
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if (theParams.get(BaseResource.SP_RES_ID) != null) {
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StringParam idParm = (StringParam) theParams.get(BaseResource.SP_RES_ID).get(0).get(0);
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@ -148,6 +155,133 @@ public class FhirSearchDao extends BaseHapiFhirDao<IBaseResource> implements ISe
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return retVal;
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}
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@Transactional()
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@Override
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public List<Long> search(String theResourceName, SearchParameterMap theParams) {
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return doSearch(theResourceName, theParams, null);
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}
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@Override
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public List<Suggestion> suggestKeywords(String theContext, String theSearchParam, String theText) {
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Validate.notBlank(theContext, "theContext must be provided");
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Validate.notBlank(theSearchParam, "theSearchParam must be provided");
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Validate.notBlank(theText, "theSearchParam must be provided");
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long start = System.currentTimeMillis();
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String[] contextParts = StringUtils.split(theContext, '/');
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if (contextParts.length != 3 || "Patient".equals(contextParts[0]) == false || "$everything".equals(contextParts[2]) == false) {
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throw new InvalidRequestException("Invalid context: " + theContext);
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}
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IdDt contextId = new IdDt(contextParts[0], contextParts[1]);
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Long pid = BaseHapiFhirDao.translateForcedIdToPid(contextId, myEntityManager);
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FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
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QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(ResourceTable.class).get();
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//@formatter:off
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Query textQuery = qb
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.phrase()
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.withSlop(2)
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.onField("myContentText").boostedTo(4.0f)
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.andField("myContentTextEdgeNGram").boostedTo(2.0f)
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.andField("myContentTextNGram").boostedTo(1.0f)
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.andField("myContentTextPhonetic").boostedTo(0.5f)
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.sentence(theText.toLowerCase()).createQuery();
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Query query = qb.bool()
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.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(pid).createQuery())
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.must(textQuery)
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.createQuery();
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//@formatter:on
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FullTextQuery ftq = em.createFullTextQuery(query, ResourceTable.class);
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ftq.setProjection("myContentText");
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ftq.setMaxResults(20);
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List<?> resultList = ftq.getResultList();
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List<Suggestion> suggestions = Lists.newArrayList();
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for (Object next : resultList) {
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Object[] nextAsArray = (Object[]) next;
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String nextValue = (String) nextAsArray[0];
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try {
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MySuggestionFormatter formatter = new MySuggestionFormatter(suggestions);
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Scorer scorer = new QueryScorer(textQuery);
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Highlighter highlighter = new Highlighter(formatter, scorer);
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Analyzer analyzer = em.getSearchFactory().getAnalyzer(ResourceTable.class);
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highlighter.getBestFragment(analyzer.tokenStream("myContentText", nextValue), nextValue);
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highlighter.getBestFragment(analyzer.tokenStream("myContentTextNGram", nextValue), nextValue);
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highlighter.getBestFragment(analyzer.tokenStream("myContentTextEdgeNGram", nextValue), nextValue);
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highlighter.getBestFragment(analyzer.tokenStream("myContentTextPhonetic", nextValue), nextValue);
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} catch (Exception e) {
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throw new InternalErrorException(e);
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}
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}
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Collections.sort(suggestions);
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Set<String> terms = Sets.newHashSet();
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for (Iterator<Suggestion> iter = suggestions.iterator(); iter.hasNext(); ) {
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if (!terms.add(iter.next().getTerm())) {
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iter.remove();
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}
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}
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long delay = System.currentTimeMillis()- start;
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ourLog.info("Provided {} suggestions for term {} in {} ms", new Object[] {terms.size(), theText, delay});
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return suggestions;
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}
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public static class Suggestion implements Comparable<Suggestion> {
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public Suggestion(String theTerm, float theScore) {
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myTerm = theTerm;
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myScore = theScore;
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}
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public String getTerm() {
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return myTerm;
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}
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public float getScore() {
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return myScore;
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}
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private String myTerm;
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private float myScore;
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@Override
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public int compareTo(Suggestion theO) {
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return Float.compare(theO.myScore, myScore);
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}
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@Override
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public String toString() {
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return "Suggestion[myTerm=" + myTerm + ", myScore=" + myScore + "]";
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}
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}
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public class MySuggestionFormatter implements Formatter {
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private List<Suggestion> mySuggestions;
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public MySuggestionFormatter(List<Suggestion> theSuggestions) {
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mySuggestions = theSuggestions;
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}
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@Override
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public String highlightTerm(String theOriginalText, TokenGroup theTokenGroup) {
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if (theTokenGroup.getTotalScore() > 0) {
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mySuggestions.add(new Suggestion(theOriginalText, theTokenGroup.getTotalScore()));
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}
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return null;
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}
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}
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}
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@ -22,8 +22,12 @@ package ca.uhn.fhir.jpa.dao;
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import java.util.List;
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import ca.uhn.fhir.jpa.dao.FhirSearchDao.Suggestion;
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public interface ISearchDao {
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List<Suggestion> suggestKeywords(String theContext, String theSearchParam, String theText);
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List<Long> search(String theResourceName, SearchParameterMap theParams);
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List<Long> everything(String theResourceName, SearchParameterMap theParams);
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@ -36,7 +36,6 @@ import javax.persistence.Table;
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import org.apache.commons.lang3.Validate;
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import org.apache.commons.lang3.builder.EqualsBuilder;
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import org.apache.commons.lang3.builder.HashCodeBuilder;
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import org.hibernate.search.annotations.ContainedIn;
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import org.hibernate.search.annotations.Field;
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@Entity
|
||||
@ -72,9 +71,9 @@ public class ResourceLink implements Serializable {
|
||||
@Column(name = "TARGET_RESOURCE_ID", insertable = false, updatable = false, nullable = false)
|
||||
@Field()
|
||||
private Long myTargetResourcePid;
|
||||
|
||||
|
||||
public ResourceLink() {
|
||||
// nothing
|
||||
super();
|
||||
}
|
||||
|
||||
public ResourceLink(String theSourcePath, ResourceTable theSourceResource, ResourceTable theTargetResource) {
|
||||
@ -101,7 +100,7 @@ public class ResourceLink implements Serializable {
|
||||
EqualsBuilder b = new EqualsBuilder();
|
||||
b.append(mySourcePath, obj.mySourcePath);
|
||||
b.append(mySourceResource, obj.mySourceResource);
|
||||
b.append(myTargetResource, obj.myTargetResource);
|
||||
b.append(myTargetResourcePid, obj.myTargetResourcePid);
|
||||
return b.isEquals();
|
||||
}
|
||||
|
||||
@ -130,7 +129,7 @@ public class ResourceLink implements Serializable {
|
||||
HashCodeBuilder b = new HashCodeBuilder();
|
||||
b.append(mySourcePath);
|
||||
b.append(mySourceResource);
|
||||
b.append(myTargetResource);
|
||||
b.append(myTargetResourcePid);
|
||||
return b.toHashCode();
|
||||
}
|
||||
|
||||
|
||||
@ -29,7 +29,6 @@ import java.util.Set;
|
||||
|
||||
import javax.persistence.CascadeType;
|
||||
import javax.persistence.Column;
|
||||
import javax.persistence.Embedded;
|
||||
import javax.persistence.Entity;
|
||||
import javax.persistence.FetchType;
|
||||
import javax.persistence.GeneratedValue;
|
||||
@ -42,9 +41,29 @@ import javax.persistence.Transient;
|
||||
|
||||
import org.apache.commons.lang3.builder.ToStringBuilder;
|
||||
import org.apache.commons.lang3.builder.ToStringStyle;
|
||||
import org.apache.lucene.analysis.core.KeywordTokenizerFactory;
|
||||
import org.apache.lucene.analysis.core.LowerCaseFilterFactory;
|
||||
import org.apache.lucene.analysis.core.StopFilterFactory;
|
||||
import org.apache.lucene.analysis.miscellaneous.WordDelimiterFilterFactory;
|
||||
import org.apache.lucene.analysis.ngram.EdgeNGramFilterFactory;
|
||||
import org.apache.lucene.analysis.ngram.NGramFilterFactory;
|
||||
import org.apache.lucene.analysis.pattern.PatternReplaceFilterFactory;
|
||||
import org.apache.lucene.analysis.phonetic.PhoneticFilterFactory;
|
||||
import org.apache.lucene.analysis.snowball.SnowballPorterFilterFactory;
|
||||
import org.apache.lucene.analysis.standard.StandardFilterFactory;
|
||||
import org.apache.lucene.analysis.standard.StandardTokenizerFactory;
|
||||
import org.hibernate.search.annotations.Analyze;
|
||||
import org.hibernate.search.annotations.Analyzer;
|
||||
import org.hibernate.search.annotations.AnalyzerDef;
|
||||
import org.hibernate.search.annotations.AnalyzerDefs;
|
||||
import org.hibernate.search.annotations.Field;
|
||||
import org.hibernate.search.annotations.Fields;
|
||||
import org.hibernate.search.annotations.Indexed;
|
||||
import org.hibernate.search.annotations.IndexedEmbedded;
|
||||
import org.hibernate.search.annotations.Parameter;
|
||||
import org.hibernate.search.annotations.Store;
|
||||
import org.hibernate.search.annotations.TokenFilterDef;
|
||||
import org.hibernate.search.annotations.TokenizerDef;
|
||||
|
||||
import ca.uhn.fhir.jpa.search.IndexNonDeletedInterceptor;
|
||||
import ca.uhn.fhir.model.primitive.IdDt;
|
||||
@ -60,6 +79,62 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
||||
@Index(name = "IDX_RES_PROFILE", columnList="RES_PROFILE"),
|
||||
@Index(name = "IDX_INDEXSTATUS", columnList="SP_INDEX_STATUS")
|
||||
})
|
||||
@AnalyzerDefs({
|
||||
@AnalyzerDef(name = "autocompleteEdgeAnalyzer",
|
||||
tokenizer = @TokenizerDef(factory = KeywordTokenizerFactory.class),
|
||||
filters = {
|
||||
@TokenFilterDef(factory = PatternReplaceFilterFactory.class, params = {
|
||||
@Parameter(name = "pattern",value = "([^a-zA-Z0-9\\.])"),
|
||||
@Parameter(name = "replacement", value = " "),
|
||||
@Parameter(name = "replace", value = "all")
|
||||
}),
|
||||
@TokenFilterDef(factory = LowerCaseFilterFactory.class),
|
||||
@TokenFilterDef(factory = StopFilterFactory.class),
|
||||
@TokenFilterDef(factory = EdgeNGramFilterFactory.class, params = {
|
||||
@Parameter(name = "minGramSize", value = "3"),
|
||||
@Parameter(name = "maxGramSize", value = "50")
|
||||
})
|
||||
}),
|
||||
@AnalyzerDef(name = "autocompletePhoneticAnalyzer",
|
||||
tokenizer = @TokenizerDef(factory=StandardTokenizerFactory.class),
|
||||
filters = {
|
||||
@TokenFilterDef(factory=StandardFilterFactory.class),
|
||||
@TokenFilterDef(factory=StopFilterFactory.class),
|
||||
@TokenFilterDef(factory=PhoneticFilterFactory.class, params = {
|
||||
@Parameter(name="encoder", value="DoubleMetaphone")
|
||||
}),
|
||||
@TokenFilterDef(factory=SnowballPorterFilterFactory.class, params = {
|
||||
@Parameter(name="language", value="English")
|
||||
})
|
||||
}),
|
||||
@AnalyzerDef(name = "autocompleteNGramAnalyzer",
|
||||
tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
|
||||
filters = {
|
||||
@TokenFilterDef(factory = WordDelimiterFilterFactory.class),
|
||||
@TokenFilterDef(factory = LowerCaseFilterFactory.class),
|
||||
@TokenFilterDef(factory = NGramFilterFactory.class, params = {
|
||||
@Parameter(name = "minGramSize", value = "3"),
|
||||
@Parameter(name = "maxGramSize", value = "20")
|
||||
}),
|
||||
// @TokenFilterDef(factory = PatternReplaceFilterFactory.class, params = {
|
||||
// @Parameter(name = "pattern",value = "([^a-zA-Z0-9\\.])"),
|
||||
// @Parameter(name = "replacement", value = " "),
|
||||
// @Parameter(name = "replace", value = "all")
|
||||
// })
|
||||
}),
|
||||
@AnalyzerDef(name = "standardAnalyzer",
|
||||
tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
|
||||
filters = {
|
||||
// @TokenFilterDef(factory = WordDelimiterFilterFactory.class),
|
||||
@TokenFilterDef(factory = LowerCaseFilterFactory.class),
|
||||
// @TokenFilterDef(factory = PatternReplaceFilterFactory.class, params = {
|
||||
// @Parameter(name = "pattern", value = "([^a-zA-Z0-9\\.])"),
|
||||
// @Parameter(name = "replacement", value = " "),
|
||||
// @Parameter(name = "replace", value = "all")
|
||||
// })
|
||||
}) // Def
|
||||
}
|
||||
)
|
||||
//@formatter:on
|
||||
public class ResourceTable extends BaseHasResource implements Serializable {
|
||||
private static final int MAX_LANGUAGE_LENGTH = 20;
|
||||
@ -72,8 +147,15 @@ public class ResourceTable extends BaseHasResource implements Serializable {
|
||||
/**
|
||||
* Holds the narrative text only - Used for Fulltext searching but not directly stored in the DB
|
||||
*/
|
||||
//@formatter:off
|
||||
@Transient()
|
||||
@Field()
|
||||
@Fields({
|
||||
@Field(name = "myContentText", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
|
||||
@Field(name = "myContentTextEdgeNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteEdgeAnalyzer")),
|
||||
@Field(name = "myContentTextNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteNGramAnalyzer")),
|
||||
@Field(name = "myContentTextPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
|
||||
})
|
||||
//@formatter:on
|
||||
private String myContentText;
|
||||
|
||||
@Column(name = "SP_HAS_LINKS")
|
||||
|
||||
@ -1,5 +1,9 @@
|
||||
package ca.uhn.fhir.jpa.provider;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
/*
|
||||
* #%L
|
||||
* HAPI FHIR JPA Server
|
||||
@ -29,11 +33,15 @@ import javax.servlet.http.HttpServletRequest;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
|
||||
import ca.uhn.fhir.jpa.dao.FhirSearchDao.Suggestion;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
|
||||
import ca.uhn.fhir.jpa.dao.ISearchDao;
|
||||
import ca.uhn.fhir.model.api.annotation.Description;
|
||||
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Bundle;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Parameters;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Parameters.Parameter;
|
||||
import ca.uhn.fhir.model.primitive.DecimalDt;
|
||||
import ca.uhn.fhir.model.primitive.IntegerDt;
|
||||
import ca.uhn.fhir.model.primitive.StringDt;
|
||||
import ca.uhn.fhir.rest.annotation.Operation;
|
||||
@ -41,12 +49,16 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
|
||||
import ca.uhn.fhir.rest.annotation.Transaction;
|
||||
import ca.uhn.fhir.rest.annotation.TransactionParam;
|
||||
import ca.uhn.fhir.rest.method.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
|
||||
public class JpaSystemProviderDstu2 extends BaseJpaSystemProvider<Bundle> {
|
||||
|
||||
@Autowired()
|
||||
@Qualifier("mySystemDaoDstu2")
|
||||
private IFhirSystemDao<Bundle> mySystemDao;
|
||||
|
||||
@Autowired
|
||||
private ISearchDao mySearchDao;
|
||||
|
||||
//@formatter:off
|
||||
// This is generated by hand:
|
||||
@ -176,12 +188,43 @@ public class JpaSystemProviderDstu2 extends BaseJpaSystemProvider<Bundle> {
|
||||
@OperationParam(name="return", type=MetaDt.class)
|
||||
})
|
||||
//@formatter:on
|
||||
public Parameters operation() {
|
||||
public Parameters meta() {
|
||||
Parameters parameters = new Parameters();
|
||||
parameters.addParameter().setName("return").setValue(getDao().metaGetOperation());
|
||||
return parameters;
|
||||
}
|
||||
|
||||
@Operation(name="$suggest-keywords", idempotent=true)
|
||||
public Parameters suggestKeywords(
|
||||
@OperationParam(name="context", min=1, max=1) String theContext,
|
||||
@OperationParam(name="searchParam", min=1, max=1) String theSearchParam,
|
||||
@OperationParam(name="text", min=1, max=1) String theText
|
||||
) {
|
||||
|
||||
if (isBlank(theContext)) {
|
||||
throw new InvalidRequestException("Parameter 'context' must be provided");
|
||||
}
|
||||
if (isBlank(theSearchParam)) {
|
||||
throw new InvalidRequestException("Parameter 'searchParam' must be provided");
|
||||
}
|
||||
if (isBlank(theText)) {
|
||||
throw new InvalidRequestException("Parameter 'text' must be provided");
|
||||
}
|
||||
|
||||
List<Suggestion> keywords = mySearchDao.suggestKeywords(theContext, theSearchParam, theText);
|
||||
|
||||
Parameters retVal = new Parameters();
|
||||
for (Suggestion next : keywords) {
|
||||
//@formatter:off
|
||||
retVal.addParameter()
|
||||
.addPart(new Parameter().setName("keyword").setValue(new StringDt(next.getTerm())))
|
||||
.addPart(new Parameter().setName("score").setValue(new DecimalDt(next.getScore())));
|
||||
//@formatter:on
|
||||
}
|
||||
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Transaction
|
||||
public Bundle transaction(RequestDetails theRequestDetails, @TransactionParam Bundle theResources) {
|
||||
startRequest(theRequestDetails);
|
||||
|
||||
@ -7,7 +7,6 @@ import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
|
||||
import javax.persistence.EntityManager;
|
||||
import javax.persistence.PersistenceContext;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.hibernate.search.jpa.FullTextEntityManager;
|
||||
@ -77,7 +76,8 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
|
||||
|
||||
@Autowired
|
||||
protected ApplicationContext myAppCtx;
|
||||
|
||||
@Autowired
|
||||
protected ISearchDao mySearchDao;
|
||||
@Autowired
|
||||
@Qualifier("myConceptMapDaoDstu2")
|
||||
protected IFhirResourceDao<ConceptMap> myConceptMapDao;
|
||||
|
||||
@ -4,8 +4,7 @@ import static org.hamcrest.Matchers.contains;
|
||||
import static org.hamcrest.Matchers.containsInAnyOrder;
|
||||
import static org.hamcrest.Matchers.empty;
|
||||
import static org.hamcrest.Matchers.not;
|
||||
import static org.junit.Assert.assertNotEquals;
|
||||
import static org.junit.Assert.assertThat;
|
||||
import static org.junit.Assert.*;
|
||||
import static org.mockito.Mockito.mock;
|
||||
|
||||
import java.util.List;
|
||||
@ -15,6 +14,7 @@ import javax.servlet.http.HttpServletRequest;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.Test;
|
||||
|
||||
import ca.uhn.fhir.jpa.dao.FhirSearchDao.Suggestion;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Device;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Observation;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Patient;
|
||||
@ -27,6 +27,72 @@ import ca.uhn.fhir.rest.server.Constants;
|
||||
public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2SearchFtTest.class);
|
||||
|
||||
@Test
|
||||
public void testSuggest() {
|
||||
Patient patient = new Patient();
|
||||
patient.addName().addFamily("testSuggest");
|
||||
IIdType ptId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
|
||||
|
||||
Observation obs = new Observation();
|
||||
obs.getSubject().setReference(ptId);
|
||||
obs.getCode().setText("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL");
|
||||
myObservationDao.create(obs);
|
||||
|
||||
obs = new Observation();
|
||||
obs.getSubject().setReference(ptId);
|
||||
obs.getCode().setText("MNBVCXZ");
|
||||
myObservationDao.create(obs);
|
||||
|
||||
obs = new Observation();
|
||||
obs.getSubject().setReference(ptId);
|
||||
obs.getCode().setText("ZXC HELLO");
|
||||
myObservationDao.create(obs);
|
||||
|
||||
/*
|
||||
* These shouldn't match since they're for another patient
|
||||
*/
|
||||
patient = new Patient();
|
||||
patient.addName().addFamily("testSuggest2");
|
||||
IIdType ptId2 = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
|
||||
|
||||
Observation obs2 = new Observation();
|
||||
obs2.getSubject().setReference(ptId2);
|
||||
obs2.getCode().setText("ZXCVBNMZZ");
|
||||
myObservationDao.create(obs2);
|
||||
|
||||
List<Suggestion> output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "ZXCVBNM");
|
||||
ourLog.info("Found: " + output);
|
||||
assertEquals(4, output.size());
|
||||
assertEquals("ZXCVBNM", output.get(0).getTerm());
|
||||
assertEquals("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL", output.get(1).getTerm());
|
||||
assertEquals("ZXC", output.get(2).getTerm());
|
||||
assertEquals("ZXC HELLO", output.get(3).getTerm());
|
||||
|
||||
output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "ZXC");
|
||||
ourLog.info("Found: " + output);
|
||||
assertEquals(4, output.size());
|
||||
assertEquals("ZXC", output.get(0).getTerm());
|
||||
assertEquals("ZXC HELLO", output.get(1).getTerm());
|
||||
assertEquals("ZXCVBNM", output.get(2).getTerm());
|
||||
assertEquals("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL", output.get(3).getTerm());
|
||||
|
||||
output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "HELO");
|
||||
ourLog.info("Found: " + output);
|
||||
assertEquals(1, output.size());
|
||||
assertEquals("HELLO", output.get(0).getTerm());
|
||||
|
||||
output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "Z");
|
||||
ourLog.info("Found: " + output);
|
||||
assertEquals(0, output.size());
|
||||
|
||||
output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "ZX");
|
||||
ourLog.info("Found: " + output);
|
||||
assertEquals(1, output.size());
|
||||
assertEquals("ZXC", output.get(0).getTerm());
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testSearchAndReindex() {
|
||||
@ -320,7 +386,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
|
||||
IIdType pId1;
|
||||
{
|
||||
Patient patient = new Patient();
|
||||
patient.addName().addGiven("methodName");
|
||||
patient.addName().addGiven(methodName);
|
||||
patient.addAddress().addLine("My fulltext address");
|
||||
pId1 = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
@ -6,15 +6,9 @@ import static org.junit.Assert.assertThat;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
import org.hibernate.search.jpa.FullTextEntityManager;
|
||||
import org.hibernate.search.jpa.Search;
|
||||
import org.junit.Before;
|
||||
import org.junit.Test;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
import org.springframework.transaction.annotation.Transactional;
|
||||
|
||||
import ca.uhn.fhir.jpa.entity.ResourceTable;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Organization;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Patient;
|
||||
import ca.uhn.fhir.rest.param.StringAndListParam;
|
||||
@ -27,14 +21,6 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
|
||||
@Autowired
|
||||
private ISearchDao mySearchDao;
|
||||
|
||||
@Before
|
||||
@Transactional
|
||||
public void beforeFlushFT() {
|
||||
FullTextEntityManager ftem = Search.getFullTextEntityManager(myEntityManager);
|
||||
ftem.purgeAll(ResourceTable.class);
|
||||
ftem.flushToIndexes();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testContentSearch() {
|
||||
Long id1;
|
||||
|
||||
@ -21,9 +21,12 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
|
||||
import org.eclipse.jetty.server.Server;
|
||||
import org.eclipse.jetty.servlet.ServletContextHandler;
|
||||
import org.eclipse.jetty.servlet.ServletHolder;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.Before;
|
||||
import org.junit.Test;
|
||||
import org.springframework.transaction.annotation.Propagation;
|
||||
import org.springframework.transaction.annotation.Transactional;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.dao.BaseJpaDstu2Test;
|
||||
@ -32,12 +35,16 @@ import ca.uhn.fhir.jpa.rp.dstu2.OrganizationResourceProvider;
|
||||
import ca.uhn.fhir.jpa.rp.dstu2.PatientResourceProvider;
|
||||
import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Bundle;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Observation;
|
||||
import ca.uhn.fhir.model.dstu2.resource.OperationDefinition;
|
||||
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Parameters;
|
||||
import ca.uhn.fhir.model.dstu2.resource.Patient;
|
||||
import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
|
||||
import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
|
||||
import ca.uhn.fhir.model.primitive.DecimalDt;
|
||||
import ca.uhn.fhir.model.primitive.IdDt;
|
||||
import ca.uhn.fhir.model.primitive.StringDt;
|
||||
import ca.uhn.fhir.rest.client.IGenericClient;
|
||||
import ca.uhn.fhir.rest.server.EncodingEnum;
|
||||
import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
|
||||
@ -177,6 +184,90 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
|
||||
}
|
||||
}
|
||||
|
||||
@Transactional(propagation=Propagation.NEVER)
|
||||
@Test
|
||||
public void testSuggestKeywords() throws Exception {
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.addName().addFamily("testSuggest");
|
||||
IIdType ptId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
|
||||
|
||||
Observation obs = new Observation();
|
||||
obs.getCode().setText("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL");
|
||||
obs.getSubject().setReference(ptId);
|
||||
IIdType obsId = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
|
||||
|
||||
obs = new Observation();
|
||||
obs.setId(obsId);
|
||||
obs.getSubject().setReference(ptId);
|
||||
obs.getCode().setText("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL");
|
||||
myObservationDao.update(obs);
|
||||
|
||||
HttpGet get = new HttpGet(ourServerBase + "/$suggest-keywords?context=Patient/" + ptId.getIdPart() + "/$everything&searchParam=_content&text=zxc&_pretty=true&_format=xml");
|
||||
CloseableHttpResponse http = ourHttpClient.execute(get);
|
||||
try {
|
||||
assertEquals(200, http.getStatusLine().getStatusCode());
|
||||
String output = IOUtils.toString(http.getEntity().getContent());
|
||||
ourLog.info(output);
|
||||
|
||||
Parameters parameters = ourCtx.newXmlParser().parseResource(Parameters.class, output);
|
||||
assertEquals(2, parameters.getParameter().size());
|
||||
assertEquals("keyword", parameters.getParameter().get(0).getPart().get(0).getName());
|
||||
assertEquals(new StringDt("ZXCVBNM"), parameters.getParameter().get(0).getPart().get(0).getValue());
|
||||
assertEquals("score", parameters.getParameter().get(0).getPart().get(1).getName());
|
||||
assertEquals(new DecimalDt("1.0"), parameters.getParameter().get(0).getPart().get(1).getValue());
|
||||
|
||||
} finally {
|
||||
http.close();
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSuggestKeywordsInvalid() throws Exception {
|
||||
Patient patient = new Patient();
|
||||
patient.addName().addFamily("testSuggest");
|
||||
IIdType ptId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
|
||||
|
||||
Observation obs = new Observation();
|
||||
obs.getSubject().setReference(ptId);
|
||||
obs.getCode().setText("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL");
|
||||
myObservationDao.create(obs);
|
||||
|
||||
HttpGet get = new HttpGet(ourServerBase + "/$suggest-keywords");
|
||||
CloseableHttpResponse http = ourHttpClient.execute(get);
|
||||
try {
|
||||
assertEquals(400, http.getStatusLine().getStatusCode());
|
||||
String output = IOUtils.toString(http.getEntity().getContent());
|
||||
ourLog.info(output);
|
||||
assertThat(output, containsString("Parameter 'context' must be provided"));
|
||||
} finally {
|
||||
http.close();
|
||||
}
|
||||
|
||||
get = new HttpGet(ourServerBase + "/$suggest-keywords?context=Patient/" + ptId.getIdPart() + "/$everything");
|
||||
http = ourHttpClient.execute(get);
|
||||
try {
|
||||
assertEquals(400, http.getStatusLine().getStatusCode());
|
||||
String output = IOUtils.toString(http.getEntity().getContent());
|
||||
ourLog.info(output);
|
||||
assertThat(output, containsString("Parameter 'searchParam' must be provided"));
|
||||
} finally {
|
||||
http.close();
|
||||
}
|
||||
|
||||
get = new HttpGet(ourServerBase + "/$suggest-keywords?context=Patient/" + ptId.getIdPart() + "/$everything&searchParam=aa");
|
||||
http = ourHttpClient.execute(get);
|
||||
try {
|
||||
assertEquals(400, http.getStatusLine().getStatusCode());
|
||||
String output = IOUtils.toString(http.getEntity().getContent());
|
||||
ourLog.info(output);
|
||||
assertThat(output, containsString("Parameter 'text' must be provided"));
|
||||
} finally {
|
||||
http.close();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testGetOperationDefinition() {
|
||||
OperationDefinition op = ourClient.read(OperationDefinition.class, "get-resource-counts");
|
||||
|
||||
10
pom.xml
10
pom.xml
@ -367,6 +367,16 @@
|
||||
<artifactId>httpcore</artifactId>
|
||||
<version>4.4</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.lucene</groupId>
|
||||
<artifactId>lucene-highlighter</artifactId>
|
||||
<version>5.3.0</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.lucene</groupId>
|
||||
<artifactId>lucene-analyzers-phonetic</artifactId>
|
||||
<version>5.3.0</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.maven.doxia</groupId>
|
||||
<artifactId>doxia-module-markdown</artifactId>
|
||||
|
||||
Loading…
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Reference in New Issue
Block a user