Merge branch 'master' of github.com:jamesagnew/hapi-fhir

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.entity;
 import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
 import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
+import ca.uhn.fhir.util.ValidateUtil;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
@@ -10,6 +11,7 @@ import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.search.annotations.*;
 import org.hl7.fhir.r4.model.Coding;
+import org.springframework.validation.ValidationUtils;
 
 import javax.annotation.Nonnull;
 import javax.persistence.*;
@@ -185,6 +187,7 @@ public class TermConcept implements Serializable {
 	}
 
 	public void setCode(String theCode) {
+		ValidateUtil.isNotBlankOrThrowInvalidRequest(theCode, "Code must not be null or empty");
 		myCode = theCode;
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java

@@ -432,7 +432,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 
 		fetchParents(concept, retVal);
 
-		ourLog.info("Fetched {} codes above code {} in {}ms", new Object[] {retVal.size(), theCode, stopwatch.getMillis()});
+		ourLog.info("Fetched {} codes above code {} in {}ms", retVal.size(), theCode, stopwatch.getMillis());
 		return retVal;
 	}
 
@@ -463,7 +463,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 
 		fetchChildren(concept, retVal);
 
-		ourLog.info("Fetched {} codes below code {} in {}ms", new Object[] {retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS)});
+		ourLog.info("Fetched {} codes below code {} in {}ms", retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS));
 		return retVal;
 	}
 
@@ -537,7 +537,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	}
 
 	private void processDeferredConceptMaps() {
-		int count = Math.min(myDeferredConceptMaps.size(), 5);
+		int count = Math.min(myDeferredConceptMaps.size(), 20);
 		for (ConceptMap nextConceptMap : new ArrayList<>(myDeferredConceptMaps.subList(0, count))) {
 			ourLog.info("Creating ConceptMap: {}", nextConceptMap.getId());
 			createOrUpdateConceptMap(nextConceptMap);
@@ -559,7 +559,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 
 		if (codeCount > 0) {
 			ourLog.info("Saved {} deferred concepts ({} codes remain and {} relationships remain) in {}ms ({}ms / code)",
-				new Object[] {codeCount, myDeferredConcepts.size(), myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount)});
+				codeCount, myDeferredConcepts.size(), myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount));
 		}
 
 		if (codeCount == 0) {
@@ -580,7 +580,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 
 		if (relCount > 0) {
 			ourLog.info("Saved {} deferred relationships ({} remain) in {}ms ({}ms / code)",
-				new Object[] {relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount)});
+				relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount));
 		}
 
 		if ((myDeferredConcepts.size() + myConceptLinksToSaveLater.size()) == 0) {
@@ -589,13 +589,13 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	}
 
 	private void processDeferredValueSets() {
-		int count = Math.min(myDeferredValueSets.size(), 5);
+		int count = Math.min(myDeferredValueSets.size(), 20);
 		for (ValueSet nextValueSet : new ArrayList<>(myDeferredValueSets.subList(0, count))) {
 			ourLog.info("Creating ValueSet: {}", nextValueSet.getId());
 			createOrUpdateValueSet(nextValueSet);
 			myDeferredValueSets.remove(nextValueSet);
 		}
-		ourLog.info("Saved {} deferred ValueSet resources, have {} remaining", count, myDeferredConceptMaps.size());
+		ourLog.info("Saved {} deferred ValueSet resources, have {} remaining", count, myDeferredValueSets.size());
 	}
 
 	private void processReindexing() {
@@ -668,7 +668,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 					count++;
 				}
 
-				ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] {count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count)});
+				ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count));
 			}
 		});
 
@@ -758,6 +758,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 		// Grab the existing versions so we can delete them later
 		List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystemResourcePid);
 
+//		verifyNoDuplicates(theCodeSystemVersion.getConcepts(), new HashSet<String>());
+
 		/*
 		 * For now we always delete old versions.. At some point it would be nice to allow configuration to keep old versions
 		 */
@@ -909,6 +911,15 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 		return retVal;
 	}
 
+	private void verifyNoDuplicates(Collection<TermConcept> theConcepts, Set<String> theCodes) {
+		for (TermConcept next : theConcepts) {
+			if (!theCodes.add(next.getCode())) {
+				throw new InvalidRequestException("Duplicate code " + next.getCode() + " found in codesystem after checking " + theCodes.size() + " codes");
+			}
+			verifyNoDuplicates(next.getChildren().stream().map(TermConceptParentChildLink::getChild).collect(Collectors.toList()), theCodes);
+		}
+	}
+
 	/**
 	 * This method is present only for unit tests, do not call from client code
 	 */

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java

@@ -240,7 +240,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		iterateOverZipFile(theDescriptors, LOINC_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC);
 
 		// Answer lists (ValueSets of potential answers/values for loinc "questions")
-		handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, propertyNames, valueSets);
+		handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, propertyNames, valueSets, conceptMaps);
 		iterateOverZipFile(theDescriptors, LOINC_ANSWERLIST_FILE, handler, ',', QuoteMode.NON_NUMERIC);
 
 		// Answer list links (connects loinc observation codes to answerlist codes)

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java

@@ -23,9 +23,8 @@ package ca.uhn.fhir.jpa.term.loinc;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
-import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.apache.commons.csv.CSVRecord;
-import org.hl7.fhir.r4.model.Enumerations;
+import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ValueSet;
 
 import java.util.HashMap;
@@ -33,10 +32,9 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.*;
-import static org.apache.commons.lang3.StringUtils.trim;
 
-public class LoincAnswerListHandler implements IRecordHandler {
+public class LoincAnswerListHandler extends BaseHandler {
 
 	private final Map<String, TermConcept> myCode2Concept;
 	private final TermCodeSystemVersion myCodeSystemVersion;
@@ -44,7 +42,8 @@ public class LoincAnswerListHandler implements IRecordHandler {
 	private final List<ValueSet> myValueSets;
 	private final Map<String, ValueSet> myIdToValueSet = new HashMap<>();
 
-	public LoincAnswerListHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept, Set<String> thePropertyNames, List<ValueSet> theValueSets) {
+	public LoincAnswerListHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept, Set<String> thePropertyNames, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
+		super(theCode2concept, theValueSets, theConceptMaps);
 		myCodeSystemVersion = theCodeSystemVersion;
 		myCode2Concept = theCode2concept;
 		myPropertyNames = thePropertyNames;
@@ -70,6 +69,10 @@ public class LoincAnswerListHandler implements IRecordHandler {
 		String extCodeSystem = trim(theRecord.get("ExtCodeSystem"));
 		String extCodeSystemVersion = trim(theRecord.get("ExtCodeSystemVersion"));
 
+		if (isBlank(answerString)) {
+			return;
+		}
+
 		// Answer list code
 		if (!myCode2Concept.containsKey(answerListId)) {
 			TermConcept concept = new TermConcept(myCodeSystemVersion, answerListId);
@@ -88,21 +91,13 @@ public class LoincAnswerListHandler implements IRecordHandler {
 		}
 
 		// Answer list ValueSet
-		ValueSet vs;
+		ValueSet vs = getValueSet(answerListId, "urn:oid:" + answerListOid, answerListName);
-		if (!myIdToValueSet.containsKey(answerListId)) {
+		if (vs.getIdentifier().isEmpty()) {
-			vs = new ValueSet();
-			vs.setUrl("urn:oid:" + answerListOid);
 			vs.addIdentifier()
 				.setSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
 				.setValue(answerListId);
-			vs.setId(answerListId);
-			vs.setName(answerListName);
-			vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
-			myIdToValueSet.put(answerListId, vs);
-			myValueSets.add(vs);
-		} else {
-			vs = myIdToValueSet.get(answerListId);
 		}
+
 		vs
 			.getCompose()
 			.getIncludeFirstRep()

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincPartHandler.java

@@ -58,8 +58,12 @@ public class LoincPartHandler implements IRecordHandler {
 //			return;
 //		}
 
-		TermConcept concept = new TermConcept(myCodeSystemVersion, partNumber);
+		TermConcept concept = myCode2Concept.get(partNumber);
+		if (concept == null) {
+			concept = new TermConcept(myCodeSystemVersion, partNumber);
 			concept.setDisplay(partName);
+			myCode2Concept.put(partNumber, concept);
+		}
 		
 		if (isNotBlank(partDisplayName)) {
 			concept.addDesignation()
@@ -68,7 +72,6 @@ public class LoincPartHandler implements IRecordHandler {
 				.setValue(partDisplayName);
 		}
 
-		myCode2Concept.put(partDisplayName, concept);
 	}
 
 }

src/site/xdoc/doc_jpa.xml

@@ -241,7 +241,7 @@ public DaoConfig daoConfig() {
 				</p>
 				<div class="source">
 				<pre>
-					Cache-Control: nocache
+					Cache-Control: no-cache
 				</pre>
 				</div>
 				<p><b>Disable Paging at the Request Level</b></p>