Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search

# Conflicts:
#	hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml

azure-pipelines.yml

@@ -19,7 +19,7 @@ jobs:
     steps:
       - task: Cache@2
         inputs:
-          key: 'maven | "$(Agent.OS)" | **/pom.xml'
+          key: 'maven | "$(Agent.OS)" | ./pom.xml'
           path: $(MAVEN_CACHE_FOLDER)
       - task: Bash@3
         inputs:

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/1679-delta-migrators-no-transient-fields.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 1679
+title: "An issue with the new flyway migrator hashCode generation was resolved. 
+   Thanks to Jafer Khan for the pull request!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml

@@ -82,6 +82,9 @@ Sean McIlvenna for reporting!"
    title: "When using a custom structure that changes the cardinality from 0..* to 0..1, the Parser was encoding
        a plain field instead of an array (as required by the FHIR specification). Thanks to 
        Petro Mykhailysyn for the pull request!"
+- item:
+   type: "fix"
+   title: "A meomery leak was resolved in the JPA terminology service delta upload operations."
 - item:
      type: "add"
      title: "Searching Location.position by latitude, longitude and distance for DSTU3, R4 and R5 is now supported using a simple 'box' search.

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

@@ -97,7 +97,7 @@ public class TermConcept implements Serializable {
 	@Column(name = "PARENT_PIDS", nullable = true)
 	private String myParentPids;
 	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "myChild")
-	private Collection<TermConceptParentChildLink> myParents;
+	private List<TermConceptParentChildLink> myParents;
 	@Column(name = "CODE_SEQUENCE", nullable = true)
 	private Integer mySequence;
 
@@ -269,7 +269,7 @@ public class TermConcept implements Serializable {
 		return myParentPids;
 	}
 
-	public Collection<TermConceptParentChildLink> getParents() {
+	public List<TermConceptParentChildLink> getParents() {
 		if (myParents == null) {
 			myParents = new ArrayList<>();
 		}

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

@@ -24,10 +24,21 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
-import ca.uhn.fhir.jpa.dao.data.*;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
-import ca.uhn.fhir.jpa.entity.*;
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
+import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import ca.uhn.fhir.jpa.entity.TermConceptProperty;
+import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
@@ -166,10 +177,17 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			TypedQuery<TermConcept> typedQuery = myEntityManager.createQuery(query.select(root));
 			org.hibernate.query.Query<TermConcept> hibernateQuery = (org.hibernate.query.Query<TermConcept>) typedQuery;
 			ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
+			int count = 0;
 			try (ScrollableResultsIterator<TermConcept> scrollableResultsIterator = new ScrollableResultsIterator<>(scrollableResults)) {
 				while (scrollableResultsIterator.hasNext()) {
 					TermConcept next = scrollableResultsIterator.next();
 					codeToConceptPid.put(next.getCode(), next.getId());
+
+					// We don't want to keep the loaded entities in the L1 cache because they can take up a loooot of memory
+					if (count % 100 == 0) {
+						myEntityManager.clear();
+					}
+					count++;
 				}
 			}
 			ourLog.info("Loaded {} concepts in {}", codeToConceptPid.size(), sw.toString());
@@ -199,12 +217,20 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 					String childCode = next.getChild().getCode();
 					parentCodeToChildCodes.put(parentCode, childCode);
 					childCodeToParentCodes.put(childCode, parentCode);
+
+					// We don't want to keep the loaded entities in the L1 cache because they can take up a loooot of memory
+					if (count % 100 == 0) {
+						myEntityManager.clear();
+					}
+
 					count++;
 				}
 			}
 			ourLog.info("Loaded {} parent/child relationships in {}", count, sw.toString());
 		}
 
+		ourLog.trace("Starting delta application");
+
 		// Account for root codes in the parent->child map
 		for (String nextCode : codeToConceptPid.keySet()) {
 			if (childCodeToParentCodes.get(nextCode).isEmpty()) {
@@ -217,13 +243,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		// Add root concepts
 		for (TermConcept nextRootConcept : theAdditions.getRootConcepts()) {
 			List<String> parentCodes = Collections.emptyList();
-			addConcept(csv, codeToConceptPid, parentCodes, nextRootConcept, parentCodeToChildCodes, retVal, true);
+			addConcept(csv, codeToConceptPid, parentCodes, nextRootConcept, parentCodeToChildCodes, retVal, theAdditions.getRootConceptCodes(), true);
-		}
-
-		// Add unanchored child concepts
-		for (TermConcept nextUnanchoredChild : theAdditions.getUnanchoredChildConceptsToParentCodes().keySet()) {
-			List<String> nextParentCodes = theAdditions.getUnanchoredChildConceptsToParentCodes().get(nextUnanchoredChild);
-			addConcept(csv, codeToConceptPid, nextParentCodes, nextUnanchoredChild, parentCodeToChildCodes, retVal, true);
 		}
 
 		return retVal;
@@ -499,10 +519,11 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		Validate.isTrue(myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3), "Terminology operations only supported in DSTU3+ mode");
 	}
 
-	private void addConcept(TermCodeSystemVersion theCsv, Map<String, Long> theCodeToConceptPid, Collection<String> theParentCodes, TermConcept theConceptToAdd, ListMultimap<String, String> theParentCodeToChildCodes, UploadStatistics theStatisticsTracker, boolean theForceResequence) {
+	private void addConcept(TermCodeSystemVersion theCsv, Map<String, Long> theCodeToConceptPid, Collection<String> theParentCodes, TermConcept theConceptToAdd, ListMultimap<String, String> theParentCodeToChildCodes, UploadStatistics theStatisticsTracker, Set<String> theAdditionSetRootConceptCodes, boolean theRootConcept) {
-		TermConcept nextConceptToAdd = theConceptToAdd;
+		TermConcept conceptToAdd = theConceptToAdd;
+		List<TermConceptParentChildLink> childrenToAdd = theConceptToAdd.getChildren();
 
-		String nextCodeToAdd = nextConceptToAdd.getCode();
+		String nextCodeToAdd = conceptToAdd.getCode();
 		String parentDescription = "(root concept)";
 		Set<TermConcept> parentConcepts = new HashSet<>();
 		if (!theParentCodes.isEmpty()) {
@@ -522,12 +543,12 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 
 			TermConcept existingCode = myConceptDao.getOne(theCodeToConceptPid.get(nextCodeToAdd));
 			existingCode.setIndexStatus(null);
-			existingCode.setDisplay(nextConceptToAdd.getDisplay());
+			existingCode.setDisplay(conceptToAdd.getDisplay());
-			nextConceptToAdd = existingCode;
+			conceptToAdd = existingCode;
 
 		}
 
-		if (theConceptToAdd.getSequence() == null || theForceResequence) {
+		if (conceptToAdd.getSequence() == null || !theRootConcept) {
 			// If this is a new code, give it a sequence number based on how many concepts the
 			// parent already has (or the highest number, if the code has multiple parents)
 			int sequence = 0;
@@ -539,17 +560,15 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 				theParentCodeToChildCodes.put("", nextCodeToAdd);
 				sequence = Math.max(sequence, theParentCodeToChildCodes.get("").size());
 			}
-			nextConceptToAdd.setSequence(sequence);
+			conceptToAdd.setSequence(sequence);
 		}
 
-
 		// Drop any old parent-child links if they aren't explicitly specified in the
 		// hierarchy being added
-		for (Iterator<TermConceptParentChildLink> iter = nextConceptToAdd.getParents().iterator(); iter.hasNext(); ) {
+		if (!theRootConcept) {
-			TermConceptParentChildLink nextLink = iter.next();
+			for (Iterator<TermConceptParentChildLink> iter = conceptToAdd.getParents().iterator(); iter.hasNext(); ) {
-			String parentCode = nextLink.getParent().getCode();
+				TermConceptParentChildLink nextLink = iter.next();
-			boolean shouldRemove = !theParentCodes.contains(parentCode);
+				String parentCode = nextLink.getParent().getCode();
-			if (shouldRemove) {
 				ourLog.info("Dropping existing parent/child link from {} -> {}", parentCode, nextCodeToAdd);
 				myConceptParentChildLinkDao.delete(nextLink);
 				iter.remove();
@@ -559,42 +578,49 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			}
 		}
 
-		nextConceptToAdd.setParentPids(null);
+		// Null out the hierarchy PIDs for this concept always. We do this because we're going to
-		nextConceptToAdd.setCodeSystemVersion(theCsv);
+		// force a reindex, and it'll be regenerated then
-		nextConceptToAdd = myConceptDao.save(nextConceptToAdd);
+		conceptToAdd.setParentPids(null);
+		conceptToAdd.setCodeSystemVersion(theCsv);
+		conceptToAdd = myConceptDao.save(conceptToAdd);
 
-		Long nextConceptPid = nextConceptToAdd.getId();
+		Long nextConceptPid = conceptToAdd.getId();
 		Validate.notNull(nextConceptPid);
 		theCodeToConceptPid.put(nextCodeToAdd, nextConceptPid);
 		theStatisticsTracker.incrementUpdatedConceptCount();
 
-		// Add link to new child to the parent if this link doesn't already exist (this will be the
+		// Add link to new child to the parent
-		// case for concepts being added to an existing child concept, but won't be the case when
-		// we're recursively adding children)
 		for (TermConcept nextParentConcept : parentConcepts) {
-			if (nextParentConcept.getChildren().stream().noneMatch(t -> t.getChild().getCode().equals(nextCodeToAdd))) {
+			TermConceptParentChildLink parentLink = new TermConceptParentChildLink();
-				TermConceptParentChildLink parentLink = new TermConceptParentChildLink();
+			parentLink.setParent(nextParentConcept);
-				parentLink.setParent(nextParentConcept);
+			parentLink.setChild(conceptToAdd);
-				parentLink.setChild(nextConceptToAdd);
+			parentLink.setCodeSystem(theCsv);
-				parentLink.setCodeSystem(theCsv);
+			parentLink.setRelationshipType(TermConceptParentChildLink.RelationshipTypeEnum.ISA);
-				parentLink.setRelationshipType(TermConceptParentChildLink.RelationshipTypeEnum.ISA);
+			nextParentConcept.getChildren().add(parentLink);
-				nextParentConcept.getChildren().add(parentLink);
+			conceptToAdd.getParents().add(parentLink);
-				nextConceptToAdd.getParents().add(parentLink);
+			ourLog.info("Saving parent/child link - Parent[{}] Child[{}]", parentLink.getParent().getCode(), parentLink.getChild().getCode());
-				myConceptParentChildLinkDao.save(parentLink);
+			myConceptParentChildLinkDao.save(parentLink);
-			}
 		}
 
+		ourLog.trace("About to save parent-child links");
+
 		// Save children recursively
-		for (TermConceptParentChildLink nextChildConceptLink : nextConceptToAdd.getChildren()) {
+		for (TermConceptParentChildLink nextChildConceptLink : new ArrayList<>(childrenToAdd)) {
 
 			TermConcept nextChild = nextChildConceptLink.getChild();
-			Collection<String> parentCodes = nextChild.getParents().stream().map(t -> t.getParent().getCode()).collect(Collectors.toList());
-			addConcept(theCsv, theCodeToConceptPid, parentCodes, nextChild, theParentCodeToChildCodes, theStatisticsTracker, false);
 
-			if (nextChildConceptLink.getId() == null) {
+			for (int i = 0; i < nextChild.getParents().size(); i++) {
-				nextChildConceptLink.setCodeSystem(theCsv);
+				if (nextChild.getParents().get(i).getId() == null) {
-				myConceptParentChildLinkDao.save(nextChildConceptLink);
+					String parentCode = nextChild.getParents().get(i).getParent().getCode();
+					Long parentPid = theCodeToConceptPid.get(parentCode);
+					TermConcept parentConcept = myConceptDao.findById(parentPid).orElseThrow(() -> new IllegalArgumentException("Unknown parent code: " + parentCode));
+					nextChild.getParents().get(i).setParent(parentConcept);
+				}
 			}
+
+			Collection<String> parentCodes = nextChild.getParents().stream().map(t -> t.getParent().getCode()).collect(Collectors.toList());
+			addConcept(theCsv, theCodeToConceptPid, parentCodes, nextChild, theParentCodeToChildCodes, theStatisticsTracker, theAdditionSetRootConceptCodes, false);
+
 		}
 
 	}

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

@@ -28,40 +28,38 @@ import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
-import com.google.common.collect.Multimaps;
 import org.apache.commons.csv.QuoteMode;
 import org.apache.commons.lang3.Validate;
 
 import javax.annotation.Nonnull;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 public class CustomTerminologySet {
 
 	private final int mySize;
-	private final ListMultimap<TermConcept, String> myUnanchoredChildConceptsToParentCodes;
 	private final List<TermConcept> myRootConcepts;
 
 	/**
 	 * Constructor for an empty object
 	 */
 	public CustomTerminologySet() {
-		this(0, ArrayListMultimap.create(), new ArrayList<>());
+		this(0, new ArrayList<>());
 	}
 
 	/**
 	 * Constructor
 	 */
-	private CustomTerminologySet(int theSize, ListMultimap<TermConcept, String> theUnanchoredChildConceptsToParentCodes, Collection<TermConcept> theRootConcepts) {
+	private CustomTerminologySet(int theSize, List<TermConcept> theRootConcepts) {
-		this(theSize, theUnanchoredChildConceptsToParentCodes, new ArrayList<>(theRootConcepts));
-	}
-
-	/**
-	 * Constructor
-	 */
-	private CustomTerminologySet(int theSize, ListMultimap<TermConcept, String> theUnanchoredChildConceptsToParentCodes, List<TermConcept> theRootConcepts) {
 		mySize = theSize;
-		myUnanchoredChildConceptsToParentCodes = theUnanchoredChildConceptsToParentCodes;
 		myRootConcepts = theRootConcepts;
 	}
 
@@ -80,10 +78,6 @@ public class CustomTerminologySet {
 	}
 
 
-	public ListMultimap<TermConcept, String> getUnanchoredChildConceptsToParentCodes() {
-		return Multimaps.unmodifiableListMultimap(myUnanchoredChildConceptsToParentCodes);
-	}
-
 	public int getSize() {
 		return mySize;
 	}
@@ -111,22 +105,9 @@ public class CustomTerminologySet {
 		return Collections.unmodifiableList(myRootConcepts);
 	}
 
-	public void addUnanchoredChildConcept(String theParentCode, String theCode, String theDisplay) {
-		Validate.notBlank(theParentCode);
-		Validate.notBlank(theCode);
-
-		TermConcept code = new TermConcept()
-			.setCode(theCode)
-			.setDisplay(theDisplay);
-		myUnanchoredChildConceptsToParentCodes.put(code, theParentCode);
-	}
-
 	public void validateNoCycleOrThrowInvalidRequest() {
 		Set<String> codes = new HashSet<>();
 		validateNoCycleOrThrowInvalidRequest(codes, getRootConcepts());
-		for (TermConcept next : myUnanchoredChildConceptsToParentCodes.keySet()) {
-			validateNoCycleOrThrowInvalidRequest(codes, next);
-		}
 	}
 
 	private void validateNoCycleOrThrowInvalidRequest(Set<String> theCodes, List<TermConcept> theRootConcepts) {
@@ -142,25 +123,30 @@ public class CustomTerminologySet {
 		validateNoCycleOrThrowInvalidRequest(theCodes, next.getChildCodes());
 	}
 
+	public Set<String> getRootConceptCodes() {
+		return getRootConcepts()
+			.stream()
+			.map(TermConcept::getCode)
+			.collect(Collectors.toSet());
+	}
 
 	@Nonnull
 	public static CustomTerminologySet load(LoadedFileDescriptors theDescriptors, boolean theFlat) {
 
 		final Map<String, TermConcept> code2concept = new LinkedHashMap<>();
-		ArrayListMultimap<TermConcept, String> unanchoredChildConceptsToParentCodes = ArrayListMultimap.create();
 
 		// Concepts
 		IRecordHandler conceptHandler = new ConceptHandler(code2concept);
 		TermLoaderSvcImpl.iterateOverZipFile(theDescriptors, TermLoaderSvcImpl.CUSTOM_CONCEPTS_FILE, conceptHandler, ',', QuoteMode.NON_NUMERIC, false);
 		if (theFlat) {
 
-			return new CustomTerminologySet(code2concept.size(), ArrayListMultimap.create(), code2concept.values());
+			return new CustomTerminologySet(code2concept.size(), new ArrayList<>(code2concept.values()));
 
 		} else {
 
 			// Hierarchy
 			if (theDescriptors.hasFile(TermLoaderSvcImpl.CUSTOM_HIERARCHY_FILE)) {
-				IRecordHandler hierarchyHandler = new HierarchyHandler(code2concept, unanchoredChildConceptsToParentCodes);
+				IRecordHandler hierarchyHandler = new HierarchyHandler(code2concept);
 				TermLoaderSvcImpl.iterateOverZipFile(theDescriptors, TermLoaderSvcImpl.CUSTOM_HIERARCHY_FILE, hierarchyHandler, ',', QuoteMode.NON_NUMERIC, false);
 			}
 
@@ -178,7 +164,7 @@ public class CustomTerminologySet {
 				}
 
 				// Sort children so they appear in the same order as they did in the concepts.csv file
-				nextConcept.getChildren().sort((o1,o2)->{
+				nextConcept.getChildren().sort((o1, o2) -> {
 					String code1 = o1.getChild().getCode();
 					String code2 = o2.getChild().getCode();
 					int order1 = codesInOrder.get(code1);
@@ -188,7 +174,7 @@ public class CustomTerminologySet {
 
 			}
 
-			return new CustomTerminologySet(code2concept.size(), unanchoredChildConceptsToParentCodes, rootConcepts);
+			return new CustomTerminologySet(code2concept.size(), rootConcepts);
 		}
 	}
 

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

@@ -24,7 +24,6 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import ca.uhn.fhir.util.ValidateUtil;
-import com.google.common.collect.ArrayListMultimap;
 import org.apache.commons.csv.CSVRecord;
 
 import java.util.Map;
@@ -37,11 +36,9 @@ public class HierarchyHandler implements IRecordHandler {
 	public static final String PARENT = "PARENT";
 	public static final String CHILD = "CHILD";
 	private final Map<String, TermConcept> myCode2Concept;
-	private final ArrayListMultimap<TermConcept, String> myUnanchoredChildConceptsToParentCodes;
 
-	public HierarchyHandler(Map<String, TermConcept> theCode2concept, ArrayListMultimap<TermConcept, String> theunanchoredChildConceptsToParentCodes) {
+	public HierarchyHandler(Map<String, TermConcept> theCode2concept) {
 		myCode2Concept = theCode2concept;
-		myUnanchoredChildConceptsToParentCodes = theunanchoredChildConceptsToParentCodes;
 	}
 
 	@Override
@@ -51,14 +48,12 @@ public class HierarchyHandler implements IRecordHandler {
 		if (isNotBlank(parent) && isNotBlank(child)) {
 
 			TermConcept childConcept = myCode2Concept.get(child);
-			ValidateUtil.isNotNullOrThrowUnprocessableEntity(childConcept, "Child code %s not found", child);
+			ValidateUtil.isNotNullOrThrowUnprocessableEntity(childConcept, "Child code %s not found in file", child);
 
 			TermConcept parentConcept = myCode2Concept.get(parent);
-			if (parentConcept == null) {
+			ValidateUtil.isNotNullOrThrowUnprocessableEntity(parentConcept, "Parent code %s not found in file", child);
-				myUnanchoredChildConceptsToParentCodes.put(childConcept, parent);
+
-			} else {
+			parentConcept.addChild(childConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
-				parentConcept.addChild(childConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
-			}
 		}
 	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcDeltaR4Test.java

@@ -2,8 +2,6 @@ package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.context.support.IContextValidationSupport;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
-import ca.uhn.fhir.jpa.entity.TermCodeSystem;
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -12,23 +10,26 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.TestUtil;
-import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.CodeType;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.test.context.TestPropertySource;
 
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
 import java.util.stream.Collectors;
 
 import static org.hamcrest.CoreMatchers.containsString;
-import static org.hamcrest.Matchers.contains;
+import static org.junit.Assert.assertEquals;
-import static org.hamcrest.Matchers.empty;
+import static org.junit.Assert.assertThat;
-import static org.junit.Assert.*;
+import static org.junit.Assert.fail;
 
 public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 	private static final Logger ourLog = LoggerFactory.getLogger(TerminologySvcDeltaR4Test.class);
@@ -114,8 +115,9 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 		});
 
 		delta = new CustomTerminologySet();
-		delta.addUnanchoredChildConcept("RootA", "ChildAA", "Child AA");
+		TermConcept root = delta.addRootConcept("RootA", "Root A");
-		delta.addUnanchoredChildConcept("RootA", "ChildAB", "Child AB");
+		root.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
+		root.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAB").setDisplay("Child AB");
 		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
 		assertHierarchyContains(
 			"RootA seq=1",
@@ -135,25 +137,29 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 
 		delta = new CustomTerminologySet();
 		delta.addRootConcept("RootA", "Root A")
-			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAA").setDisplay("Child AAA");
 		delta.addRootConcept("RootB", "Root B");
 		outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
 		assertHierarchyContains(
 			"RootA seq=1",
 			" ChildAA seq=1",
+			"  ChildAAA seq=1",
 			"RootB seq=2"
 		);
-		assertEquals(3, outcome.getUpdatedConceptCount());
+		assertEquals(4, outcome.getUpdatedConceptCount());
 
 		delta = new CustomTerminologySet();
-		delta.addUnanchoredChildConcept("RootB", "ChildAA", "Child AA");
+		delta.addRootConcept("RootB", "Root B")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
 		outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
-		assertEquals(1, outcome.getUpdatedConceptCount());
 		assertHierarchyContains(
 			"RootA seq=1",
 			"RootB seq=2",
-			" ChildAA seq=1"
+			" ChildAA seq=1",
+			"  ChildAAA seq=1"
 		);
+		assertEquals(2, outcome.getUpdatedConceptCount());
 
 	}
 
@@ -166,11 +172,6 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
 		myCodeSystemDao.create(cs);
 
-		CodeSystem delta = new CodeSystem();
-		delta
-			.addConcept()
-			.setCode("codeA")
-			.setDisplay("displayA");
 		try {
 			myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo", new CustomTerminologySet());
 			fail();
@@ -180,6 +181,44 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testAddChildToExistingChild() {
+		CustomTerminologySet set;
+
+		// Create not-present
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		myCodeSystemDao.create(cs);
+
+		// Add parent with 1 child
+		set = new CustomTerminologySet();
+		set.addRootConcept("ParentA", "Parent A")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildA").setDisplay("Child A");
+		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo", set);
+
+		// Check so far
+		assertHierarchyContains(
+			"ParentA seq=1",
+			" ChildA seq=1"
+		);
+
+		// Add sub-child to existing child
+		ourLog.info("*** Adding child to existing child");
+		set = new CustomTerminologySet();
+		set.addRootConcept("ChildA", "Child A")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
+		myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo", set);
+
+		// Check so far
+		assertHierarchyContains(
+			"ParentA seq=1",
+			" ChildA seq=1",
+			"  ChildAA seq=1"
+		);
+
+	}
+
 	@Test
 	public void testAddWithoutPreExistingCodeSystem() {
 
@@ -229,27 +268,6 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 		assertEquals("CODEA1", myTermSvc.lookupCode(myFhirCtx, "http://foo", "codea").getCodeDisplay());
 	}
 
-	@Test
-	public void testAddUnanchoredWithUnknownParent() {
-		createNotPresentCodeSystem();
-
-		// Add root code
-		CustomTerminologySet delta = new CustomTerminologySet();
-		delta.addRootConcept("CodeA", "Code A");
-		UploadStatistics outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo", delta);
-		assertEquals(1, outcome.getUpdatedConceptCount());
-
-		// Try to add child to nonexistent root code
-		delta = new CustomTerminologySet();
-		delta.addUnanchoredChildConcept("CodeB", "CodeBB", "Code BB");
-		try {
-			myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
-			fail();
-		} catch (InvalidRequestException e) {
-			assertThat(e.getMessage(), containsString("Unable to add code \"CodeBB\" to unknown parent: CodeB"));
-		}
-	}
-
 	@Test
 	public void testAddRelocateHierarchy() {
 		createNotPresentCodeSystem();
@@ -280,9 +298,11 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 		// Move a single child code to a new spot and make sure the hierarchy comes along
 		// for the ride..
 		delta = new CustomTerminologySet();
-		delta.addUnanchoredChildConcept("CodeB", "CodeAA", "Code AA");
+		delta
+			.addRootConcept("CodeB", "Code B")
+			.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAA").setDisplay("Code AA");
 		outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
-		assertEquals(3, outcome.getUpdatedConceptCount());
+		assertEquals(2, outcome.getUpdatedConceptCount());
 		assertHierarchyContains(
 			"CodeA seq=1",
 			"CodeB seq=2",
@@ -431,8 +451,6 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
 	}
 
 
-
-
 	private ValueSet expandNotPresentCodeSystem() {
 		ValueSet vs = new ValueSet();
 		vs.setUrl("http://foo/vs");

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/RenameColumnTask.java

@@ -146,8 +146,6 @@ public class RenameColumnTask extends BaseTableTask<RenameColumnTask> {
 
 		return new EqualsBuilder()
 			.appendSuper(super.equals(theO))
-			.append(myIsOkayIfNeitherColumnExists, that.myIsOkayIfNeitherColumnExists)
-			.append(myDeleteTargetColumnFirstIfBothExist, that.myDeleteTargetColumnFirstIfBothExist)
 			.append(myOldName, that.myOldName)
 			.append(myNewName, that.myNewName)
 			.isEquals();