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Merge remote-tracking branch 'remotes/origin/master' into expunge-hooks 

# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
This commit is contained in:
Ken Stevens 2019-07-12 13:27:11 -04:00
parent b445df3e05 a5a9950e77
commit 8d817b364c
55 changed files with 1810 additions and 979 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

35
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
View File

@ -1401,6 +1401,41 @@ public enum Pointcut {
"ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails"
),
/**
* Invoked when the storage engine is about to reuse the results of
* a previously cached search.
* <p>
* Hooks may accept the following parameters:
* </p>
* <ul>
* <li>
* ca.uhn.fhir.jpa.searchparam.SearchParameterMap - Contains the details of the search being checked
* </li>
* <li>
* ca.uhn.fhir.rest.api.server.RequestDetails - A bean containing details about the request that is about to be processed, including details such as the
* resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
* pulled out of the servlet request. Note that the bean
* properties are not all guaranteed to be populated, depending on how early during processing the
* exception occurred. <b>Note that this parameter may be null in contexts where the request is not
* known, such as while processing searches</b>
* </li>
* <li>
* ca.uhn.fhir.rest.server.servlet.ServletRequestDetails - A bean containing details about the request that is about to be processed, including details such as the
* resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
* pulled out of the servlet request. This parameter is identical to the RequestDetails parameter above but will
* only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
* </li>
* </ul>
* <p>
* Hooks should return <code>void</code>.
* </p>
*/
JPA_PERFTRACE_SEARCH_REUSING_CACHED(boolean.class,
"ca.uhn.fhir.jpa.searchparam.SearchParameterMap",
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails"
),
/**
* Note that this is a performance tracing hook. Use with caution in production
* systems, since calling it may (or may not) carry a cost.

33
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -34,6 +34,7 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.hl7.fhir.instance.model.api.*;
import javax.annotation.Nullable;
import java.io.*;
import java.lang.reflect.Modifier;
import java.util.*;
@ -65,6 +66,7 @@ public abstract class BaseParser implements IParser {
private boolean mySummaryMode;
private boolean mySuppressNarratives;
private Set<String> myDontStripVersionsFromReferencesAtPaths;
/**
* Constructor
*/
@ -165,8 +167,6 @@ public abstract class BaseParser implements IParser {
myNext = null;
} else if (!myNext.shouldBeEncoded(theContainedResource)) {
myNext = null;
} else if (isSummaryMode() && !myNext.getDef().isSummary()) {
myNext = null;
} else if (myNext.getDef() instanceof RuntimeChildNarrativeDefinition) {
if (isSuppressNarratives() || isSummaryMode()) {
myNext = null;
@ -1004,7 +1004,7 @@ public abstract class BaseParser implements IParser {
private final RuntimeResourceDefinition myResDef;
private final EncodeContext myEncodeContext;
public CompositeChildElement(CompositeChildElement theParent, BaseRuntimeChildDefinition theDef, EncodeContext theEncodeContext) {
public CompositeChildElement(CompositeChildElement theParent, @Nullable BaseRuntimeChildDefinition theDef, EncodeContext theEncodeContext) {
myDef = theDef;
myParent = theParent;
myResDef = null;
@ -1015,7 +1015,9 @@ public abstract class BaseParser implements IParser {
StringBuilder path = theParent.buildPath();
if (path != null) {
path.append('.');
if (myDef != null) {
path.append(myDef.getElementName());
}
ourLog.trace(" * Next path: {}", path.toString());
}
}
@ -1165,6 +1167,21 @@ public abstract class BaseParser implements IParser {
if (theContainedResource) {
retVal = !notEncodeForContainedResource.contains(myDef.getElementName());
}
if (retVal && isSummaryMode() && (getDef() == null || !getDef().isSummary())) {
String resourceName = myEncodeContext.getLeafResourceName();
// Technically the spec says we shouldn't include extensions in CapabilityStatement
// but we will do so because there are people who depend on this behaviour, at least
// as of 2019-07. See
// https://github.com/smart-on-fhir/Swift-FHIR/issues/26
// for example.
if (("Conformance".equals(resourceName) || "CapabilityStatement".equals(resourceName)) &&
("extension".equals(myDef.getElementName()) || "extension".equals(myEncodeContext.getLeafElementName())
)) {
// skip
} else {
retVal = false;
}
}
return retVal;
}
@ -1183,7 +1200,7 @@ public abstract class BaseParser implements IParser {
@Override
public String toString() {
return myPath.stream().map(t->t.toString()).collect(Collectors.joining("."));
return myPath.stream().map(t -> t.toString()).collect(Collectors.joining("."));
}
protected List<EncodeContextPathElement> getPath() {
@ -1251,6 +1268,14 @@ public abstract class BaseParser implements IParser {
return myResourcePath;
}
public String getLeafElementName() {
return getPath().get(getPath().size() - 1).getName();
}
public String getLeafResourceName() {
return myResourcePath.get(myResourcePath.size() - 1).getName();
}
public String getLeafResourcePathFirstField() {
String retVal = null;
for (int i = getPath().size() - 1; i >= 0; i--) {

115
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -80,7 +80,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
theListToAddTo.add(null);
}
if (theListToAddTo.get(valueIdx) == null) {
theListToAddTo.set(valueIdx, new ArrayList<String>());
theListToAddTo.set(valueIdx, new ArrayList<>());
}
theListToAddTo.get(valueIdx).addAll(theCommentsToAdd);
return true;
@ -89,21 +89,34 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private boolean addToHeldExtensions(int valueIdx, List<? extends IBaseExtension<?, ?>> ext, ArrayList<ArrayList<HeldExtension>> list, boolean theIsModifier, CompositeChildElement theChildElem,
CompositeChildElement theParent) {
CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource, IBase theContainingElement) {
boolean retVal = false;
if (ext.size() > 0) {
Boolean encodeExtension = null;
for (IBaseExtension<?, ?> next : ext) {
// Make sure we respect _summary and _elements
if (encodeExtension == null) {
encodeExtension = isEncodeExtension(theParent, theEncodeContext, theContainedResource, theContainingElement);
}
if (encodeExtension) {
HeldExtension extension = new HeldExtension(next, theIsModifier, theChildElem, theParent);
list.ensureCapacity(valueIdx);
while (list.size() <= valueIdx) {
list.add(null);
}
if (list.get(valueIdx) == null) {
list.set(valueIdx, new ArrayList<JsonParser.HeldExtension>());
ArrayList<HeldExtension> extensionList = list.get(valueIdx);
if (extensionList == null) {
extensionList = new ArrayList<>();
list.set(valueIdx, extensionList);
}
for (IBaseExtension<?, ?> next : ext) {
list.get(valueIdx).add(new HeldExtension(next, theIsModifier, theChildElem, theParent));
extensionList.add(extension);
retVal = true;
}
return true;
}
return false;
}
return retVal;
}
private void addToHeldIds(int theValueIdx, ArrayList<String> theListToAddTo, String theId) {
@ -342,7 +355,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
if (nextChildElem.getDef().getElementName().equals("extension") || nextChildElem.getDef().getElementName().equals("modifierExtension")
|| nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
if (!haveWrittenExtensions) {
extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent, theEncodeContext);
extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent, theEncodeContext, theContainedResource);
haveWrittenExtensions = true;
}
continue;
@ -433,20 +446,20 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
if (primitive) {
if (nextValue instanceof ISupportsUndeclaredExtensions) {
List<ExtensionDt> ext = ((ISupportsUndeclaredExtensions) nextValue).getUndeclaredExtensions();
force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent);
force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent, theEncodeContext, theContainedResource, theElement);
ext = ((ISupportsUndeclaredExtensions) nextValue).getUndeclaredModifierExtensions();
force |= addToHeldExtensions(valueIdx, ext, modifierExtensions, true, nextChildElem, theParent);
force |= addToHeldExtensions(valueIdx, ext, modifierExtensions, true, nextChildElem, theParent, theEncodeContext, theContainedResource, theElement);
} else {
if (nextValue instanceof IBaseHasExtensions) {
IBaseHasExtensions element = (IBaseHasExtensions) nextValue;
List<? extends IBaseExtension<?, ?>> ext = element.getExtension();
force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent);
force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent, theEncodeContext, theContainedResource, theElement);
}
if (nextValue instanceof IBaseHasModifierExtensions) {
IBaseHasModifierExtensions element = (IBaseHasModifierExtensions) nextValue;
List<? extends IBaseExtension<?, ?>> ext = element.getModifierExtension();
force |= addToHeldExtensions(valueIdx, ext, extensions, true, nextChildElem, theParent);
force |= addToHeldExtensions(valueIdx, ext, extensions, true, nextChildElem, theParent, theEncodeContext, theContainedResource, theElement);
}
}
if (nextValue.hasFormatComment()) {
@ -486,6 +499,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
theEventWriter.endArray();
}
if (!extensions.isEmpty() || !modifierExtensions.isEmpty() || !comments.isEmpty()) {
if (inArray) {
// If this is a repeatable field, the extensions go in an array too
@ -541,7 +555,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
theEventWriter.endArray();
}
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, heldExts, heldModExts, theEncodeContext);
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, heldExts, heldModExts, theEncodeContext, theContainedResource);
if (inArray) {
theEventWriter.endObject();
}
@ -626,7 +640,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
final List<HeldExtension> extensions = new ArrayList<>(0);
final List<HeldExtension> modifierExtensions = new ArrayList<>(0);
// Undeclared extensions
extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null);
extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null, theEncodeContext, theContainedResource);
boolean haveExtension = false;
if (!extensions.isEmpty()) {
haveExtension = true;
@ -638,7 +652,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
writeCommentsPreAndPost(theResourceId, theEventWriter);
}
if (haveExtension) {
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext);
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext, theContainedResource);
}
theEventWriter.endObject();
}
@ -741,12 +755,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
* called _name): resource extensions, and extension extensions
*/
private void extractAndWriteExtensionsAsDirectChild(IBase theElement, JsonLikeWriter theEventWriter, BaseRuntimeElementDefinition<?> theElementDef, RuntimeResourceDefinition theResDef,
IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent, EncodeContext theEncodeContext) throws IOException {
IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
List<HeldExtension> extensions = new ArrayList<>(0);
List<HeldExtension> modifierExtensions = new ArrayList<>(0);
// Undeclared extensions
extractUndeclaredExtensions(theElement, extensions, modifierExtensions, theChildElem, theParent);
extractUndeclaredExtensions(theElement, extensions, modifierExtensions, theChildElem, theParent, theEncodeContext, theContainedResource);
// Declared extensions
if (theElementDef != null) {
@ -754,7 +768,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
// Write the extensions
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext);
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext, theContainedResource);
}
private void extractDeclaredExtensions(IBase theResource, BaseRuntimeElementDefinition<?> resDef, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions,
@ -782,7 +796,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void extractUndeclaredExtensions(IBase theElement, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions, CompositeChildElement theChildElem,
CompositeChildElement theParent) {
CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource) {
if (theElement instanceof ISupportsUndeclaredExtensions) {
ISupportsUndeclaredExtensions element = (ISupportsUndeclaredExtensions) theElement;
List<ExtensionDt> ext = element.getUndeclaredExtensions();
@ -804,11 +818,21 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
if (theElement instanceof IBaseHasExtensions) {
IBaseHasExtensions element = (IBaseHasExtensions) theElement;
List<? extends IBaseExtension<?, ?>> ext = element.getExtension();
Boolean encodeExtension = null;
for (IBaseExtension<?, ?> next : ext) {
if (next == null || (ElementUtil.isEmpty(next.getValue()) && next.getExtension().isEmpty())) {
continue;
}
extensions.add(new HeldExtension(next, false, theChildElem, theParent));
// Make sure we respect _elements and _summary
if (encodeExtension == null) {
encodeExtension = isEncodeExtension(theParent, theEncodeContext, theContainedResource, element);
}
if (encodeExtension) {
HeldExtension extension = new HeldExtension(next, false, theChildElem, theParent);
extensions.add(extension);
}
}
}
if (theElement instanceof IBaseHasModifierExtensions) {
@ -818,12 +842,28 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
if (next == null || next.isEmpty()) {
continue;
}
modifierExtensions.add(new HeldExtension(next, true, theChildElem, theParent));
HeldExtension extension = new HeldExtension(next, true, theChildElem, theParent);
modifierExtensions.add(extension);
}
}
}
}
private boolean isEncodeExtension(CompositeChildElement theParent, EncodeContext theEncodeContext, boolean theContainedResource, IBase theElement) {
// theEncodeContext.pushPath("extension", false);
BaseRuntimeElementDefinition<?> runtimeElementDefinition = myContext.getElementDefinition(theElement.getClass());
boolean retVal = true;
if (runtimeElementDefinition instanceof BaseRuntimeElementCompositeDefinition) {
BaseRuntimeElementCompositeDefinition definition = (BaseRuntimeElementCompositeDefinition) runtimeElementDefinition;
BaseRuntimeChildDefinition childDef = definition.getChildByName("extension");
CompositeChildElement c = new CompositeChildElement(theParent, childDef, theEncodeContext);
retVal = c.shouldBeEncoded(theContainedResource);
}
// theEncodeContext.popPath();
return retVal;
}
@Override
public EncodingEnum getEncoding() {
return EncodingEnum.JSON;
@ -1275,21 +1315,24 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void writeExtensionsAsDirectChild(IBaseResource theResource, JsonLikeWriter theEventWriter, RuntimeResourceDefinition resDef, List<HeldExtension> extensions,
List<HeldExtension> modifierExtensions, EncodeContext theEncodeContext) throws IOException {
List<HeldExtension> modifierExtensions, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
// Write Extensions
if (extensions.isEmpty() == false) {
theEncodeContext.pushPath("extension", false);
beginArray(theEventWriter, "extension");
for (HeldExtension next : extensions) {
next.write(resDef, theResource, theEventWriter, theEncodeContext);
next.write(resDef, theResource, theEventWriter, theEncodeContext, theContainedResource);
}
theEventWriter.endArray();
theEncodeContext.popPath();
}
// Write ModifierExtensions
if (modifierExtensions.isEmpty() == false) {
theEncodeContext.pushPath("modifierExtension", false);
beginArray(theEventWriter, "modifierExtension");
for (HeldExtension next : modifierExtensions) {
next.write(resDef, theResource, theEventWriter, theEncodeContext);
next.write(resDef, theResource, theEventWriter, theEncodeContext, theContainedResource);
}
theEventWriter.endArray();
theEncodeContext.popPath();
@ -1353,12 +1396,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
return url1.compareTo(url2);
}
private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName, EncodeContext theEncodeContext) throws IOException {
private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
// Undeclared extensions
extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null);
extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null, theEncodeContext, theContainedResource);
// Declared extensions
if (def != null) {
extractDeclaredExtensions(theValue, def, extensions, modifierExtensions, myParent);
@ -1369,15 +1412,15 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
if (haveContent) {
beginObject(theEventWriter, '_' + childName);
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext);
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions, theEncodeContext, theContainedResource);
theEventWriter.endObject();
}
}
}
public void write(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, EncodeContext theEncodeContext) throws IOException {
public void write(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
if (myUndeclaredExtension != null) {
writeUndeclaredExtension(theResDef, theResource, theEventWriter, myUndeclaredExtension, theEncodeContext);
writeUndeclaredExtension(theResDef, theResource, theEventWriter, myUndeclaredExtension, theEncodeContext, theContainedResource);
} else {
theEventWriter.beginObject();
@ -1410,18 +1453,18 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
BaseRuntimeElementDefinition<?> def = myDef.getChildElementDefinitionByDatatype(myValue.getClass());
if (def.getChildType() == ChildTypeEnum.RESOURCE_BLOCK) {
extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem, null, theEncodeContext);
extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem, null, theEncodeContext, theContainedResource);
} else {
String childName = myDef.getChildNameByDatatype(myValue.getClass());
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false, myParent, false, theEncodeContext);
managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName, theEncodeContext);
managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName, theEncodeContext, theContainedResource);
}
theEventWriter.endObject();
}
}
private void writeUndeclaredExtension(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, IBaseExtension<?, ?> ext, EncodeContext theEncodeContext) throws IOException {
private void writeUndeclaredExtension(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, IBaseExtension<?, ?> ext, EncodeContext theEncodeContext, boolean theContainedResource) throws IOException {
IBase value = ext.getValue();
final String extensionUrl = getExtensionUrl(ext.getUrl());
@ -1465,7 +1508,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
for (Object next : ext.getExtension()) {
writeUndeclaredExtension(theResDef, theResource, theEventWriter, (IBaseExtension<?, ?>) next, theEncodeContext);
writeUndeclaredExtension(theResDef, theResource, theEventWriter, (IBaseExtension<?, ?>) next, theEncodeContext, theContainedResource);
}
theEventWriter.endArray();
@ -1473,6 +1516,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
// Write value
if (!noValue) {
theEncodeContext.pushPath("value", false);
/*
* Pre-process value - This is called in case the value is a reference
@ -1490,8 +1534,9 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
}
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, false, myParent,false, theEncodeContext);
managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName, theEncodeContext);
managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName, theEncodeContext, theContainedResource);
theEncodeContext.popPath();
}
}

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
View File

@ -51,15 +51,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* This class is the FHIR XML parser/encoder. Users should not interact with this class directly, but should use
* {@link FhirContext#newXmlParser()} to get an instance.
*/
public class XmlParser extends BaseParser /* implements IParser */ {
public class XmlParser extends BaseParser {
static final String ATOM_NS = "http://www.w3.org/2005/Atom";
static final String FHIR_NS = "http://hl7.org/fhir";
static final String OPENSEARCH_NS = "http://a9.com/-/spec/opensearch/1.1/";
static final String RESREF_DISPLAY = "display";
static final String RESREF_REFERENCE = "reference";
static final String TOMBSTONES_NS = "http://purl.org/atompub/tombstones/1.0";
static final String XHTML_NS = "http://www.w3.org/1999/xhtml";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParser.class);
// private static final Set<String> RESOURCE_NAMESPACES;

16
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ValidateUtil.java
View File

@ -23,7 +23,7 @@ package ca.uhn.fhir.util;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.*;
public class ValidateUtil {
@ -37,7 +37,7 @@ public class ValidateUtil {
}
/**
* Throws {@link IllegalArgumentException} if theValue is <= theMinimum
* Throws {@link IllegalArgumentException} if theValue is < theMinimum
*/
public static void isGreaterThanOrEqualTo(long theValue, long theMinimum, String theMessage) {
if (theValue < theMinimum) {
@ -45,6 +45,12 @@ public class ValidateUtil {
}
}
public static void isNotBlankOrThrowIllegalArgument(String theString, String theMessage) {
if (isBlank(theString)) {
throw new IllegalArgumentException(theMessage);
}
}
public static void isNotBlankOrThrowInvalidRequest(String theString, String theMessage) {
if (isBlank(theString)) {
throw new InvalidRequestException(theMessage);
@ -57,6 +63,12 @@ public class ValidateUtil {
}
}
public static void isNotTooLongOrThrowIllegalArgument(String theString, int theMaxLength, String theMessage) {
if (length(theString) > theMaxLength) {
throw new IllegalArgumentException(theMessage);
}
}
public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage) {
if (theSuccess == false) {
throw new InvalidRequestException(theMessage);

2
hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseHasExtensions.java
View File

@ -22,7 +22,7 @@ package org.hl7.fhir.instance.model.api;
import java.util.List;
public interface IBaseHasExtensions {
public interface IBaseHasExtensions extends IBase {
IBaseExtension<?, ?> addExtension();

3
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -115,8 +115,9 @@ ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor.noParam=Note that cascadi
ca.uhn.fhir.jpa.provider.BaseJpaProvider.cantCombintAtAndSince=Unable to combine _at and _since parameters for history operation
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}

32
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
View File

@ -145,6 +145,10 @@ public class DaoConfig {
private boolean myEnableInMemorySubscriptionMatching = true;
private boolean myEnforceReferenceTargetTypes = true;
private ClientIdStrategyEnum myResourceClientIdStrategy = ClientIdStrategyEnum.ALPHANUMERIC;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code false}!
*/
private boolean myPreExpandValueSetsExperimental = false;
/**
* Constructor
@ -1600,6 +1604,34 @@ public class DaoConfig {
myModelConfig.setWebsocketContextPath(theWebsocketContextPath);
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
* future optimization of the $expand operation on large ValueSets.
* </p>
* <p>
* The default value for this setting is {@code false}.
* </p>
*/
public boolean isPreExpandValueSetsExperimental() {
return myPreExpandValueSetsExperimental;
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
* future optimization of the $expand operation on large ValueSets.
* </p>
* <p>
* The default value for this setting is {@code false}.
* </p>
*/
public void setPreExpandValueSetsExperimental(boolean thePreExpandValueSetsExperimental) {
myPreExpandValueSetsExperimental = thePreExpandValueSetsExperimental;
}
public enum IndexEnabledEnum {
ENABLED,
DISABLED

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
View File

@ -32,6 +32,7 @@ import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.model.util.StringNormalizer;
import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
@ -60,7 +61,6 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
@ -113,10 +113,6 @@ public class SearchBuilder implements ISearchBuilder {
*/
private static final int MAXIMUM_PAGE_SIZE = 800;
private static Long NO_MORE = -1L;
private static HandlerTypeEnum ourLastHandlerMechanismForUnitTest;
private static SearchParameterMap ourLastHandlerParamsForUnitTest;
private static String ourLastHandlerThreadForUnitTest;
private static boolean ourTrackHandlersForUnitTest;
private final boolean myDontUseHashesForSearch;
private final DaoConfig myDaoConfig;
@Autowired
@ -1546,12 +1542,6 @@ public class SearchBuilder implements ISearchBuilder {
myBuilder = myEntityManager.getCriteriaBuilder();
mySearchUuid = theSearchRuntimeDetails.getSearchUuid();
if (ourTrackHandlersForUnitTest) {
ourLastHandlerParamsForUnitTest = theParams;
ourLastHandlerMechanismForUnitTest = HandlerTypeEnum.STANDARD_QUERY;
ourLastHandlerThreadForUnitTest = Thread.currentThread().getName();
}
if (myPidSet == null) {
myPidSet = new HashSet<>();
}
@ -2214,9 +2204,16 @@ public class SearchBuilder implements ISearchBuilder {
if (sb != null) {
String indexString = sb.toString();
ourLog.debug("Checking for unique index for query: {}", indexString);
if (ourTrackHandlersForUnitTest) {
ourLastHandlerMechanismForUnitTest = HandlerTypeEnum.UNIQUE_INDEX;
}
// Interceptor broadcast: JPA_PERFTRACE_INFO
StorageProcessingMessage msg = new StorageProcessingMessage()
.setMessage("Using unique index for query for search: " + indexString);
HookParams params = new HookParams()
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(StorageProcessingMessage.class, msg);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.JPA_PERFTRACE_INFO, params);
addPredicateCompositeStringUnique(theParams, indexString);
}
}
@ -2788,24 +2785,6 @@ public class SearchBuilder implements ISearchBuilder {
return query.getResultList();
}
@VisibleForTesting
public static HandlerTypeEnum getLastHandlerMechanismForUnitTest() {
return ourLastHandlerMechanismForUnitTest;
}
@VisibleForTesting
public static String getLastHandlerParamsForUnitTest() {
return ourLastHandlerParamsForUnitTest.toString() + " on thread [" + ourLastHandlerThreadForUnitTest + "]";
}
@VisibleForTesting
public static void resetLastHandlerMechanismForUnitTest() {
ourLastHandlerMechanismForUnitTest = null;
ourLastHandlerParamsForUnitTest = null;
ourLastHandlerThreadForUnitTest = null;
ourTrackHandlersForUnitTest = true;
}
private static Predicate[] toArray(List<Predicate> thePredicates) {
return thePredicates.toArray(new Predicate[0]);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermCodeSystemDao.java
View File

@ -34,7 +34,7 @@ public interface ITermCodeSystemDao extends JpaRepository<TermCodeSystem, Long>
TermCodeSystem findByCodeSystemUri(@Param("code_system_uri") String theCodeSystemUri);
@Query("SELECT cs FROM TermCodeSystem cs WHERE cs.myResourcePid = :resource_pid")
TermCodeSystem findByResourcePid(@Param("resource_pid") Long theReourcePid);
TermCodeSystem findByResourcePid(@Param("resource_pid") Long theResourcePid);
@Query("SELECT cs FROM TermCodeSystem cs WHERE cs.myCurrentVersion.myId = :csv_pid")
Optional<TermCodeSystem> findWithCodeSystemVersionAsCurrentVersion(@Param("csv_pid") Long theCodeSystemVersionPid);

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetCodeDao.java Normal file
View File

@ -0,0 +1,35 @@
package ca.uhn.fhir.jpa.dao.data;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.entity.TermValueSetCode;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
public interface ITermValueSetCodeDao extends JpaRepository<TermValueSetCode, Long> {
@Query("DELETE FROM TermValueSetCode vsc WHERE vsc.myValueSet.myId = :pid")
@Modifying
void deleteTermValueSetCodesByValueSetId(@Param("pid") Long theValueSetId);
}

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java Normal file
View File

@ -0,0 +1,43 @@
package ca.uhn.fhir.jpa.dao.data;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.entity.TermValueSet;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import java.util.Optional;
public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
@Query("DELETE FROM TermValueSet vs WHERE vs.myId = :pid")
@Modifying
void deleteTermValueSetById(@Param("pid") Long theId);
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myResourcePid = :resource_pid")
Optional<TermValueSet> findByResourcePid(@Param("resource_pid") Long theResourcePid);
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url")
Optional<TermValueSet> findByUrl(@Param("url") String theUrl);
}

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -23,11 +23,15 @@ package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
@ -37,6 +41,8 @@ import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
@ -45,14 +51,18 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
@Autowired
@Qualifier("myJpaValidationSupportChainDstu3")
private IValidationSupport myValidationSupport;
@ -295,4 +305,26 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
// nothing
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (retVal.getDeleted() == null) {
try {
ValueSet valueSet = (ValueSet) theResource;
org.hl7.fhir.r4.model.ValueSet converted = VersionConvertor_30_40.convertValueSet(valueSet);
myHapiTerminologySvc.storeTermValueSetAndChildren(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
}
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
}
}
return retVal;
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
View File

@ -96,6 +96,8 @@ public class ExpungeEverythingService {
counter.addAndGet(expungeEverythingByType(ResourceLink.class));
counter.addAndGet(expungeEverythingByType(SearchResult.class));
counter.addAndGet(expungeEverythingByType(SearchInclude.class));
counter.addAndGet(expungeEverythingByType(TermValueSetCode.class));
counter.addAndGet(expungeEverythingByType(TermValueSet.class));
counter.addAndGet(expungeEverythingByType(TermConceptParentChildLink.class));
counter.addAndGet(expungeEverythingByType(TermConceptMapGroupElementTarget.class));
counter.addAndGet(expungeEverythingByType(TermConceptMapGroupElement.class));

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
View File

@ -57,6 +57,14 @@ public class IdHelperService {
myForcedIdDao.delete(forcedId);
}
/**
* @throws ResourceNotFoundException If the ID can not be found
*/
@Nonnull
public Long translateForcedIdToPid(IIdType theId, RequestDetails theRequestDetails) {
return translateForcedIdToPid(theId.getResourceType(), theId.getIdPart(), theRequestDetails);
}
/**
* @throws ResourceNotFoundException If the ID can not be found
*/

62
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -20,34 +20,43 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.Collections;
import java.util.List;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.ValueSet.*;
import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
@Autowired
@Qualifier("myJpaValidationSupportChainR4")
private IValidationSupport myValidationSupport;
@ -296,4 +305,21 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
// nothing
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSetAndChildren(retVal, valueSet);
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
}
}
return retVal;
}
}

28
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java
View File

@ -21,13 +21,16 @@ package ca.uhn.fhir.jpa.entity;
*/
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
//@formatter:off
@Table(name = "TRM_CODESYSTEM", uniqueConstraints = {
@ -37,9 +40,11 @@ import static org.apache.commons.lang3.StringUtils.left;
//@formatter:on
public class TermCodeSystem implements Serializable {
private static final long serialVersionUID = 1L;
public static final int CS_NAME_LENGTH = 200;
@Column(name = "CODE_SYSTEM_URI", nullable = false)
private static final int MAX_NAME_LENGTH = 200;
public static final int MAX_URL_LENGTH = 200;
@Column(name = "CODE_SYSTEM_URI", nullable = false, length = MAX_URL_LENGTH)
private String myCodeSystemUri;
@OneToOne()
@ -55,7 +60,7 @@ public class TermCodeSystem implements Serializable {
private ResourceTable myResource;
@Column(name = "RES_ID", insertable = false, updatable = false)
private Long myResourcePid;
@Column(name = "CS_NAME", nullable = true)
@Column(name = "CS_NAME", nullable = true, length = MAX_NAME_LENGTH)
private String myName;
public String getCodeSystemUri() {
@ -66,16 +71,21 @@ public class TermCodeSystem implements Serializable {
return myName;
}
public void setCodeSystemUri(String theCodeSystemUri) {
public TermCodeSystem setCodeSystemUri(@Nonnull String theCodeSystemUri) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCodeSystemUri, "theCodeSystemUri must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCodeSystemUri, MAX_URL_LENGTH,
"URI exceeds maximum length (" + MAX_URL_LENGTH + "): " + length(theCodeSystemUri));
myCodeSystemUri = theCodeSystemUri;
return this;
}
public TermCodeSystemVersion getCurrentVersion() {
return myCurrentVersion;
}
public void setCurrentVersion(TermCodeSystemVersion theCurrentVersion) {
public TermCodeSystem setCurrentVersion(TermCodeSystemVersion theCurrentVersion) {
myCurrentVersion = theCurrentVersion;
return this;
}
public Long getPid() {
@ -86,12 +96,14 @@ public class TermCodeSystem implements Serializable {
return myResource;
}
public void setName(String theName) {
myName = left(theName, CS_NAME_LENGTH);
public TermCodeSystem setName(String theName) {
myName = left(theName, MAX_NAME_LENGTH);
return this;
}
public void setResource(ResourceTable theResource) {
public TermCodeSystem setResource(ResourceTable theResource) {
myResource = theResource;
return this;
}
@Override

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java
View File

@ -22,12 +22,15 @@ package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ValidateUtil;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import static org.apache.commons.lang3.StringUtils.length;
//@formatter:off
@Table(name = "TRM_CODESYSTEM_VER"
// Note, we used to have a constraint named IDX_CSV_RESOURCEPID_AND_VER (don't reuse this)
@ -37,6 +40,8 @@ import java.util.Collection;
public class TermCodeSystemVersion implements Serializable {
private static final long serialVersionUID = 1L;
static final int MAX_VERSION_LENGTH = 200;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myCodeSystem")
private Collection<TermConcept> myConcepts;
@ -50,7 +55,7 @@ public class TermCodeSystemVersion implements Serializable {
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CODESYSVER_RES_ID"))
private ResourceTable myResource;
@Column(name = "CS_VERSION_ID", nullable = true, updatable = false)
@Column(name = "CS_VERSION_ID", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)
private String myCodeSystemVersionId;
/**
* This was added in HAPI FHIR 3.3.0 and is nullable just to avoid migration
@ -104,16 +109,21 @@ public class TermCodeSystemVersion implements Serializable {
return myCodeSystem;
}
public void setCodeSystem(TermCodeSystem theCodeSystem) {
public TermCodeSystemVersion setCodeSystem(TermCodeSystem theCodeSystem) {
myCodeSystem = theCodeSystem;
return this;
}
public String getCodeSystemVersionId() {
return myCodeSystemVersionId;
}
public void setCodeSystemVersionId(String theCodeSystemVersionId) {
public TermCodeSystemVersion setCodeSystemVersionId(String theCodeSystemVersionId) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(
theCodeSystemVersionId, MAX_VERSION_LENGTH,
"Version ID exceeds maximum length (" + MAX_VERSION_LENGTH + "): " + length(theCodeSystemVersionId));
myCodeSystemVersionId = theCodeSystemVersionId;
return this;
}
public Collection<TermConcept> getConcepts() {
@ -131,8 +141,9 @@ public class TermCodeSystemVersion implements Serializable {
return myResource;
}
public void setResource(ResourceTable theResource) {
public TermCodeSystemVersion setResource(ResourceTable theResource) {
myResource = theResource;
return this;
}
@Override

77
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -1,25 +1,5 @@
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;
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 javax.annotation.Nonnull;
import javax.persistence.*;
import javax.persistence.Index;
import java.io.Serializable;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
* HAPI FHIR JPA Server
@ -40,6 +20,27 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* #L%
*/
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;
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 javax.annotation.Nonnull;
import javax.persistence.Index;
import javax.persistence.*;
import java.io.Serializable;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Indexed(interceptor = DeferConceptIndexingInterceptor.class)
@Table(name = "TRM_CONCEPT", uniqueConstraints = {
@ -49,16 +50,17 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
@Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
})
public class TermConcept implements Serializable {
public static final int CODE_LENGTH = 500;
protected static final int MAX_DESC_LENGTH = 400;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
private static final long serialVersionUID = 1L;
public static final int MAX_CODE_LENGTH = 500;
public static final int MAX_DESC_LENGTH = 400;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade = {})
private Collection<TermConceptParentChildLink> myChildren;
@Column(name = "CODE", length = CODE_LENGTH, nullable = false)
@Column(name = "CODE", nullable = false, length = MAX_CODE_LENGTH)
@Fields({@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),})
private String myCode;
@Temporal(TemporalType.TIMESTAMP)
@ -70,7 +72,7 @@ public class TermConcept implements Serializable {
@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
@Fields({@Field(name = "myCodeSystemVersionPid")})
private long myCodeSystemVersionPid;
@Column(name = "DISPLAY", length = MAX_DESC_LENGTH, nullable = true)
@Column(name = "DISPLAY", nullable = true, length = MAX_DESC_LENGTH)
@Fields({
@Field(name = "myDisplay", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
@Field(name = "myDisplayEdgeNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteEdgeAnalyzer")),
@ -187,20 +189,24 @@ public class TermConcept implements Serializable {
return myCode;
}
public void setCode(String theCode) {
ValidateUtil.isNotBlankOrThrowInvalidRequest(theCode, "Code must not be null or empty");
public TermConcept setCode(@Nonnull String theCode) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, MAX_CODE_LENGTH,
"Code exceeds maximum length (" + MAX_CODE_LENGTH + "): " + length(theCode));
myCode = theCode;
return this;
}
public TermCodeSystemVersion getCodeSystemVersion() {
return myCodeSystem;
}
public void setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
public TermConcept setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
myCodeSystem = theCodeSystemVersion;
if (theCodeSystemVersion.getPid() != null) {
myCodeSystemVersionPid = theCodeSystemVersion.getPid();
}
return this;
}
public List<Coding> getCodingProperties(String thePropertyName) {
@ -231,10 +237,7 @@ public class TermConcept implements Serializable {
}
public TermConcept setDisplay(String theDisplay) {
myDisplay = theDisplay;
if (isNotBlank(theDisplay) && theDisplay.length() > MAX_DESC_LENGTH) {
myDisplay = myDisplay.substring(0, MAX_DESC_LENGTH);
}
myDisplay = left(theDisplay, MAX_DESC_LENGTH);
return this;
}
@ -246,8 +249,9 @@ public class TermConcept implements Serializable {
return myIndexStatus;
}
public void setIndexStatus(Long theIndexStatus) {
public TermConcept setIndexStatus(Long theIndexStatus) {
myIndexStatus = theIndexStatus;
return this;
}
public String getParentPidsAsString() {
@ -272,8 +276,9 @@ public class TermConcept implements Serializable {
return mySequence;
}
public void setSequence(Integer theSequence) {
public TermConcept setSequence(Integer theSequence) {
mySequence = theSequence;
return this;
}
public List<String> getStringProperties(String thePropertyName) {
@ -300,8 +305,9 @@ public class TermConcept implements Serializable {
return myUpdated;
}
public void setUpdated(Date theUpdated) {
public TermConcept setUpdated(Date theUpdated) {
myUpdated = theUpdated;
return this;
}
@Override
@ -355,8 +361,9 @@ public class TermConcept implements Serializable {
myParentPids = b.toString();
}
public void setParentPids(String theParentPids) {
public TermConcept setParentPids(String theParentPids) {
myParentPids = theParentPids;
return this;
}
@Override

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java
View File

@ -20,16 +20,24 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.util.ValidateUtil;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_DESIG", uniqueConstraints = {
}, indexes = {
})
public class TermConceptDesignation implements Serializable {
private static final long serialVersionUID = 1L;
private static final int MAX_LENGTH = 500;
@ManyToOne
@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTDESIG_CONCEPT"))
private TermConcept myConcept;
@ -38,15 +46,15 @@ public class TermConceptDesignation implements Serializable {
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_DESIG_PID")
@Column(name = "PID")
private Long myId;
@Column(name = "LANG", length = 500, nullable = true)
@Column(name = "LANG", nullable = true, length = MAX_LENGTH)
private String myLanguage;
@Column(name = "USE_SYSTEM", length = 500, nullable = true)
@Column(name = "USE_SYSTEM", nullable = true, length = MAX_LENGTH)
private String myUseSystem;
@Column(name = "USE_CODE", length = 500, nullable = true)
@Column(name = "USE_CODE", nullable = true, length = MAX_LENGTH)
private String myUseCode;
@Column(name = "USE_DISPLAY", length = 500, nullable = true)
@Column(name = "USE_DISPLAY", nullable = true, length = MAX_LENGTH)
private String myUseDisplay;
@Column(name = "VAL", length = 500, nullable = false)
@Column(name = "VAL", nullable = false, length = MAX_LENGTH)
private String myValue;
/**
* TODO: Make this non-null
@ -62,6 +70,8 @@ public class TermConceptDesignation implements Serializable {
}
public TermConceptDesignation setLanguage(String theLanguage) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theLanguage, MAX_LENGTH,
"Language exceeds maximum length (" + MAX_LENGTH + "): " + length(theLanguage));
myLanguage = theLanguage;
return this;
}
@ -71,6 +81,8 @@ public class TermConceptDesignation implements Serializable {
}
public TermConceptDesignation setUseCode(String theUseCode) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUseCode, MAX_LENGTH,
"Use code exceeds maximum length (" + MAX_LENGTH + "): " + length(theUseCode));
myUseCode = theUseCode;
return this;
}
@ -80,7 +92,7 @@ public class TermConceptDesignation implements Serializable {
}
public TermConceptDesignation setUseDisplay(String theUseDisplay) {
myUseDisplay = theUseDisplay;
myUseDisplay = left(theUseDisplay, MAX_LENGTH);
return this;
}
@ -89,6 +101,9 @@ public class TermConceptDesignation implements Serializable {
}
public TermConceptDesignation setUseSystem(String theUseSystem) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUseSystem, MAX_LENGTH,
"Use system exceeds maximum length (" + MAX_LENGTH + "): " + length(theUseSystem));
myUseSystem = theUseSystem;
return this;
}
@ -97,7 +112,10 @@ public class TermConceptDesignation implements Serializable {
return myValue;
}
public TermConceptDesignation setValue(String theValue) {
public TermConceptDesignation setValue(@Nonnull String theValue) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theValue, "theValue must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theValue, MAX_LENGTH,
"Value exceeds maximum length (" + MAX_LENGTH + "): " + length(theValue));
myValue = theValue;
return this;
}

47
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMap.java
View File

@ -21,19 +21,27 @@ package ca.uhn.fhir.jpa.entity;
*/
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_MAP", uniqueConstraints = {
@UniqueConstraint(name = "IDX_CONCEPT_MAP_URL", columnNames = {"URL"})
})
public class TermConceptMap implements Serializable {
private static final long serialVersionUID = 1L;
static final int MAX_URL_LENGTH = 200;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_MAP_PID", sequenceName = "SEQ_CONCEPT_MAP_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_MAP_PID")
@ -47,13 +55,13 @@ public class TermConceptMap implements Serializable {
@Column(name = "RES_ID", insertable = false, updatable = false)
private Long myResourcePid;
@Column(name = "SOURCE_URL", nullable = true, length = 200)
@Column(name = "SOURCE_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String mySource;
@Column(name = "TARGET_URL", nullable = true, length = 200)
@Column(name = "TARGET_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String myTarget;
@Column(name = "URL", length = 200, nullable = false)
@Column(name = "URL", nullable = false, length = MAX_URL_LENGTH)
private String myUrl;
@OneToMany(mappedBy = "myConceptMap")
@ -75,47 +83,58 @@ public class TermConceptMap implements Serializable {
return myResource;
}
public void setResource(ResourceTable resource) {
myResource = resource;
public TermConceptMap setResource(ResourceTable theResource) {
myResource = theResource;
return this;
}
public Long getResourcePid() {
return myResourcePid;
}
public void setResourcePid(Long resourcePid) {
myResourcePid = resourcePid;
public TermConceptMap setResourcePid(Long theResourcePid) {
myResourcePid = theResourcePid;
return this;
}
public String getSource() {
return mySource;
}
public void setSource(String source) {
mySource = source;
public TermConceptMap setSource(String theSource) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSource, TermValueSet.MAX_URL_LENGTH,
"Source exceeds maximum length (" + TermValueSet.MAX_URL_LENGTH + "): " + length(theSource));
mySource = theSource;
return this;
}
public String getTarget() {
return myTarget;
}
public void setTarget(String target) {
myTarget = target;
public TermConceptMap setTarget(String theTarget) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theTarget, TermValueSet.MAX_URL_LENGTH,
"Target exceeds maximum length (" + TermValueSet.MAX_URL_LENGTH + "): " + length(theTarget));
myTarget = theTarget;
return this;
}
public String getUrl() {
return myUrl;
}
public void setUrl(String theUrl) {
public TermConceptMap setUrl(@Nonnull String theUrl) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theUrl, "theUrl must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUrl, MAX_URL_LENGTH,
"URL exceeds maximum length (" + MAX_URL_LENGTH + "): " + length(theUrl));
myUrl = theUrl;
return this;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append("myResource", myResource.toString())
.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
.append("myResourcePid", myResourcePid)
.append("mySource", mySource)

47
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroup.java
View File

@ -20,17 +20,23 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_MAP_GROUP")
public class TermConceptMapGroup implements Serializable {
private static final long serialVersionUID = 1L;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_MAP_GROUP_PID", sequenceName = "SEQ_CONCEPT_MAP_GROUP_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_MAP_GROUP_PID")
@ -41,36 +47,37 @@ public class TermConceptMapGroup implements Serializable {
@JoinColumn(name = "CONCEPT_MAP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGROUP_CONCEPTMAP"))
private TermConceptMap myConceptMap;
@Column(name = "SOURCE_URL", nullable = false, length = 200)
@Column(name = "SOURCE_URL", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
private String mySource;
@Column(name = "SOURCE_VERSION", length = 100)
@Column(name = "SOURCE_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
private String mySourceVersion;
@Column(name = "TARGET_URL", nullable = false, length = 200)
@Column(name = "TARGET_URL", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
private String myTarget;
@Column(name = "TARGET_VERSION", length = 100)
@Column(name = "TARGET_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
private String myTargetVersion;
@OneToMany(mappedBy = "myConceptMapGroup")
private List<TermConceptMapGroupElement> myConceptMapGroupElements;
@Column(name= "CONCEPT_MAP_URL", length = 200, nullable = true)
@Column(name= "CONCEPT_MAP_URL", nullable = true, length = TermConceptMap.MAX_URL_LENGTH)
private String myConceptMapUrl;
@Column(name= "SOURCE_VS", length = 200, nullable = true)
@Column(name= "SOURCE_VS", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String mySourceValueSet;
@Column(name= "TARGET_VS", length = 200, nullable = true)
@Column(name= "TARGET_VS", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String myTargetValueSet;
public TermConceptMap getConceptMap() {
return myConceptMap;
}
public void setConceptMap(TermConceptMap theTermConceptMap) {
public TermConceptMapGroup setConceptMap(TermConceptMap theTermConceptMap) {
myConceptMap = theTermConceptMap;
return this;
}
public List<TermConceptMapGroupElement> getConceptMapGroupElements() {
@ -96,8 +103,12 @@ public class TermConceptMapGroup implements Serializable {
return mySource;
}
public void setSource(String theSource) {
public TermConceptMapGroup setSource(@Nonnull String theSource) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theSource, "theSource must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSource, TermCodeSystem.MAX_URL_LENGTH,
"Source exceeds maximum length (" + TermCodeSystem.MAX_URL_LENGTH + "): " + length(theSource));
this.mySource = theSource;
return this;
}
public String getSourceValueSet() {
@ -111,16 +122,23 @@ public class TermConceptMapGroup implements Serializable {
return mySourceVersion;
}
public void setSourceVersion(String theSourceVersion) {
public TermConceptMapGroup setSourceVersion(String theSourceVersion) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSourceVersion, TermCodeSystemVersion.MAX_VERSION_LENGTH,
"Source version ID exceeds maximum length (" + TermCodeSystemVersion.MAX_VERSION_LENGTH + "): " + length(theSourceVersion));
mySourceVersion = theSourceVersion;
return this;
}
public String getTarget() {
return myTarget;
}
public void setTarget(String theTarget) {
public TermConceptMapGroup setTarget(@Nonnull String theTarget) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theTarget, "theTarget must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theTarget, TermCodeSystem.MAX_URL_LENGTH,
"Target exceeds maximum length (" + TermCodeSystem.MAX_URL_LENGTH + "): " + length(theTarget));
this.myTarget = theTarget;
return this;
}
public String getTargetValueSet() {
@ -134,13 +152,16 @@ public class TermConceptMapGroup implements Serializable {
return myTargetVersion;
}
public void setTargetVersion(String theTargetVersion) {
public TermConceptMapGroup setTargetVersion(String theTargetVersion) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theTargetVersion, TermCodeSystemVersion.MAX_VERSION_LENGTH,
"Target version ID exceeds maximum length (" + TermCodeSystemVersion.MAX_VERSION_LENGTH + "): " + length(theTargetVersion));
myTargetVersion = theTargetVersion;
return this;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConceptMap != null ? ("myConceptMap - id=" + myConceptMap.getId()) : ("myConceptMap=(null)"))
.append("mySource", mySource)

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElement.java
View File

@ -20,22 +20,28 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import org.apache.commons.lang3.Validate;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_MAP_GRP_ELEMENT", indexes = {
@Index(name = "IDX_CNCPT_MAP_GRP_CD", columnList = "SOURCE_CODE")
})
public class TermConceptMapGroupElement implements Serializable {
private static final long serialVersionUID = 1L;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_MAP_GRP_ELM_PID", sequenceName = "SEQ_CONCEPT_MAP_GRP_ELM_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_MAP_GRP_ELM_PID")
@ -46,7 +52,7 @@ public class TermConceptMapGroupElement implements Serializable {
@JoinColumn(name = "CONCEPT_MAP_GROUP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGELEMENT_GROUP"))
private TermConceptMapGroup myConceptMapGroup;
@Column(name = "SOURCE_CODE", nullable = false, length = TermConcept.CODE_LENGTH)
@Column(name = "SOURCE_CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
private String myCode;
@Column(name = "SOURCE_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)
@ -55,33 +61,37 @@ public class TermConceptMapGroupElement implements Serializable {
@OneToMany(mappedBy = "myConceptMapGroupElement")
private List<TermConceptMapGroupElementTarget> myConceptMapGroupElementTargets;
@Column(name = "CONCEPT_MAP_URL", length = 200)
@Column(name = "CONCEPT_MAP_URL", nullable = true, length = TermConceptMap.MAX_URL_LENGTH)
private String myConceptMapUrl;
@Column(name = "SYSTEM_URL", length = 200)
@Column(name = "SYSTEM_URL", nullable = true, length = TermCodeSystem.MAX_URL_LENGTH)
private String mySystem;
@Column(name = "SYSTEM_VERSION", length = 200)
@Column(name = "SYSTEM_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
private String mySystemVersion;
@Column(name = "VALUESET_URL", length = 200)
@Column(name = "VALUESET_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String myValueSet;
public String getCode() {
return myCode;
}
public void setCode(String theCode) {
Validate.notBlank(theCode, "theCode must not be blank");
public TermConceptMapGroupElement setCode(@Nonnull String theCode) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, TermConcept.MAX_CODE_LENGTH,
"Code exceeds maximum length (" + TermConcept.MAX_CODE_LENGTH + "): " + length(theCode));
myCode = theCode;
return this;
}
public TermConceptMapGroup getConceptMapGroup() {
return myConceptMapGroup;
}
public void setConceptMapGroup(TermConceptMapGroup theTermConceptMapGroup) {
public TermConceptMapGroupElement setConceptMapGroup(TermConceptMapGroup theTermConceptMapGroup) {
myConceptMapGroup = theTermConceptMapGroup;
return this;
}
public List<TermConceptMapGroupElementTarget> getConceptMapGroupElementTargets() {
@ -103,8 +113,9 @@ public class TermConceptMapGroupElement implements Serializable {
return myDisplay;
}
public void setDisplay(String theDisplay) {
myDisplay = theDisplay;
public TermConceptMapGroupElement setDisplay(String theDisplay) {
myDisplay = left(theDisplay, TermConcept.MAX_DESC_LENGTH);
return this;
}
public Long getId() {
@ -158,7 +169,7 @@ public class TermConceptMapGroupElement implements Serializable {
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConceptMapGroup != null ? ("myConceptMapGroup - id=" + myConceptMapGroup.getId()) : ("myConceptMapGroup=(null)"))
.append("myCode", myCode)

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElementTarget.java
View File

@ -20,20 +20,28 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_MAP_GRP_ELM_TGT", indexes = {
@Index(name = "IDX_CNCPT_MP_GRP_ELM_TGT_CD", columnList = "TARGET_CODE")
})
public class TermConceptMapGroupElementTarget implements Serializable {
private static final long serialVersionUID = 1L;
static final int MAX_EQUIVALENCE_LENGTH = 50;
@Id()
@SequenceGenerator(name = "SEQ_CNCPT_MAP_GRP_ELM_TGT_PID", sequenceName = "SEQ_CNCPT_MAP_GRP_ELM_TGT_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CNCPT_MAP_GRP_ELM_TGT_PID")
@ -44,31 +52,38 @@ public class TermConceptMapGroupElementTarget implements Serializable {
@JoinColumn(name = "CONCEPT_MAP_GRP_ELM_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGETARGET_ELEMENT"))
private TermConceptMapGroupElement myConceptMapGroupElement;
@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.CODE_LENGTH)
@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
private String myCode;
@Column(name = "TARGET_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)
@Column(name = "TARGET_DISPLAY", nullable = true, length = TermConcept.MAX_DESC_LENGTH)
private String myDisplay;
@Enumerated(EnumType.STRING)
@Column(name = "TARGET_EQUIVALENCE", length = 50)
@Column(name = "TARGET_EQUIVALENCE", nullable = true, length = MAX_EQUIVALENCE_LENGTH)
private ConceptMapEquivalence myEquivalence;
@Column(name = "CONCEPT_MAP_URL", length = 200)
@Column(name = "CONCEPT_MAP_URL", nullable = true, length = TermConceptMap.MAX_URL_LENGTH)
private String myConceptMapUrl;
@Column(name = "SYSTEM_URL", length = 200)
@Column(name = "SYSTEM_URL", nullable = true, length = TermCodeSystem.MAX_URL_LENGTH)
private String mySystem;
@Column(name = "SYSTEM_VERSION", length = 200)
@Column(name = "SYSTEM_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
private String mySystemVersion;
@Column(name = "VALUESET_URL", length = 200)
@Column(name = "VALUESET_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String myValueSet;
public String getCode() {
return myCode;
}
public void setCode(String theCode) {
public TermConceptMapGroupElementTarget setCode(@Nonnull String theCode) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, TermConcept.MAX_CODE_LENGTH,
"Code exceeds maximum length (" + TermConcept.MAX_CODE_LENGTH + "): " + length(theCode));
myCode = theCode;
return this;
}
public TermConceptMapGroupElement getConceptMapGroupElement() {
@ -90,16 +105,18 @@ public class TermConceptMapGroupElementTarget implements Serializable {
return myDisplay;
}
public void setDisplay(String theDisplay) {
public TermConceptMapGroupElementTarget setDisplay(String theDisplay) {
myDisplay = theDisplay;
return this;
}
public ConceptMapEquivalence getEquivalence() {
return myEquivalence;
}
public void setEquivalence(ConceptMapEquivalence theEquivalence) {
public TermConceptMapGroupElementTarget setEquivalence(ConceptMapEquivalence theEquivalence) {
myEquivalence = theEquivalence;
return this;
}
public Long getId() {
@ -155,7 +172,7 @@ public class TermConceptMapGroupElementTarget implements Serializable {
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConceptMapGroupElement != null ? ("myConceptMapGroupElement - id=" + myConceptMapGroupElement.getId()) : ("myConceptMapGroupElement=(null)"))
.append("myCode", myCode)

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
View File

@ -20,21 +20,9 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import javax.persistence.*;
import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.EnumType;
import javax.persistence.Enumerated;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
@Entity
@Table(name = "TRM_CONCEPT_PC_LINK")
public class TermConceptParentChildLink implements Serializable {
@ -136,20 +124,24 @@ public class TermConceptParentChildLink implements Serializable {
return result;
}
public void setChild(TermConcept theChild) {
public TermConceptParentChildLink setChild(TermConcept theChild) {
myChild = theChild;
return this;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
public TermConceptParentChildLink setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
return this;
}
public void setParent(TermConcept theParent) {
public TermConceptParentChildLink setParent(TermConcept theParent) {
myParent = theParent;
return this;
}
public void setRelationshipType(RelationshipTypeEnum theRelationshipType) {
public TermConceptParentChildLink setRelationshipType(RelationshipTypeEnum theRelationshipType) {
myRelationshipType = theRelationshipType;
return this;
}
public enum RelationshipTypeEnum {

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
View File

@ -20,21 +20,29 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.validator.constraints.NotBlank;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_PROPERTY", uniqueConstraints = {
}, indexes = {
})
public class TermConceptProperty implements Serializable {
static final int MAX_PROPTYPE_ENUM_LENGTH = 6;
private static final long serialVersionUID = 1L;
private static final int MAX_LENGTH = 500;
static final int MAX_PROPTYPE_ENUM_LENGTH = 6;
@ManyToOne
@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CONCEPT"))
private TermConcept myConcept;
@ -51,22 +59,22 @@ public class TermConceptProperty implements Serializable {
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PROP_PID")
@Column(name = "PID")
private Long myId;
@Column(name = "PROP_KEY", length = 500, nullable = false)
@Column(name = "PROP_KEY", nullable = false, length = MAX_LENGTH)
@NotBlank
private String myKey;
@Column(name = "PROP_VAL", length = 500, nullable = true)
@Column(name = "PROP_VAL", nullable = true, length = MAX_LENGTH)
private String myValue;
@Column(name = "PROP_TYPE", length = MAX_PROPTYPE_ENUM_LENGTH, nullable = false)
@Column(name = "PROP_TYPE", nullable = false, length = MAX_PROPTYPE_ENUM_LENGTH)
private TermConceptPropertyTypeEnum myType;
/**
* Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
*/
@Column(name = "PROP_CODESYSTEM", length = 500, nullable = true)
@Column(name = "PROP_CODESYSTEM", length = MAX_LENGTH, nullable = true)
private String myCodeSystem;
/**
* Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
*/
@Column(name = "PROP_DISPLAY", length = 500, nullable = true)
@Column(name = "PROP_DISPLAY", length = MAX_LENGTH, nullable = true)
private String myDisplay;
/**
@ -80,6 +88,8 @@ public class TermConceptProperty implements Serializable {
* Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
*/
public TermConceptProperty setCodeSystem(String theCodeSystem) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCodeSystem, MAX_LENGTH,
"Property code system exceeds maximum length (" + MAX_LENGTH + "): " + length(theCodeSystem));
myCodeSystem = theCodeSystem;
return this;
}
@ -95,7 +105,7 @@ public class TermConceptProperty implements Serializable {
* Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
*/
public TermConceptProperty setDisplay(String theDisplay) {
myDisplay = theDisplay;
myDisplay = left(theDisplay, MAX_LENGTH);
return this;
}
@ -103,15 +113,20 @@ public class TermConceptProperty implements Serializable {
return myKey;
}
public void setKey(String theKey) {
public TermConceptProperty setKey(@Nonnull String theKey) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theKey, "theKey must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theKey, MAX_LENGTH,
"Code exceeds maximum length (" + MAX_LENGTH + "): " + length(theKey));
myKey = theKey;
return this;
}
public TermConceptPropertyTypeEnum getType() {
return myType;
}
public TermConceptProperty setType(TermConceptPropertyTypeEnum theType) {
public TermConceptProperty setType(@Nonnull TermConceptPropertyTypeEnum theType) {
Validate.notNull(theType);
myType = theType;
return this;
}
@ -128,8 +143,9 @@ public class TermConceptProperty implements Serializable {
* This will contain the value for a {@link TermConceptPropertyTypeEnum#STRING string}
* property, and the code for a {@link TermConceptPropertyTypeEnum#CODING coding} property.
*/
public void setValue(String theValue) {
myValue = theValue;
public TermConceptProperty setValue(String theValue) {
myValue = left(theValue, MAX_LENGTH);
return this;
}
public TermConceptProperty setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
@ -137,8 +153,9 @@ public class TermConceptProperty implements Serializable {
return this;
}
public void setConcept(TermConcept theConcept) {
public TermConceptProperty setConcept(TermConcept theConcept) {
myConcept = theConcept;
return this;
}
@Override

144
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java Normal file
View File

@ -0,0 +1,144 @@
package ca.uhn.fhir.jpa.entity;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Table(name = "TRM_VALUESET", uniqueConstraints = {
@UniqueConstraint(name = "IDX_VALUESET_URL", columnNames = {"URL"})
})
@Entity()
public class TermValueSet implements Serializable {
private static final long serialVersionUID = 1L;
public static final int MAX_NAME_LENGTH = 200;
public static final int MAX_URL_LENGTH = 200;
@Id()
@SequenceGenerator(name = "SEQ_VALUESET_PID", sequenceName = "SEQ_VALUESET_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_VALUESET_PID")
@Column(name = "PID")
private Long myId;
@Column(name = "URL", nullable = false, length = MAX_URL_LENGTH)
private String myUrl;
@OneToOne()
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMVALUESET_RES"))
private ResourceTable myResource;
@Column(name = "RES_ID", insertable = false, updatable = false)
private Long myResourcePid;
@Column(name = "NAME", nullable = true, length = MAX_NAME_LENGTH)
private String myName;
@OneToMany(mappedBy = "myValueSet")
private List<TermValueSetCode> myCodes;
public Long getId() {
return myId;
}
public String getUrl() {
return myUrl;
}
public TermValueSet setUrl(@Nonnull String theUrl) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theUrl, "theUrl must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUrl, MAX_URL_LENGTH,
"URL exceeds maximum length (" + MAX_URL_LENGTH + "): " + length(theUrl));
myUrl = theUrl;
return this;
}
public ResourceTable getResource() {
return myResource;
}
public TermValueSet setResource(ResourceTable theResource) {
myResource = theResource;
return this;
}
public String getName() {
return myName;
}
public TermValueSet setName(String theName) {
myName = left(theName, MAX_NAME_LENGTH);
return this;
}
public List<TermValueSetCode> getCodes() {
if (myCodes == null) {
myCodes = new ArrayList<>();
}
return myCodes;
}
@Override
public boolean equals(Object theO) {
if (this == theO) return true;
if (!(theO instanceof TermValueSet)) return false;
TermValueSet that = (TermValueSet) theO;
return new EqualsBuilder()
.append(getUrl(), that.getUrl())
.isEquals();
}
@Override
public int hashCode() {
return new HashCodeBuilder(17, 37)
.append(getUrl())
.toHashCode();
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append("myUrl", myUrl)
.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
.append("myResourcePid", myResourcePid)
.append("myName", myName)
.append(myCodes != null ? ("myCodes - size=" + myCodes.size()) : ("myCodes=(null)"))
.toString();
}
}

166
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetCode.java Normal file
View File

@ -0,0 +1,166 @@
package ca.uhn.fhir.jpa.entity;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Table(name = "TRM_VALUESET_CODE", indexes = {
@Index(name = "IDX_VALUESET_CODE_CS_CD", columnList = "SYSTEM, CODE")
})
@Entity()
public class TermValueSetCode implements Serializable {
private static final long serialVersionUID = 1L;
@Id()
@SequenceGenerator(name = "SEQ_VALUESET_CODE_PID", sequenceName = "SEQ_VALUESET_CODE_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_VALUESET_CODE_PID")
@Column(name = "PID")
private Long myId;
@ManyToOne()
@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_PID"))
private TermValueSet myValueSet;
@Transient
private String myValueSetUrl;
@Transient
private String myValueSetName;
@Column(name = "SYSTEM", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
private String mySystem;
@Column(name = "CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
private String myCode;
@Column(name = "DISPLAY", nullable = true, length = TermConcept.MAX_DESC_LENGTH)
private String myDisplay;
public Long getId() {
return myId;
}
public TermValueSet getValueSet() {
return myValueSet;
}
public TermValueSetCode setValueSet(TermValueSet theValueSet) {
myValueSet = theValueSet;
return this;
}
public String getValueSetUrl() {
if (myValueSetUrl == null) {
myValueSetUrl = getValueSet().getUrl();
}
return myValueSetUrl;
}
public String getValueSetName() {
if (myValueSetName == null) {
myValueSetName = getValueSet().getName();
}
return myValueSetName;
}
public String getSystem() {
return mySystem;
}
public TermValueSetCode setSystem(@Nonnull String theSystem) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theSystem, "theSystem must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSystem, TermCodeSystem.MAX_URL_LENGTH,
"System exceeds maximum length (" + TermCodeSystem.MAX_URL_LENGTH + "): " + length(theSystem));
mySystem = theSystem;
return this;
}
public String getCode() {
return myCode;
}
public TermValueSetCode setCode(@Nonnull String theCode) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, TermConcept.MAX_CODE_LENGTH,
"Code exceeds maximum length (" + TermConcept.MAX_CODE_LENGTH + "): " + length(theCode));
myCode = theCode;
return this;
}
public String getDisplay() {
return myDisplay;
}
public TermValueSetCode setDisplay(String theDisplay) {
myDisplay = left(theDisplay, TermConcept.MAX_DESC_LENGTH);
return this;
}
@Override
public boolean equals(Object theO) {
if (this == theO) return true;
if (!(theO instanceof TermValueSetCode)) return false;
TermValueSetCode that = (TermValueSetCode) theO;
return new EqualsBuilder()
.append(getValueSetUrl(), that.getValueSetUrl())
.append(getSystem(), that.getSystem())
.append(getCode(), that.getCode())
.isEquals();
}
@Override
public int hashCode() {
return new HashCodeBuilder(17, 37)
.append(getValueSetUrl())
.append(getSystem())
.append(getCode())
.toHashCode();
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
.append("myValueSetUrl", this.getValueSetUrl())
.append("myValueSetName", this.getValueSetName())
.append("mySystem", mySystem)
.append("myCode", myCode)
.append("myDisplay", myDisplay)
.toString();
}
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -410,6 +410,14 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
PersistedJpaBundleProvider retVal = null;
if (searchToUse != null) {
ourLog.debug("Reusing search {} from cache", searchToUse.getUuid());
// Interceptor call: JPA_PERFTRACE_SEARCH_REUSING_CACHED
params = new HookParams()
.add(SearchParameterMap.class, theParams)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_SEARCH_REUSING_CACHED, params);
searchToUse.setSearchLastReturned(new Date());
mySearchDao.updateSearchLastReturned(searchToUse.getId(), new Date());

102
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
View File

@ -119,6 +119,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Autowired
protected ITermConceptDesignationDao myConceptDesignationDao;
@Autowired
protected ITermValueSetDao myValueSetDao;
@Autowired
protected ITermValueSetCodeDao myValueSetCodeDao;
@Autowired
protected FhirContext myContext;
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@ -388,6 +392,31 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
deleteConceptMap(theResourceTable);
}
public void deleteValueSet(ResourceTable theResourceTable) {
// Get existing entity so it can be deleted.
Optional<TermValueSet> optionalExistingTermValueSetById = myValueSetDao.findByResourcePid(theResourceTable.getId());
if (optionalExistingTermValueSetById.isPresent()) {
TermValueSet existingTermValueSet = optionalExistingTermValueSetById.get();
ourLog.info("Deleting existing TermValueSet {} and its children...", existingTermValueSet.getId());
myValueSetCodeDao.deleteTermValueSetCodesByValueSetId(existingTermValueSet.getId());
myValueSetDao.deleteTermValueSetById(existingTermValueSet.getId());
ourLog.info("Done deleting existing TermValueSet {} and its children.", existingTermValueSet.getId());
ourLog.info("Flushing...");
myValueSetCodeDao.flush();
myValueSetDao.flush();
ourLog.info("Done flushing.");
}
}
@Override
@Transactional
public void deleteValueSetAndChildren(ResourceTable theResourceTable) {
deleteValueSet(theResourceTable);
}
private <T> void doDelete(String theDescriptor, Supplier<Slice<T>> theLoader, Supplier<Integer> theCounter, JpaRepository<T, ?> theDao) {
int count;
ourLog.info(" * Deleting {}", theDescriptor);
@ -690,7 +719,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
private void expandWithoutHibernateSearch(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
ourLog.trace("Hibernate search is not enabled");
Validate.isTrue(theExpansionComponent.getParameter().isEmpty(), "Can not exapnd ValueSet with parameters - Hibernate Search is not enabled on this server.");
Validate.isTrue(theExpansionComponent.getParameter().isEmpty(), "Can not expand ValueSet with parameters - Hibernate Search is not enabled on this server.");
Validate.isTrue(theInclude.getFilter().isEmpty(), "Can not expand ValueSet with filters - Hibernate Search is not enabled on this server.");
Validate.isTrue(isNotBlank(theSystem), "Can not expand ValueSet without explicit system - Hibernate Search is not enabled on this server.");
@ -1144,7 +1173,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
myCodeSystemDao.save(codeSystem);
} else {
if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemVersion.getResource().getId())) {
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri,
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
@ -1310,7 +1339,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
myConceptMapGroupElementTargetDao.save(termConceptMapGroupElementTarget);
if (codesSaved++ % 250 == 0) {
ourLog.info("Have saved {} codes in conceptmap", codesSaved);
ourLog.info("Have saved {} codes in ConceptMap", codesSaved);
myConceptMapGroupElementTargetDao.flush();
}
}
@ -1334,6 +1363,69 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
ourLog.info("Done storing TermConceptMap.");
}
@Override
@Transactional
public void storeTermValueSetAndChildren(ResourceTable theResourceTable, ValueSet theValueSet) {
ourLog.info("Storing TermValueSet {}", theValueSet.getIdElement().getValue());
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theValueSet.getUrl(), "ValueSet has no value for ValueSet.url");
TermValueSet termValueSet = new TermValueSet();
termValueSet.setResource(theResourceTable);
termValueSet.setUrl(theValueSet.getUrl());
termValueSet.setName(theValueSet.hasName() ? theValueSet.getName() : null);
// We delete old versions; we don't support versioned ValueSets.
deleteValueSet(theResourceTable);
/*
* Do the upload.
*/
String url = termValueSet.getUrl();
Optional<TermValueSet> optionalExistingTermValueSetByUrl = myValueSetDao.findByUrl(url);
if (!optionalExistingTermValueSetByUrl.isPresent()) {
myValueSetDao.save(termValueSet);
int codesSaved = 0;
ValueSet expandedValueSet = expandValueSet(theValueSet);
if (expandedValueSet.hasExpansion()) {
if (expandedValueSet.getExpansion().hasTotal() && expandedValueSet.getExpansion().getTotal() > 0) {
TermValueSetCode code;
for (ValueSet.ValueSetExpansionContainsComponent contains : expandedValueSet.getExpansion().getContains()) {
ValidateUtil.isNotBlankOrThrowInvalidRequest(contains.getSystem(), "ValueSet contains a code with no system value");
ValidateUtil.isNotBlankOrThrowInvalidRequest(contains.getCode(), "ValueSet contains a code with no code value");
code = new TermValueSetCode();
code.setValueSet(termValueSet);
code.setSystem(contains.getSystem());
code.setCode(contains.getCode());
code.setDisplay(contains.hasDisplay() ? contains.getDisplay() : null);
myValueSetCodeDao.save(code);
if (codesSaved++ % 250 == 0) {
ourLog.info("Have pre-expanded {} codes in ValueSet", codesSaved);
myValueSetCodeDao.flush();
}
}
}
}
} else {
TermValueSet existingTermValueSet = optionalExistingTermValueSetByUrl.get();
String msg = myContext.getLocalizer().getMessage(
BaseHapiTerminologySvcImpl.class,
"cannotCreateDuplicateValueSetUrl",
url,
existingTermValueSet.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
ourLog.info("Done storing TermValueSet.");
}
@Override
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
VersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA);
@ -1581,9 +1673,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
private int validateConceptForStorage(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, ArrayList<String> theConceptsStack,
IdentityHashMap<TermConcept, Object> theAllConcepts) {
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() != null, "CodesystemValue is null");
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() != null, "CodeSystemVersion is null");
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() == theCodeSystem, "CodeSystems are not equal");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "Codesystem contains a code with no code value");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "CodeSystem contains a code with no code value");
if (theConceptsStack.contains(theConcept.getCode())) {
throw new InvalidRequestException("CodeSystem contains circular reference around code " + theConcept.getCode());

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java
View File

@ -81,8 +81,12 @@ public interface IHapiTerminologySvc {
void deleteConceptMapAndChildren(ResourceTable theResourceTable);
void deleteValueSetAndChildren(ResourceTable theResourceTable);
void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap);
void storeTermValueSetAndChildren(ResourceTable theResourceTable, ValueSet theValueSet);
boolean supportsSystem(String theCodeSystem);
List<TermConceptMapGroupElementTarget> translate(TranslationRequest theTranslationRequest);

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
View File

@ -5,7 +5,6 @@ import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import net.ttddyy.dsproxy.listener.SingleQueryCountHolder;
import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import org.springframework.context.annotation.Bean;
@ -104,7 +103,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
DataSource dataSource = ProxyDataSourceBuilder
.create(retVal)
.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
// .logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
// .logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
// .countQuery(new ThreadQueryCountHolder())
.beforeQuery(new BlockLargeNumbersOfParamsListener())

49
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -1,31 +1,13 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsStringIgnoringCase;
import static org.hamcrest.Matchers.empty;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.util.*;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.*;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.TokenParam;
@ -35,6 +17,25 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
@ -226,7 +227,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
myCodeSystemDao.create(codeSystem, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
assertEquals("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
}
}

345
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UniqueSearchParamTest.java
View File

@ -1,345 +0,0 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.dao.SearchBuilder;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.test.context.TestPropertySource;
import java.util.List;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.empty;
import static org.junit.Assert.*;
@SuppressWarnings({"unchecked", "deprecation"})
@TestPropertySource(properties = {
// Since scheduled tasks can cause searches, which messes up the
// value returned by SearchBuilder.getLastHandlerMechanismForUnitTest()
"scheduling_disabled=true"
})
public class FhirResourceDaoDstu3UniqueSearchParamTest extends BaseJpaDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3UniqueSearchParamTest.class);
@After
public void after() {
myModelConfig.setDefaultSearchParamsCanBeOverridden(new ModelConfig().isDefaultSearchParamsCanBeOverridden());
}
@Before
public void before() {
myModelConfig.setDefaultSearchParamsCanBeOverridden(true);
}
private void createUniqueBirthdateAndGenderSps() {
SearchParameter sp = new SearchParameter();
sp.setId("SearchParameter/patient-gender");
sp.setType(Enumerations.SearchParamType.TOKEN);
sp.setCode("gender");
sp.setExpression("Patient.gender");
sp.setStatus(PublicationStatus.ACTIVE);
sp.addBase("Patient");
mySearchParameterDao.update(sp);
sp = new SearchParameter();
sp.setId("SearchParameter/patient-birthdate");
sp.setType(Enumerations.SearchParamType.DATE);
sp.setCode("birthdate");
sp.setExpression("Patient.birthDate");
sp.setStatus(PublicationStatus.ACTIVE);
sp.addBase("Patient");
mySearchParameterDao.update(sp);
sp = new SearchParameter();
sp.setId("SearchParameter/patient-gender-birthdate");
sp.setType(Enumerations.SearchParamType.COMPOSITE);
sp.setStatus(PublicationStatus.ACTIVE);
sp.addBase("Patient");
sp.addComponent()
.setExpression("Patient")
.setDefinition(new Reference("SearchParameter/patient-gender"));
sp.addComponent()
.setExpression("Patient")
.setDefinition(new Reference("SearchParameter/patient-birthdate"));
sp.addExtension()
.setUrl(SearchParamConstants.EXT_SP_UNIQUE)
.setValue(new BooleanType(true));
mySearchParameterDao.update(sp);
mySearchParamRegistry.forceRefresh();
}
private void createUniqueIndexCoverageBeneficiary() {
SearchParameter sp = new SearchParameter();
sp.setId("SearchParameter/coverage-beneficiary");
sp.setCode("beneficiary");
sp.setExpression("Coverage.beneficiary");
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.setStatus(PublicationStatus.ACTIVE);
sp.addBase("Coverage");
mySearchParameterDao.update(sp);
sp = new SearchParameter();
sp.setId("SearchParameter/coverage-identifier");
sp.setCode("identifier");
sp.setExpression("Coverage.identifier");
sp.setType(Enumerations.SearchParamType.TOKEN);
sp.setStatus(PublicationStatus.ACTIVE);
sp.addBase("Coverage");
mySearchParameterDao.update(sp);
sp = new SearchParameter();
sp.setId("SearchParameter/coverage-beneficiary-identifier");
sp.setCode("coverage-beneficiary-identifier");
sp.setExpression("Coverage.beneficiary");
sp.setType(Enumerations.SearchParamType.COMPOSITE);
sp.setStatus(PublicationStatus.ACTIVE);
sp.addBase("Coverage");
sp.addComponent()
.setExpression("Coverage")
.setDefinition(new Reference("/SearchParameter/coverage-beneficiary"));
sp.addComponent()
.setExpression("Coverage")
.setDefinition(new Reference("/SearchParameter/coverage-identifier"));
sp.addExtension()
.setUrl(SearchParamConstants.EXT_SP_UNIQUE)
.setValue(new BooleanType(true));
mySearchParameterDao.update(sp);
mySearchParamRegistry.forceRefresh();
}
private void createUniqueNameAndManagingOrganizationSps() {
SearchParameter sp = new SearchParameter();
sp.setId("SearchParameter/patient-name");
sp.setType(Enumerations.SearchParamType.STRING);
sp.setCode("name");
sp.setExpression("Patient.name");
sp.setStatus(PublicationStatus.ACTIVE);
sp.addBase("Patient");
mySearchParameterDao.update(sp);
sp = new SearchParameter();
sp.setId("SearchParameter/patient-organization");
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.setCode("organization");
sp.setExpression("Patient.managingOrganization");
sp.setStatus(PublicationStatus.ACTIVE);
sp.addBase("Patient");
mySearchParameterDao.update(sp);
sp = new SearchParameter();
sp.setId("SearchParameter/patient-name-organization");
sp.setType(Enumerations.SearchParamType.COMPOSITE);
sp.setStatus(PublicationStatus.ACTIVE);
sp.addBase("Patient");
sp.addComponent()
.setExpression("Patient")
.setDefinition(new Reference("SearchParameter/patient-name"));
sp.addComponent()
.setExpression("Patient")
.setDefinition(new Reference("SearchParameter/patient-organization"));
sp.addExtension()
.setUrl(SearchParamConstants.EXT_SP_UNIQUE)
.setValue(new BooleanType(true));
mySearchParameterDao.update(sp);
mySearchParamRegistry.forceRefresh();
}
@Test
public void testDetectUniqueSearchParams() {
createUniqueBirthdateAndGenderSps();
List<JpaRuntimeSearchParam> params = mySearchParamRegistry.getActiveUniqueSearchParams("Patient");
assertEquals(1, params.size());
assertEquals(params.get(0).isUnique(), true);
assertEquals(2, params.get(0).getCompositeOf().size());
// Should be alphabetical order
assertEquals("birthdate", params.get(0).getCompositeOf().get(0).getName());
assertEquals("gender", params.get(0).getCompositeOf().get(1).getName());
}
@Test
public void testDuplicateUniqueValuesAreRejected() {
createUniqueBirthdateAndGenderSps();
Patient pt1 = new Patient();
pt1.setGender(Enumerations.AdministrativeGender.MALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
try {
myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
fail();
} catch (PreconditionFailedException e) {
// good
}
Patient pt2 = new Patient();
pt2.setGender(Enumerations.AdministrativeGender.MALE);
IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
pt2 = new Patient();
pt2.setId(id2);
pt2.setGender(Enumerations.AdministrativeGender.MALE);
pt2.setBirthDateElement(new DateType("2011-01-01"));
try {
myPatientDao.update(pt2);
fail();
} catch (PreconditionFailedException e) {
// good
}
}
@Test
public void testReplaceOneWithAnother() {
createUniqueBirthdateAndGenderSps();
Patient pt1 = new Patient();
pt1.setGender(Enumerations.AdministrativeGender.MALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
IIdType id1 = myPatientDao.create(pt1).getId().toUnqualified();
assertNotNull(id1);
ourLog.info("** Replacing");
pt1 = new Patient();
pt1.setId(id1);
pt1.setGender(Enumerations.AdministrativeGender.FEMALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
id1 = myPatientDao.update(pt1).getId().toUnqualified();
assertNotNull(id1);
assertEquals("2", id1.getVersionIdPart());
Patient pt2 = new Patient();
pt2.setGender(Enumerations.AdministrativeGender.MALE);
pt2.setBirthDateElement(new DateType("2011-01-01"));
IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
SearchBuilder.resetLastHandlerMechanismForUnitTest();
SearchParameterMap params = new SearchParameterMap();
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
params.add("birthdate", new DateParam("2011-01-01"));
IBundleProvider results = myPatientDao.search(params);
String searchId = results.getUuid();
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id2.getValue()));
assertEquals(SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
}
@Test
public void testSearchSynchronousUsingUniqueComposite() {
createUniqueBirthdateAndGenderSps();
Patient pt1 = new Patient();
pt1.setGender(Enumerations.AdministrativeGender.MALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
Patient pt2 = new Patient();
pt2.setGender(Enumerations.AdministrativeGender.MALE);
pt2.setBirthDateElement(new DateType("2011-01-02"));
IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
SearchBuilder.resetLastHandlerMechanismForUnitTest();
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(100);
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
params.add("birthdate", new DateParam("2011-01-01"));
IBundleProvider results = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1.getValue()));
assertEquals(SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
}
@Test
public void testSearchUsingUniqueComposite() {
createUniqueBirthdateAndGenderSps();
Patient pt1 = new Patient();
pt1.setGender(Enumerations.AdministrativeGender.MALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
assertNotNull(id1);
Patient pt2 = new Patient();
pt2.setGender(Enumerations.AdministrativeGender.MALE);
pt2.setBirthDateElement(new DateType("2011-01-02"));
IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
SearchBuilder.resetLastHandlerMechanismForUnitTest();
SearchParameterMap params = new SearchParameterMap();
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
params.add("birthdate", new DateParam("2011-01-01"));
IBundleProvider results = myPatientDao.search(params);
String searchId = results.getUuid();
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1.getValue()));
assertEquals(SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
// Other order
SearchBuilder.resetLastHandlerMechanismForUnitTest();
params = new SearchParameterMap();
params.add("birthdate", new DateParam("2011-01-01"));
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
results = myPatientDao.search(params);
assertEquals(searchId, results.getUuid());
String id1Value = id1.getValue();
List<String> actualValues = toUnqualifiedVersionlessIdValues(results);
assertThat(actualValues, containsInAnyOrder(id1Value));
// Null because we just reuse the last search
assertEquals(null, SearchBuilder.getLastHandlerMechanismForUnitTest());
SearchBuilder.resetLastHandlerMechanismForUnitTest();
params = new SearchParameterMap();
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
params.add("birthdate", new DateParam("2011-01-03"));
results = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIdValues(results), empty());
assertEquals(SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
SearchBuilder.resetLastHandlerMechanismForUnitTest();
params = new SearchParameterMap();
params.add("birthdate", new DateParam("2011-01-03"));
results = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIdValues(results), empty());
assertEquals(SearchBuilder.HandlerTypeEnum.STANDARD_QUERY, SearchBuilder.getLastHandlerMechanismForUnitTest());
}
@Test
public void testUniqueValuesAreIndexed_DateAndToken() {
createUniqueBirthdateAndGenderSps();
Patient pt1 = new Patient();
pt1.setGender(Enumerations.AdministrativeGender.MALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
List<ResourceIndexedCompositeStringUnique> uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
assertEquals(1, uniques.size());
assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
assertEquals("Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale", uniques.get(0).getIndexString());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -118,6 +118,10 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Qualifier("myCodeSystemDaoR4")
protected IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
@Autowired
protected ITermCodeSystemDao myTermCodeSystemDao;
@Autowired
protected ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
@Autowired
@Qualifier("myCompartmentDefinitionDaoR4")
protected IFhirResourceDao<CompartmentDefinition> myCompartmentDefinitionDao;
@Autowired
@ -287,6 +291,10 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Qualifier("myValueSetDaoR4")
protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
@Autowired
protected ITermValueSetDao myTermValueSetDao;
@Autowired
protected ITermValueSetCodeDao myTermValueSetCodeDao;
@Autowired
protected ITermConceptMapDao myTermConceptMapDao;
@Autowired
protected ITermConceptMapGroupElementTargetDao myTermConceptMapGroupElementTargetDao;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
View File

@ -222,7 +222,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
myCodeSystemDao.create(codeSystem, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
assertEquals("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
}
}

210
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java
View File

@ -1,15 +1,18 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.SearchBuilder;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
@ -17,6 +20,7 @@ import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
@ -25,6 +29,7 @@ import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.mockito.ArgumentMatchers;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.TestPropertySource;
import org.springframework.transaction.TransactionStatus;
@ -32,6 +37,7 @@ import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.UUID;
@ -40,8 +46,10 @@ import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.INDEX_STATUS_INDEXED;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
@SuppressWarnings({"unchecked", "deprecation"})
@TestPropertySource(properties = {
// Since scheduled tasks can cause searches, which messes up the
// value returned by SearchBuilder.getLastHandlerMechanismForUnitTest()
@ -52,6 +60,8 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4UniqueSearchParamTest.class);
@Autowired
private ISearchParamRegistry mySearchParamRegistry;
private IInterceptorBroadcaster myInterceptorBroadcaster;
private List<String> myMessages = new ArrayList<>();
@After
public void after() {
@ -66,9 +76,31 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
myModelConfig.setDefaultSearchParamsCanBeOverridden(true);
myDaoConfig.setSchedulingDisabled(true);
myDaoConfig.setUniqueIndexesEnabled(true);
SearchBuilder.resetLastHandlerMechanismForUnitTest();
myInterceptorBroadcaster = mock(IInterceptorBroadcaster.class);
when(mySrd.getInterceptorBroadcaster()).thenReturn(myInterceptorBroadcaster);
when(mySrd.getServer().getPagingProvider()).thenReturn(new DatabaseBackedPagingProvider());
when(myInterceptorBroadcaster.hasHooks(eq(Pointcut.JPA_PERFTRACE_WARNING))).thenReturn(true);
when(myInterceptorBroadcaster.hasHooks(eq(Pointcut.JPA_PERFTRACE_INFO))).thenReturn(true);
when(myInterceptorBroadcaster.callHooks(eq(Pointcut.JPA_PERFTRACE_INFO), ArgumentMatchers.any(HookParams.class))).thenAnswer(t -> {
HookParams params = t.getArgument(1, HookParams.class);
myMessages.add("INFO " + params.get(StorageProcessingMessage.class).getMessage());
return null;
});
when(myInterceptorBroadcaster.callHooks(eq(Pointcut.JPA_PERFTRACE_WARNING), ArgumentMatchers.any(HookParams.class))).thenAnswer(t -> {
HookParams params = t.getArgument(1, HookParams.class);
myMessages.add("WARN " + params.get(StorageProcessingMessage.class).getMessage());
return null;
});
when(myInterceptorBroadcaster.callHooks(eq(Pointcut.JPA_PERFTRACE_SEARCH_REUSING_CACHED), ArgumentMatchers.any(HookParams.class))).thenAnswer(t -> {
HookParams params = t.getArgument(1, HookParams.class);
myMessages.add("REUSING CACHED SEARCH");
return null;
});
}
private void createUniqueBirthdateAndGenderSps() {
SearchParameter sp = new SearchParameter();
sp.setId("SearchParameter/patient-gender");
@ -106,7 +138,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
mySearchParamRegistry.forceRefresh();
SearchBuilder.resetLastHandlerMechanismForUnitTest();
myMessages.clear();
}
private void createUniqueIndexCoverageBeneficiary() {
@ -322,19 +354,6 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
mySearchParamRegistry.forceRefresh();
}
@Test
public void testDetectUniqueSearchParams() {
createUniqueBirthdateAndGenderSps();
List<JpaRuntimeSearchParam> params = mySearchParamRegistry.getActiveUniqueSearchParams("Patient");
assertEquals(1, params.size());
assertTrue(params.get(0).isUnique());
assertEquals(2, params.get(0).getCompositeOf().size());
// Should be alphabetical order
assertEquals("birthdate", params.get(0).getCompositeOf().get(0).getName());
assertEquals("gender", params.get(0).getCompositeOf().get(1).getName());
}
@Test
public void testDoubleMatchingOnAnd_Search() {
createUniqueIndexPatientIdentifier();
@ -981,15 +1000,19 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
myCaptureQueriesListener.clear();
SearchBuilder.resetLastHandlerMechanismForUnitTest();
myMessages.clear();
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(100);
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
params.add("birthdate", new DateParam("2011-01-01"));
IBundleProvider results = myPatientDao.search(params);
IBundleProvider results = myPatientDao.search(params, mySrd);
myCaptureQueriesListener.logFirstSelectQueryForCurrentThread();
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1.getValue()));
assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
logCapturedMessages();
assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale"));
myMessages.clear();
}
@ -1007,40 +1030,50 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
pt2.setBirthDateElement(new DateType("2011-01-02"));
myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
SearchBuilder.resetLastHandlerMechanismForUnitTest();
myMessages.clear();
SearchParameterMap params = new SearchParameterMap();
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
params.add("birthdate", new DateParam("2011-01-01"));
IBundleProvider results = myPatientDao.search(params);
IBundleProvider results = myPatientDao.search(params, mySrd);
String searchId = results.getUuid();
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1));
assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
logCapturedMessages();
assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale"));
myMessages.clear();
// Other order
SearchBuilder.resetLastHandlerMechanismForUnitTest();
myMessages.clear();
params = new SearchParameterMap();
params.add("birthdate", new DateParam("2011-01-01"));
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
results = myPatientDao.search(params);
results = myPatientDao.search(params, mySrd);
assertEquals(searchId, results.getUuid());
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1));
// Null because we just reuse the last search
assertNull(SearchBuilder.getLastHandlerMechanismForUnitTest());
// Because we just reuse the last search
logCapturedMessages();
assertThat(myMessages.toString(), containsString("REUSING"));
assertThat(myMessages.toString(), not(containsString("Using unique index")));
myMessages.clear();
SearchBuilder.resetLastHandlerMechanismForUnitTest();
myMessages.clear();
params = new SearchParameterMap();
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
params.add("birthdate", new DateParam("2011-01-03"));
results = myPatientDao.search(params);
results = myPatientDao.search(params, mySrd);
assertThat(toUnqualifiedVersionlessIdValues(results), empty());
assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
logCapturedMessages();
assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?birthdate=2011-01-03&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale"));
myMessages.clear();
SearchBuilder.resetLastHandlerMechanismForUnitTest();
myMessages.clear();
params = new SearchParameterMap();
params.add("birthdate", new DateParam("2011-01-03"));
results = myPatientDao.search(params);
results = myPatientDao.search(params, mySrd);
assertThat(toUnqualifiedVersionlessIdValues(results), empty());
assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.STANDARD_QUERY, SearchBuilder.getLastHandlerMechanismForUnitTest());
// STANDARD QUERY
logCapturedMessages();
assertThat(myMessages.toString(), not(containsString("unique index")));
myMessages.clear();
}
@ -1104,9 +1137,12 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
pt1.addName().setFamily("FAMILY1");
pt1.setManagingOrganization(new Reference("Organization/ORG"));
SearchBuilder.resetLastHandlerMechanismForUnitTest();
IIdType id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization:Organization=ORG").getId().toUnqualifiedVersionless();
assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
IIdType id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization:Organization=ORG", mySrd).getId().toUnqualifiedVersionless();
logCapturedMessages();
assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?name=FAMILY1&organization=Organization%2FORG"));
myMessages.clear();
uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
assertEquals(1, uniques.size());
assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
@ -1118,9 +1154,12 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
pt1.addName().setFamily("FAMILY1");
pt1.setManagingOrganization(new Reference("Organization/ORG"));
SearchBuilder.resetLastHandlerMechanismForUnitTest();
id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization:Organization=ORG").getId().toUnqualifiedVersionless();
assertEquals(SearchBuilder.getLastHandlerParamsForUnitTest(), SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
id1 = myPatientDao.update(pt1, "Patient?name=FAMILY1&organization:Organization=ORG", mySrd).getId().toUnqualifiedVersionless();
logCapturedMessages();
assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?name=FAMILY1&organization=Organization%2FORG"));
myMessages.clear();
uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
assertEquals(1, uniques.size());
assertEquals("Patient/" + id1.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
@ -1128,6 +1167,10 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
}
private void logCapturedMessages() {
ourLog.info("Messages:\n {}", String.join("\n ", myMessages));
}
@Test
public void testUniqueValuesAreIndexed_StringAndReference() {
createUniqueNameAndManagingOrganizationSps();
@ -1375,6 +1418,93 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
}
@Test
public void testDetectUniqueSearchParams() {
createUniqueBirthdateAndGenderSps();
List<JpaRuntimeSearchParam> params = mySearchParamRegistry.getActiveUniqueSearchParams("Patient");
assertEquals(1, params.size());
assertEquals(params.get(0).isUnique(), true);
assertEquals(2, params.get(0).getCompositeOf().size());
// Should be alphabetical order
assertEquals("birthdate", params.get(0).getCompositeOf().get(0).getName());
assertEquals("gender", params.get(0).getCompositeOf().get(1).getName());
}
@Test
public void testDuplicateUniqueValuesAreRejected() {
createUniqueBirthdateAndGenderSps();
Patient pt1 = new Patient();
pt1.setGender(Enumerations.AdministrativeGender.MALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
try {
myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
fail();
} catch (PreconditionFailedException e) {
// good
}
Patient pt2 = new Patient();
pt2.setGender(Enumerations.AdministrativeGender.MALE);
IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
pt2 = new Patient();
pt2.setId(id2);
pt2.setGender(Enumerations.AdministrativeGender.MALE);
pt2.setBirthDateElement(new DateType("2011-01-01"));
try {
myPatientDao.update(pt2);
fail();
} catch (PreconditionFailedException e) {
// good
}
}
@Test
public void testReplaceOneWithAnother() {
createUniqueBirthdateAndGenderSps();
Patient pt1 = new Patient();
pt1.setGender(Enumerations.AdministrativeGender.MALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
IIdType id1 = myPatientDao.create(pt1).getId().toUnqualified();
assertNotNull(id1);
ourLog.info("** Replacing");
pt1 = new Patient();
pt1.setId(id1);
pt1.setGender(Enumerations.AdministrativeGender.FEMALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
id1 = myPatientDao.update(pt1).getId().toUnqualified();
assertNotNull(id1);
assertEquals("2", id1.getVersionIdPart());
Patient pt2 = new Patient();
pt2.setGender(Enumerations.AdministrativeGender.MALE);
pt2.setBirthDateElement(new DateType("2011-01-01"));
IIdType id2 = myPatientDao.create(pt2).getId().toUnqualifiedVersionless();
myMessages.clear();
SearchParameterMap params = new SearchParameterMap();
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
params.add("birthdate", new DateParam("2011-01-01"));
IBundleProvider results = myPatientDao.search(params, mySrd);
String searchId = results.getUuid();
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id2.getValue()));
logCapturedMessages();
assertThat(myMessages.toString(), containsString("Using unique index for query for search: Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale"));
myMessages.clear();
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

30
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValueSetTest.java
View File

@ -1,34 +1,20 @@
package ca.uhn.fhir.jpa.dao.r4;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import java.io.IOException;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.util.TestUtil;
import java.io.IOException;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
@ -224,7 +210,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
@Test
public void testValiedateCodeAgainstBuiltInValueSetAndCodeSystemWithValidCode() {
public void testValidateCodeAgainstBuiltInValueSetAndCodeSystemWithValidCode() {
IPrimitiveType<String> display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu3Test.java
View File

@ -36,6 +36,7 @@ import java.util.concurrent.CountDownLatch;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.*;
@ -471,6 +472,9 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(SubscriptionMatchingStrategy.IN_MEMORY.toString(), tag.getCode());
assertEquals("In-memory", tag.getDisplay());
// Wait for subscription to be moved to active
await().until(()-> Subscription.SubscriptionStatus.ACTIVE.equals(ourClient.read().resource(Subscription.class).withId(subscriptionId.toUnqualifiedVersionless()).execute().getStatus()));
Subscription subscriptionActivated = ourClient.read().resource(Subscription.class).withId(subscriptionId.toUnqualifiedVersionless()).execute();
assertEquals(Subscription.SubscriptionStatus.ACTIVE, subscriptionActivated.getStatus());
tags = subscriptionActivated.getMeta().getTag();
@ -495,6 +499,9 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(SubscriptionMatchingStrategy.DATABASE.toString(), tag.getCode());
assertEquals("Database", tag.getDisplay());
// Wait for subscription to be moved to active
await().until(()-> Subscription.SubscriptionStatus.ACTIVE.equals(ourClient.read().resource(Subscription.class).withId(subscriptionId.toUnqualifiedVersionless()).execute().getStatus()));
Subscription subscription = ourClient.read().resource(Subscription.class).withId(subscriptionId.toUnqualifiedVersionless()).execute();
assertEquals(Subscription.SubscriptionStatus.ACTIVE, subscription.getStatus());
tags = subscription.getMeta().getTag();

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -177,7 +177,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
assertThat(e.getMessage(), containsString("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
}
}

126
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

@ -2,17 +2,12 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.UriType;
import org.junit.*;
import org.junit.rules.ExpectedException;
import org.slf4j.Logger;
@ -21,6 +16,7 @@ import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
@ -31,6 +27,8 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Rule
public final ExpectedException expectedException = ExpectedException.none();
private IIdType myConceptMapId;
private IIdType myExtensionalCsId;
private IIdType myExtensionalVsId;
@Before
public void before() {
@ -40,6 +38,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@After
public void after() {
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
}
private void createAndPersistConceptMap() {
@ -56,6 +55,39 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
});
}
private void loadAndPersistCodeSystemAndValueSet() throws IOException {
loadAndPersistCodeSystem();
loadAndPersistValueSet();
}
private void loadAndPersistCodeSystem() throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
persistCodeSystem(codeSystem);
}
private void persistCodeSystem(CodeSystem theCodeSystem) {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
}
});
}
private void loadAndPersistValueSet() throws IOException {
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
persistValueSet(valueSet);
}
private void persistValueSet(ValueSet theValueSet) {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalVsId = myValueSetDao.create(theValueSet, mySrd).getId().toUnqualifiedVersionless();
}
});
}
@Test
public void testCreateConceptMapWithMissingSourceSystem() {
ConceptMap conceptMap = new ConceptMap();
@ -137,6 +169,16 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
}
@Test
public void testDuplicateCodeSystemUrls() throws Exception {
loadAndPersistCodeSystem();
expectedException.expect(UnprocessableEntityException.class);
expectedException.expectMessage("Can not create multiple CodeSystem resources with CodeSystem.url \"http://acme.org\", already have one with resource ID: CodeSystem/" + myExtensionalCsId.getIdPart());
loadAndPersistCodeSystem();
}
@Test
public void testDuplicateConceptMapUrls() {
createAndPersistConceptMap();
@ -147,6 +189,19 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
createAndPersistConceptMap();
}
@Test
public void testDuplicateValueSetUrls() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
// DM 2019-03-05 - We pre-load our custom CodeSystem otherwise pre-expansion of the ValueSet will fail.
loadAndPersistCodeSystemAndValueSet();
expectedException.expect(UnprocessableEntityException.class);
expectedException.expectMessage("Can not create multiple ValueSet resources with ValueSet.url \"http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2\", already have one with resource ID: ValueSet/" + myExtensionalVsId.getIdPart());
loadAndPersistValueSet();
}
@Test
public void testStoreTermConceptMapAndChildren() {
createAndPersistConceptMap();
@ -325,6 +380,63 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
});
}
@Test
public void testStoreTermValueSetAndChildren() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSet();
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsId.getIdPartAsLong());
assertTrue(optionalValueSetByResourcePid.isPresent());
Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
assertTrue(optionalValueSetByUrl.isPresent());
TermValueSet valueSet = optionalValueSetByUrl.get();
assertSame(optionalValueSetByResourcePid.get(), valueSet);
ourLog.info("ValueSet:\n" + valueSet.toString());
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", valueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", valueSet.getName());
assertEquals(codeSystem.getConcept().size(), valueSet.getCodes().size());
TermValueSetCode code = valueSet.getCodes().get(0);
ourLog.info("Code:\n" + code.toString());
assertEquals("http://acme.org", code.getSystem());
assertEquals("8450-9", code.getCode());
assertEquals("Systolic blood pressure--expiration", code.getDisplay());
code = valueSet.getCodes().get(1);
ourLog.info("Code:\n" + code.toString());
assertEquals("http://acme.org", code.getSystem());
assertEquals("11378-7", code.getCode());
assertEquals("Systolic blood pressure at First encounter", code.getDisplay());
// ...
code = valueSet.getCodes().get(22);
ourLog.info("Code:\n" + code.toString());
assertEquals("http://acme.org", code.getSystem());
assertEquals("8491-3", code.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", code.getDisplay());
code = valueSet.getCodes().get(23);
ourLog.info("Code:\n" + code.toString());
assertEquals("http://acme.org", code.getSystem());
assertEquals("8492-1", code.getCode());
assertEquals("Systolic blood pressure 8 hour minimum", code.getDisplay());
}
});
}
@Test
public void testTranslateByCodeSystemsAndSourceCodeOneToMany() {
createAndPersistConceptMap();

2
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTypeTask.java
View File

@ -102,7 +102,7 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
Validate.notNull(myNullable);
if (myColumnType == ColumnTypeEnum.STRING) {
Validate.notNull(myColumnLength);
Validate.notNull(myColumnLength, "No length specified for " + ColumnTypeEnum.STRING + " column {}.", getColumnName());
} else {
Validate.isTrue(myColumnLength == null);
}

40
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -20,6 +20,9 @@ package ca.uhn.fhir.jpa.migrate.tasks;
* #L%
*/
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.taskdef.AddColumnTask;
import ca.uhn.fhir.jpa.migrate.taskdef.ArbitrarySqlTask;
@ -56,7 +59,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
init400();
}
private void init400() {
protected void init400() {
Builder version = forVersion(VersionEnum.V4_0_0);
version.onTable("TRM_CONCEPT_MAP_GROUP")
@ -75,6 +78,41 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.renameColumn("mySystem", "SYSTEM_URL")
.renameColumn("mySystemVersion", "SYSTEM_VERSION")
.renameColumn("myValueSet", "VALUESET_URL");
// TermValueSet
version.startSectionWithMessage("Processing table: TRM_VALUESET");
version.addIdGenerator("SEQ_VALUESET_PID");
Builder.BuilderAddTableByColumns termValueSetTable = version.addTableByColumns("TRM_VALUESET", "PID");
termValueSetTable.addColumn("PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetTable.addColumn("URL").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermValueSet.MAX_URL_LENGTH);
termValueSetTable
.addIndex("IDX_VALUESET_URL")
.unique(true)
.withColumns("URL");
termValueSetTable.addColumn("RES_ID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetTable
.addForeignKey("FK_TRMVALUESET_RES")
.toColumn("RES_ID")
.references("HFJ_RESOURCE", "RES_ID");
termValueSetTable.addColumn("NAME").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermValueSet.MAX_NAME_LENGTH);
// TermValueSetCode
version.startSectionWithMessage("Processing table: TRM_VALUESET_CODE");
version.addIdGenerator("SEQ_VALUESET_CODE_PID");
Builder.BuilderAddTableByColumns termValueSetCodeTable = version.addTableByColumns("TRM_VALUESET_CODE", "PID");
termValueSetCodeTable.addColumn("PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetCodeTable.addColumn("VALUESET_PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetCodeTable
.addForeignKey("FK_TRM_VALUESET_PID")
.toColumn("VALUESET_PID")
.references("TRM_VALUESET", "PID");
termValueSetCodeTable.addColumn("SYSTEM").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermCodeSystem.MAX_URL_LENGTH);
termValueSetCodeTable.addColumn("CODE").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermConcept.MAX_CODE_LENGTH);
termValueSetCodeTable
.addIndex("IDX_VALUESET_CODE_CS_CD")
.unique(false)
.withColumns("SYSTEM", "CODE");
termValueSetCodeTable.addColumn("DISPLAY").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, TermConcept.MAX_DESC_LENGTH);
}

2
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/SearchParameterMap.java
View File

@ -446,7 +446,7 @@ public class SearchParameterMap implements Serializable {
public String toString() {
ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
if (isEmpty() == false) {
b.append("params", super.toString());
b.append("params", mySearchParameterMap);
}
if (getIncludes().isEmpty() == false) {
b.append("includes", getIncludes());

6
hapi-fhir-structures-dstu2/pom.xml
View File

@ -210,6 +210,12 @@
<artifactId>spring-web</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>

41
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/PreferTest.java
View File

@ -1,14 +1,18 @@
package ca.uhn.fhir.rest.server;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.emptyOrNullString;
import static org.hamcrest.Matchers.is;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertThat;
import java.util.concurrent.TimeUnit;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpPost;
@ -26,19 +30,12 @@ import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import java.util.concurrent.TimeUnit;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.emptyOrNullString;
import static org.junit.Assert.*;
public class PreferTest {
private static CloseableHttpClient ourClient;

302
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/InterceptorUserDataMapDstu2Test.java
View File

@ -1,19 +1,27 @@
package ca.uhn.fhir.rest.server.interceptor;
import static org.hamcrest.Matchers.contains;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertThat;
import static org.mockito.Mockito.mock;
import java.util.*;
import java.util.concurrent.TimeUnit;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Interceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
import ca.uhn.fhir.model.dstu2.valueset.IdentifierUseEnum;
import ca.uhn.fhir.model.primitive.DateDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.CloseableHttpResponse;
@ -24,37 +32,30 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.junit.*;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
import ca.uhn.fhir.model.dstu2.valueset.IdentifierUseEnum;
import ca.uhn.fhir.model.primitive.*;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import java.util.*;
import java.util.concurrent.TimeUnit;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.Matchers.contains;
import static org.junit.Assert.*;
public class InterceptorUserDataMapDstu2Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(InterceptorUserDataMapDstu2Test.class);
private static CloseableHttpClient ourClient;
private static FhirContext ourCtx = FhirContext.forDstu2();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(InterceptorUserDataMapDstu2Test.class);
private static int ourPort;
private static Server ourServer;
private static RestfulServer servlet;
private final Object myKey = "KEY";
private final Object myValue = "VALUE";
private Map<Object, Object> myMap;
private Set<String> myMapCheckMethods;
private final Object myValue = "VALUE";
@Before
public void before() {
@ -66,7 +67,7 @@ public class InterceptorUserDataMapDstu2Test {
@Before
public void beforePurgeMap() {
myMap = null;
myMapCheckMethods= new LinkedHashSet<>();
myMapCheckMethods = new LinkedHashSet<>();
}
@ -78,7 +79,7 @@ public class InterceptorUserDataMapDstu2Test {
IOUtils.closeQuietly(status.getEntity().getContent());
ourLog.info(myMapCheckMethods.toString());
assertThat(myMapCheckMethods, contains("incomingRequestPostProcessed", "incomingRequestPreHandled", "preProcessOutgoingException", "handleException", "processingCompleted"));
await().until(() -> myMapCheckMethods, contains("incomingRequestPostProcessed", "incomingRequestPreHandled", "preProcessOutgoingException", "handleException", "processingCompleted"));
}
@Test
@ -95,8 +96,7 @@ public class InterceptorUserDataMapDstu2Test {
}
ourLog.info(myMapCheckMethods.toString());
assertThat(myMapCheckMethods.toString(), myMapCheckMethods, contains("incomingRequestPostProcessed", "incomingRequestPreHandled", "outgoingResponse", "processingCompletedNormally", "processingCompleted"));
await().until(() -> myMapCheckMethods, contains("incomingRequestPostProcessed", "incomingRequestPreHandled", "outgoingResponse", "processingCompletedNormally", "processingCompleted"));
}
private void updateMapUsing(Map<Object, Object> theUserData, String theMethod) {
@ -111,125 +111,6 @@ public class InterceptorUserDataMapDstu2Test {
myMapCheckMethods.add(theMethod);
}
@AfterClass
public static void afterClassClearContext() throws Exception {
JettyUtil.closeServer(ourServer);
TestUtil.clearAllStaticFieldsForUnitTest();
}
@BeforeClass
public static void beforeClass() throws Exception {
ourServer = new Server(0);
ServletHandler proxyHandler = new ServletHandler();
servlet = new RestfulServer(ourCtx);
servlet.setResourceProviders(new DummyPatientResourceProvider());
servlet.setPlainProviders(new PlainProvider());
ServletHolder servletHolder = new ServletHolder(servlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
ourServer.setHandler(proxyHandler);
JettyUtil.startServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourClient = builder.build();
}
public static class DummyPatientResourceProvider implements IResourceProvider {
private Patient createPatient1() {
Patient patient = new Patient();
patient.addIdentifier();
patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
patient.getIdentifier().get(0).setValue("00001");
patient.addName();
patient.getName().get(0).addFamily("Test");
patient.getName().get(0).addGiven("PatientOne");
patient.setGender(AdministrativeGenderEnum.MALE);
patient.getId().setValue("1");
return patient;
}
public Map<String, Patient> getIdToPatient() {
Map<String, Patient> idToPatient = new HashMap<String, Patient>();
{
Patient patient = createPatient1();
idToPatient.put("1", patient);
}
{
Patient patient = new Patient();
patient.getIdentifier().add(new IdentifierDt());
patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
patient.getIdentifier().get(0).setValue("00002");
patient.getName().add(new HumanNameDt());
patient.getName().get(0).addFamily("Test");
patient.getName().get(0).addGiven("PatientTwo");
patient.setGender(AdministrativeGenderEnum.FEMALE);
patient.getId().setValue("2");
idToPatient.put("2", patient);
}
return idToPatient;
}
/**
* Retrieve the resource by its identifier
*
* @param theId
* The resource identity
* @return The resource
*/
@Read()
public Patient getResourceById(@IdParam IdDt theId) {
if (theId.getIdPart().equals("EX")) {
throw new InvalidRequestException("FOO");
}
String key = theId.getIdPart();
Patient retVal = getIdToPatient().get(key);
return retVal;
}
/**
* Retrieve the resource by its identifier
*
* @param theId
* The resource identity
* @return The resource
*/
@Search()
public List<Patient> getResourceById(@RequiredParam(name = "_id") String theId) {
throw new InvalidRequestException("FOO");
}
@Override
public Class<Patient> getResourceType() {
return Patient.class;
}
@Operation(name = "$everything", idempotent = true)
public Bundle patientTypeOperation(@OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
Bundle retVal = new Bundle();
// Populate bundle with matching resources
return retVal;
}
@Operation(name = "$everything", idempotent = true)
public Bundle patientTypeOperation(@IdParam IdDt theId, @OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
Bundle retVal = new Bundle();
// Populate bundle with matching resources
return retVal;
}
}
@Interceptor
public class MyInterceptor {
@ -276,6 +157,94 @@ public class InterceptorUserDataMapDstu2Test {
}
public static class DummyPatientResourceProvider implements IResourceProvider {
private Patient createPatient1() {
Patient patient = new Patient();
patient.addIdentifier();
patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
patient.getIdentifier().get(0).setValue("00001");
patient.addName();
patient.getName().get(0).addFamily("Test");
patient.getName().get(0).addGiven("PatientOne");
patient.setGender(AdministrativeGenderEnum.MALE);
patient.getId().setValue("1");
return patient;
}
public Map<String, Patient> getIdToPatient() {
Map<String, Patient> idToPatient = new HashMap<String, Patient>();
{
Patient patient = createPatient1();
idToPatient.put("1", patient);
}
{
Patient patient = new Patient();
patient.getIdentifier().add(new IdentifierDt());
patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
patient.getIdentifier().get(0).setValue("00002");
patient.getName().add(new HumanNameDt());
patient.getName().get(0).addFamily("Test");
patient.getName().get(0).addGiven("PatientTwo");
patient.setGender(AdministrativeGenderEnum.FEMALE);
patient.getId().setValue("2");
idToPatient.put("2", patient);
}
return idToPatient;
}
/**
* Retrieve the resource by its identifier
*
* @param theId The resource identity
* @return The resource
*/
@Read()
public Patient getResourceById(@IdParam IdDt theId) {
if (theId.getIdPart().equals("EX")) {
throw new InvalidRequestException("FOO");
}
String key = theId.getIdPart();
Patient retVal = getIdToPatient().get(key);
return retVal;
}
/**
* Retrieve the resource by its identifier
*
* @param theId The resource identity
* @return The resource
*/
@Search()
public List<Patient> getResourceById(@RequiredParam(name = "_id") String theId) {
throw new InvalidRequestException("FOO");
}
@Override
public Class<Patient> getResourceType() {
return Patient.class;
}
@Operation(name = "$everything", idempotent = true)
public Bundle patientTypeOperation(@OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
Bundle retVal = new Bundle();
// Populate bundle with matching resources
return retVal;
}
@Operation(name = "$everything", idempotent = true)
public Bundle patientTypeOperation(@IdParam IdDt theId, @OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
Bundle retVal = new Bundle();
// Populate bundle with matching resources
return retVal;
}
}
public static class PlainProvider {
@Operation(name = "$everything", idempotent = true)
@ -288,4 +257,33 @@ public class InterceptorUserDataMapDstu2Test {
}
@AfterClass
public static void afterClassClearContext() throws Exception {
JettyUtil.closeServer(ourServer);
TestUtil.clearAllStaticFieldsForUnitTest();
}
@BeforeClass
public static void beforeClass() throws Exception {
ourServer = new Server(0);
ServletHandler proxyHandler = new ServletHandler();
servlet = new RestfulServer(ourCtx);
servlet.setResourceProviders(new DummyPatientResourceProvider());
servlet.setPlainProviders(new PlainProvider());
ServletHolder servletHolder = new ServletHolder(servlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
ourServer.setHandler(proxyHandler);
JettyUtil.startServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourClient = builder.build();
}
}

188
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -18,9 +18,9 @@ import net.sf.json.JsonConfig;
import org.apache.commons.io.IOUtils;
import org.hamcrest.Matchers;
import org.hamcrest.core.StringContains;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Address.AddressUse;
import org.hl7.fhir.dstu3.model.Address.AddressUseEnumFactory;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.CapabilityStatement.UnknownContentCode;
@ -33,7 +33,6 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.junit.*;
import org.mockito.ArgumentCaptor;
import org.mockito.Mockito;
import java.io.IOException;
import java.io.StringReader;
@ -45,9 +44,8 @@ import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.eq;
import static org.mockito.Matchers.isNull;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.*;
import static org.mockito.Mockito.nullable;
import static org.mockito.Mockito.*;
@ -110,16 +108,16 @@ public class JsonParserDstu3Test {
// Deserialize then check that valueReference value is still correct
fhirPat = parser.parseResource(Patient.class, output);
List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
Assert.assertEquals(1, extlst.size());
Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
List<Extension> extensions = fhirPat.getExtensionsByUrl("x1");
Assert.assertEquals(1, extensions.size());
Assert.assertEquals(refVal, ((Reference) extensions.get(0).getValue()).getReference());
}
/**
* See #544
*/
@Test
public void testBundleStitchReferencesByUuid() throws Exception {
public void testBundleStitchReferencesByUuid() {
Bundle bundle = new Bundle();
DocumentManifest dm = new DocumentManifest();
@ -175,7 +173,7 @@ public class JsonParserDstu3Test {
}
@Test
public void testCustomUrlExtensioninBundle() {
public void testCustomUrlExtensionInBundle() {
final String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}}]}";
final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
@ -213,7 +211,7 @@ public class JsonParserDstu3Test {
* See #276
*/
@Test
public void testDoubleEncodingContainedResources() throws Exception {
public void testDoubleEncodingContainedResources() {
Patient patient = new Patient();
patient.setId("#patient-1");
patient.setActive(true);
@ -236,7 +234,7 @@ public class JsonParserDstu3Test {
}
@Test
public void testEncodeAndParseExtensions() throws Exception {
public void testEncodeAndParseExtensions() {
Patient patient = new Patient();
patient.addIdentifier().setUse(IdentifierUse.OFFICIAL).setSystem("urn:example").setValue("7000135");
@ -402,6 +400,7 @@ public class JsonParserDstu3Test {
/**
* See #336
*/
@SuppressWarnings("SpellCheckingInspection")
@Test
public void testEncodeAndParseNullPrimitiveWithExtensions() {
@ -458,7 +457,7 @@ public class JsonParserDstu3Test {
Patient p = new Patient();
p.addName().setFamily("FAMILY");
List<Coding> labels = new ArrayList<Coding>();
List<Coding> labels = new ArrayList<>();
labels.add(new Coding().setSystem("SYSTEM1").setCode("CODE1").setDisplay("DISPLAY1").setVersion("VERSION1"));
labels.add(new Coding().setSystem("SYSTEM2").setCode("CODE2").setDisplay("DISPLAY2").setVersion("VERSION2"));
p.getMeta().getSecurity().addAll(labels);
@ -602,7 +601,7 @@ public class JsonParserDstu3Test {
*/
@Test
public void testEncodeEmptyTag() {
ArrayList<Coding> tagList = new ArrayList<Coding>();
ArrayList<Coding> tagList = new ArrayList<>();
tagList.add(new Coding());
tagList.add(new Coding().setDisplay("Label"));
@ -618,7 +617,7 @@ public class JsonParserDstu3Test {
*/
@Test
public void testEncodeEmptyTag2() {
ArrayList<Coding> tagList = new ArrayList<Coding>();
ArrayList<Coding> tagList = new ArrayList<>();
tagList.add(new Coding().setSystem("scheme").setCode("code"));
tagList.add(new Coding().setDisplay("Label"));
@ -715,13 +714,26 @@ public class JsonParserDstu3Test {
.setValue(new Reference("Practitioner/A"));
IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
parser.setDontEncodeElements(new HashSet<String>(Arrays.asList("*.id", "*.meta")));
parser.setDontEncodeElements(new HashSet<>(Arrays.asList("*.id", "*.meta")));
String encoded = parser.encodeResourceToString(p);
ourLog.info(encoded);
assertThat(encoded, containsString("http://foo"));
assertThat(encoded, containsString("Practitioner/A"));
// Now with exclude
parser = ourCtx.newJsonParser().setPrettyPrint(true);
parser.setDontEncodeElements(new HashSet<>(Arrays.asList("*.id", "*.meta", "*.extension")));
encoded = parser.encodeResourceToString(p);
ourLog.info(encoded);
assertThat(encoded, not(containsString("http://foo")));
assertThat(encoded, not(containsString("Practitioner/A")));
}
@Test
@ -818,7 +830,7 @@ public class JsonParserDstu3Test {
TestPatientFor327 patient = new TestPatientFor327();
patient.setBirthDateElement(new DateType("2016-04-14"));
List<Reference> conditions = new ArrayList<Reference>();
List<Reference> conditions = new ArrayList<>();
Condition condition = new Condition();
condition.addBodySite().setText("BODY SITE");
conditions.add(new Reference(condition));
@ -896,7 +908,7 @@ public class JsonParserDstu3Test {
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<String>());
parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<>());
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
@ -930,12 +942,12 @@ public class JsonParserDstu3Test {
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(Arrays.asList("Patient.managingOrganization"));
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(Collections.singletonList("Patient.managingOrganization"));
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(new HashSet<String>(Arrays.asList("Patient.managingOrganization")));
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(new HashSet<>(Collections.singletonList("Patient.managingOrganization")));
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
@ -1013,7 +1025,7 @@ public class JsonParserDstu3Test {
}
@Test
public void testEncodeNarrativeSuppressed() throws Exception {
public void testEncodeNarrativeSuppressed() {
Patient patient = new Patient();
patient.setId("Patient/1/_history/1");
patient.getText().setDivAsString("<div>THE DIV</div>");
@ -1064,6 +1076,57 @@ public class JsonParserDstu3Test {
assertThat(encoded, not(containsString("maritalStatus")));
}
/**
* We specifically include extensions on CapabilityStatment even in
* summary mode, since this is behaviour that people depend on
*/
@Test
public void testEncodeSummaryCapabilityStatementExtensions() {
CapabilityStatement cs = new CapabilityStatement();
CapabilityStatement.CapabilityStatementRestComponent rest = cs.addRest();
rest.setMode(CapabilityStatement.RestfulCapabilityMode.CLIENT);
rest.getSecurity()
.addExtension()
.setUrl("http://foo")
.setValue(new StringType("bar"));
cs.getVersionElement().addExtension()
.setUrl("http://goo")
.setValue(new StringType("ber"));
String encoded = ourCtx.newJsonParser().setSummaryMode(true).setPrettyPrint(true).setPrettyPrint(true).encodeResourceToString(cs);
ourLog.info(encoded);
assertThat(encoded, (containsString("http://foo")));
assertThat(encoded, (containsString("bar")));
assertThat(encoded, (containsString("http://goo")));
assertThat(encoded, (containsString("ber")));
}
@Test
public void testEncodeSummaryPatientExtensions() {
Patient cs = new Patient();
Address address = cs.addAddress();
address.setCity("CITY");
address
.addExtension()
.setUrl("http://foo")
.setValue(new StringType("bar"));
address.getCityElement().addExtension()
.setUrl("http://goo")
.setValue(new StringType("ber"));
String encoded = ourCtx.newJsonParser().setSummaryMode(true).setPrettyPrint(true).setPrettyPrint(true).encodeResourceToString(cs);
ourLog.info(encoded);
assertThat(encoded, not(containsString("http://foo")));
assertThat(encoded, not(containsString("bar")));
assertThat(encoded, not(containsString("http://goo")));
assertThat(encoded, not(containsString("ber")));
}
@Test
public void testEncodeSummary2() {
Patient patient = new Patient();
@ -1107,7 +1170,7 @@ public class JsonParserDstu3Test {
* See #241
*/
@Test
public void testEncodeThenParseShouldNotAddSpuriousId() throws Exception {
public void testEncodeThenParseShouldNotAddSpuriousId() {
Condition condition = new Condition().setVerificationStatus(ConditionVerificationStatus.CONFIRMED);
Bundle bundle = new Bundle();
BundleEntryComponent entry = new Bundle.BundleEntryComponent();
@ -1126,7 +1189,7 @@ public class JsonParserDstu3Test {
}
@Test
public void testEncodeUndeclaredBlock() throws Exception {
public void testEncodeUndeclaredBlock() {
FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
source.getMessageHeaderApplicationId().setValue("APPID");
source.setName("NAME");
@ -1153,7 +1216,7 @@ public class JsonParserDstu3Test {
Patient patient = new Patient();
patient.addAddress().setUse(AddressUse.HOME);
EnumFactory<AddressUse> fact = new AddressUseEnumFactory();
PrimitiveType<AddressUse> enumeration = new Enumeration<AddressUse>(fact).setValue(AddressUse.HOME);
PrimitiveType<AddressUse> enumeration = new Enumeration<>(fact).setValue(AddressUse.HOME);
patient.addExtension().setUrl("urn:foo").setValue(enumeration);
String val = parser.encodeResourceToString(patient);
@ -1168,7 +1231,7 @@ public class JsonParserDstu3Test {
}
@Test
public void testEncodeWithDontEncodeElements() throws Exception {
public void testEncodeWithDontEncodeElements() {
Patient patient = new Patient();
patient.setId("123");
@ -1224,7 +1287,7 @@ public class JsonParserDstu3Test {
{
IParser p = ourCtx.newJsonParser();
p.setDontEncodeElements(Sets.newHashSet("Patient.meta"));
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
p.setEncodeElements(new HashSet<>(Collections.singletonList("Patient.name")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(patient);
ourLog.info(out);
@ -1438,7 +1501,7 @@ public class JsonParserDstu3Test {
String res = "{ \"resourceType\": \"ValueSet\", \"url\": \"http://sample/ValueSet/education-levels\", \"version\": \"1\", \"name\": \"Education Levels\", \"status\": \"draft\", \"compose\": { \"include\": [ { \"filter\": [ { \"property\": \"n\", \"op\": \"n\", \"value\": \"365460000\" } ], \"system\": \"http://snomed.info/sct\" } ], \"exclude\": [ { \"concept\": [ { \"code\": \"224298008\" }, { \"code\": \"365460000\" }, { \"code\": \"473462005\" }, { \"code\": \"424587006\" } ], \"system\": \"http://snomed.info/sct\" } ] }, \"description\": \"A selection of Education Levels\", \"text\": { \"status\": \"generated\", \"div\": \"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\"><h2>Education Levels</h2><tt>http://csiro.au/ValueSet/education-levels</tt><p>A selection of Education Levels</p></div>\" }, \"experimental\": true, \"date\": \"2016-07-26\" }";
IParser parser = ourCtx.newJsonParser();
parser.setParserErrorHandler(new StrictErrorHandler());
ValueSet parsed = parser.parseResource(ValueSet.class, res);
parser.parseResource(ValueSet.class, res);
fail("DataFormat Invalid attribute exception should be thrown");
}
@ -1671,53 +1734,6 @@ public class JsonParserDstu3Test {
assertThat(reencoded, containsString("contained"));
}
@Test
@Ignore
public void testParseAndEncodeBundleNewStyle() throws Exception {
String content = IOUtils.toString(JsonParserDstu3Test.class.getResourceAsStream("/bundle-example.json"), StandardCharsets.UTF_8);
Bundle parsed = ourCtx.newJsonParser().parseResource(Bundle.class, content);
assertEquals("Bundle/example/_history/1", parsed.getIdElement().getValue());
assertEquals("1", parsed.getIdElement().getVersionIdPart());
assertEquals("2014-08-18T01:43:30Z", parsed.getMeta().getLastUpdatedElement().getValueAsString());
assertEquals("searchset", parsed.getType());
assertEquals(3, parsed.getTotal());
assertEquals("https://example.com/base/MedicationRequest?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2", parsed.getLink().get(0).getUrlElement().getValueAsString());
assertEquals("https://example.com/base/MedicationRequest?patient=347&_include=MedicationRequest.medication", parsed.getLink().get(1).getUrlElement().getValueAsString());
assertEquals(2, parsed.getEntry().size());
assertEquals("alternate", parsed.getEntry().get(0).getLink().get(0).getRelation());
assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", parsed.getEntry().get(0).getLink().get(0).getUrl());
assertEquals("http://foo?search", parsed.getEntry().get(0).getRequest().getUrlElement().getValueAsString());
MedicationRequest p = (MedicationRequest) parsed.getEntry().get(0).getResource();
assertEquals("Patient/347", p.getSubject().getReference());
assertEquals("2014-08-16T05:31:17Z", p.getMeta().getLastUpdatedElement().getValueAsString());
assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", p.getId());
// assertEquals("3123", p.getId());
Medication m = (Medication) parsed.getEntry().get(1).getResource();
assertEquals("http://example.com/base/Medication/example", m.getId());
assertSame(((Reference) p.getMedication()).getResource(), m);
String reencoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(parsed);
ourLog.info(reencoded);
JsonConfig cfg = new JsonConfig();
JSON expected = JSONSerializer.toJSON(content.trim(), cfg);
JSON actual = JSONSerializer.toJSON(reencoded.trim(), cfg);
String exp = expected.toString().replace("\\r\\n", "\\n"); // .replace("&sect;", "§");
String act = actual.toString().replace("\\r\\n", "\\n");
ourLog.info("Expected: {}", exp);
ourLog.info("Actual : {}", act);
assertEquals(exp, act);
}
@Test
public void testParseAndEncodeBundleWithUuidBase() {
//@formatter:off
@ -2221,20 +2237,18 @@ public class JsonParserDstu3Test {
@Test(expected = DataFormatException.class)
public void testParseWithTrailingContent() {
//@formatter:off
String bundle = "{\n" +
" \"resourceType\" : \"Bundle\",\n" +
" \"total\" : 1\n" +
"}}";
//@formatter:on
Bundle b = ourCtx.newJsonParser().parseResource(Bundle.class, bundle);
ourCtx.newJsonParser().parseResource(Bundle.class, bundle);
}
@Test
@Ignore
public void testParseWithWrongTypeObjectShouldBeArray() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/invalid_metadata.json"));
String input = IOUtils.toString(getClass().getResourceAsStream("/invalid_metadata.json"), Charsets.UTF_8);
try {
ourCtx.newJsonParser().parseResource(CapabilityStatement.class, input);
fail();
@ -2346,14 +2360,14 @@ public class JsonParserDstu3Test {
ArgumentCaptor<ValueType> actual = ArgumentCaptor.forClass(ValueType.class);
ArgumentCaptor<ScalarType> expectedScalar = ArgumentCaptor.forClass(ScalarType.class);
ArgumentCaptor<ScalarType> actualScalar = ArgumentCaptor.forClass(ScalarType.class);
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.nullable(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalar.capture(), actual.capture(),
verify(errorHandler, atLeastOnce()).incorrectJsonType(nullable(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalar.capture(), actual.capture(),
actualScalar.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.nullable(IParseLocation.class), Mockito.eq("_id"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR),
verify(errorHandler, atLeastOnce()).incorrectJsonType(nullable(IParseLocation.class), eq("_id"), eq(ValueType.OBJECT), expectedScalar.capture(), eq(ValueType.SCALAR),
actualScalar.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.nullable(IParseLocation.class), Mockito.eq("__v"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR),
verify(errorHandler, atLeastOnce()).incorrectJsonType(nullable(IParseLocation.class), eq("__v"), eq(ValueType.OBJECT), expectedScalar.capture(), eq(ValueType.SCALAR),
actualScalar.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.nullable(IParseLocation.class), Mockito.eq("_status"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(),
Mockito.eq(ValueType.SCALAR), actualScalar.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(nullable(IParseLocation.class), eq("_status"), eq(ValueType.OBJECT), expectedScalar.capture(),
eq(ValueType.SCALAR), actualScalar.capture());
assertEquals("_id", elementName.getAllValues().get(0));
assertEquals(ValueType.OBJECT, expected.getAllValues().get(0));
@ -2363,7 +2377,7 @@ public class JsonParserDstu3Test {
}
@Test
public void testValidateCustomStructure() throws Exception {
public void testValidateCustomStructure() {
FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
source.getMessageHeaderApplicationId().setValue("APPID");
@ -2392,13 +2406,13 @@ public class JsonParserDstu3Test {
containedOrganization.getMeta().addProfile(UUID.randomUUID().toString());
containedOrganization.getMeta().setLastUpdated(new Date());
containedOrganization.getMeta().setVersionId(UUID.randomUUID().toString());
containedOrganization.getMeta().setSecurity(Arrays.asList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
containedOrganization.getMeta().setTag(Arrays.asList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
containedOrganization.getMeta().setSecurity(Collections.singletonList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
containedOrganization.getMeta().setTag(Collections.singletonList(new Coding(UUID.randomUUID().toString(), UUID.randomUUID().toString(), UUID.randomUUID().toString())));
Patient patient = new Patient();
patient.setId(UUID.randomUUID().toString());
patient.getMeta().addProfile(UUID.randomUUID().toString());
patient.setGeneralPractitioner(Arrays.asList(new Reference(containedOrganization)));
patient.setGeneralPractitioner(Collections.singletonList(new Reference(containedOrganization)));
HashSet<String> excludeElementsInEncoded = new HashSet<>(); // ResourceMetaParams.EXCLUDE_ELEMENTS_IN_ENCODED
excludeElementsInEncoded.add("id");

30
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
View File

@ -12,6 +12,7 @@ import com.google.common.collect.Sets;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
import org.hamcrest.Matchers;
import org.hamcrest.collection.IsEmptyCollection;
import org.hamcrest.core.StringContains;
import org.hamcrest.text.StringContainsInOrder;
@ -69,6 +70,35 @@ public class XmlParserDstu3Test {
ourCtx.setNarrativeGenerator(null);
}
/**
* We specifically include extensions on CapabilityStatment even in
* summary mode, since this is behaviour that people depend on
*/
@Test
public void testEncodeSummaryCapabilityStatementExtensions() {
CapabilityStatement cs = new CapabilityStatement();
CapabilityStatement.CapabilityStatementRestComponent rest = cs.addRest();
rest.setMode(CapabilityStatement.RestfulCapabilityMode.CLIENT);
rest.getSecurity()
.addExtension()
.setUrl("http://foo")
.setValue(new StringType("bar"));
cs.getVersionElement().addExtension()
.setUrl("http://goo")
.setValue(new StringType("ber"));
String encoded = ourCtx.newXmlParser().setSummaryMode(true).setPrettyPrint(true).setPrettyPrint(true).encodeResourceToString(cs);
ourLog.info(encoded);
assertThat(encoded, Matchers.containsString("http://foo"));
assertThat(encoded, Matchers.containsString("bar"));
assertThat(encoded, Matchers.containsString("http://goo"));
assertThat(encoded, Matchers.containsString("ber"));
}
@Test
public void testEncodeInvalidMetaTime() {

10
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ElementsParamR4Test.java
View File

@ -264,6 +264,16 @@ public class ElementsParamR4Test {
assertEquals("mg", ((Quantity) procedure.getExtension().get(0).getValue()).getCode());
});
verifyXmlAndJson(
"http://localhost:" + ourPort + "/Procedure?_elements=Procedure.extension.value",
bundle -> {
Procedure procedure = (Procedure) bundle.getEntry().get(0).getResource();
assertEquals("SUBSETTED", procedure.getMeta().getTag().get(0).getCode());
assertEquals(0, procedure.getReasonCode().size());
assertEquals("1.1", ((Quantity) procedure.getExtension().get(0).getValue()).getValueElement().getValueAsString());
assertEquals("mg", ((Quantity) procedure.getExtension().get(0).getValue()).getCode());
});
verifyXmlAndJson(
"http://localhost:" + ourPort + "/Procedure?_elements=Procedure.extension.value.value",
bundle -> {

5
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/SummaryParamR4Test.java
View File

@ -18,6 +18,7 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hamcrest.CoreMatchers;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
@ -31,6 +32,8 @@ import java.util.List;
import java.util.concurrent.TimeUnit;
import java.util.function.Consumer;
import static org.hamcrest.CoreMatchers.containsStringIgnoringCase;
import static org.hamcrest.CoreMatchers.containsStringIgnoringCase;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
@ -220,7 +223,7 @@ public class SummaryParamR4Test {
assertThat(responseContent, (containsString("entry")));
assertThat(responseContent, (containsString(">TEXT<")));
assertThat(responseContent, (containsString("Medication/123")));
assertThat(responseContent, not(containsStringIgnoringCase("note")));
assertThat(responseContent, not(CoreMatchers.containsStringIgnoringCase("note")));
}
);

5
hapi-fhir-test-utilities/pom.xml
View File

@ -46,6 +46,11 @@
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
</dependency>
</dependencies>
<build>

60
pom.xml
View File

@ -1022,6 +1022,25 @@
<artifactId>velocity-tools</artifactId>
<version>2.0</version>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<version>3.1.6</version>
<exclusions>
<exclusion>
<groupId>org.hamcrest</groupId>
<artifactId>java-hamcrest</artifactId>
</exclusion>
<exclusion>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
</exclusion>
<exclusion>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-library</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.codehaus.plexus</groupId>
<artifactId>plexus-compiler-api</artifactId>
@ -1792,23 +1811,6 @@
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
<inherited>false</inherited>
<executions>
<execution>
<id>update-project-license</id>
<phase>package</phase>
<goals>
<goal>update-project-license</goal>
</goals>
<configuration>
<licenseName>apache_v2</licenseName>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<inherited>false</inherited>
@ -2196,9 +2198,27 @@
<profiles>
<profile>
<id>DIST</id>
<modules>
<!--<module>hapi-fhir-osgi-core</module>-->
</modules>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
<inherited>false</inherited>
<executions>
<execution>
<id>update-project-license</id>
<phase>package</phase>
<goals>
<goal>update-project-license</goal>
</goals>
<configuration>
<licenseName>apache_v2</licenseName>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>ROOT</id>

4
src/changes/changes.xml
View File

@ -266,6 +266,10 @@
A new server interceptor hook called PROCESSING_COMPLETED has been added. This
hook is called by the server at the end of processing every request (success and failure).
</action>
<action type="fix">
The <![CDATA[<code>_summary</code>]]> element was not always respected when encoding
JSON resources.
</action>
</release>
<release version="3.8.0" date="2019-05-30" description="Hippo">
<action type="fix">

4
src/site/xdoc/doc_jpa.xml
View File

@ -276,7 +276,7 @@ public DaoConfig daoConfig() {
If the client knows that they will only want a small number of results
(for example, a UI containing 20 results is being shown and the client
knows that they will never load the next page of results) the client
may also use the <code>nostore</code> directive along with a HAPI FHIR
may also use the <code>no-store</code> directive along with a HAPI FHIR
extension called <code>max-results</code> in order to specify that
only the given number of results should be fetched. This directive
disabled paging entirely for the request and causes the request to
@ -285,7 +285,7 @@ public DaoConfig daoConfig() {
</p>
<div class="source">
<pre>
Cache-Control: nostore, max-results=20
Cache-Control: no-store, max-results=20
</pre>
</div>