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Merge branch 'master' into issue-3144-multi-threaded-bundle-validation

This commit is contained in:
Jaison B 2021-12-02 14:53:05 -07:00
parent 613f0de95c 2fbbf31431
commit 72515c2094
102 changed files with 3353 additions and 476 deletions
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80
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ParserOptions.java
View File

@ -22,7 +22,12 @@ package ca.uhn.fhir.context;
import ca.uhn.fhir.parser.IParser;
import java.util.*;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
/**
* This object supplies default configuration to all {@link IParser parser} instances
@ -37,31 +42,40 @@ public class ParserOptions {
private boolean myStripVersionsFromReferences = true;
private Set<String> myDontStripVersionsFromReferencesAtPaths = Collections.emptySet();
private boolean myOverrideResourceIdWithBundleEntryFullUrl = true;
private boolean myAutoContainReferenceTargetsWithNoId = true;
/**
* If supplied value(s), any resource references at the specified paths will have their
* resource versions encoded instead of being automatically stripped during the encoding
* process. This setting has no effect on the parsing process.
* If set to {@literal true} (which is the default), contained resources may be specified by
* populating the target (contained) resource directly in {@link org.hl7.fhir.instance.model.api.IBaseReference#setReference(String)}
* and the parser will automatically locate it and insert it into <code>Resource.contained</code> when
* serializing. This is convenient, but also imposes a performance cost when serializing large numbers
* of resources, so this can be disabled if it is not needed.
* <p>
* This method provides a finer-grained level of control than {@link #setStripVersionsFromReferences(boolean)}
* and any paths specified by this method will be encoded even if {@link #setStripVersionsFromReferences(boolean)}
* has been set to <code>true</code> (which is the default)
* If disabled, only resources that are directly placed in <code>Resource.contained</code> will be
* serialized.
* </p>
*
* @param thePaths A collection of paths for which the resource versions will not be removed automatically
* when serializing, e.g. "Patient.managingOrganization" or "AuditEvent.object.reference". Note that
* only resource name and field names with dots separating is allowed here (no repetition
* indicators, FluentPath expressions, etc.)
* @return Returns a reference to <code>this</code> parser so that method calls can be chained together
* @see #setStripVersionsFromReferences(boolean)
* @since 6.0.0
*/
public ParserOptions setDontStripVersionsFromReferencesAtPaths(String... thePaths) {
if (thePaths == null) {
setDontStripVersionsFromReferencesAtPaths((List<String>) null);
} else {
setDontStripVersionsFromReferencesAtPaths(Arrays.asList(thePaths));
}
return this;
public boolean isAutoContainReferenceTargetsWithNoId() {
return myAutoContainReferenceTargetsWithNoId;
}
/**
* If set to {@literal true} (which is the default), contained resources may be specified by
* populating the target (contained) resource directly in {@link org.hl7.fhir.instance.model.api.IBaseReference#setReference(String)}
* and the parser will automatically locate it and insert it into <code>Resource.contained</code> when
* serializing. This is convenient, but also imposes a performance cost when serializing large numbers
* of resources, so this can be disabled if it is not needed.
* <p>
* If disabled, only resources that are directly placed in <code>Resource.contained</code> will be
* serialized.
* </p>
*
* @since 6.0.0
*/
public void setAutoContainReferenceTargetsWithNoId(boolean theAllowAutoContainedReferences) {
myAutoContainReferenceTargetsWithNoId = theAllowAutoContainedReferences;
}
/**
@ -109,6 +123,32 @@ public class ParserOptions {
return myDontStripVersionsFromReferencesAtPaths;
}
/**
* If supplied value(s), any resource references at the specified paths will have their
* resource versions encoded instead of being automatically stripped during the encoding
* process. This setting has no effect on the parsing process.
* <p>
* This method provides a finer-grained level of control than {@link #setStripVersionsFromReferences(boolean)}
* and any paths specified by this method will be encoded even if {@link #setStripVersionsFromReferences(boolean)}
* has been set to <code>true</code> (which is the default)
* </p>
*
* @param thePaths A collection of paths for which the resource versions will not be removed automatically
* when serializing, e.g. "Patient.managingOrganization" or "AuditEvent.object.reference". Note that
* only resource name and field names with dots separating is allowed here (no repetition
* indicators, FluentPath expressions, etc.)
* @return Returns a reference to <code>this</code> parser so that method calls can be chained together
* @see #setStripVersionsFromReferences(boolean)
*/
public ParserOptions setDontStripVersionsFromReferencesAtPaths(String... thePaths) {
if (thePaths == null) {
setDontStripVersionsFromReferencesAtPaths((List<String>) null);
} else {
setDontStripVersionsFromReferencesAtPaths(Arrays.asList(thePaths));
}
return this;
}
/**
* If supplied value(s), any resource references at the specified paths will have their
* resource versions encoded instead of being automatically stripped during the encoding

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
View File

@ -214,6 +214,15 @@ public interface IValidationSupport {
return false;
}
/**
* Returns <code>true</code> if a Remote Terminology Service is currently configured
*
* @return Returns <code>true</code> if a Remote Terminology Service is currently configured
*/
default boolean isRemoteTerminologyServiceConfigured() {
return false;
}
/**
* Fetch the given ValueSet by URL
*/

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -45,6 +45,7 @@ import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import org.apache.commons.io.output.StringBuilderWriter;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
@ -268,7 +269,7 @@ public abstract class BaseParser implements IParser {
@Override
public String encodeResourceToString(IBaseResource theResource) throws DataFormatException {
Writer stringWriter = new StringWriter();
Writer stringWriter = new StringBuilderWriter();
try {
encodeResourceToWriter(theResource, stringWriter);
} catch (IOException e) {
@ -615,7 +616,7 @@ public abstract class BaseParser implements IParser {
if (isBlank(resourceId.getValue())) {
resourceId.setValue(fullUrl);
} else {
if (fullUrl.startsWith("urn:") && fullUrl.endsWith(":" + resourceId.getIdPart())) {
if (fullUrl.startsWith("urn:") && fullUrl.length() > resourceId.getIdPart().length() && fullUrl.charAt(fullUrl.length() - resourceId.getIdPart().length() - 1) == ':' && fullUrl.endsWith(resourceId.getIdPart())) {
resourceId.setValue(fullUrl);
} else {
IIdType fullUrlId = myContext.getVersion().newIdType();

19
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -57,6 +57,7 @@ import java.io.Writer;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
@ -939,7 +940,9 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
JsonLikeObject alternate = alternateVal.getAsObject();
for (String nextKey : alternate.keySet()) {
for (Iterator<String> keyIter = alternate.keyIterator(); keyIter.hasNext(); ) {
String nextKey = keyIter.next();
JsonLikeValue nextVal = alternate.get(nextKey);
if ("extension".equals(nextKey)) {
boolean isModifier = false;
@ -962,12 +965,11 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void parseChildren(JsonLikeObject theObject, ParserState<?> theState) {
Set<String> keySet = theObject.keySet();
int allUnderscoreNames = 0;
int handledUnderscoreNames = 0;
for (String nextName : keySet) {
for (Iterator<String> keyIter = theObject.keyIterator(); keyIter.hasNext(); ) {
String nextName = keyIter.next();
if ("resourceType".equals(nextName)) {
continue;
} else if ("extension".equals(nextName)) {
@ -1013,7 +1015,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
* for example.
*/
if (allUnderscoreNames > handledUnderscoreNames) {
for (String alternateName : keySet) {
for (Iterator<String> keyIter = theObject.keyIterator(); keyIter.hasNext(); ) {
String alternateName = keyIter.next();
if (alternateName.startsWith("_") && alternateName.length() > 1) {
JsonLikeValue nextValue = theObject.get(alternateName);
if (nextValue != null) {
@ -1116,7 +1119,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
url = getExtensionUrl(jsonElement.getAsString());
}
theState.enteringNewElementExtension(null, url, theIsModifier, getServerBaseUrl());
for (String next : nextExtObj.keySet()) {
for (Iterator<String> keyIter = nextExtObj.keyIterator(); keyIter.hasNext(); ) {
String next = keyIter.next();
if ("url".equals(next)) {
continue;
} else if ("extension".equals(next)) {
@ -1146,7 +1150,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
* for example.
*/
if (allUnderscoreNames > handledUnderscoreNames) {
for (String alternateName : nextExtObj.keySet()) {
for (Iterator<String> keyIter = nextExtObj.keyIterator(); keyIter.hasNext(); ) {
String alternateName = keyIter.next();
if (alternateName.startsWith("_") && alternateName.length() > 1) {
JsonLikeValue nextValue = nextExtObj.get(alternateName);
if (nextValue != null) {

12
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/JsonLikeObject.java
View File

@ -1,6 +1,6 @@
package ca.uhn.fhir.parser.json;
import java.util.Set;
import java.util.Iterator;
/*
* #%L
@ -28,7 +28,7 @@ public abstract class JsonLikeObject extends JsonLikeValue {
public ValueType getJsonType() {
return ValueType.OBJECT;
}
@Override
public ScalarType getDataType() {
return null;
@ -49,8 +49,8 @@ public abstract class JsonLikeObject extends JsonLikeValue {
return null;
}
public abstract Set<String> keySet ();
public abstract JsonLikeValue get (String key);
public abstract Iterator<String> keyIterator();
public abstract JsonLikeValue get(String key);
}

65
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/jackson/JacksonStructure.java
View File

@ -31,6 +31,7 @@ import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.json.JsonMapper;
import com.fasterxml.jackson.databind.node.ArrayNode;
import com.fasterxml.jackson.databind.node.DecimalNode;
import com.fasterxml.jackson.databind.node.JsonNodeFactory;
@ -46,9 +47,6 @@ import java.util.ArrayList;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;
public class JacksonStructure implements JsonLikeStructure {
@ -153,8 +151,6 @@ public class JacksonStructure implements JsonLikeStructure {
private static class JacksonJsonObject extends JsonLikeObject {
private final ObjectNode nativeObject;
private final Map<String, JsonLikeValue> jsonLikeMap = new LinkedHashMap<>();
private Set<String> keySet = null;
public JacksonJsonObject(ObjectNode json) {
this.nativeObject = json;
@ -166,30 +162,17 @@ public class JacksonStructure implements JsonLikeStructure {
}
@Override
public Set<String> keySet() {
if (null == keySet) {
final Iterable<Map.Entry<String, JsonNode>> iterable = nativeObject::fields;
keySet = StreamSupport.stream(iterable.spliterator(), false)
.map(Map.Entry::getKey)
.collect(Collectors.toCollection(EntryOrderedSet::new));
}
return keySet;
public Iterator<String> keyIterator() {
return nativeObject.fieldNames();
}
@Override
public JsonLikeValue get(String key) {
JsonLikeValue result = null;
if (jsonLikeMap.containsKey(key)) {
result = jsonLikeMap.get(key);
} else {
JsonNode child = nativeObject.get(key);
if (child != null) {
result = new JacksonJsonValue(child);
}
jsonLikeMap.put(key, result);
JsonNode child = nativeObject.get(key);
if (child != null) {
return new JacksonJsonValue(child);
}
return result;
return null;
}
}
@ -300,19 +283,28 @@ public class JacksonStructure implements JsonLikeStructure {
@Override
public ValueType getJsonType() {
if (null == nativeValue || nativeValue.isNull()) {
if (null == nativeValue) {
return ValueType.NULL;
}
if (nativeValue.isObject()) {
return ValueType.OBJECT;
switch (nativeValue.getNodeType()) {
case NULL:
case MISSING:
return ValueType.NULL;
case OBJECT:
return ValueType.OBJECT;
case ARRAY:
return ValueType.ARRAY;
case POJO:
case BINARY:
case STRING:
case NUMBER:
case BOOLEAN:
default:
break;
}
if (nativeValue.isArray()) {
return ValueType.ARRAY;
}
if (nativeValue.isValueNode()) {
return ValueType.SCALAR;
}
return null;
return ValueType.SCALAR;
}
@Override
@ -378,7 +370,10 @@ public class JacksonStructure implements JsonLikeStructure {
}
private static ObjectMapper createObjectMapper() {
ObjectMapper retVal = new ObjectMapper();
ObjectMapper retVal =
JsonMapper
.builder()
.build();
retVal = retVal.setNodeFactory(new JsonNodeFactory(true));
retVal = retVal.enable(DeserializationFeature.USE_BIG_DECIMAL_FOR_FLOATS);
retVal = retVal.enable(DeserializationFeature.FAIL_ON_TRAILING_TOKENS);

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
View File

@ -73,6 +73,7 @@ public class Constants {
public static final String CT_OCTET_STREAM = "application/octet-stream";
public static final String CT_TEXT = "text/plain";
public static final String CT_TEXT_WITH_UTF8 = CT_TEXT + CHARSET_UTF8_CTSUFFIX;
public static final String CT_TEXT_CDA = "text/xml+cda";
public static final String CT_X_FORM_URLENCODED = "application/x-www-form-urlencoded";
public static final String CT_XML = "application/xml";
public static final String CT_XML_PATCH = "application/xml-patch+xml";
@ -201,6 +202,14 @@ public class Constants {
public static final String PARAM_TAGS = "_tags";
public static final String PARAM_TEXT = "_text";
public static final String PARAM_VALIDATE = "_validate";
/**
* $member-match operation
*/
public static final String PARAM_MEMBER_PATIENT = "MemberPatient";
public static final String PARAM_OLD_COVERAGE = "OldCoverage";
public static final String PARAM_NEW_COVERAGE = "NewCoverage";
public static final String PARAMQUALIFIER_MISSING = ":missing";
public static final String PARAMQUALIFIER_MISSING_FALSE = "false";
public static final String PARAMQUALIFIER_MISSING_TRUE = "true";

53
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -83,7 +83,6 @@ import static org.apache.commons.lang3.StringUtils.substring;
public class FhirTerser {
private static final Pattern COMPARTMENT_MATCHER_PATH = Pattern.compile("([a-zA-Z.]+)\\.where\\(resolve\\(\\) is ([a-zA-Z]+)\\)");
private static final EnumSet<OptionsEnum> EMPTY_OPTION_SET = EnumSet.noneOf(OptionsEnum.class);
private static final String USER_DATA_KEY_CONTAIN_RESOURCES_COMPLETED = FhirTerser.class.getName() + "_CONTAIN_RESOURCES_COMPLETED";
private final FhirContext myContext;
@ -323,11 +322,11 @@ public class FhirTerser {
}
public Optional<String> getSinglePrimitiveValue(IBase theTarget, String thePath) {
return getSingleValue(theTarget, thePath, IPrimitiveType.class).map(t->t.getValueAsString());
return getSingleValue(theTarget, thePath, IPrimitiveType.class).map(t -> t.getValueAsString());
}
public String getSinglePrimitiveValueOrNull(IBase theTarget, String thePath) {
return getSingleValue(theTarget, thePath, IPrimitiveType.class).map(t->t.getValueAsString()).orElse(null);
return getSingleValue(theTarget, thePath, IPrimitiveType.class).map(t -> t.getValueAsString()).orElse(null);
}
public <T extends IBase> Optional<T> getSingleValue(IBase theTarget, String thePath, Class<T> theWantedType) {
@ -712,9 +711,9 @@ public class FhirTerser {
* Returns <code>true</code> if <code>theSource</code> is in the compartment named <code>theCompartmentName</code>
* belonging to resource <code>theTarget</code>
*
* @param theCompartmentName The name of the compartment
* @param theSource The potential member of the compartment
* @param theTarget The owner of the compartment. Note that both the resource type and ID must be filled in on this IIdType or the method will throw an {@link IllegalArgumentException}
* @param theCompartmentName The name of the compartment
* @param theSource The potential member of the compartment
* @param theTarget The owner of the compartment. Note that both the resource type and ID must be filled in on this IIdType or the method will throw an {@link IllegalArgumentException}
* @param theAdditionalCompartmentParamNames If provided, search param names provided here will be considered as included in the given compartment for this comparison.
* @return <code>true</code> if <code>theSource</code> is in the compartment or one of the additional parameters matched.
* @throws IllegalArgumentException If theTarget does not contain both a resource type and ID
@ -1112,7 +1111,7 @@ public class FhirTerser {
});
}
private void containResourcesForEncoding(ContainedResources theContained, IBaseResource theResource, EnumSet<OptionsEnum> theOptions) {
private void containResourcesForEncoding(ContainedResources theContained, IBaseResource theResource, boolean theModifyResource) {
List<IBaseReference> allReferences = getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
for (IBaseReference next : allReferences) {
IBaseResource resource = next.getResource();
@ -1121,7 +1120,7 @@ public class FhirTerser {
IBaseResource potentialTarget = theContained.getExistingIdToContainedResource().remove(next.getReferenceElement().getValue());
if (potentialTarget != null) {
theContained.addContained(next.getReferenceElement(), potentialTarget);
containResourcesForEncoding(theContained, potentialTarget, theOptions);
containResourcesForEncoding(theContained, potentialTarget, theModifyResource);
}
}
}
@ -1136,15 +1135,13 @@ public class FhirTerser {
continue;
}
IIdType id = theContained.addContained(resource);
if (theOptions.contains(OptionsEnum.MODIFY_RESOURCE)) {
if (theModifyResource) {
getContainedResourceList(theResource).add(resource);
next.setReference(id.getValue());
}
if (resource.getIdElement().isLocal() && theContained.hasExistingIdToContainedResource()) {
theContained.getExistingIdToContainedResource().remove(resource.getIdElement().getValue());
}
} else {
continue;
}
}
@ -1161,9 +1158,20 @@ public class FhirTerser {
* @since 5.4.0
*/
public ContainedResources containResources(IBaseResource theResource, OptionsEnum... theOptions) {
EnumSet<OptionsEnum> options = toOptionSet(theOptions);
boolean storeAndReuse = false;
boolean modifyResource = false;
for (OptionsEnum next : theOptions) {
switch (next) {
case MODIFY_RESOURCE:
modifyResource = true;
break;
case STORE_AND_REUSE_RESULTS:
storeAndReuse = true;
break;
}
}
if (options.contains(OptionsEnum.STORE_AND_REUSE_RESULTS)) {
if (storeAndReuse) {
Object cachedValue = theResource.getUserData(USER_DATA_KEY_CONTAIN_RESOURCES_COMPLETED);
if (cachedValue != null) {
return (ContainedResources) cachedValue;
@ -1184,25 +1192,17 @@ public class FhirTerser {
contained.addContained(next);
}
containResourcesForEncoding(contained, theResource, options);
if (myContext.getParserOptions().isAutoContainReferenceTargetsWithNoId()) {
containResourcesForEncoding(contained, theResource, modifyResource);
}
if (options.contains(OptionsEnum.STORE_AND_REUSE_RESULTS)) {
if (storeAndReuse) {
theResource.setUserData(USER_DATA_KEY_CONTAIN_RESOURCES_COMPLETED, contained);
}
return contained;
}
private EnumSet<OptionsEnum> toOptionSet(OptionsEnum[] theOptions) {
EnumSet<OptionsEnum> options;
if (theOptions == null || theOptions.length == 0) {
options = EMPTY_OPTION_SET;
} else {
options = EnumSet.of(theOptions[0], theOptions);
}
return options;
}
@SuppressWarnings("unchecked")
private <T extends IBaseResource> List<T> getContainedResourceList(T theResource) {
List<T> containedResources = Collections.emptyList();
@ -1404,14 +1404,13 @@ public class FhirTerser {
/**
* Clones a resource object, copying all data elements from theSource into a new copy of the same type.
*
* <p>
* Note that:
* <ul>
* <li>Only FHIR data elements are copied (i.e. user data maps are not copied)</li>
* <li>If a class extending a HAPI FHIR type (e.g. an instance of a class extending the Patient class) is supplied, an instance of the base type will be returned.</li>
* </ul>
*
*
* @param theSource The source resource
* @return A copy of the source resource
* @since 5.6.0

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java
View File

@ -80,7 +80,6 @@ public enum VersionEnum {
V5_5_3,
V5_6_0,
V5_7_0
;
public static VersionEnum latestVersion() {

6
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -183,3 +183,9 @@ ca.uhn.fhir.jpa.provider.DiffProvider.cantDiffDifferentTypes=Unable to diff two
ca.uhn.fhir.jpa.interceptor.validation.RuleRequireProfileDeclaration.noMatchingProfile=Resource of type "{0}" does not declare conformance to profile from: {1}
ca.uhn.fhir.jpa.interceptor.validation.RuleRequireProfileDeclaration.illegalProfile=Resource of type "{0}" must not declare conformance to profile: {1}
operation.member.match.error.coverage.not.found=Could not find coverage for member based on coverage id or coverage identifier.
operation.member.match.error.beneficiary.not.found=Could not find beneficiary for coverage.
operation.member.match.error.missing.parameter=Parameter "{0}" is required.
operation.member.match.error.beneficiary.without.identifier=Coverage beneficiary does not have an identifier.

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3136-add-operation-validate-code-to-remoteterminologyservice.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: add
issue: 3136
title: "Provided a Remote Terminology Service implementation for the $validate-code Operation."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3172-implement-support-for-member-match-operation.yml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 3172
title: "Implement support for $member-match operation by coverage-id or coverage-identifier.
(Beneficiary demographic matching not supported)"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3173-add-message-key-to-messages.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 3158
title: "Add the concept of `messageKey` to the BaseResourceMessage class. This is to support brokers which permit key-based
partitioning."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3173-update-eid-system-to-support-multiple-resources.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: change
issue: 3158
title: "Previously in configuring MDM, you were only allowed to set a single `eidSystem` which was global regardless of how many resource types you were performing
MDM on. This has been changed. That field is now deprecated, and a new field called `eidSystems` (a json object) should be used instead. This will allow you to have granular
control over which resource types use which EIDs. See the [documentation](/hapi-fhir/docs/server_jpa_mdm/mdm_rules.html) of `eidSystems` for more information."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3197-add-option-to-not-auto-contain.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: perf
issue: 3197
title: "A new configuration option has been added to ParserOptions called `setAutoContainReferenceTargetsWithNoId`. This
setting disables the automatic creation of contained resources in cases where the target/contained resource is set
to a Reference instance but not actually added to the `Resource.contained` list. Disabling this automatic containing
yields a minor performance improvement in systems that do not need this functionality."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3197-load-performance-improvements.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: perf
issue: 3197
title: "A number of minor optimizations have been added to the JsonParser serializer module as well as to the
transaction processor. These optimizations lead to a significant performance improvement when processing
large transaction bundles (i.e. transaction bundles containing a larger number of entries)."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3198-package-loading-woes.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: change
issue: 3198
jira: SMILE-3452
title: "Fixed a regression where packages would fail to load if HAPI-FHIR was operating in DATABASE binary storage mode."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3211-reindex-performance.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
jira: SMILE-3472
title: "Fixed a serious performance issue with the `$reindex` operation."

11
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/changes.yaml Normal file
View File

@ -0,0 +1,11 @@
---
- item:
type: "add"
title: "The version of a few dependencies have been bumped to the latest versions
(dependent HAPI modules listed in brackets):
<ul>
<li>Spring (JPA): 5.3.7 -> 5.3.13</li>
<li>Thymeleaf (Testpage Overlay): 3.0.12.RELEASE -> 3.0.13.RELEASE (Addresses CVE-2021-43466)</li>
</ul>
"

17
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_rules.md
View File

@ -99,7 +99,11 @@ Here is an example of a full HAPI MDM rules json document:
"lastname-jaro,phone,birthday": "POSSIBLE_MATCH",
"firstname-jaro,phone,birthday": "POSSIBLE_MATCH",
"org-name": "MATCH"
}
},
"eidSystems": {
"Organization": "https://hapifhir.org/identifier/naming/business-number",
"Practitioner": "https://hapifhir.org/identifier/naming/license-number"
}
}
```
@ -483,6 +487,13 @@ These entries convert combinations of successful matchFields into an MDM Match R
}
```
### eidSystem
### eidSystems
The external EID systems that the HAPI MDM system can expect to see on incoming resources. These are defined on a per-resource basis. Alternatively, you may use `*` to indicate
that an EID is valid for all managed resource types. The values must be valid URIs, and the keys must be valid resource types, or `*`.
See [MDM EID](/hapi-fhir/docs/server_jpa_mdm/mdm_eid.html) for details on how EIDs are managed by HAPI MDM.
<p class="helpInfoCalloutBox">
Note that this field used to be called `eidSystem`. While that field is deprecated, it will continue to work. In the background, it effectively sets the eid for resource type `*`.
</p>
The external EID system that the HAPI MDM system should expect to see on incoming Patient resources. Must be a valid URI. See [MDM EID](/hapi-fhir/docs/server_jpa_mdm/mdm_eid.html) for details on how EIDs are managed by HAPI MDM.

4
hapi-fhir-jpaserver-base/pom.xml
View File

@ -197,8 +197,8 @@
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>io.swagger</groupId>
<artifactId>swagger-annotations</artifactId>
<groupId>org.springdoc</groupId>
<artifactId>springdoc-openapi-ui</artifactId>
</dependency>
<dependency>

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -86,6 +86,7 @@ import ca.uhn.fhir.jpa.provider.DiffProvider;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
import ca.uhn.fhir.jpa.provider.r4.MemberMatcherR4Helper;
import ca.uhn.fhir.jpa.reindex.ReindexJobSubmitterImpl;
import ca.uhn.fhir.jpa.sched.AutowiringSpringBeanJobFactory;
import ca.uhn.fhir.jpa.sched.HapiSchedulerServiceImpl;
@ -942,6 +943,14 @@ public abstract class BaseConfig {
return new UnknownCodeSystemWarningValidationSupport(fhirContext());
}
@Lazy
@Bean
public MemberMatcherR4Helper memberMatcherR4Helper(FhirContext theFhirContext) {
return new MemberMatcherR4Helper(theFhirContext);
}
public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) {
theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer()));
theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");

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

@ -117,8 +117,8 @@ public class TransactionProcessor extends BaseTransactionProcessor {
}
@Override
protected Map<IBase, IIdType> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName, TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries, StopWatch theTransactionStopWatch) {
protected EntriesToProcessMap doTransactionWriteOperations(final RequestDetails theRequest, String theActionName, TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
IdSubstitutionMap theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries, StopWatch theTransactionStopWatch) {
ITransactionProcessorVersionAdapter versionAdapter = getVersionAdapter();
RequestPartitionId requestPartitionId = null;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.binstore.NullBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.dao.data.INpmPackageDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionResourceDao;
@ -198,7 +199,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
* @throws IOException
*/
private byte[] fetchBlobFromBinary(IBaseBinary theBinary) throws IOException {
if (myBinaryStorageSvc != null) {
if (myBinaryStorageSvc != null && !(myBinaryStorageSvc instanceof NullBinaryStorageSvcImpl)) {
return myBinaryStorageSvc.fetchDataBlobFromBinary(theBinary);
} else {
byte[] value = BinaryUtil.getOrCreateData(myCtx, theBinary).getValue();

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/NpmPackageMetadataJson.java
View File

@ -27,15 +27,14 @@ import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import io.swagger.annotations.ApiModel;
import io.swagger.annotations.ApiModelProperty;
import io.swagger.v3.oas.annotations.media.Schema;
import javax.annotation.Nonnull;
import java.util.Date;
import java.util.LinkedHashMap;
import java.util.Map;
@ApiModel("Represents an NPM package metadata response")
@Schema(description = "Represents an NPM package metadata response")
@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonAutoDetect(creatorVisibility = JsonAutoDetect.Visibility.NONE, fieldVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
public class NpmPackageMetadataJson {
@ -108,7 +107,7 @@ public class NpmPackageMetadataJson {
private String myDescription;
@JsonProperty("fhirVersion")
private String myFhirVersion;
@ApiModelProperty(value = "The size of this package in bytes", example = "1000")
@Schema(description = "The size of this package in bytes", example = "1000")
@JsonProperty("_bytes")
private long myBytes;

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/NpmPackageSearchResultJson.java
View File

@ -23,13 +23,12 @@ package ca.uhn.fhir.jpa.packages;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import io.swagger.annotations.ApiModel;
import io.swagger.annotations.ApiModelProperty;
import io.swagger.v3.oas.annotations.media.Schema;
import java.util.ArrayList;
import java.util.List;
@ApiModel("Represents an NPM package search response")
@Schema(description = "Represents an NPM package search response")
@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonAutoDetect(creatorVisibility = JsonAutoDetect.Visibility.NONE, fieldVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
public class NpmPackageSearchResultJson {
@ -95,7 +94,7 @@ public class NpmPackageSearchResultJson {
private String myDescription;
@JsonProperty("fhirVersion")
private List<String> myFhirVersion;
@ApiModelProperty(value = "The size of this package in bytes", example = "1000")
@Schema(description = "The size of this package in bytes", example = "1000")
@JsonProperty("_bytes")
private long myBytes;

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

@ -23,12 +23,12 @@ package ca.uhn.fhir.jpa.packages;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import io.swagger.annotations.ApiModel;
import io.swagger.v3.oas.annotations.media.Schema;
import java.util.ArrayList;
import java.util.List;
@ApiModel("Represents an NPM package deletion response")
@Schema(description = "Represents an NPM package deletion response")
@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonAutoDetect(creatorVisibility = JsonAutoDetect.Visibility.NONE, fieldVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
public class PackageDeleteOutcomeJson {

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

@ -23,14 +23,14 @@ package ca.uhn.fhir.jpa.packages;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import io.swagger.annotations.ApiModel;
import io.swagger.v3.oas.annotations.media.Schema;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@ApiModel("Represents an NPM package installation response")
@Schema(description = "Represents an NPM package installation response")
@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonAutoDetect(creatorVisibility = JsonAutoDetect.Visibility.NONE, fieldVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
public class PackageInstallOutcomeJson {

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallationSpec.java
View File

@ -27,15 +27,14 @@ import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonPropertyOrder;
import io.swagger.annotations.ApiModel;
import io.swagger.annotations.ApiModelProperty;
import io.swagger.v3.oas.annotations.media.Schema;
import java.util.ArrayList;
import java.util.List;
import java.util.function.Supplier;
@ApiModel(
value = "PackageInstallationSpec",
@Schema(
name = "PackageInstallationSpec",
description =
"Defines a set of instructions for package installation"
)
@ -47,25 +46,25 @@ import java.util.function.Supplier;
@JsonAutoDetect(creatorVisibility = JsonAutoDetect.Visibility.NONE, fieldVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
public class PackageInstallationSpec {
@ApiModelProperty("The direct package URL")
@Schema(description = "The direct package URL")
@JsonProperty("packageUrl")
private String myPackageUrl;
@ApiModelProperty("The NPM package Name")
@Schema(description = "The NPM package Name")
@JsonProperty("name")
private String myName;
@ApiModelProperty("The direct package version")
@Schema(description = "The direct package version")
@JsonProperty("version")
private String myVersion;
@ApiModelProperty("Should resources from this package be extracted from the package and installed into the repository individually")
@Schema(description = "Should resources from this package be extracted from the package and installed into the repository individually")
@JsonProperty("installMode")
private InstallModeEnum myInstallMode;
@ApiModelProperty("If resources are being installed individually, this is list provides the resource types to install. By default, all conformance resources will be installed.")
@Schema(description = "If resources are being installed individually, this is list provides the resource types to install. By default, all conformance resources will be installed.")
@JsonProperty("installResourceTypes")
private List<String> myInstallResourceTypes;
@ApiModelProperty("Should dependencies be automatically resolved, fetched and installed with the same settings")
@Schema(description = "Should dependencies be automatically resolved, fetched and installed with the same settings")
@JsonProperty("fetchDependencies")
private boolean myFetchDependencies;
@ApiModelProperty("Any values provided here will be interpreted as a regex. Dependencies with an ID matching any regex will be skipped.")
@Schema(description = "Any values provided here will be interpreted as a regex. Dependencies with an ID matching any regex will be skipped.")
private List<String> myDependencyExcludes;
@JsonIgnore
private byte[] myPackageContents;

53
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/ValueSetOperationProvider.java
View File

@ -20,11 +20,14 @@ package ca.uhn.fhir.jpa.provider;
* #L%
*/
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.rest.annotation.IdParam;
@ -34,6 +37,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.util.ParametersUtil;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.ICompositeType;
@ -42,6 +46,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import javax.servlet.http.HttpServletRequest;
@ -56,6 +61,9 @@ public class ValueSetOperationProvider extends BaseJpaProvider {
private DaoRegistry myDaoRegistry;
@Autowired
private ITermReadSvc myTermReadSvc;
@Autowired
@Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT_CHAIN)
private ValidationSupportChain myValidationSupportChain;
public void setDaoConfig(DaoConfig theDaoConfig) {
myDaoConfig = theDaoConfig;
@ -69,6 +77,10 @@ public class ValueSetOperationProvider extends BaseJpaProvider {
myTermReadSvc = theTermReadSvc;
}
public void setValidationSupportChain(ValidationSupportChain theValidationSupportChain) {
myValidationSupportChain = theValidationSupportChain;
}
@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true, typeName = "ValueSet")
public IBaseResource expand(
HttpServletRequest theServletRequest,
@ -142,24 +154,37 @@ public class ValueSetOperationProvider extends BaseJpaProvider {
RequestDetails theRequestDetails
) {
IValidationSupport.CodeValidationResult result;
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<IBaseResource, ICompositeType, ICompositeType> dao = getDao();
IPrimitiveType<String> valueSetIdentifier;
if (theValueSetVersion != null) {
valueSetIdentifier = (IPrimitiveType<String>) getContext().getElementDefinition("uri").newInstance();
valueSetIdentifier.setValue(theValueSetUrl.getValue() + "|" + theValueSetVersion);
// If a Remote Terminology Server has been configured, use it
if (myValidationSupportChain != null && myValidationSupportChain.isRemoteTerminologyServiceConfigured()) {
String theSystemString = (theSystem != null && theSystem.hasValue()) ? theSystem.getValueAsString() : null;
String theCodeString = (theCode != null && theCode.hasValue()) ? theCode.getValueAsString() : null;
String theDisplayString = (theDisplay != null && theDisplay.hasValue()) ? theDisplay.getValueAsString() : null;
String theValueSetUrlString = (theValueSetUrl != null && theValueSetUrl.hasValue()) ?
theValueSetUrl.getValueAsString() : null;
result = myValidationSupportChain.validateCode(new ValidationSupportContext(myValidationSupportChain),
new ConceptValidationOptions(), theSystemString, theCodeString, theDisplayString, theValueSetUrlString);
} else {
valueSetIdentifier = theValueSetUrl;
// Otherwise, use the local DAO layer to validate the code
IFhirResourceDaoValueSet<IBaseResource, ICompositeType, ICompositeType> dao = getDao();
IPrimitiveType<String> valueSetIdentifier;
if (theValueSetUrl != null && theValueSetVersion != null) {
valueSetIdentifier = (IPrimitiveType<String>) getContext().getElementDefinition("uri").newInstance();
valueSetIdentifier.setValue(theValueSetUrl.getValue() + "|" + theValueSetVersion);
} else {
valueSetIdentifier = theValueSetUrl;
}
IPrimitiveType<String> codeSystemIdentifier;
if (theSystem != null && theSystemVersion != null) {
codeSystemIdentifier = (IPrimitiveType<String>) getContext().getElementDefinition("uri").newInstance();
codeSystemIdentifier.setValue(theSystem.getValue() + "|" + theSystemVersion);
} else {
codeSystemIdentifier = theSystem;
}
result = dao.validateCode(valueSetIdentifier, theId, theCode, codeSystemIdentifier, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
}
IPrimitiveType<String> codeSystemIdentifier;
if (theSystemVersion != null) {
codeSystemIdentifier = (IPrimitiveType<String>) getContext().getElementDefinition("uri").newInstance();
codeSystemIdentifier.setValue(theSystem.getValue() + "|" + theSystemVersion);
} else {
codeSystemIdentifier = theSystem;
}
IValidationSupport.CodeValidationResult result = dao.validateCode(valueSetIdentifier, theId, theCode, codeSystemIdentifier, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
return BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
} finally {
endRequest(theServletRequest);

45
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java
View File

@ -1,13 +1,19 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
@ -17,6 +23,8 @@ 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.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import javax.servlet.http.HttpServletRequest;
import java.util.List;
@ -43,6 +51,13 @@ import java.util.List;
public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<CodeSystem> {
@Autowired
@Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT_CHAIN)
private ValidationSupportChain myValidationSupportChain;
@Autowired
protected ITermReadSvcR4 myTermSvc;
/**
* $lookup operation
*/
@ -133,11 +148,35 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
RequestDetails theRequestDetails
) {
IValidationSupport.CodeValidationResult result = null;
startRequest(theServletRequest);
try {
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IValidationSupport.CodeValidationResult result = dao.validateCode(theId, theCodeSystemUrl, theVersion, theCode, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
// If a Remote Terminology Server has been configured, use it
if (myValidationSupportChain.isRemoteTerminologyServiceConfigured()) {
String codeSystemUrl = (theCodeSystemUrl != null && theCodeSystemUrl.hasValue()) ?
theCodeSystemUrl.asStringValue() : null;
String code = (theCode != null && theCode.hasValue()) ? theCode.asStringValue() : null;
String display = (theDisplay != null && theDisplay.hasValue()) ? theDisplay.asStringValue() : null;
if (theCoding != null) {
if (theCoding.hasSystem()) {
if (codeSystemUrl != null && !codeSystemUrl.equalsIgnoreCase(theCoding.getSystem())) {
throw new InvalidRequestException("Coding.system '" + theCoding.getSystem() + "' does not equal param url '" + theCodeSystemUrl + "'. Unable to validate-code.");
}
codeSystemUrl = theCoding.getSystem();
code = theCoding.getCode();
display = theCoding.getDisplay();
result = myValidationSupportChain.validateCode(
new ValidationSupportContext(myValidationSupportChain), new ConceptValidationOptions(),
codeSystemUrl, code, display, null);
}
}
} else {
// Otherwise, use the local DAO layer to validate the code
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
result = dao.validateCode(theId, theCodeSystemUrl, theVersion, theCode, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
}
return (Parameters) BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
} finally {
endRequest(theServletRequest);

91
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderPatientR4.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.valueset.BundleTypeEnum;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
@ -18,13 +19,20 @@ import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import org.hl7.fhir.r4.model.Coverage;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UnsignedIntType;
import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletRequest;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -50,6 +58,10 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class BaseJpaResourceProviderPatientR4 extends JpaResourceProviderR4<Patient> {
@Autowired
private MemberMatcherR4Helper myMemberMatcherR4Helper;
/**
* Patient/123/$everything
*/
@ -150,6 +162,85 @@ public class BaseJpaResourceProviderPatientR4 extends JpaResourceProviderR4<Pati
}
/**
* /Patient/$member-match operation
* Basic implementation matching by coverage id or by coverage identifier. Not matching by
* Beneficiary (Patient) demographics in this version
*/
@Operation(name = ProviderConstants.OPERATION_MEMBER_MATCH, idempotent = true, returnParameters = {
@OperationParam(name = "MemberIdentifier", type = StringDt.class)
})
public Parameters patientMemberMatch(
javax.servlet.http.HttpServletRequest theServletRequest,
@Description(shortDefinition = "The target of the operation. Will be returned with Identifier for matched coverage added.")
@OperationParam(name = Constants.PARAM_MEMBER_PATIENT, min = 1, max = 1)
Patient theMemberPatient,
@Description(shortDefinition = "Old coverage information as extracted from beneficiary's card.")
@OperationParam(name = Constants.PARAM_OLD_COVERAGE, min = 1, max = 1)
Coverage oldCoverage,
@Description(shortDefinition = "New Coverage information. Provided as a reference. Optionally returned unmodified.")
@OperationParam(name = Constants.PARAM_NEW_COVERAGE, min = 1, max = 1)
Coverage newCoverage,
RequestDetails theRequestDetails
) {
return doMemberMatchOperation(theServletRequest, theMemberPatient, oldCoverage, newCoverage, theRequestDetails);
}
private Parameters doMemberMatchOperation(HttpServletRequest theServletRequest, Patient theMemberPatient,
Coverage theCoverageToMatch, Coverage theCoverageToLink, RequestDetails theRequestDetails) {
validateParams(theMemberPatient, theCoverageToMatch, theCoverageToLink);
Optional<Coverage> coverageOpt = myMemberMatcherR4Helper.findMatchingCoverage(theCoverageToMatch);
if ( ! coverageOpt.isPresent()) {
String i18nMessage = getContext().getLocalizer().getMessage(
"operation.member.match.error.coverage.not.found");
throw new UnprocessableEntityException(i18nMessage);
}
Coverage coverage = coverageOpt.get();
Optional<Patient> patientOpt = myMemberMatcherR4Helper.getBeneficiaryPatient(coverage);
if (! patientOpt.isPresent()) {
String i18nMessage = getContext().getLocalizer().getMessage(
"operation.member.match.error.beneficiary.not.found");
throw new UnprocessableEntityException(i18nMessage);
}
Patient patient = patientOpt.get();
if (patient.getIdentifier().isEmpty()) {
String i18nMessage = getContext().getLocalizer().getMessage(
"operation.member.match.error.beneficiary.without.identifier");
throw new UnprocessableEntityException(i18nMessage);
}
myMemberMatcherR4Helper.addMemberIdentifierToMemberPatient(theMemberPatient, patient.getIdentifierFirstRep());
return myMemberMatcherR4Helper.buildSuccessReturnParameters(theMemberPatient, theCoverageToLink);
}
private void validateParams(Patient theMemberPatient, Coverage theOldCoverage, Coverage theNewCoverage) {
validateParam(theMemberPatient, Constants.PARAM_MEMBER_PATIENT);
validateParam(theOldCoverage, Constants.PARAM_OLD_COVERAGE);
validateParam(theNewCoverage, Constants.PARAM_NEW_COVERAGE);
}
private void validateParam(Object theParam, String theParamName) {
if (theParam == null) {
String i18nMessage = getContext().getLocalizer().getMessage(
"operation.member.match.error.missing.parameter", theParamName);
throw new UnprocessableEntityException(i18nMessage);
}
}
/**
* Given a list of string types, return only the ID portions of any parameters passed in.
*/

172
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/MemberMatcherR4Helper.java Normal file
View File

@ -0,0 +1,172 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.util.ParametersUtil;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Coverage;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import java.util.Optional;
import static ca.uhn.fhir.rest.api.Constants.PARAM_MEMBER_PATIENT;
import static ca.uhn.fhir.rest.api.Constants.PARAM_NEW_COVERAGE;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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%
*/
public class MemberMatcherR4Helper {
private static final String OUT_COVERAGE_IDENTIFIER_CODE_SYSTEM = "http://terminology.hl7.org/CodeSystem/v2-0203";
private static final String OUT_COVERAGE_IDENTIFIER_CODE = "UMB";
private static final String OUT_COVERAGE_IDENTIFIER_TEXT = "Member Number";
private static final String COVERAGE_TYPE = "Coverage";
private final FhirContext myFhirContext;
@Autowired
private IFhirResourceDao<Coverage> myCoverageDao;
@Autowired
private IFhirResourceDao<Patient> myPatientDao;
public MemberMatcherR4Helper(FhirContext theContext) {
myFhirContext = theContext;
}
/**
* Find Coverage matching the received member (Patient) by coverage id or by coverage identifier
* Matching by member patient demographics is not supported.
*/
public Optional<Coverage> findMatchingCoverage(Coverage theCoverageToMatch) {
// search by received old coverage id
List<IBaseResource> foundCoverages = findCoverageByCoverageId(theCoverageToMatch);
if (foundCoverages.size() == 1 && isCoverage(foundCoverages.get(0))) {
return Optional.of( (Coverage) foundCoverages.get(0) );
}
// search by received old coverage identifier
foundCoverages = findCoverageByCoverageIdentifier(theCoverageToMatch);
if (foundCoverages.size() == 1 && isCoverage(foundCoverages.get(0))) {
return Optional.of( (Coverage) foundCoverages.get(0) );
}
return Optional.empty();
}
private List<IBaseResource> findCoverageByCoverageIdentifier(Coverage theCoverageToMatch) {
TokenOrListParam identifierParam = new TokenOrListParam();
for (Identifier identifier : theCoverageToMatch.getIdentifier()) {
identifierParam.add(identifier.getSystem(), identifier.getValue());
}
SearchParameterMap paramMap = new SearchParameterMap()
.add("identifier", identifierParam);
ca.uhn.fhir.rest.api.server.IBundleProvider retVal = myCoverageDao.search(paramMap);
return retVal.getAllResources();
}
private boolean isCoverage(IBaseResource theIBaseResource) {
return theIBaseResource.fhirType().equals(COVERAGE_TYPE);
}
private List<IBaseResource> findCoverageByCoverageId(Coverage theCoverageToMatch) {
SearchParameterMap paramMap = new SearchParameterMap()
.add("_id", new StringParam(theCoverageToMatch.getId()));
ca.uhn.fhir.rest.api.server.IBundleProvider retVal = myCoverageDao.search(paramMap);
return retVal.getAllResources();
}
public Parameters buildSuccessReturnParameters(Patient theMemberPatient, Coverage theCoverage) {
IBaseParameters parameters = ParametersUtil.newInstance(myFhirContext);
ParametersUtil.addParameterToParameters(myFhirContext, parameters, PARAM_MEMBER_PATIENT, theMemberPatient);
ParametersUtil.addParameterToParameters(myFhirContext, parameters, PARAM_NEW_COVERAGE, theCoverage);
return (Parameters) parameters;
}
public void addMemberIdentifierToMemberPatient(Patient theMemberPatient, Identifier theNewIdentifier) {
Coding coding = new Coding()
.setSystem(OUT_COVERAGE_IDENTIFIER_CODE_SYSTEM)
.setCode(OUT_COVERAGE_IDENTIFIER_CODE)
.setDisplay(OUT_COVERAGE_IDENTIFIER_TEXT)
.setUserSelected(false);
CodeableConcept concept = new CodeableConcept()
.setCoding(Lists.newArrayList(coding))
.setText(OUT_COVERAGE_IDENTIFIER_TEXT);
Identifier newIdentifier = new Identifier()
.setUse(Identifier.IdentifierUse.USUAL)
.setType(concept)
.setSystem(theNewIdentifier.getSystem())
.setValue(theNewIdentifier.getValue());
theMemberPatient.addIdentifier(newIdentifier);
}
public Optional<Patient> getBeneficiaryPatient(Coverage theCoverage) {
if (theCoverage.getBeneficiaryTarget() == null && theCoverage.getBeneficiary() == null) {
return Optional.empty();
}
if (theCoverage.getBeneficiaryTarget() != null
&& ! theCoverage.getBeneficiaryTarget().getIdentifier().isEmpty()) {
return Optional.of(theCoverage.getBeneficiaryTarget());
}
Reference beneficiaryRef = theCoverage.getBeneficiary();
if (beneficiaryRef == null) {
return Optional.empty();
}
if (beneficiaryRef.getResource() != null) {
return Optional.of((Patient) beneficiaryRef.getResource());
}
if (beneficiaryRef.getReference() == null) {
return Optional.empty();
}
Patient beneficiary = myPatientDao.read(new IdDt(beneficiaryRef.getReference()));
return Optional.ofNullable(beneficiary);
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexWriter.java
View File

@ -56,7 +56,7 @@ public class ReindexWriter implements ItemWriter<List<Long>> {
// Note that since our chunk size is 1, there will always be exactly one list
for (List<Long> pidList : thePidLists) {
partitionRunner.runInPartitionedThreads(new SliceImpl<>(pidList), pids -> reindexPids(pidList));
partitionRunner.runInPartitionedThreads(new SliceImpl<>(pidList), pids -> reindexPids(pids));
}
}

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

@ -125,13 +125,13 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
private PartitionSettings myPartitionSettings;
//This constructor used to inject a dummy partitionsettings in test.
public ElasticsearchSvcImpl(PartitionSettings thePartitionSetings, String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
this(theHostname, theUsername, thePassword);
public ElasticsearchSvcImpl(PartitionSettings thePartitionSetings, String theProtocol, String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
this(theProtocol, theHostname, theUsername, thePassword);
this.myPartitionSettings = thePartitionSetings;
}
public ElasticsearchSvcImpl(String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient("http", theHostname, theUsername, thePassword);
public ElasticsearchSvcImpl(String theProtocol, String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theProtocol, theHostname, theUsername, thePassword);
try {
createObservationIndexIfMissing();

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestJPAConfig.java
View File

@ -30,7 +30,13 @@ import javax.persistence.EntityManagerFactory;
public class TestJPAConfig {
@Bean
public DaoConfig daoConfig() {
return new DaoConfig();
DaoConfig retVal = new DaoConfig();
if ("true".equals(System.getProperty("mass_ingestion_mode"))) {
retVal.setMassIngestionMode(true);
}
return retVal;
}
@Bean

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

@ -53,6 +53,9 @@ public class TestR4Config extends BaseJavaConfigR4 {
if ("true".equals(System.getProperty("single_db_connection"))) {
ourMaxThreads = 1;
}
if ("true".equals(System.getProperty("unlimited_db_connection"))) {
ourMaxThreads = 100;
}
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticsearchClient.java
View File

@ -21,7 +21,7 @@ public class TestR4ConfigWithElasticsearchClient extends TestR4ConfigWithElastic
public ElasticsearchSvcImpl myElasticsearchSvc() {
int elasticsearchPort = elasticContainer().getMappedPort(9200);
String host = elasticContainer().getHost();
return new ElasticsearchSvcImpl(host + ":" + elasticsearchPort, null, null);
return new ElasticsearchSvcImpl("http", host + ":" + elasticsearchPort, null, null);
}
@PreDestroy

65
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
View File

@ -39,29 +39,27 @@ import org.hl7.fhir.r4.model.ServiceRequest;
import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.MethodOrderer;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestMethodOrder;
import javax.annotation.Nonnull;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.StringTokenizer;
import java.util.concurrent.Callable;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.in;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.when;
@TestMethodOrder(MethodOrderer.MethodName.class)
public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4QueryCountTest.class);
@ -70,7 +68,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
myDaoConfig.setResourceMetaCountHardLimit(new DaoConfig().getResourceMetaCountHardLimit());
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
myDaoConfig.setDeleteEnabled(new DaoConfig().isDeleteEnabled());
myDaoConfig.setMatchUrlCache(new DaoConfig().getMatchUrlCache());
myDaoConfig.setMatchUrlCacheEnabled(new DaoConfig().isMatchUrlCacheEnabled());
myDaoConfig.setHistoryCountMode(DaoConfig.DEFAULT_HISTORY_COUNT_MODE);
myDaoConfig.setMassIngestionMode(new DaoConfig().isMassIngestionMode());
myModelConfig.setAutoVersionReferenceAtPaths(new ModelConfig().getAutoVersionReferenceAtPaths());
@ -811,7 +809,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(5, myCaptureQueriesListener.countInsertQueries());
assertEquals(1, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(()->assertEquals(4, myResourceTableDao.count()));
runInTransaction(() -> assertEquals(4, myResourceTableDao.count()));
// Run it again - This time even the match URL should be cached
@ -822,7 +820,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(4, myCaptureQueriesListener.countInsertQueries());
assertEquals(1, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(()->assertEquals(7, myResourceTableDao.count()));
runInTransaction(() -> assertEquals(7, myResourceTableDao.count()));
// Once more for good measure
@ -833,28 +831,28 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(4, myCaptureQueriesListener.countInsertQueries());
assertEquals(1, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(()->assertEquals(10, myResourceTableDao.count()));
runInTransaction(() -> assertEquals(10, myResourceTableDao.count()));
}
@Nonnull
private Bundle createTransactionWithCreatesAndOneMatchUrl() {
BundleBuilder bb = new BundleBuilder(myFhirCtx);
BundleBuilder bb = new BundleBuilder(myFhirCtx);
Patient p = new Patient();
p.setId(IdType.newRandomUuid());
p.setActive(true);
bb.addTransactionCreateEntry(p);
Patient p = new Patient();
p.setId(IdType.newRandomUuid());
p.setActive(true);
bb.addTransactionCreateEntry(p);
Encounter enc = new Encounter();
enc.setSubject(new Reference(p.getId()));
enc.addParticipant().setIndividual(new Reference("Practitioner?identifier=foo|bar"));
bb.addTransactionCreateEntry(enc);
Encounter enc = new Encounter();
enc.setSubject(new Reference(p.getId()));
enc.addParticipant().setIndividual(new Reference("Practitioner?identifier=foo|bar"));
bb.addTransactionCreateEntry(enc);
enc = new Encounter();
enc.setSubject(new Reference(p.getId()));
enc.addParticipant().setIndividual(new Reference("Practitioner?identifier=foo|bar"));
bb.addTransactionCreateEntry(enc);
enc = new Encounter();
enc.setSubject(new Reference(p.getId()));
enc.addParticipant().setIndividual(new Reference("Practitioner?identifier=foo|bar"));
bb.addTransactionCreateEntry(enc);
return (Bundle) bb.getBundle();
}
@ -870,6 +868,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
Practitioner pract = new Practitioner();
pract.addIdentifier().setSystem("foo").setValue("bar");
myPractitionerDao.create(pract);
runInTransaction(() -> assertEquals(1, myResourceTableDao.count(), () -> myResourceTableDao.findAll().stream().map(t -> t.getIdDt().toUnqualifiedVersionless().getValue()).collect(Collectors.joining(","))));
// First pass
@ -881,7 +880,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(5, myCaptureQueriesListener.countInsertQueries());
assertEquals(1, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(()->assertEquals(4, myResourceTableDao.count()));
runInTransaction(() -> assertEquals(4, myResourceTableDao.count(), () -> myResourceTableDao.findAll().stream().map(t -> t.getIdDt().toUnqualifiedVersionless().getValue()).collect(Collectors.joining(","))));
// Run it again - This time even the match URL should be cached
@ -892,7 +891,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(4, myCaptureQueriesListener.countInsertQueries());
assertEquals(1, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(()->assertEquals(7, myResourceTableDao.count()));
runInTransaction(() -> assertEquals(7, myResourceTableDao.count()));
// Once more for good measure
@ -903,7 +902,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(4, myCaptureQueriesListener.countInsertQueries());
assertEquals(1, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(()->assertEquals(10, myResourceTableDao.count()));
runInTransaction(() -> assertEquals(10, myResourceTableDao.count()));
}
@ -923,9 +922,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
pt2.addIdentifier().setSystem("http://foo").setValue("456");
bb.addTransactionCreateEntry(pt2);
runInTransaction(() -> {
assertEquals(0, myResourceTableDao.count());
});
runInTransaction(() -> assertEquals(0, myResourceTableDao.count()));
ourLog.info("About to start transaction");
@ -940,9 +937,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
runInTransaction(() -> {
assertEquals(2, myResourceTableDao.count());
});
runInTransaction(() -> assertEquals(2, myResourceTableDao.count()));
}
@Test
@ -1299,7 +1294,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
* Third time with mass ingestion mode enabled
*/
myDaoConfig.setMassIngestionMode(true);
myDaoConfig.setMatchUrlCache(true);
myDaoConfig.setMatchUrlCacheEnabled(true);
myCaptureQueriesListener.clear();
outcome = mySystemDao.transaction(mySrd, input.get());
@ -1331,7 +1326,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
@Test
public void testTransactionWithConditionalCreate_MatchUrlCacheEnabled() {
myDaoConfig.setMatchUrlCache(true);
myDaoConfig.setMatchUrlCacheEnabled(true);
Supplier<Bundle> bundleCreator = () -> {
BundleBuilder bb = new BundleBuilder(myFhirCtx);
@ -2155,7 +2150,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
@Test
public void testMassIngestionMode_TransactionWithChanges() {
myDaoConfig.setDeleteEnabled(false);
myDaoConfig.setMatchUrlCache(true);
myDaoConfig.setMatchUrlCacheEnabled(true);
myDaoConfig.setMassIngestionMode(true);
myFhirCtx.getParserOptions().setStripVersionsFromReferences(false);
myModelConfig.setRespectVersionsForSearchIncludes(true);
@ -2219,7 +2214,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
@Test
public void testMassIngestionMode_TransactionWithChanges_2() throws IOException {
myDaoConfig.setDeleteEnabled(false);
myDaoConfig.setMatchUrlCache(true);
myDaoConfig.setMatchUrlCacheEnabled(true);
myDaoConfig.setMassIngestionMode(true);
myFhirCtx.getParserOptions().setStripVersionsFromReferences(false);
myModelConfig.setRespectVersionsForSearchIncludes(true);

106
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -55,9 +55,7 @@ import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.param.UriParamQualifierEnum;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.util.CollectionUtil;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.ResourceUtil;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
@ -133,11 +131,6 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.CsvFileSource;
import org.junit.jupiter.params.provider.CsvSource;
import org.junit.jupiter.params.provider.MethodSource;
import org.mockito.ArgumentCaptor;
import org.mockito.ArgumentMatchers;
import org.springframework.beans.factory.annotation.Autowired;
@ -149,12 +142,9 @@ import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import javax.servlet.http.HttpServletRequest;
import java.io.BufferedReader;
import java.io.IOException;
import java.math.BigDecimal;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
@ -162,7 +152,6 @@ import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import static ca.uhn.fhir.rest.api.Constants.PARAM_TYPE;
import static org.apache.commons.lang3.StringUtils.countMatches;
@ -190,17 +179,12 @@ import static org.mockito.Mockito.verify;
@SuppressWarnings({"unchecked", "Duplicates"})
@TestPropertySource(properties = {
BaseJpaTest.CONFIG_ENABLE_LUCENE_FALSE
})
})
public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4SearchNoFtTest.class);
@Autowired
MatchUrlService myMatchUrlService;
@BeforeAll
public static void beforeAllTest(){
System.setProperty("user.timezone", "EST");
}
@AfterEach
public void afterResetSearchSize() {
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
@ -209,6 +193,9 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
myModelConfig.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
myModelConfig.setAutoSupportDefaultSearchParams(true);
mySearchParamRegistry.resetForUnitTest();
}
@BeforeEach
@ -217,6 +204,35 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Test
public void testDisableAutoSupportDefaultSearchParams() {
myModelConfig.setAutoSupportDefaultSearchParams(false);
mySearchParamRegistry.resetForUnitTest();
Patient patient = new Patient();
patient.setActive(true);
patient.addName().setFamily("FAMILY");
myPatientDao.create(patient);
runInTransaction(() -> {
assertEquals(0, myResourceIndexedSearchParamStringDao.count());
assertEquals(0, myResourceIndexedSearchParamTokenDao.count());
});
SearchParameterMap map = SearchParameterMap.newSynchronous("name", new StringParam("FAMILY"));
try {
myPatientDao.search(map, mySrd);
fail();
} catch (InvalidRequestException e) {
// good
}
// Make sure we can support mandatory SPs
map = SearchParameterMap.newSynchronous("url", new UriParam("http://foo"));
myCodeSystemDao.search(map, mySrd); // should not fail
}
@Test
public void testSearchInExistingTransaction() {
createPatient(withBirthdate("2021-01-01"));
@ -237,8 +253,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testCanonicalReference() {
StructureDefinition sd = new StructureDefinition();
@ -665,7 +679,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
/**
* See #1053
*/
@ -1061,7 +1074,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testHasParameterChained() {
IIdType pid0;
@ -1415,15 +1427,15 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
Bundle bundleResponse = mySystemDao.transaction(new SystemRequestDetails(), firstBundle);
bundleResponse.getEntry()
.forEach( entry -> assertThat(entry.getResponse().getStatus(), is(equalTo("201 Created"))));
.forEach(entry -> assertThat(entry.getResponse().getStatus(), is(equalTo("201 Created"))));
IBundleProvider search = myOrganizationDao.search(new SearchParameterMap().setLoadSynchronous(true));
assertEquals(1, search.getAllResources().size());
//Running the bundle again should just result in 0 new resources created, as the org should already exist, and there is no update to the SR.
bundleResponse= mySystemDao.transaction(new SystemRequestDetails(), duplicateBundle);
bundleResponse = mySystemDao.transaction(new SystemRequestDetails(), duplicateBundle);
bundleResponse.getEntry()
.forEach( entry -> {
.forEach(entry -> {
assertThat(entry.getResponse().getStatus(), is(equalTo("200 OK")));
});
@ -1574,7 +1586,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testPeriodWithNoStart() {
ServiceRequest serviceRequest = new ServiceRequest();
@ -1611,7 +1622,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
});
}
@Test
public void testSearchByIdParamInverse() {
String id1;
@ -1641,7 +1651,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testSearchByIdParam_QueryIsMinimal() {
// With only an _id parameter
@ -1919,7 +1928,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testSearchWithIncludeStarQualified() {
@ -1984,7 +1992,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(ids, containsInAnyOrder(obsId, encId));
}
@Test
public void testComponentQuantity() {
Observation o1 = new Observation();
@ -2061,7 +2068,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchDate_TimingValueUsingPeriod() {
ServiceRequest p1 = new ServiceRequest();
@ -2081,7 +2087,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchDateWrongParam() {
Patient p1 = new Patient();
@ -2105,7 +2110,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testDateRangeOnPeriod_SearchByDateTime_NoUpperBound() {
Encounter enc = new Encounter();
@ -2153,7 +2157,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(ids, empty());
}
@Test
public void testDateRangeOnPeriod_SearchByDate_NoUpperBound() {
Encounter enc = new Encounter();
@ -2201,7 +2204,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(ids, empty());
}
@Test
public void testDateRangeOnPeriod_SearchByDateTime_NoLowerBound() {
Encounter enc = new Encounter();
@ -2249,7 +2251,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(ids, contains(id1));
}
@Test
public void testDateRangeOnPeriod_SearchByDate_NoLowerBound() {
Encounter enc = new Encounter();
@ -2297,7 +2298,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(ids, contains(id1));
}
@Test
public void testDatePeriodParamEndOnly() {
{
@ -2436,7 +2436,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
/**
* See #1174
*/
@ -2546,7 +2545,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchLastUpdatedParam() {
String methodName = "testSearchLastUpdatedParam";
@ -2861,7 +2859,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchNumberParam() {
RiskAssessment e1 = new RiskAssessment();
@ -2985,7 +2982,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchParamChangesType() {
String name = "testSearchParamChangesType";
@ -3133,7 +3129,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testSearchResourceLinkWithChain() {
Patient patient = new Patient();
@ -3417,7 +3412,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testSearchTokenListWithMixedCombinations() {
@ -3665,7 +3659,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertEquals(5, countMatches(searchQuery.toUpperCase(), "LEFT OUTER JOIN"), searchQuery);
}
@Test
public void testSearchWithDateRange() {
@ -3792,7 +3785,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchDoubleToken() {
Patient patient = new Patient();
@ -3829,7 +3821,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchDoubleString() {
Patient patient = new Patient();
@ -4297,7 +4288,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchReferenceUntyped() {
Patient p = new Patient();
@ -4334,7 +4324,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertEquals("This search uses an unqualified resource(a parameter in a chain without a resource type). This is less efficient than using a qualified type. If you know what you're looking for, try qualifying it using the form: 'entity:[resourceType]'", message.getMessage());
}
@Test
public void testSearchWithDateAndReusesExistingJoin() {
// Add a search parameter to Observation.issued, so that between that one
@ -4434,7 +4423,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testSearchWithFetchSizeDefaultMaximum() {
myDaoConfig.setFetchSizeDefaultMaximum(5);
@ -5119,7 +5107,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
p.addName().setFamily("A1");
myPatientDao.create(p);
runInTransaction(()->assertEquals(0, mySearchEntityDao.count()));
runInTransaction(() -> assertEquals(0, mySearchEntityDao.count()));
SearchParameterMap map = new SearchParameterMap();
StringOrListParam or = new StringOrListParam();
@ -5130,7 +5118,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
map.add(Patient.SP_NAME, or);
IBundleProvider results = myPatientDao.search(map);
assertEquals(1, results.getResources(0, 10).size());
runInTransaction(()->assertEquals(1, mySearchEntityDao.count()));
runInTransaction(() -> assertEquals(1, mySearchEntityDao.count()));
map = new SearchParameterMap();
or = new StringOrListParam();
@ -5143,7 +5131,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
results = myPatientDao.search(map);
assertEquals(1, results.getResources(0, 10).size());
// We expect a new one because we don't cache the search URL for very long search URLs
runInTransaction(()->assertEquals(2, mySearchEntityDao.count()));
runInTransaction(() -> assertEquals(2, mySearchEntityDao.count()));
}
@Test
@ -5189,7 +5177,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testDateSearchParametersShouldBeTimezoneIndependent() {
@ -5316,7 +5303,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
));
}
private void createObservationWithEffective(String theId, String theEffective) {
Observation obs = new Observation();
obs.setId(theId);
@ -5337,7 +5323,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
p.addName().setFamily("A1");
myPatientDao.create(p);
runInTransaction(()->assertEquals(0, mySearchEntityDao.count()));
runInTransaction(() -> assertEquals(0, mySearchEntityDao.count()));
SearchParameterMap map = new SearchParameterMap();
StringOrListParam or = new StringOrListParam();
@ -5348,7 +5334,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
map.add(Patient.SP_NAME, or);
IBundleProvider results = myPatientDao.search(map);
assertEquals(1, results.getResources(0, 10).size());
assertEquals(1, runInTransaction(()->mySearchEntityDao.count()));
assertEquals(1, runInTransaction(() -> mySearchEntityDao.count()));
map = new SearchParameterMap();
or = new StringOrListParam();
@ -5359,7 +5345,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
map.add(Patient.SP_NAME, or);
results = myPatientDao.search(map);
assertEquals(1, results.getResources(0, 10).size());
assertEquals(1, runInTransaction(()->mySearchEntityDao.count()));
assertEquals(1, runInTransaction(() -> mySearchEntityDao.count()));
}
@ -5404,7 +5390,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(toUnqualifiedVersionlessIdValues(outcome), contains(crId));
}
@Test
public void testSearchWithTwoChainedDates() {
// Matches
@ -5457,7 +5442,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testCircularReferencesDontBreakRevIncludes() {
@ -5495,7 +5479,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
private String toStringMultiline(List<?> theResults) {
StringBuilder b = new StringBuilder();
for (Object next : theResults) {
@ -5505,5 +5488,10 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
return b.toString();
}
@BeforeAll
public static void beforeAllTest() {
System.setProperty("user.timezone", "EST");
}
}

20
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
View File

@ -136,6 +136,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
myDaoConfig.setBundleBatchMaxPoolSize(new DaoConfig().getBundleBatchMaxPoolSize());
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(new DaoConfig().isAutoCreatePlaceholderReferenceTargets());
myModelConfig.setAutoVersionReferenceAtPaths(new ModelConfig().getAutoVersionReferenceAtPaths());
myFhirCtx.getParserOptions().setAutoContainReferenceTargetsWithNoId(true);
}
@BeforeEach
@ -1043,6 +1044,25 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
assertThat(task.getBasedOn().get(0).getReference(), matchesPattern("Patient/[0-9]+"));
}
@Test
public void testTransactionNoContainedRedux_ContainedProcessingDisabled() throws IOException {
myFhirCtx.getParserOptions().setAutoContainReferenceTargetsWithNoId(false);
//Pre-create the patient, which will cause the ifNoneExist to prevent a new creation during bundle transaction
Patient patient = loadResourceFromClasspath(Patient.class, "/r4/preexisting-patient.json");
myPatientDao.create(patient);
//Post the Bundle containing a conditional POST with an identical patient from the above resource.
Bundle request = loadResourceFromClasspath(Bundle.class, "/r4/transaction-no-contained-2.json");
Bundle outcome = mySystemDao.transaction(mySrd, request);
IdType taskId = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
Task task = myTaskDao.read(taskId, mySrd);
assertThat(task.getBasedOn().get(0).getReference(), matchesPattern("Patient/[0-9]+"));
}
@Test
public void testTransactionNoContained() throws IOException {

203
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SyntheaPerfTest.java Normal file
View File

@ -0,0 +1,203 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.config.TestR4Config;
import ca.uhn.fhir.jpa.config.TestR4WithLuceneDisabledConfig;
import ca.uhn.fhir.jpa.dao.BaseJpaTest;
import ca.uhn.fhir.jpa.dao.BaseTransactionProcessor;
import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.search.reindex.BlockPolicy;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.StopWatch;
import org.apache.commons.compress.utils.Lists;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Meta;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.transaction.PlatformTransactionManager;
import java.io.FileReader;
import java.io.IOException;
import java.nio.file.FileSystems;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
@ExtendWith(SpringExtension.class)
@ContextConfiguration(classes = {TestR4WithLuceneDisabledConfig.class})
@DirtiesContext
public class SyntheaPerfTest extends BaseJpaTest {
@BeforeAll
public static void beforeAll() {
System.setProperty("unlimited_db_connection", "true");
System.setProperty("mass_ingestion_mode", "true");
}
@AfterAll
public static void afterAll() {
System.clearProperty("unlimited_db_connection");
System.clearProperty("mass_ingestion_mode");
}
@AfterEach
public void afterEach() {
myCtx.getParserOptions().setAutoContainReferenceTargetsWithNoId(true);
}
private static final Logger ourLog = LoggerFactory.getLogger(SyntheaPerfTest.class);
private static final FhirContext ourCtx = FhirContext.forR4Cached();
public static final String PATH_TO_SYNTHEA_OUTPUT = "../../synthea/output/fhir/";
public static final int CONCURRENCY = 4;
@Autowired
private FhirContext myCtx;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private IFhirSystemDao<Bundle, Meta> mySystemDao;
@Disabled
@Test
public void testLoadSynthea() throws Exception {
assertEquals(100, TestR4Config.getMaxThreads());
myDaoConfig.setResourceEncoding(ResourceEncodingEnum.JSON);
myDaoConfig.setTagStorageMode(DaoConfig.TagStorageModeEnum.INLINE);
myDaoConfig.setMatchUrlCacheEnabled(true);
myDaoConfig.setDeleteEnabled(false);
myCtx.getParserOptions().setAutoContainReferenceTargetsWithNoId(false);
assertTrue(myDaoConfig.isMassIngestionMode());
List<Path> files = Files
.list(FileSystems.getDefault().getPath(PATH_TO_SYNTHEA_OUTPUT))
.filter(t->t.toString().endsWith(".json"))
.collect(Collectors.toList());
List<Path> meta = files.stream().filter(t -> t.toString().contains("hospital") || t.toString().contains("practitioner")).collect(Collectors.toList());
new Uploader(meta);
List<Path> nonMeta = files.stream().filter(t -> !t.toString().contains("hospital") && !t.toString().contains("practitioner")).collect(Collectors.toList());
// new Uploader(Collections.singletonList(nonMeta.remove(0)));
// new Uploader(Collections.singletonList(nonMeta.remove(0)));
// new Uploader(Collections.singletonList(nonMeta.remove(0)));
new Uploader(Collections.singletonList(nonMeta.remove(0)));
new Uploader(nonMeta);
}
@Override
protected FhirContext getContext() {
return myCtx;
}
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
private class Uploader {
private final ThreadPoolTaskExecutor myExecutor;
private final int myTotal;
private final StopWatch mySw;
private final AtomicInteger myFilesCounter = new AtomicInteger(0);
private final AtomicInteger myResourcesCounter = new AtomicInteger(0);
public Uploader(List<Path> thePaths) throws ExecutionException, InterruptedException {
Validate.isTrue(thePaths.size() > 0);
myTotal = thePaths.size();
myExecutor = new ThreadPoolTaskExecutor();
myExecutor.setCorePoolSize(0);
myExecutor.setMaxPoolSize(CONCURRENCY);
myExecutor.setQueueCapacity(100);
myExecutor.setAllowCoreThreadTimeOut(true);
myExecutor.setThreadNamePrefix("Uploader-");
myExecutor.setRejectedExecutionHandler(new BlockPolicy());
myExecutor.initialize();
mySw = new StopWatch();
List<Future<?>> futures = new ArrayList<>();
for (Path next : thePaths) {
futures.add(myExecutor.submit(new MyTask(next)));
}
for (Future<?> next : futures) {
next.get();
}
ourLog.info("Finished uploading {} files with {} resources in {} - {} files/sec - {} res/sec",
myFilesCounter.get(),
myResourcesCounter.get(),
mySw,
mySw.formatThroughput(myFilesCounter.get(), TimeUnit.SECONDS),
mySw.formatThroughput(myResourcesCounter.get(), TimeUnit.SECONDS));
}
private class MyTask implements Runnable {
private final Path myPath;
public MyTask(Path thePath) {
myPath = thePath;
}
@Override
public void run() {
Bundle bundle;
try (FileReader reader = new FileReader(myPath.toFile())) {
bundle = ourCtx.newJsonParser().parseResource(Bundle.class, reader);
} catch (IOException e) {
throw new InternalErrorException(e);
}
mySystemDao.transaction(new SystemRequestDetails(myInterceptorRegistry), bundle);
int fileCount = myFilesCounter.incrementAndGet();
myResourcesCounter.addAndGet(bundle.getEntry().size());
if (fileCount % 10 == 0) {
ourLog.info("Have uploaded {} files with {} resources in {} - {} files/sec - {} res/sec",
myFilesCounter.get(),
myResourcesCounter.get(),
mySw,
mySw.formatThroughput(myFilesCounter.get(), TimeUnit.SECONDS),
mySw.formatThroughput(myResourcesCounter.get(), TimeUnit.SECONDS));
}
}
}
}
}

241
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MemberMatcherR4HelperTest.java Normal file
View File

@ -0,0 +1,241 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import com.google.common.collect.Lists;
import org.hl7.fhir.r4.model.Coverage;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Answers;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.springframework.test.util.ReflectionTestUtils;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import static ca.uhn.fhir.rest.api.Constants.PARAM_MEMBER_PATIENT;
import static ca.uhn.fhir.rest.api.Constants.PARAM_NEW_COVERAGE;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.ArgumentMatchers.isA;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
class MemberMatcherR4HelperTest {
private final FhirContext myFhirContext = FhirContext.forR4();
@Mock private IFhirResourceDao<Coverage> myCoverageDao;
@Mock private IFhirResourceDao<Patient> myPatientDao;
private MemberMatcherR4Helper myTestedHelper;
@Mock private Coverage myCoverageToMatch;
@Mock private Patient myPatient;
@Mock private IBundleProvider myBundleProvider;
private final Coverage myMatchedCoverage = new Coverage();
private final Identifier myMatchingIdentifier = new Identifier()
.setSystem("identifier-system").setValue("identifier-value");
@Captor ArgumentCaptor<SearchParameterMap> mySearchParameterMapCaptor;
@BeforeEach
public void beforeEach() {
myTestedHelper = new MemberMatcherR4Helper(myFhirContext);
// @InjectMocks didn't work
ReflectionTestUtils.setField(myTestedHelper, "myCoverageDao", myCoverageDao);
ReflectionTestUtils.setField(myTestedHelper, "myPatientDao", myPatientDao);
}
@Test
void findMatchingCoverageMatchByIdReturnsMatched() {
when(myCoverageToMatch.getId()).thenReturn("cvg-to-match-id");
when(myCoverageDao.search(isA(SearchParameterMap.class))).thenReturn(myBundleProvider);
when(myBundleProvider.getAllResources()).thenReturn(Collections.singletonList(myMatchedCoverage));
Optional<Coverage> result = myTestedHelper.findMatchingCoverage(myCoverageToMatch);
assertEquals(Optional.of(myMatchedCoverage), result);
verify(myCoverageDao).search(mySearchParameterMapCaptor.capture());
SearchParameterMap spMap = mySearchParameterMapCaptor.getValue();
assertTrue(spMap.containsKey("_id"));
List<List<IQueryParameterType>> listListParams = spMap.get("_id");
assertEquals(1, listListParams.size());
assertEquals(1, listListParams.get(0).size());
IQueryParameterType param = listListParams.get(0).get(0);
assertEquals("cvg-to-match-id", param.getValueAsQueryToken(myFhirContext));
}
@Test
void findMatchingCoverageMatchByIdentifierReturnsMatched() {
when(myCoverageToMatch.getId()).thenReturn("non-matching-id");
when(myCoverageToMatch.getIdentifier()).thenReturn(Collections.singletonList(myMatchingIdentifier));
when(myCoverageDao.search(isA(SearchParameterMap.class))).thenReturn(myBundleProvider);
when(myBundleProvider.getAllResources()).thenReturn(
Collections.emptyList(), Collections.singletonList(myMatchedCoverage));
Optional<Coverage> result = myTestedHelper.findMatchingCoverage(myCoverageToMatch);
assertEquals(Optional.of(myMatchedCoverage), result);
verify(myCoverageDao, times(2)).search(mySearchParameterMapCaptor.capture());
List<SearchParameterMap> spMap = mySearchParameterMapCaptor.getAllValues();
assertTrue(spMap.get(0).containsKey("_id"));
assertTrue(spMap.get(1).containsKey("identifier"));
List<List<IQueryParameterType>> listListParams = spMap.get(1).get("identifier");
assertEquals(1, listListParams.size());
assertEquals(1, listListParams.get(0).size());
IQueryParameterType param = listListParams.get(0).get(0);
assertEquals(myMatchingIdentifier.getSystem() + "|" + myMatchingIdentifier.getValue(),
param.getValueAsQueryToken(myFhirContext));
}
@Test
void findMatchingCoverageNoMatchReturnsEmpty() {
when(myCoverageToMatch.getId()).thenReturn("non-matching-id");
when(myCoverageToMatch.getIdentifier()).thenReturn(Collections.singletonList(myMatchingIdentifier));
when(myCoverageDao.search(isA(SearchParameterMap.class))).thenReturn(myBundleProvider);
when(myBundleProvider.getAllResources()).thenReturn(Collections.emptyList(), Collections.emptyList());
Optional<Coverage> result = myTestedHelper.findMatchingCoverage(myCoverageToMatch);
assertFalse(result.isPresent());
}
@Test
void buildSuccessReturnParameters() {
Patient patient = new Patient();
Coverage coverage = new Coverage();
Parameters result = myTestedHelper.buildSuccessReturnParameters(patient, coverage);
assertEquals(PARAM_MEMBER_PATIENT, result.getParameter().get(0).getName());
assertEquals(patient, result.getParameter().get(0).getResource());
assertEquals(PARAM_NEW_COVERAGE, result.getParameter().get(1).getName());
assertEquals(coverage, result.getParameter().get(1).getResource());
}
@Test
void addMemberIdentifierToMemberPatient() {
Identifier originalIdentifier = new Identifier()
.setSystem("original-identifier-system").setValue("original-identifier-value");
Identifier newIdentifier = new Identifier()
.setSystem("new-identifier-system").setValue("new-identifier-value");
Patient patient = new Patient().setIdentifier(Lists.newArrayList(originalIdentifier));
myTestedHelper.addMemberIdentifierToMemberPatient(patient, newIdentifier);
assertEquals(2, patient.getIdentifier().size());
assertEquals("original-identifier-system", patient.getIdentifier().get(0).getSystem());
assertEquals("original-identifier-value", patient.getIdentifier().get(0).getValue());
assertEquals("new-identifier-system", patient.getIdentifier().get(1).getSystem());
assertEquals("new-identifier-value", patient.getIdentifier().get(1).getValue());
}
@Nested
public class TestGetBeneficiaryPatient {
@Mock(answer = Answers.RETURNS_DEEP_STUBS)
private Coverage coverage;
@Test
void noBeneficiaryOrBeneficiaryTargetReturnsEmpty() {
when(coverage.getBeneficiaryTarget()).thenReturn(null);
when(coverage.getBeneficiary()).thenReturn(null);
Optional<Patient> result = myTestedHelper.getBeneficiaryPatient(coverage);
assertFalse(result.isPresent());
}
@Test
void beneficiaryTargetWithNoIdentifierReturnsEmpty() {
when(coverage.getBeneficiary()).thenReturn(null);
when(coverage.getBeneficiaryTarget()).thenReturn(new Patient());
Optional<Patient> result = myTestedHelper.getBeneficiaryPatient(coverage);
assertFalse(result.isPresent());
}
@Test
void beneficiaryTargetWithIdentifierReturnsBeneficiary() {
Patient patient = new Patient().setIdentifier(Collections.singletonList(new Identifier()));
when(coverage.getBeneficiaryTarget()).thenReturn(patient);
Optional<Patient> result = myTestedHelper.getBeneficiaryPatient(coverage);
assertTrue(result.isPresent());
assertEquals(patient, result.get());
}
@Test
void beneficiaryReferenceResourceReturnsBeneficiary() {
Patient patient = new Patient().setIdentifier(Collections.singletonList(new Identifier()));
when(coverage.getBeneficiaryTarget()).thenReturn(null);
when(coverage.getBeneficiary().getResource()).thenReturn(patient);
Optional<Patient> result = myTestedHelper.getBeneficiaryPatient(coverage);
assertTrue(result.isPresent());
assertEquals(patient, result.get());
}
@Test
void beneficiaryReferenceNoResourceOrReferenceReturnsEmpty() {
when(coverage.getBeneficiaryTarget()).thenReturn(null);
when(coverage.getBeneficiary()).thenReturn(new Reference());
Optional<Patient> result = myTestedHelper.getBeneficiaryPatient(coverage);
assertFalse(result.isPresent());
}
@Test
void beneficiaryReferenceReferenceReturnsReadPatient() {
when(coverage.getBeneficiaryTarget()).thenReturn(null);
when(coverage.getBeneficiary().getResource()).thenReturn(null);
when(coverage.getBeneficiary().getReference()).thenReturn("patient-id");
myTestedHelper.getBeneficiaryPatient(coverage);
verify(myPatientDao).read(new IdDt("patient-id"));
}
}
}

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package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.client.apache.ResourceEntity;
import ca.uhn.fhir.util.ParametersUtil;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Coverage;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import java.nio.charset.StandardCharsets;
import java.util.Collections;
import java.util.List;
import static ca.uhn.fhir.rest.api.Constants.PARAM_MEMBER_PATIENT;
import static ca.uhn.fhir.rest.api.Constants.PARAM_NEW_COVERAGE;
import static ca.uhn.fhir.rest.api.Constants.PARAM_OLD_COVERAGE;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@SuppressWarnings("Duplicates")
public class PatientMemberMatchOperationR4Test extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(PatientMemberMatchOperationR4Test.class);
private static final String ourQuery = "/Patient/$member-match?_format=json";
private static final String EXISTING_COVERAGE_ID = "cov-id-123";
private static final String EXISTING_COVERAGE_IDENT_SYSTEM = "http://centene.com/insurancePlanIds";
private static final String EXISTING_COVERAGE_IDENT_VALUE = "U1234567890";
private static final String EXISTING_COVERAGE_PATIENT_IDENT_SYSTEM = "http://oldhealthplan.example.com";
private static final String EXISTING_COVERAGE_PATIENT_IDENT_VALUE = "DHU-55678";
private Identifier ourExistingCoverageIdentifier;
@BeforeEach
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Override
@AfterEach
public void after() throws Exception {
super.after();
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
myDaoConfig.setEverythingIncludesFetchPageSize(new DaoConfig().getEverythingIncludesFetchPageSize());
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
}
@Override
@BeforeEach
public void before() throws Exception {
super.before();
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
}
private void createCoverageWithBeneficiary(
boolean theAssociateBeneficiaryPatient, boolean includeBeneficiaryIdentifier) {
Patient member = null;
if (theAssociateBeneficiaryPatient) {
// Patient
member = new Patient().setName(Lists.newArrayList(new HumanName()
.setUse(HumanName.NameUse.OFFICIAL).setFamily("Person").addGiven("Patricia").addGiven("Ann")));
if (includeBeneficiaryIdentifier) {
member.setIdentifier(Collections.singletonList(new Identifier()
.setSystem(EXISTING_COVERAGE_PATIENT_IDENT_SYSTEM).setValue(EXISTING_COVERAGE_PATIENT_IDENT_VALUE)));
}
myClient.create().resource(member).execute().getId().toUnqualifiedVersionless().getValue();
}
// Coverage
ourExistingCoverageIdentifier = new Identifier()
.setSystem(EXISTING_COVERAGE_IDENT_SYSTEM).setValue(EXISTING_COVERAGE_IDENT_VALUE);
Coverage ourExistingCoverage = new Coverage()
.setStatus(Coverage.CoverageStatus.ACTIVE)
.setIdentifier(Collections.singletonList(ourExistingCoverageIdentifier));
if (theAssociateBeneficiaryPatient) {
// this doesn't work
// myOldCoverage.setBeneficiaryTarget(patient)
ourExistingCoverage.setBeneficiary(new Reference(member))
.setId(EXISTING_COVERAGE_ID);
}
myClient.create().resource(ourExistingCoverage).execute().getId().toUnqualifiedVersionless().getValue();
}
@Test
public void testMemberMatchByCoverageId() throws Exception {
createCoverageWithBeneficiary(true, true);
// patient doesn't participate in match
Patient patient = new Patient().setGender(Enumerations.AdministrativeGender.FEMALE);
// Old Coverage
Coverage oldCoverage = new Coverage();
oldCoverage.setId(EXISTING_COVERAGE_ID); // must match field
// New Coverage (must return unchanged)
Coverage newCoverage = new Coverage();
newCoverage.setId("AA87654");
newCoverage.setIdentifier(Lists.newArrayList(
new Identifier().setSystem("http://newealthplan.example.com").setValue("234567")));
Parameters inputParameters = buildInputParameters(patient, oldCoverage, newCoverage);
Parameters parametersResponse = performOperation(ourServerBase + ourQuery,
EncodingEnum.JSON, inputParameters);
validateMemberPatient(parametersResponse);
validateNewCoverage(parametersResponse, newCoverage);
}
@Test
public void testCoverageNoBeneficiaryReturns422() throws Exception {
createCoverageWithBeneficiary(false, false);
// patient doesn't participate in match
Patient patient = new Patient().setGender(Enumerations.AdministrativeGender.FEMALE);
// Old Coverage
Coverage oldCoverage = new Coverage();
oldCoverage.setId(EXISTING_COVERAGE_ID); // must match field
// New Coverage (must return unchanged)
Coverage newCoverage = new Coverage();
newCoverage.setId("AA87654");
newCoverage.setIdentifier(Lists.newArrayList(
new Identifier().setSystem("http://newealthplan.example.com").setValue("234567")));
Parameters inputParameters = buildInputParameters(patient, oldCoverage, newCoverage);
performOperationExpecting422(ourServerBase + ourQuery, EncodingEnum.JSON, inputParameters,
"Could not find beneficiary for coverage.");
}
@Test
public void testCoverageBeneficiaryNoIdentifierReturns422() throws Exception {
createCoverageWithBeneficiary(true, false);
// patient doesn't participate in match
Patient patient = new Patient().setGender(Enumerations.AdministrativeGender.FEMALE);
// Old Coverage
Coverage oldCoverage = new Coverage();
oldCoverage.setId(EXISTING_COVERAGE_ID); // must match field
// New Coverage (must return unchanged)
Coverage newCoverage = new Coverage();
newCoverage.setId("AA87654");
newCoverage.setIdentifier(Lists.newArrayList(
new Identifier().setSystem("http://newealthplan.example.com").setValue("234567")));
Parameters inputParameters = buildInputParameters(patient, oldCoverage, newCoverage);
performOperationExpecting422(ourServerBase + ourQuery, EncodingEnum.JSON, inputParameters,
"Coverage beneficiary does not have an identifier.");
}
@Nested
public class ValidateParameterErrors {
private Patient ourPatient;
private Coverage ourOldCoverage;
private Coverage ourNewCoverage;
@BeforeEach
public void beforeValidateParameterErrors() {
ourPatient = new Patient().setGender(Enumerations.AdministrativeGender.FEMALE);
ourOldCoverage = new Coverage();
ourOldCoverage.setId(EXISTING_COVERAGE_ID);
ourNewCoverage = new Coverage();
ourNewCoverage.setId("AA87654");
ourNewCoverage.setIdentifier(Lists.newArrayList(
new Identifier().setSystem("http://newealthplan.example.com").setValue("234567")));
}
@Test
public void testInvalidPatient() throws Exception {
Parameters inputParameters = buildInputParameters(new Patient(), ourOldCoverage, ourNewCoverage);
performOperationExpecting422(ourServerBase + ourQuery, EncodingEnum.JSON, inputParameters,
"Parameter \\\"" + PARAM_MEMBER_PATIENT + "\\\" is required.");
}
@Test
public void testInvalidOldCoverage() throws Exception {
Parameters inputParameters = buildInputParameters(ourPatient, new Coverage(), ourNewCoverage);
performOperationExpecting422(ourServerBase + ourQuery, EncodingEnum.JSON, inputParameters,
"Parameter \\\"" + PARAM_OLD_COVERAGE + "\\\" is required.");
}
@Test
public void testInvalidNewCoverage() throws Exception {
Parameters inputParameters = buildInputParameters(ourPatient, ourOldCoverage, new Coverage());
performOperationExpecting422(ourServerBase + ourQuery, EncodingEnum.JSON, inputParameters,
"Parameter \\\"" + PARAM_NEW_COVERAGE + "\\\" is required.");
}
}
@Test
public void testMemberMatchByCoverageIdentifier() throws Exception {
createCoverageWithBeneficiary(true, true);
// patient doesn't participate in match
Patient patient = new Patient().setGender(Enumerations.AdministrativeGender.FEMALE);
// Old Coverage
Coverage oldCoverage = new Coverage();
oldCoverage.setId("9876B1");
oldCoverage.setIdentifier(Lists.newArrayList(ourExistingCoverageIdentifier)); // must match field
// New Coverage (must return unchanged)
Coverage newCoverage = new Coverage();
newCoverage.setId("AA87654");
newCoverage.setIdentifier(Lists.newArrayList(
new Identifier().setSystem("http://newealthplan.example.com").setValue("234567")));
Parameters inputParameters = buildInputParameters(patient, oldCoverage, newCoverage);
Parameters parametersResponse = performOperation(ourServerBase + ourQuery, EncodingEnum.JSON, inputParameters);
validateMemberPatient(parametersResponse);
validateNewCoverage(parametersResponse, newCoverage);
}
/**
* Validates that second resource from the response is same as the received coverage
*/
private void validateNewCoverage(Parameters theResponse, Coverage theOriginalCoverage) {
List<IBase> patientList = ParametersUtil.getNamedParameters(getContext(), theResponse, PARAM_NEW_COVERAGE);
assertEquals(1, patientList.size());
Coverage respCoverage = (Coverage) theResponse.getParameter().get(1).getResource();
assertEquals("Coverage/" + theOriginalCoverage.getId(), respCoverage.getId());
assertEquals(theOriginalCoverage.getIdentifierFirstRep().getSystem(), respCoverage.getIdentifierFirstRep().getSystem());
assertEquals(theOriginalCoverage.getIdentifierFirstRep().getValue(), respCoverage.getIdentifierFirstRep().getValue());
}
private void validateMemberPatient(Parameters response) {
// parameter MemberPatient must have a new identifier with:
// {
// "use": "usual",
// "type": {
// "coding": [
// {
// "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
// "code": "UMB",
// "display": "Member Number",
// "userSelected": false
// }
// ],
// "text": "Member Number"
// },
// "system": COVERAGE_PATIENT_IDENT_SYSTEM,
// "value": COVERAGE_PATIENT_IDENT_VALUE
// }
List<IBase> patientList = ParametersUtil.getNamedParameters(getContext(), response, PARAM_MEMBER_PATIENT);
assertEquals(1, patientList.size());
Patient resultPatient = (Patient) response.getParameter().get(0).getResource();
assertNotNull(resultPatient.getIdentifier());
assertEquals(1, resultPatient.getIdentifier().size());
Identifier addedIdentifier = resultPatient.getIdentifier().get(0);
assertEquals(Identifier.IdentifierUse.USUAL, addedIdentifier.getUse());
checkCoding(addedIdentifier.getType());
assertEquals(EXISTING_COVERAGE_PATIENT_IDENT_SYSTEM, addedIdentifier.getSystem());
assertEquals(EXISTING_COVERAGE_PATIENT_IDENT_VALUE, addedIdentifier.getValue());
}
@Test
public void testNoCoverageMatchFound() throws Exception {
// Patient doesn't participate in match
Patient patient = new Patient().setGender(Enumerations.AdministrativeGender.FEMALE);
// Old Coverage
Coverage oldCoverage = new Coverage();
oldCoverage.setId("9876B1");
oldCoverage.setIdentifier(Lists.newArrayList(
new Identifier().setSystem("http://oldhealthplan.example.com").setValue("DH10001235")));
// New Coverage
Organization newOrg = new Organization();
newOrg.setId("Organization/ProviderOrg1");
newOrg.setName("New Health Plan");
Coverage newCoverage = new Coverage();
newCoverage.setId("AA87654");
newCoverage.getContained().add(newOrg);
newCoverage.setIdentifier(Lists.newArrayList(
new Identifier().setSystem("http://newealthplan.example.com").setValue("234567")));
Parameters inputParameters = buildInputParameters(patient, oldCoverage, newCoverage);
performOperationExpecting422(ourServerBase + ourQuery, EncodingEnum.JSON, inputParameters,
"Could not find coverage for member");
}
private Parameters buildInputParameters(Patient thePatient, Coverage theOldCoverage, Coverage theNewCoverage) {
Parameters p = new Parameters();
ParametersUtil.addParameterToParameters(getContext(), p, PARAM_MEMBER_PATIENT, thePatient);
ParametersUtil.addParameterToParameters(getContext(), p, PARAM_OLD_COVERAGE, theOldCoverage);
ParametersUtil.addParameterToParameters(getContext(), p, PARAM_NEW_COVERAGE, theNewCoverage);
return p;
}
private Parameters performOperation(String theUrl,
EncodingEnum theEncoding, Parameters theInputParameters) throws Exception {
HttpPost post = new HttpPost(theUrl);
post.addHeader(Constants.HEADER_ACCEPT_ENCODING, theEncoding.toString());
post.setEntity(new ResourceEntity(getContext(), theInputParameters));
ourLog.info("Request: {}", post);
try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
assertEquals(200, response.getStatusLine().getStatusCode());
return theEncoding.newParser(myFhirCtx).parseResource(Parameters.class,
IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8));
}
}
private void performOperationExpecting422(String theUrl, EncodingEnum theEncoding,
Parameters theInputParameters, String theExpectedErrorMsg) throws Exception {
HttpPost post = new HttpPost(theUrl);
post.addHeader(Constants.HEADER_ACCEPT_ENCODING, theEncoding.toString());
post.setEntity(new ResourceEntity(getContext(), theInputParameters));
ourLog.info("Request: {}", post);
try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info("Response: {}", responseString);
assertEquals(422, response.getStatusLine().getStatusCode());
assertThat(responseString, containsString(theExpectedErrorMsg));
}
}
private void checkCoding(CodeableConcept theType) {
// must match:
// "coding": [
// {
// "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
// "code": "UMB",
// "display": "Member Number",
// "userSelected": false
// }
// * ]
Coding coding = theType.getCoding().get(0);
assertEquals("http://terminology.hl7.org/CodeSystem/v2-0203", coding.getSystem());
assertEquals("UMB", coding.getCode());
assertEquals("Member Number", coding.getDisplay());
assertFalse(coding.getUserSelected());
}
}

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package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
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 org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
import javax.servlet.http.HttpServletRequest;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
/*
* This set of Unit Tests simulates the call to a remote server and therefore, only tests the code in the
* {@link org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport#invokeRemoteValidateCode}
* method, before and after it makes that remote client call.
*/
public class RemoteTerminologyServiceResourceProviderR4Test {
private static final String DISPLAY = "DISPLAY";
private static final String CODE_SYSTEM = "CODE_SYS";
private static final String CODE = "CODE";
private static final String VALUE_SET_URL = "http://value.set/url";
private static final String SAMPLE_MESSAGE = "This is a sample message";
private static FhirContext ourCtx = FhirContext.forR4();
private MyCodeSystemProvider myCodeSystemProvider = new MyCodeSystemProvider();
private MyValueSetProvider myValueSetProvider = new MyValueSetProvider();
@RegisterExtension
public RestfulServerExtension myRestfulServerExtension = new RestfulServerExtension(ourCtx, myCodeSystemProvider,
myValueSetProvider);
private RemoteTerminologyServiceValidationSupport mySvc;
@BeforeEach
public void before_ConfigureService() {
String myBaseUrl = "http://localhost:" + myRestfulServerExtension.getPort();
mySvc = new RemoteTerminologyServiceValidationSupport(ourCtx, myBaseUrl);
}
@AfterEach
public void after_UnregisterProviders() {
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.ONCE);
myRestfulServerExtension.getRestfulServer().getInterceptorService().unregisterAllInterceptors();
}
@Test
public void testValidateCodeInCodeSystem_BlankCode_ReturnsNull() {
IValidationSupport.CodeValidationResult outcome = mySvc
.validateCode(null, null, CODE_SYSTEM, null, DISPLAY, null);
assertNull(outcome);
}
@Test
public void testValidateCodeInCodeSystem_ProvidingMinimalInputs_ReturnsSuccess() {
createNextCodeSystemReturnParameters(true, null, null);
IValidationSupport.CodeValidationResult outcome = mySvc
.validateCode(null, null, CODE_SYSTEM, CODE, null, null);
assertEquals(CODE, outcome.getCode());
assertEquals(null, outcome.getSeverity());
assertEquals(null, outcome.getMessage());
assertEquals(CODE, myCodeSystemProvider.myLastCode.getCode());
assertEquals(CODE_SYSTEM, myCodeSystemProvider.myLastUrl.getValueAsString());
}
@Test
public void testValidateCodeInCodeSystem_WithMessageValue_ReturnsMessage() {
createNextCodeSystemReturnParameters(true, DISPLAY, SAMPLE_MESSAGE);
IValidationSupport.CodeValidationResult outcome = mySvc
.validateCode(null, null, CODE_SYSTEM, CODE, DISPLAY, null);
assertEquals(CODE, outcome.getCode());
assertEquals(DISPLAY, outcome.getDisplay());
assertEquals(null, outcome.getSeverity());
assertEquals(null, outcome.getMessage());
assertEquals(CODE, myCodeSystemProvider.myLastCode.getCode());
assertEquals(DISPLAY, myCodeSystemProvider.myLastDisplay.getValue());
assertEquals(CODE_SYSTEM, myCodeSystemProvider.myLastUrl.getValueAsString());
assertEquals(SAMPLE_MESSAGE, myCodeSystemProvider.myNextReturnParams.getParameter("message").toString());
}
@Test
public void testValidateCodeInCodeSystem_AssumeFailure_ReturnsFailureCodeAndFailureMessage() {
createNextCodeSystemReturnParameters(false, null, SAMPLE_MESSAGE);
IValidationSupport.CodeValidationResult outcome = mySvc
.validateCode(null, null, CODE_SYSTEM, CODE, null, null);
assertEquals(IValidationSupport.IssueSeverity.ERROR, outcome.getSeverity());
assertEquals(SAMPLE_MESSAGE, outcome.getMessage());
assertEquals(false, ((BooleanType)myCodeSystemProvider.myNextReturnParams.getParameter("result")).booleanValue());
}
@Test
public void testValidateCodeInValueSet_ProvidingMinimalInputs_ReturnsSuccess() {
createNextValueSetReturnParameters(true, null, null);
IValidationSupport.CodeValidationResult outcome = mySvc
.validateCode(null, null, CODE_SYSTEM, CODE, null, VALUE_SET_URL);
assertEquals(CODE, outcome.getCode());
assertEquals(null, outcome.getSeverity());
assertEquals(null, outcome.getMessage());
assertEquals(CODE, myValueSetProvider.myLastCode.getCode());
assertEquals(VALUE_SET_URL, myValueSetProvider.myLastUrl.getValueAsString());
}
@Test
public void testValidateCodeInValueSet_WithMessageValue_ReturnsMessage() {
createNextValueSetReturnParameters(true, DISPLAY, SAMPLE_MESSAGE);
IValidationSupport.CodeValidationResult outcome = mySvc
.validateCode(null, null, CODE_SYSTEM, CODE, DISPLAY, VALUE_SET_URL);
assertEquals(CODE, outcome.getCode());
assertEquals(DISPLAY, outcome.getDisplay());
assertEquals(null, outcome.getSeverity());
assertEquals(null, outcome.getMessage());
assertEquals(CODE, myValueSetProvider.myLastCode.getCode());
assertEquals(DISPLAY, myValueSetProvider.myLastDisplay.getValue());
assertEquals(VALUE_SET_URL, myValueSetProvider.myLastUrl.getValueAsString());
assertEquals(SAMPLE_MESSAGE, myValueSetProvider.myNextReturnParams.getParameter("message").toString());
}
private void createNextCodeSystemReturnParameters(boolean theResult, String theDisplay, String theMessage) {
myCodeSystemProvider.myNextReturnParams = new Parameters();
myCodeSystemProvider.myNextReturnParams.addParameter("result", theResult);
myCodeSystemProvider.myNextReturnParams.addParameter("display", theDisplay);
if (theMessage != null) {
myCodeSystemProvider.myNextReturnParams.addParameter("message", theMessage);
}
}
private void createNextValueSetReturnParameters(boolean theResult, String theDisplay, String theMessage) {
myValueSetProvider.myNextReturnParams = new Parameters();
myValueSetProvider.myNextReturnParams.addParameter("result", theResult);
myValueSetProvider.myNextReturnParams.addParameter("display", theDisplay);
if (theMessage != null) {
myValueSetProvider.myNextReturnParams.addParameter("message", theMessage);
}
}
private static class MyCodeSystemProvider implements IResourceProvider {
private UriParam myLastUrlParam;
private List<CodeSystem> myNextReturnCodeSystems;
private int myInvocationCount;
private UriType myLastUrl;
private CodeType myLastCode;
private StringType myLastDisplay;
private Parameters myNextReturnParams;
@Operation(name = "validate-code", idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1),
@OperationParam(name = "message", type = StringType.class),
@OperationParam(name = "display", type = StringType.class)
})
public Parameters validateCode(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theCodeSystemUrl,
@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay
) {
myInvocationCount++;
myLastUrl = theCodeSystemUrl;
myLastCode = theCode;
myLastDisplay = theDisplay;
return myNextReturnParams;
}
@Search
public List<CodeSystem> find(@RequiredParam(name = "url") UriParam theUrlParam) {
myLastUrlParam = theUrlParam;
assert myNextReturnCodeSystems != null;
return myNextReturnCodeSystems;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return CodeSystem.class;
}
}
private static class MyValueSetProvider implements IResourceProvider {
private Parameters myNextReturnParams;
private List<ValueSet> myNextReturnValueSets;
private UriType myLastUrl;
private CodeType myLastCode;
private int myInvocationCount;
private UriType myLastSystem;
private StringType myLastDisplay;
private ValueSet myLastValueSet;
private UriParam myLastUrlParam;
@Operation(name = "validate-code", idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1),
@OperationParam(name = "message", type = StringType.class),
@OperationParam(name = "display", type = StringType.class)
})
public Parameters validateCode(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theValueSetUrl,
@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay,
@OperationParam(name = "valueSet") ValueSet theValueSet
) {
myInvocationCount++;
myLastUrl = theValueSetUrl;
myLastCode = theCode;
myLastSystem = theSystem;
myLastDisplay = theDisplay;
myLastValueSet = theValueSet;
return myNextReturnParams;
}
@Search
public List<ValueSet> find(@RequiredParam(name = "url") UriParam theUrlParam) {
myLastUrlParam = theUrlParam;
assert myNextReturnValueSets != null;
return myNextReturnValueSets;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return ValueSet.class;
}
}
}

270
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4RemoteTerminologyTest.java Normal file
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@ -0,0 +1,270 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.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 org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import javax.servlet.http.HttpServletRequest;
import java.util.ArrayList;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertThrows;
/*
* This set of Unit Tests instantiates and injects an instance of
* {@link org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport}
* into the ValidationSupportChain, which tests the logic of dynamically selecting the correct Remote Terminology
* implementation. It also exercises the code found in
* {@link org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport#invokeRemoteValidateCode}
*/
public class ResourceProviderR4RemoteTerminologyTest extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4RemoteTerminologyTest.class);
private static final String DISPLAY = "DISPLAY";
private static final String DISPLAY_BODY_MASS_INDEX = "Body mass index (BMI) [Ratio]";
private static final String CODE_BODY_MASS_INDEX = "39156-5";
private static FhirContext ourCtx = FhirContext.forR4();
private MyCodeSystemProvider myCodeSystemProvider = new MyCodeSystemProvider();
private MyValueSetProvider myValueSetProvider = new MyValueSetProvider();
@RegisterExtension
public RestfulServerExtension myRestfulServerExtension = new RestfulServerExtension(ourCtx, myCodeSystemProvider,
myValueSetProvider);
private RemoteTerminologyServiceValidationSupport mySvc;
@Autowired
@Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT_CHAIN)
private ValidationSupportChain myValidationSupportChain;
@BeforeEach
public void before_addRemoteTerminologySupport() throws Exception {
String baseUrl = "http://localhost:" + myRestfulServerExtension.getPort();
mySvc = new RemoteTerminologyServiceValidationSupport(ourCtx, baseUrl);
myValidationSupportChain.addValidationSupport(0, mySvc);
}
@AfterEach
public void after_removeRemoteTerminologySupport() {
myValidationSupportChain.removeValidationSupport(mySvc);
myRestfulServerExtension.getRestfulServer().getInterceptorService().unregisterAllInterceptors();
}
@Test
public void testValidateCodeOperationOnCodeSystem_ByCodingAndUrlWhereSystemIsDifferent_ThrowsException() {
assertThrows(InvalidRequestException.class, () -> {
Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named(JpaConstants.OPERATION_VALIDATE_CODE)
.withParameter(Parameters.class, "coding", new Coding().setSystem("http://terminology.hl7.org/CodeSystem/v2-0247").setCode("P"))
.andParameter("url", new UriType("http://terminology.hl7.org/CodeSystem/INVALID-CODESYSTEM"))
.execute();
});
}
@Test
public void testValidateCodeOperationOnCodeSystem_ByCodingAndUrl_UsingBuiltInCodeSystems() {
myCodeSystemProvider.myNextReturnCodeSystems = new ArrayList<>();
myCodeSystemProvider.myNextReturnCodeSystems.add((CodeSystem) new CodeSystem().setId("CodeSystem/v2-0247"));
createNextCodeSystemReturnParameters(true, DISPLAY, null);
Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named(JpaConstants.OPERATION_VALIDATE_CODE)
.withParameter(Parameters.class, "coding", new Coding().setSystem("http://terminology.hl7.org/CodeSystem/v2-0247").setCode("P"))
.andParameter("url", new UriType("http://terminology.hl7.org/CodeSystem/v2-0247"))
.execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType)respParam.getParameter("result")).booleanValue());
assertEquals(DISPLAY, respParam.getParameter("display").toString());
}
@Test
public void testValidateCodeOperationOnValueSet_ByUrlAndSystem_UsingBuiltInCodeSystems() {
myCodeSystemProvider.myNextReturnCodeSystems = new ArrayList<>();
myCodeSystemProvider.myNextReturnCodeSystems.add((CodeSystem) new CodeSystem().setId("CodeSystem/list-example-use-codes"));
myValueSetProvider.myNextReturnValueSets = new ArrayList<>();
myValueSetProvider.myNextReturnValueSets.add((ValueSet) new ValueSet().setId("ValueSet/list-example-codes"));
createNextValueSetReturnParameters(true, DISPLAY, null);
Parameters respParam = myClient
.operation()
.onType(ValueSet.class)
.named(JpaConstants.OPERATION_VALIDATE_CODE)
.withParameter(Parameters.class, "code", new CodeType("alerts"))
.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/list-example-use-codes"))
.andParameter("url", new UriType("http://hl7.org/fhir/ValueSet/list-example-codes"))
.useHttpGet()
.execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType)respParam.getParameter("result")).booleanValue());
assertEquals(DISPLAY, respParam.getParameter("display").toString());
}
@Test
public void testValidateCodeOperationOnValueSet_ByUrlSystemAndCode() {
myCodeSystemProvider.myNextReturnCodeSystems = new ArrayList<>();
myCodeSystemProvider.myNextReturnCodeSystems.add((CodeSystem) new CodeSystem().setId("CodeSystem/list-example-use-codes"));
myValueSetProvider.myNextReturnValueSets = new ArrayList<>();
myValueSetProvider.myNextReturnValueSets.add((ValueSet) new ValueSet().setId("ValueSet/list-example-codes"));
createNextValueSetReturnParameters(true, DISPLAY_BODY_MASS_INDEX, null);
Parameters respParam = myClient
.operation()
.onType(ValueSet.class)
.named(JpaConstants.OPERATION_VALIDATE_CODE)
.withParameter(Parameters.class, "code", new CodeType(CODE_BODY_MASS_INDEX))
.andParameter("url", new UriType("https://loinc.org"))
.andParameter("system", new UriType("http://loinc.org"))
.execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType)respParam.getParameter("result")).booleanValue());
assertEquals(DISPLAY_BODY_MASS_INDEX, respParam.getParameter("display").toString());
}
private void createNextCodeSystemReturnParameters(boolean theResult, String theDisplay, String theMessage) {
myCodeSystemProvider.myNextReturnParams = new Parameters();
myCodeSystemProvider.myNextReturnParams.addParameter("result", theResult);
myCodeSystemProvider.myNextReturnParams.addParameter("display", theDisplay);
if (theMessage != null) {
myCodeSystemProvider.myNextReturnParams.addParameter("message", theMessage);
}
}
private void createNextValueSetReturnParameters(boolean theResult, String theDisplay, String theMessage) {
myValueSetProvider.myNextReturnParams = new Parameters();
myValueSetProvider.myNextReturnParams.addParameter("result", theResult);
myValueSetProvider.myNextReturnParams.addParameter("display", theDisplay);
if (theMessage != null) {
myValueSetProvider.myNextReturnParams.addParameter("message", theMessage);
}
}
private static class MyCodeSystemProvider implements IResourceProvider {
private UriParam myLastUrlParam;
private List<CodeSystem> myNextReturnCodeSystems;
private int myInvocationCount;
private UriType myLastUrl;
private CodeType myLastCode;
private StringType myLastDisplay;
private Parameters myNextReturnParams;
@Operation(name = "validate-code", idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1),
@OperationParam(name = "message", type = StringType.class),
@OperationParam(name = "display", type = StringType.class)
})
public Parameters validateCode(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theCodeSystemUrl,
@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay
) {
myInvocationCount++;
myLastUrl = theCodeSystemUrl;
myLastCode = theCode;
myLastDisplay = theDisplay;
return myNextReturnParams;
}
@Search
public List<CodeSystem> find(@RequiredParam(name = "url") UriParam theUrlParam) {
myLastUrlParam = theUrlParam;
assert myNextReturnCodeSystems != null;
return myNextReturnCodeSystems;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return CodeSystem.class;
}
}
private static class MyValueSetProvider implements IResourceProvider {
private Parameters myNextReturnParams;
private List<ValueSet> myNextReturnValueSets;
private UriType myLastUrl;
private CodeType myLastCode;
private int myInvocationCount;
private UriType myLastSystem;
private StringType myLastDisplay;
private ValueSet myLastValueSet;
private UriParam myLastUrlParam;
@Operation(name = "validate-code", idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1),
@OperationParam(name = "message", type = StringType.class),
@OperationParam(name = "display", type = StringType.class)
})
public Parameters validateCode(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theValueSetUrl,
@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay,
@OperationParam(name = "valueSet") ValueSet theValueSet
) {
myInvocationCount++;
myLastUrl = theValueSetUrl;
myLastCode = theCode;
myLastSystem = theSystem;
myLastDisplay = theDisplay;
myLastValueSet = theValueSet;
return myNextReturnParams;
}
@Search
public List<ValueSet> find(@RequiredParam(name = "url") UriParam theUrlParam) {
myLastUrlParam = theUrlParam;
assert myNextReturnValueSets != null;
return myNextReturnValueSets;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return ValueSet.class;
}
}
}

51
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/reindex/job/ReindexWriterTest.java Normal file
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@ -0,0 +1,51 @@
package ca.uhn.fhir.jpa.reindex.job;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexer;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.springframework.transaction.PlatformTransactionManager;
import java.util.ArrayList;
import java.util.List;
import static org.mockito.ArgumentMatchers.anyLong;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.verifyNoMoreInteractions;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class ReindexWriterTest {
@Mock
private DaoConfig myDaoConfig;
@Mock
private PlatformTransactionManager myPlatformTransactionManager;
@Mock
ResourceReindexer myResourceReindexer;
@InjectMocks
private ReindexWriter myReindexWriter;
@Test
public void testReindexSplitsPidList() throws Exception {
when(myDaoConfig.getReindexBatchSize()).thenReturn(5);
when(myDaoConfig.getReindexThreadCount()).thenReturn(4);
List<Long> pidList = new ArrayList<>();
int count = 20;
for (long i = 0; i < count; ++i) {
pidList.add(i);
}
List<List<Long>> pidListList = new ArrayList<>();
pidListList.add(pidList);
myReindexWriter.write(pidListList);
verify(myResourceReindexer, times(count)).readAndReindexResourceByPid(anyLong());
verifyNoMoreInteractions(myResourceReindexer);
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcMultipleObservationsIT.java
View File

@ -67,7 +67,7 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
public void before() throws IOException {
PartitionSettings partitionSettings = new PartitionSettings();
partitionSettings.setPartitioningEnabled(false);
elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), null, null);
elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, "http", elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), null, null);
if (!indexLoaded) {
createMultiplePatientsAndObservations();

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcSingleObservationIT.java
View File

@ -90,7 +90,7 @@ public class LastNElasticsearchSvcSingleObservationIT {
public void before() {
PartitionSettings partitionSettings = new PartitionSettings();
partitionSettings.setPartitioningEnabled(false);
elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), "", "");
elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, "http", elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), "", "");
}
@AfterEach

47
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmMessageKeySvc.java Normal file
View File

@ -0,0 +1,47 @@
package ca.uhn.fhir.jpa.mdm.broker;
/*-
* #%L
* HAPI FHIR JPA Server - Master Data Management
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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.subscription.api.ISubscriptionMessageKeySvc;
import ca.uhn.fhir.mdm.model.CanonicalEID;
import ca.uhn.fhir.mdm.util.EIDHelper;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.annotation.Nullable;
import java.util.List;
@Service
public class MdmMessageKeySvc implements ISubscriptionMessageKeySvc {
@Autowired
private EIDHelper myEIDHelper;
@Nullable
@Override
public String getMessageKeyOrNull(IBaseResource theTargetResource) {
List<CanonicalEID> eidList = myEIDHelper.getExternalEid(theTargetResource);
if (eidList.isEmpty()) {
return null;
}
return eidList.get(0).getValue();
}
}

5
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmConsumerConfig.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.batch.mdm.MdmBatchJobSubmitterFactoryImpl;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDeleteSvc;
import ca.uhn.fhir.jpa.interceptor.MdmSearchExpandingInterceptor;
import ca.uhn.fhir.jpa.mdm.broker.MdmMessageHandler;
import ca.uhn.fhir.jpa.mdm.broker.MdmMessageKeySvc;
import ca.uhn.fhir.jpa.mdm.broker.MdmQueueConsumerLoader;
import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
import ca.uhn.fhir.jpa.mdm.dao.MdmLinkFactory;
@ -104,6 +105,10 @@ public class MdmConsumerConfig {
return new MdmMessageHandler();
}
@Bean
MdmMessageKeySvc mdmMessageKeySvc() {
return new MdmMessageKeySvc();
}
@Bean
MdmMatchLinkSvc mdmMatchLinkSvc() {
return new MdmMatchLinkSvc();

6
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmResourceDaoSvc.java
View File

@ -77,7 +77,7 @@ public class MdmResourceDaoSvc {
//TODO GGG MDM address this
public Optional<IAnyResource> searchGoldenResourceByEID(String theEid, String theResourceType) {
SearchParameterMap map = buildEidSearchParameterMap(theEid);
SearchParameterMap map = buildEidSearchParameterMap(theEid, theResourceType);
IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theResourceType);
IBundleProvider search = resourceDao.search(map);
@ -101,10 +101,10 @@ public class MdmResourceDaoSvc {
}
@Nonnull
private SearchParameterMap buildEidSearchParameterMap(String theTheEid) {
private SearchParameterMap buildEidSearchParameterMap(String theEid, String theResourceType) {
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add("identifier", new TokenParam(myMdmSettings.getMdmRules().getEnterpriseEIDSystem(), theTheEid));
map.add("identifier", new TokenParam(myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType(theResourceType), theEid));
map.add("_tag", new TokenParam(MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS, MdmConstants.CODE_GOLDEN_RECORD));
return map;
}

4
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java
View File

@ -327,12 +327,12 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
}
protected Patient addExternalEID(Patient thePatient, String theEID) {
thePatient.addIdentifier().setSystem(myMdmSettings.getMdmRules().getEnterpriseEIDSystem()).setValue(theEID);
thePatient.addIdentifier().setSystem(myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType("Patient")).setValue(theEID);
return thePatient;
}
protected Patient clearExternalEIDs(Patient thePatient) {
thePatient.getIdentifier().removeIf(theIdentifier -> theIdentifier.getSystem().equalsIgnoreCase(myMdmSettings.getMdmRules().getEnterpriseEIDSystem()));
thePatient.getIdentifier().removeIf(theIdentifier -> theIdentifier.getSystem().equalsIgnoreCase(myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType("Patient")));
return thePatient;
}

4
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcMultipleEidModeTest.java
View File

@ -71,11 +71,11 @@ public class MdmMatchLinkSvcMultipleEidModeTest extends BaseMdmR4Test {
//The collision should have added a new identifier with the external system.
Identifier secondIdentifier = identifier.get(1);
assertThat(secondIdentifier.getSystem(), is(equalTo(myMdmSettings.getMdmRules().getEnterpriseEIDSystem())));
assertThat(secondIdentifier.getSystem(), is(equalTo(myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType("Patient"))));
assertThat(secondIdentifier.getValue(), is(equalTo("12345")));
Identifier thirdIdentifier = identifier.get(2);
assertThat(thirdIdentifier.getSystem(), is(equalTo(myMdmSettings.getMdmRules().getEnterpriseEIDSystem())));
assertThat(thirdIdentifier.getSystem(), is(equalTo(myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType("Patient"))));
assertThat(thirdIdentifier.getValue(), is(equalTo("67890")));
}

4
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java
View File

@ -157,7 +157,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
Patient patient = getTargetResourceFromMdmLink(mdmLink.get(), "Patient");
List<CanonicalEID> externalEid = myEidHelper.getExternalEid(patient);
assertThat(externalEid.get(0).getSystem(), is(equalTo(myMdmSettings.getMdmRules().getEnterpriseEIDSystem())));
assertThat(externalEid.get(0).getSystem(), is(equalTo(myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType("Patient"))));
assertThat(externalEid.get(0).getValue(), is(equalTo(sampleEID)));
}
@ -222,7 +222,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
//The collision should have added a new identifier with the external system.
Identifier secondIdentifier = identifier.get(1);
assertThat(secondIdentifier.getSystem(), is(equalTo(myMdmSettings.getMdmRules().getEnterpriseEIDSystem())));
assertThat(secondIdentifier.getSystem(), is(equalTo(myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType("Patient"))));
assertThat(secondIdentifier.getValue(), is(equalTo("12345")));
}

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

@ -34,7 +34,6 @@ import javax.persistence.TemporalType;
import javax.persistence.Transient;
import java.util.Collection;
import java.util.Date;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.defaultString;
@ -113,12 +112,16 @@ public abstract class BaseHasResource extends BasePartitionable implements IBase
@Override
public InstantDt getPublished() {
if (myPublished != null) {
return new InstantDt(cloneDate(myPublished));
return new InstantDt(getPublishedDate());
} else {
return null;
}
}
public Date getPublishedDate() {
return cloneDate(myPublished);
}
public void setPublished(Date thePublished) {
myPublished = thePublished;
}
@ -137,7 +140,12 @@ public abstract class BaseHasResource extends BasePartitionable implements IBase
@Override
public InstantDt getUpdated() {
return new InstantDt(cloneDate(myUpdated));
return new InstantDt(getUpdatedDate());
}
@Override
public Date getUpdatedDate() {
return cloneDate(myUpdated);
}
public void setUpdated(Date theUpdated) {
@ -148,11 +156,6 @@ public abstract class BaseHasResource extends BasePartitionable implements IBase
myUpdated = theUpdated.getValue();
}
@Override
public Date getUpdatedDate() {
return cloneDate(myUpdated);
}
@Override
public abstract long getVersion();

104
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ModelConfig.java
View File

@ -28,8 +28,6 @@ import org.hl7.fhir.dstu2.model.Subscription;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.DateTimeType;
import javax.annotation.Nonnull;
import javax.annotation.PostConstruct;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
@ -102,6 +100,7 @@ public class ModelConfig {
private boolean myIndexOnContainedResources = false;
private boolean myIndexOnContainedResourcesRecursively = false;
private boolean myAllowMdmExpansion = false;
private boolean myAutoSupportDefaultSearchParams = true;
/**
* Constructor
@ -162,36 +161,6 @@ public class ModelConfig {
return myAllowContainsSearches;
}
/**
* If enabled, the server will support the use of :mdm search parameter qualifier on Reference Search Parameters.
* This Parameter Qualifier is HAPI-specific, and not defined anywhere in the FHIR specification. Using this qualifier
* will result in an MDM expansion being done on the reference, which will expand the search scope. For example, if Patient/1
* is MDM-matched to Patient/2 and you execute the search:
* Observation?subject:mdm=Patient/1 , you will receive observations for both Patient/1 and Patient/2.
* <p>
* Default is <code>false</code>
* </p>
* @since 5.4.0
*/
public boolean isAllowMdmExpansion() {
return myAllowMdmExpansion;
}
/**
* If enabled, the server will support the use of :mdm search parameter qualifier on Reference Search Parameters.
* This Parameter Qualifier is HAPI-specific, and not defined anywhere in the FHIR specification. Using this qualifier
* will result in an MDM expansion being done on the reference, which will expand the search scope. For example, if Patient/1
* is MDM-matched to Patient/2 and you execute the search:
* Observation?subject:mdm=Patient/1 , you will receive observations for both Patient/1 and Patient/2.
* <p>
* Default is <code>false</code>
* </p>
* @since 5.4.0
*/
public void setAllowMdmExpansion(boolean theAllowMdmExpansion) {
myAllowMdmExpansion = theAllowMdmExpansion;
}
/**
* If enabled, the server will support the use of :contains searches,
* which are helpful but can have adverse effects on performance.
@ -210,6 +179,38 @@ public class ModelConfig {
this.myAllowContainsSearches = theAllowContainsSearches;
}
/**
* If enabled, the server will support the use of :mdm search parameter qualifier on Reference Search Parameters.
* This Parameter Qualifier is HAPI-specific, and not defined anywhere in the FHIR specification. Using this qualifier
* will result in an MDM expansion being done on the reference, which will expand the search scope. For example, if Patient/1
* is MDM-matched to Patient/2 and you execute the search:
* Observation?subject:mdm=Patient/1 , you will receive observations for both Patient/1 and Patient/2.
* <p>
* Default is <code>false</code>
* </p>
*
* @since 5.4.0
*/
public boolean isAllowMdmExpansion() {
return myAllowMdmExpansion;
}
/**
* If enabled, the server will support the use of :mdm search parameter qualifier on Reference Search Parameters.
* This Parameter Qualifier is HAPI-specific, and not defined anywhere in the FHIR specification. Using this qualifier
* will result in an MDM expansion being done on the reference, which will expand the search scope. For example, if Patient/1
* is MDM-matched to Patient/2 and you execute the search:
* Observation?subject:mdm=Patient/1 , you will receive observations for both Patient/1 and Patient/2.
* <p>
* Default is <code>false</code>
* </p>
*
* @since 5.4.0
*/
public void setAllowMdmExpansion(boolean theAllowMdmExpansion) {
myAllowMdmExpansion = theAllowMdmExpansion;
}
/**
* If set to <code>true</code> (default is <code>false</code>) the server will allow
* resources to have references to external servers. For example if this server is
@ -385,7 +386,6 @@ public class ModelConfig {
}
/**
* This setting indicates which subscription channel types are supported by the server. Any subscriptions submitted
* to the server matching these types will be activated.
@ -769,13 +769,13 @@ public class ModelConfig {
/**
* Should indexing and searching on contained resources be enabled on this server.
* This may have performance impacts, and should be enabled only if it is needed. Default is <code>false</code>.
*
*
* @since 5.4.0
*/
public boolean isIndexOnContainedResources() {
return myIndexOnContainedResources;
}
/**
* Should indexing and searching on contained resources be enabled on this server.
* This may have performance impacts, and should be enabled only if it is needed. Default is <code>false</code>.
@ -785,7 +785,7 @@ public class ModelConfig {
public void setIndexOnContainedResources(boolean theIndexOnContainedResources) {
myIndexOnContainedResources = theIndexOnContainedResources;
}
/**
* Should recursive indexing and searching on contained resources be enabled on this server.
* This may have performance impacts, and should be enabled only if it is needed. Default is <code>false</code>.
@ -806,6 +806,38 @@ public class ModelConfig {
myIndexOnContainedResourcesRecursively = theIndexOnContainedResourcesRecursively;
}
/**
* If this is disabled by setting this to {@literal false} (default is {@literal true}),
* the server will not automatically implement and support search parameters that
* are not explcitly created in the repository.
* <p>
* Disabling this can have a dramatic improvement on performance (especially write performance)
* in servers that only need to support a small number of search parameters, or no search parameters at all.
* Disabling this obviously reduces the options for searching however.
* </p>
*
* @since 6.0.0
*/
public boolean isAutoSupportDefaultSearchParams() {
return myAutoSupportDefaultSearchParams;
}
/**
* If this is disabled by setting this to {@literal false} (default is {@literal true}),
* the server will not automatically implement and support search parameters that
* are not explcitly created in the repository.
* <p>
* Disabling this can have a dramatic improvement on performance (especially write performance)
* in servers that only need to support a small number of search parameters, or no search parameters at all.
* Disabling this obviously reduces the options for searching however.
* </p>
*
* @since 6.0.0
*/
public void setAutoSupportDefaultSearchParams(boolean theAutoSupportDefaultSearchParams) {
myAutoSupportDefaultSearchParams = theAutoSupportDefaultSearchParams;
}
private static void validateTreatBaseUrlsAsLocal(String theUrl) {
Validate.notBlank(theUrl, "Base URL must not be null or empty");

4
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java
View File

@ -638,8 +638,8 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
retVal.setVersion(myVersion);
retVal.setTransientForcedId(getTransientForcedId());
retVal.setPublished(getPublished());
retVal.setUpdated(getUpdated());
retVal.setPublished(getPublishedDate());
retVal.setUpdated(getUpdatedDate());
retVal.setFhirVersion(getFhirVersion());
retVal.setDeleted(getDeleted());
retVal.setResourceTable(this);

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

@ -991,7 +991,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
myModelConfig.isIndexOnContainedResources()
|| anySearchParameterUsesResolve(searchParams, theSearchParamType);
if (havePathWithResolveExpression) {
if (havePathWithResolveExpression && myContext.getParserOptions().isAutoContainReferenceTargetsWithNoId()) {
//TODO GGG/JA: At this point, if the Task.basedOn.reference.resource does _not_ have an ID, we will attempt to contain it internally. Wild
myContext.newTerser().containResources(theResource, FhirTerser.OptionsEnum.MODIFY_RESOURCE, FhirTerser.OptionsEnum.STORE_AND_REUSE_RESULTS);
}

14
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java
View File

@ -24,6 +24,8 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
@ -32,6 +34,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.context.IWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.ExpressionNode;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.ResourceType;
@ -45,11 +48,13 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements ISearchParamExtractor {
private Cache<String, ExpressionNode> myParsedFhirPathCache;
private FHIRPathEngine myFhirPathEngine;
/**
@ -70,8 +75,8 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
@Override
public IValueExtractor getPathValueExtractor(IBaseResource theResource, String theSinglePath) {
return () -> {
List<Base> allValues = myFhirPathEngine.evaluate((Base) theResource, theSinglePath);
return (List<IBase>) new ArrayList<IBase>(allValues);
ExpressionNode parsed = myParsedFhirPathCache.get(theSinglePath, path -> myFhirPathEngine.parse(path));
return myFhirPathEngine.evaluate((Base) theResource, parsed);
};
}
@ -89,6 +94,11 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
IWorkerContext worker = new HapiWorkerContext(getContext(), getContext().getValidationSupport());
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR4HostServices());
myParsedFhirPathCache = Caffeine
.newBuilder()
.expireAfterWrite(10, TimeUnit.MINUTES)
.build();
}

19
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java
View File

@ -24,12 +24,16 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ResourceType;
@ -38,16 +42,19 @@ import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import javax.annotation.PostConstruct;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements ISearchParamExtractor {
private FHIRPathEngine myFhirPathEngine;
private Cache<String, ExpressionNode> myParsedFhirPathCache;
public SearchParamExtractorR5() {
super();
@ -75,11 +82,19 @@ public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements
IWorkerContext worker = new HapiWorkerContext(getContext(), getContext().getValidationSupport());
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR5HostServices());
myParsedFhirPathCache = Caffeine
.newBuilder()
.expireAfterWrite(10, TimeUnit.MINUTES)
.build();
}
@Override
public IValueExtractor getPathValueExtractor(IBaseResource theResource, String nextPath) {
return () -> myFhirPathEngine.evaluate((Base) theResource, nextPath);
public IValueExtractor getPathValueExtractor(IBaseResource theResource, String theSinglePath) {
return () -> {
ExpressionNode parsed = myParsedFhirPathCache.get(theSinglePath, path -> myFhirPathEngine.parse(path));
return myFhirPathEngine.evaluate((Base) theResource, parsed);
};
}

52
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/ReadOnlySearchParamCache.java
View File

@ -26,11 +26,12 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.ClasspathUtil;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
@ -80,7 +81,11 @@ public class ReadOnlySearchParamCache {
return myUrlToParam.get(theUrl);
}
public static ReadOnlySearchParamCache fromFhirContext(FhirContext theFhirContext, SearchParameterCanonicalizer theCanonicalizer) {
public static ReadOnlySearchParamCache fromFhirContext(@Nonnull FhirContext theFhirContext, @Nonnull SearchParameterCanonicalizer theCanonicalizer) {
return fromFhirContext(theFhirContext, theCanonicalizer, null);
}
public static ReadOnlySearchParamCache fromFhirContext(@Nonnull FhirContext theFhirContext, @Nonnull SearchParameterCanonicalizer theCanonicalizer, @Nullable Set<String> theSearchParamPatternsToInclude) {
assert theCanonicalizer != null;
ReadOnlySearchParamCache retVal = new ReadOnlySearchParamCache();
@ -97,10 +102,12 @@ public class ReadOnlySearchParamCache {
base = resourceNames;
}
for (String nextBase : base) {
Map<String, RuntimeSearchParam> nameToParam = retVal.myResourceNameToSpNameToSp.computeIfAbsent(nextBase, t -> new HashMap<>());
String nextName = nextCanonical.getName();
nameToParam.putIfAbsent(nextName, nextCanonical);
for (String nextResourceName : base) {
Map<String, RuntimeSearchParam> nameToParam = retVal.myResourceNameToSpNameToSp.computeIfAbsent(nextResourceName, t -> new HashMap<>());
String nextParamName = nextCanonical.getName();
if (theSearchParamPatternsToInclude == null || searchParamMatchesAtLeastOnePattern(theSearchParamPatternsToInclude, nextResourceName, nextParamName)) {
nameToParam.putIfAbsent(nextParamName, nextCanonical);
}
}
}
}
@ -110,15 +117,42 @@ public class ReadOnlySearchParamCache {
RuntimeResourceDefinition nextResDef = theFhirContext.getResourceDefinition(resourceName);
String nextResourceName = nextResDef.getName();
Map<String, RuntimeSearchParam> nameToParam = retVal.myResourceNameToSpNameToSp.computeIfAbsent(nextResourceName, t-> new HashMap<>());
Map<String, RuntimeSearchParam> nameToParam = retVal.myResourceNameToSpNameToSp.computeIfAbsent(nextResourceName, t -> new HashMap<>());
for (RuntimeSearchParam nextSp : nextResDef.getSearchParams()) {
nameToParam.putIfAbsent(nextSp.getName(), nextSp);
String nextParamName = nextSp.getName();
if (theSearchParamPatternsToInclude == null || searchParamMatchesAtLeastOnePattern(theSearchParamPatternsToInclude, nextResourceName, nextParamName)) {
nameToParam.putIfAbsent(nextParamName, nextSp);
}
}
}
return retVal;
}
public static boolean searchParamMatchesAtLeastOnePattern(Set<String> theSearchParamPatterns, String theResourceType, String theSearchParamName) {
for (String nextPattern : theSearchParamPatterns) {
if ("*".equals(nextPattern)) {
return true;
}
int colonIdx = nextPattern.indexOf(':');
Validate.isTrue(colonIdx > 0, "Invalid search param pattern: %s", nextPattern);
String resourceType = nextPattern.substring(0, colonIdx);
String searchParamName = nextPattern.substring(colonIdx + 1);
Validate.notBlank(resourceType, "No resource type specified in pattern: %s", nextPattern);
Validate.notBlank(searchParamName, "No param name specified in pattern: %s", nextPattern);
if (!resourceType.equals("*") && !resourceType.equals(theResourceType)) {
continue;
}
if (!searchParamName.equals("*") && !searchParamName.equals(theSearchParamName)) {
continue;
}
return true;
}
return false;
}
public static ReadOnlySearchParamCache fromRuntimeSearchParamCache(RuntimeSearchParamCache theRuntimeSearchParamCache) {
return new ReadOnlySearchParamCache(theRuntimeSearchParamCache);
}
}

22
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/SearchParamRegistryImpl.java
View File

@ -37,6 +37,7 @@ import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.SearchParameterUtil;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -59,7 +60,12 @@ import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class SearchParamRegistryImpl implements ISearchParamRegistry, IResourceChangeListener, ISearchParamRegistryController {
// TODO: JA remove unused?
public static final Set<String> NON_DISABLEABLE_SEARCH_PARAMS = Collections.unmodifiableSet(Sets.newHashSet(
"*:url",
"Subscription:*",
"SearchParameter:*"
));
private static final Logger ourLog = LoggerFactory.getLogger(SearchParamRegistryImpl.class);
private static final int MAX_MANAGED_PARAM_COUNT = 10000;
@ -78,7 +84,6 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry, IResourceC
private volatile ReadOnlySearchParamCache myBuiltInSearchParams;
private volatile IPhoneticEncoder myPhoneticEncoder;
private volatile RuntimeSearchParamCache myActiveSearchParams;
@Autowired
private IInterceptorService myInterceptorBroadcaster;
private IResourceChangeListenerCache myResourceChangeListenerCache;
@ -134,6 +139,8 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry, IResourceC
params.setLoadSynchronousUpTo(MAX_MANAGED_PARAM_COUNT);
IBundleProvider allSearchParamsBp = mySearchParamProvider.search(params);
List<IBaseResource> allSearchParams = allSearchParamsBp.getResources(0, MAX_MANAGED_PARAM_COUNT);
int size = allSearchParamsBp.sizeOrThrowNpe();
ourLog.trace("Loaded {} search params from the DB", size);
@ -141,9 +148,8 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry, IResourceC
// Just in case..
if (size >= MAX_MANAGED_PARAM_COUNT) {
ourLog.warn("Unable to support >" + MAX_MANAGED_PARAM_COUNT + " search params!");
size = MAX_MANAGED_PARAM_COUNT;
}
List<IBaseResource> allSearchParams = allSearchParamsBp.getResources(0, size);
initializeActiveSearchParams(allSearchParams);
}
@ -167,7 +173,12 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry, IResourceC
private ReadOnlySearchParamCache getBuiltInSearchParams() {
if (myBuiltInSearchParams == null) {
myBuiltInSearchParams = ReadOnlySearchParamCache.fromFhirContext(myFhirContext, mySearchParameterCanonicalizer);
if (myModelConfig.isAutoSupportDefaultSearchParams()) {
myBuiltInSearchParams = ReadOnlySearchParamCache.fromFhirContext(myFhirContext, mySearchParameterCanonicalizer);
} else {
// Only the built-in search params that can not be disabled will be supported automatically
myBuiltInSearchParams = ReadOnlySearchParamCache.fromFhirContext(myFhirContext, mySearchParameterCanonicalizer, NON_DISABLEABLE_SEARCH_PARAMS);
}
}
return myBuiltInSearchParams;
}
@ -311,6 +322,7 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry, IResourceC
@VisibleForTesting
public void resetForUnitTest() {
myBuiltInSearchParams = null;
handleInit(Collections.emptyList());
}

32
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/registry/ReadOnlySearchParamCacheTest.java Normal file
View File

@ -0,0 +1,32 @@
package ca.uhn.fhir.jpa.searchparam.registry;
import org.junit.jupiter.api.Test;
import static ca.uhn.fhir.jpa.searchparam.registry.ReadOnlySearchParamCache.searchParamMatchesAtLeastOnePattern;
import static com.google.common.collect.Sets.newHashSet;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class ReadOnlySearchParamCacheTest {
@Test
void testSearchParamMatchesAtLeastOnePattern() {
assertTrue(searchParamMatchesAtLeastOnePattern(newHashSet("*"), "Patient", "name"));
assertTrue(searchParamMatchesAtLeastOnePattern(newHashSet("Patient:name"), "Patient", "name"));
assertTrue(searchParamMatchesAtLeastOnePattern(newHashSet("Patient:*"), "Patient", "name"));
assertTrue(searchParamMatchesAtLeastOnePattern(newHashSet("*:name"), "Patient", "name"));
assertFalse(searchParamMatchesAtLeastOnePattern(newHashSet("Patient:foo"), "Patient", "name"));
assertFalse(searchParamMatchesAtLeastOnePattern(newHashSet("Foo:name"), "Patient", "name"));
}
@Test
void testSearchParamMatchesAtLeastOnePattern_InvalidPattern() {
assertThrows(IllegalArgumentException.class, () -> searchParamMatchesAtLeastOnePattern(newHashSet("aaa"), "Patient", "name"));
assertThrows(IllegalArgumentException.class, () -> searchParamMatchesAtLeastOnePattern(newHashSet(":name"), "Patient", "name"));
assertThrows(IllegalArgumentException.class, () -> searchParamMatchesAtLeastOnePattern(newHashSet("Patient:"), "Patient", "name"));
}
}

40
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/api/ISubscriptionMessageKeySvc.java Normal file
View File

@ -0,0 +1,40 @@
package ca.uhn.fhir.jpa.subscription.api;
/*-
* #%L
* HAPI FHIR Subscription Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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 org.hl7.fhir.instance.model.api.IBaseResource;
import javax.annotation.Nullable;
/**
* This is used by "message" type subscriptions to provide a key to the message wrapper before submitting it to the channel
*/
public interface ISubscriptionMessageKeySvc {
/**
* Given an {@link IBaseResource}, return a key that can be used to identify the message. This key will be used to
* partition the message into a queue.
*
* @param thePayloadResource the payload resource.
* @return the key or null.
*/
@Nullable
String getMessageKeyOrNull(IBaseResource thePayloadResource);
}

20
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/channel/models/BaseChannelParameters.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.subscription.channel.models;
/*-
* #%L
* HAPI FHIR Subscription Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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.subscription.model.ChannelRetryConfiguration;
public class BaseChannelParameters {

20
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/channel/models/ProducingChannelParameters.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.subscription.channel.models;
/*-
* #%L
* HAPI FHIR Subscription Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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%
*/
public class ProducingChannelParameters extends BaseChannelParameters {
/**

20
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/channel/models/ReceivingChannelParameters.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.subscription.channel.models;
/*-
* #%L
* HAPI FHIR Subscription Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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%
*/
public class ReceivingChannelParameters extends BaseChannelParameters {
/**

1
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/message/SubscriptionDeliveringMessageSubscriber.java
View File

@ -64,6 +64,7 @@ public class SubscriptionDeliveringMessageSubscriber extends BaseSubscriptionDel
protected void doDelivery(ResourceDeliveryMessage theMsg, CanonicalSubscription theSubscription, IChannelProducer theChannelProducer, IBaseResource thePayloadResource) {
ResourceModifiedMessage payload = new ResourceModifiedMessage(myFhirContext, thePayloadResource, theMsg.getOperationType());
payload.setMessageKey(theMsg.getMessageKeyOrNull());
payload.setTransactionId(theMsg.getTransactionId());
ResourceModifiedJsonMessage message = new ResourceModifiedJsonMessage(payload);
theChannelProducer.send(message);

50
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/resthook/SubscriptionDeliveringRestHookSubscriber.java
View File

@ -44,7 +44,6 @@ import ca.uhn.fhir.rest.gclient.IClientExecutable;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.BundleBuilder;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.text.StringSubstitutor;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -57,10 +56,10 @@ import org.springframework.messaging.MessagingException;
import javax.annotation.Nullable;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -251,21 +250,10 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDe
*/
protected void sendNotification(ResourceDeliveryMessage theMsg) {
Map<String, List<String>> params = new HashMap<>();
List<Header> headers = new ArrayList<>();
if (theMsg.getSubscription().getHeaders() != null) {
theMsg.getSubscription().getHeaders().stream().filter(Objects::nonNull).forEach(h -> {
final int sep = h.indexOf(':');
if (sep > 0) {
final String name = h.substring(0, sep);
final String value = h.substring(sep + 1);
if (StringUtils.isNotBlank(name)) {
headers.add(new Header(name.trim(), value.trim()));
}
}
});
}
CanonicalSubscription subscription = theMsg.getSubscription();
List<Header> headers = parseHeadersFromSubscription(subscription);
StringBuilder url = new StringBuilder(theMsg.getSubscription().getEndpointUrl());
StringBuilder url = new StringBuilder(subscription.getEndpointUrl());
IHttpClient client = myFhirContext.getRestfulClientFactory().getHttpClient(url, params, "", RequestTypeEnum.POST, headers);
IHttpRequest request = client.createParamRequest(myFhirContext, params, null);
try {
@ -273,8 +261,36 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDe
// close connection in order to return a possible cached connection to the connection pool
response.close();
} catch (IOException e) {
ourLog.error("Error trying to reach {}: {}", theMsg.getSubscription().getEndpointUrl(), e.toString());
ourLog.error("Error trying to reach {}: {}", subscription.getEndpointUrl(), e.toString());
throw new ResourceNotFoundException(e.getMessage());
}
}
public static List<Header> parseHeadersFromSubscription(CanonicalSubscription subscription) {
List<Header> headers = null;
if (subscription != null) {
for (String h : subscription.getHeaders()) {
if (h != null) {
final int sep = h.indexOf(':');
if (sep > 0) {
final String name = h.substring(0, sep);
final String value = h.substring(sep + 1);
if (isNotBlank(name)) {
if (headers == null) {
headers = new ArrayList<>();
}
headers.add(new Header(name.trim(), value.trim()));
}
}
}
}
}
if (headers == null) {
headers = Collections.emptyList();
} else {
headers = Collections.unmodifiableList(headers);
}
return headers;
}
}

19
hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/CanonicalSubscriptionTest.java
View File

@ -16,10 +16,13 @@ import java.util.HashMap;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class CanonicalSubscriptionTest {
private static final String TAG_SYSTEM = "https://hapifhir.org/NamingSystem/managing-mdm-system";
private static final String TAG_VALUE = "HAPI-MDM";
@Test
public void testGetChannelExtension() throws IOException {
@ -54,6 +57,14 @@ public class CanonicalSubscriptionTest {
assertThat(s.getChannelExtensions("key3"), Matchers.empty());
}
@Test
public void testCanonicalSubscriptionRetainsMetaTags() throws IOException {
SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4());
CanonicalSubscription sub1 = canonicalizer.canonicalize(makeMdmSubscription());
assertTrue(sub1.getTags().keySet().contains(TAG_SYSTEM));
assertEquals(sub1.getTags().get(TAG_SYSTEM), TAG_VALUE);
}
@Test
public void emailDetailsEquals() {
SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4());
@ -69,6 +80,14 @@ public class CanonicalSubscriptionTest {
retVal.setChannel(channel);
return retVal;
}
private Subscription makeMdmSubscription() {
Subscription retVal = new Subscription();
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
channel.setType(Subscription.SubscriptionChannelType.MESSAGE);
retVal.setChannel(channel);
retVal.getMeta().addTag("https://hapifhir.org/NamingSystem/managing-mdm-system", "HAPI-MDM", "managed by hapi mdm");
return retVal;
}
private CanonicalSubscription serializeAndDeserialize(CanonicalSubscription theSubscription) throws IOException {

50
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/config/MdmRuleValidator.java
View File

@ -35,17 +35,21 @@ import ca.uhn.fhir.mdm.rules.json.MdmSimilarityJson;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.FhirTerser;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.xml.crypto.Data;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
@Service
public class MdmRuleValidator implements IMdmRuleValidator {
@ -73,7 +77,40 @@ public class MdmRuleValidator implements IMdmRuleValidator {
validateMdmTypes(theMdmRules);
validateSearchParams(theMdmRules);
validateMatchFields(theMdmRules);
validateSystemIsUri(theMdmRules);
validateSystemsAreUris(theMdmRules);
validateEidSystemsMatchMdmTypes(theMdmRules);
}
private void validateEidSystemsMatchMdmTypes(MdmRulesJson theMdmRules) {
theMdmRules.getEnterpriseEIDSystems().keySet()
.forEach(key -> {
//Ensure each key is either * or a valid resource type.
if (!key.equalsIgnoreCase("*") && !theMdmRules.getMdmTypes().contains(key)) {
throw new ConfigurationException(String.format("There is an eidSystem set for [%s] but that is not one of the mdmTypes. Valid options are [%s].", key, buildValidEidKeysMessage(theMdmRules)));
}
});
}
private String buildValidEidKeysMessage(MdmRulesJson theMdmRulesJson) {
List<String> validTypes = new ArrayList<>(theMdmRulesJson.getMdmTypes());
validTypes.add("*");
return String.join(", ", validTypes);
}
private void validateSystemsAreUris(MdmRulesJson theMdmRules) {
theMdmRules.getEnterpriseEIDSystems().entrySet()
.forEach(entry -> {
String resourceType = entry.getKey();
String uri = entry.getValue();
if (!resourceType.equals("*")) {
try {
myFhirContext.getResourceType(resourceType);
}catch (DataFormatException e) {
throw new ConfigurationException(String.format("%s is not a valid resource type, but is set in the eidSystems field.", resourceType));
}
}
validateIsUri(uri);
});
}
public void validateMdmTypes(MdmRulesJson theMdmRulesJson) {
@ -212,15 +249,10 @@ public class MdmRuleValidator implements IMdmRuleValidator {
validateFieldPathForType(theFieldMatch.getResourceType(), theFieldMatch);
}
private void validateSystemIsUri(MdmRulesJson theMdmRulesJson) {
if (theMdmRulesJson.getEnterpriseEIDSystem() == null) {
return;
}
ourLog.info("Validating system URI {}", theMdmRulesJson.getEnterpriseEIDSystem());
private void validateIsUri(String theUri) {
ourLog.info("Validating system URI {}", theUri);
try {
new URI(theMdmRulesJson.getEnterpriseEIDSystem());
new URI(theUri);
} catch (URISyntaxException e) {
throw new ConfigurationException("Enterprise Identifier System (eidSystem) must be a valid URI");
}

62
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/json/MdmRulesJson.java
View File

@ -26,6 +26,7 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import com.fasterxml.jackson.databind.util.StdConverter;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import java.util.ArrayList;
@ -34,6 +35,8 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static ca.uhn.fhir.mdm.api.MdmConstants.ALL_RESOURCE_SEARCH_PARAM_TYPE;
@JsonDeserialize(converter = MdmRulesJson.MdmRulesJsonConverter.class)
public class MdmRulesJson implements IModelJson {
@ -47,10 +50,16 @@ public class MdmRulesJson implements IModelJson {
List<MdmFieldMatchJson> myMatchFieldJsonList = new ArrayList<>();
@JsonProperty(value = "matchResultMap", required = true)
Map<String, MdmMatchResultEnum> myMatchResultMap = new HashMap<>();
/**
* This field is deprecated, use eidSystems instead.
*/
@Deprecated
@JsonProperty(value = "eidSystem")
String myEnterpriseEIDSystem;
@JsonProperty(value = "eidSystems")
Map<String, String> myEnterpriseEidSystems = new HashMap<>();
@JsonProperty(value = "mdmTypes")
List<String> myMdmTypes;
@ -112,14 +121,57 @@ public class MdmRulesJson implements IModelJson {
return Collections.unmodifiableList(myCandidateFilterSearchParams);
}
/**
* Use {@link this#getEnterpriseEIDSystemForResourceType(String)} instead.
*/
@Deprecated
public String getEnterpriseEIDSystem() {
return myEnterpriseEIDSystem;
}
/**
* Use {@link this#setEnterpriseEIDSystems(Map)} (String)} or {@link this#addEnterpriseEIDSystem(String, String)} instead.
*/
@Deprecated
public void setEnterpriseEIDSystem(String theEnterpriseEIDSystem) {
myEnterpriseEIDSystem = theEnterpriseEIDSystem;
}
public void setEnterpriseEIDSystems(Map<String, String> theEnterpriseEIDSystems) {
myEnterpriseEidSystems = theEnterpriseEIDSystems;
}
public void addEnterpriseEIDSystem(String theResourceType, String theEidSystem) {
if (myEnterpriseEidSystems == null) {
myEnterpriseEidSystems = new HashMap<>();
}
myEnterpriseEidSystems.put(theResourceType, theEidSystem);
}
public Map<String, String> getEnterpriseEIDSystems() {
//First try the new property.
if (myEnterpriseEidSystems != null && !myEnterpriseEidSystems.isEmpty()) {
return myEnterpriseEidSystems;
//If that fails, fall back to our deprecated property.
} else if (!StringUtils.isBlank(myEnterpriseEIDSystem)) {
HashMap<String , String> retVal = new HashMap<>();
retVal.put(ALL_RESOURCE_SEARCH_PARAM_TYPE, myEnterpriseEIDSystem);
return retVal;
//Otherwise, return an empty map.
} else {
return Collections.emptyMap();
}
}
public String getEnterpriseEIDSystemForResourceType(String theResourceType) {
Map<String, String> enterpriseEIDSystems = getEnterpriseEIDSystems();
if (enterpriseEIDSystems.containsKey(ALL_RESOURCE_SEARCH_PARAM_TYPE)) {
return enterpriseEIDSystems.get(ALL_RESOURCE_SEARCH_PARAM_TYPE);
} else {
return enterpriseEIDSystems.get(theResourceType);
}
}
public String getVersion() {
return myVersion;
}
@ -131,6 +183,14 @@ public class MdmRulesJson implements IModelJson {
private void validate() {
Validate.notBlank(myVersion, "version may not be blank");
Map<String, String> enterpriseEIDSystems = getEnterpriseEIDSystems();
//If we have a * eid system, there should only be one.
if (enterpriseEIDSystems.containsKey(ALL_RESOURCE_SEARCH_PARAM_TYPE)) {
Validate.isTrue(enterpriseEIDSystems.size() == 1);
}
}
public String getSummary() {

3
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/EIDHelper.java
View File

@ -63,7 +63,8 @@ public final class EIDHelper {
* @return An optional {@link CanonicalEID} representing the external EID. Absent if the EID is not present.
*/
public List<CanonicalEID> getExternalEid(IBaseResource theResource) {
return CanonicalEID.extractFromResource(myFhirContext, myMdmSettings.getMdmRules().getEnterpriseEIDSystem(), theResource);
String resourceType = myFhirContext.getResourceType(theResource);
return CanonicalEID.extractFromResource(myFhirContext, myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType(resourceType), theResource);
}
/**

10
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/GoldenResourceHelper.java
View File

@ -120,7 +120,7 @@ public class GoldenResourceHelper {
}
private void cloneAllExternalEidsIntoNewGoldenResource(BaseRuntimeChildDefinition theGoldenResourceIdentifier,
IBase theGoldenResource, IBase theNewGoldenResource) {
IAnyResource theGoldenResource, IBase theNewGoldenResource) {
// FHIR choice types - fields within fhir where we have a choice of ids
IFhirPath fhirPath = myFhirContext.newFhirPath();
List<IBase> goldenResourceIdentifiers = theGoldenResourceIdentifier.getAccessor().getValues(theGoldenResource);
@ -128,7 +128,8 @@ public class GoldenResourceHelper {
for (IBase base : goldenResourceIdentifiers) {
Optional<IPrimitiveType> system = fhirPath.evaluateFirst(base, "system", IPrimitiveType.class);
if (system.isPresent()) {
String mdmSystem = myMdmSettings.getMdmRules().getEnterpriseEIDSystem();
String resourceType = myFhirContext.getResourceType(theGoldenResource);
String mdmSystem = myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType(resourceType);
String baseSystem = system.get().getValueAsString();
if (Objects.equals(baseSystem, mdmSystem)) {
ca.uhn.fhir.util.TerserUtil.cloneEidIntoResource(myFhirContext, theGoldenResourceIdentifier, base, theNewGoldenResource);
@ -188,7 +189,7 @@ public class GoldenResourceHelper {
return theGoldenResource;
}
private void clearExternalEidsFromTheGoldenResource(BaseRuntimeChildDefinition theGoldenResourceIdentifier, IBase theGoldenResource) {
private void clearExternalEidsFromTheGoldenResource(BaseRuntimeChildDefinition theGoldenResourceIdentifier, IBaseResource theGoldenResource) {
IFhirPath fhirPath = myFhirContext.newFhirPath();
List<IBase> goldenResourceIdentifiers = theGoldenResourceIdentifier.getAccessor().getValues(theGoldenResource);
List<IBase> clonedIdentifiers = new ArrayList<>();
@ -197,7 +198,8 @@ public class GoldenResourceHelper {
for (IBase base : goldenResourceIdentifiers) {
Optional<IPrimitiveType> system = fhirPath.evaluateFirst(base, "system", IPrimitiveType.class);
if (system.isPresent()) {
String mdmSystem = myMdmSettings.getMdmRules().getEnterpriseEIDSystem();
String resourceType = myFhirContext.getResourceType(theGoldenResource);
String mdmSystem = myMdmSettings.getMdmRules().getEnterpriseEIDSystemForResourceType(resourceType);
String baseSystem = system.get().getValueAsString();
if (Objects.equals(baseSystem, mdmSystem)) {
ourLog.debug("Found EID confirming to MDM rules {}. It should not be copied, skipping", baseSystem);

20
hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/config/MdmRuleValidatorTest.java
View File

@ -12,6 +12,7 @@ import org.springframework.core.io.Resource;
import java.io.IOException;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.startsWith;
@ -161,6 +162,25 @@ public class MdmRuleValidatorTest extends BaseR4Test {
}
}
@Test
public void testBadEidResourceType() throws IOException {
try {
setMdmRuleJson("bad-rules-illegal-resource-type-eid.json");
}
catch (ConfigurationException e){
assertThat(e.getMessage(), is(equalTo("not-a-resource is not a valid resource type, but is set in the eidSystems field.")));
}
}
@Test
public void testBadEidDoesntMatchKnownMdmTypes() throws IOException {
try {
setMdmRuleJson("bad-rules-illegal-missing-resource-type.json");
}
catch (ConfigurationException e){
assertThat(e.getMessage(), is(equalTo("There is an eidSystem set for [Patient] but that is not one of the mdmTypes. Valid options are [Organization, *].")));
}
}
private void setMdmRuleJson(String theTheS) throws IOException {
MdmRuleValidator mdmRuleValidator = new MdmRuleValidator(ourFhirContext, mySearchParamRetriever);
MdmSettings mdmSettings = new MdmSettings(mdmRuleValidator);

32
hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/json/MdmRulesJsonR4Test.java
View File

@ -11,9 +11,13 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.Collections;
import java.util.HashMap;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.is;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
@ -72,4 +76,32 @@ public class MdmRulesJsonR4Test extends BaseMdmRulesR4Test {
assertEquals("There is no matchField with name bad", e.getMessage());
}
}
@Test
public void testInvalidResourceTypeDoesntDeserialize() throws IOException {
myRules = buildOldStyleEidRules();
String eidSystem = myRules.getEnterpriseEIDSystemForResourceType("Patient");
assertThat(eidSystem, is(equalTo(PATIENT_EID_FOR_TEST)));
eidSystem = myRules.getEnterpriseEIDSystemForResourceType("Practitioner");
assertThat(eidSystem, is(equalTo(PATIENT_EID_FOR_TEST)));
eidSystem = myRules.getEnterpriseEIDSystemForResourceType("Medication");
assertThat(eidSystem, is(equalTo(PATIENT_EID_FOR_TEST)));
}
@Override
protected MdmRulesJson buildActiveBirthdateIdRules() {
return super.buildActiveBirthdateIdRules();
}
private MdmRulesJson buildOldStyleEidRules() {
MdmRulesJson mdmRulesJson = super.buildActiveBirthdateIdRules();
mdmRulesJson.setEnterpriseEIDSystems(Collections.emptyMap());
//This sets the new-style eid resource type to `*`
mdmRulesJson.setEnterpriseEIDSystem(PATIENT_EID_FOR_TEST);
return mdmRulesJson;
}
}

7
hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/svc/BaseMdmRulesR4Test.java
View File

@ -18,6 +18,9 @@ public abstract class BaseMdmRulesR4Test extends BaseR4Test {
public static final String PATIENT_GIVEN = "patient-given";
public static final String PATIENT_GIVEN_FIRST = "patient-given-first";
public static final String PATIENT_FAMILY = "patient-last";
public static final String PATIENT_EID_FOR_TEST = "http://hello.com/naming/patient-eid";
public static final String MEDICATION_EID_FOR_TEST= "http://hello.com/naming/medication-eid";
public static final String PRACTITIONER_EID_FOR_TEST = "http://hello.com/naming/practitioner-eid";
public static final double NAME_THRESHOLD = 0.8;
protected MdmFieldMatchJson myGivenNameMatchField;
@ -71,6 +74,10 @@ public abstract class BaseMdmRulesR4Test extends BaseR4Test {
retval.setMdmTypes(Arrays.asList("Patient", "Practitioner", "Medication"));
retval.putMatchResult(myBothNameFields, MdmMatchResultEnum.MATCH);
retval.putMatchResult(PATIENT_GIVEN, MdmMatchResultEnum.POSSIBLE_MATCH);
retval.addEnterpriseEIDSystem("Patient", PATIENT_EID_FOR_TEST);
retval.addEnterpriseEIDSystem("Medication", MEDICATION_EID_FOR_TEST);
retval.addEnterpriseEIDSystem("Practitioner", PRACTITIONER_EID_FOR_TEST);
return retval;
}
}

2
hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/svc/EIDHelperR4Test.java
View File

@ -33,7 +33,7 @@ public class EIDHelperR4Test extends BaseR4Test {
private static final MdmRulesJson ourRules = new MdmRulesJson() {
{
setEnterpriseEIDSystem(EXTERNAL_ID_SYSTEM_FOR_TEST);
addEnterpriseEIDSystem("Patient", EXTERNAL_ID_SYSTEM_FOR_TEST);
setMdmTypes(Arrays.asList(new String[] {"Patient"}));
}
};

20
hapi-fhir-server-mdm/src/test/resources/bad-rules-illegal-missing-resource-type.json Normal file
View File

@ -0,0 +1,20 @@
{
"version": "1",
"mdmTypes": ["Organization"],
"candidateSearchParams": [],
"candidateFilterSearchParams": [],
"matchFields": [
{
"name": "name-prefix",
"resourceType": "Organization",
"resourcePath": "name",
"matcher": {
"algorithm": "STRING"
}
}
],
"matchResultMap": {},
"eidSystems": {
"Patient": "http://hello.com/uri"
}
}

20
hapi-fhir-server-mdm/src/test/resources/bad-rules-illegal-resource-type-eid.json Normal file
View File

@ -0,0 +1,20 @@
{
"version": "1",
"mdmTypes": ["Organization"],
"candidateSearchParams": [],
"candidateFilterSearchParams": [],
"matchFields": [
{
"name": "name-prefix",
"resourceType": "Organization",
"resourcePath": "name",
"matcher": {
"algorithm": "STRING"
}
}
],
"matchResultMap": {},
"eidSystems": {
"not-a-resource": "http://hello.com/uri"
}
}

15
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/BaseResourceMessage.java
View File

@ -46,6 +46,12 @@ public abstract class BaseResourceMessage implements IResourceMessage, IModelJso
@JsonProperty("mediaType")
private String myMediaType;
/**
* This is used by any message going to kafka for topic partition selection purposes.
*/
@JsonProperty("messageKey")
private String myMessageKey;
/**
* Returns an attribute stored in this message.
* <p>
@ -156,6 +162,15 @@ public abstract class BaseResourceMessage implements IResourceMessage, IModelJso
myMediaType = theMediaType;
}
@Nullable
public String getMessageKeyOrNull() {
return myMessageKey;
}
public void setMessageKey(String theMessageKey) {
myMessageKey = theMessageKey;
}
public enum OperationTypeEnum {
CREATE,
UPDATE,

1
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/ResourceOperationMessage.java
View File

@ -26,7 +26,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
public class ResourceOperationMessage extends BaseResourceModifiedMessage {
public ResourceOperationMessage() {
}

7
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/json/BaseJsonMessage.java
View File

@ -26,6 +26,8 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import org.springframework.messaging.Message;
import org.springframework.messaging.MessageHeaders;
import javax.annotation.Nullable;
public abstract class BaseJsonMessage<T> implements Message<T>, IModelJson {
private static final long serialVersionUID = 1L;
@ -58,4 +60,9 @@ public abstract class BaseJsonMessage<T> implements Message<T>, IModelJson {
public void setHeaders(HapiMessageHeaders theHeaders) {
myHeaders = theHeaders;
}
@Nullable
public String getMessageKeyOrNull() {
return null;
}
}

5
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/provider/ProviderConstants.java
View File

@ -186,6 +186,11 @@ public class ProviderConstants {
*/
public static final String OPERATION_REINDEX_RESPONSE_JOB_ID = "jobId";
/**
* Operation name for the $member-match operation
*/
public static final String OPERATION_MEMBER_MATCH = "$member-match";
@Deprecated
public static final String MARK_ALL_RESOURCES_FOR_REINDEXING = "$mark-all-resources-for-reindexing";
/**

240
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
View File

@ -108,6 +108,7 @@ import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import javax.annotation.PostConstruct;
import java.util.ArrayList;
import java.util.Collection;
@ -137,8 +138,10 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public abstract class BaseTransactionProcessor {
public static final String URN_PREFIX = "urn:";
public static final String URN_PREFIX_ESCAPED = UrlUtil.escapeUrlParam(URN_PREFIX);
public static final Pattern UNQUALIFIED_MATCH_URL_START = Pattern.compile("^[a-zA-Z0-9_]+=");
private static final Logger ourLog = LoggerFactory.getLogger(BaseTransactionProcessor.class);
public static final Pattern INVALID_PLACEHOLDER_PATTERN = Pattern.compile("[a-zA-Z]+:.*");
private BaseStorageDao myDao;
@Autowired
private PlatformTransactionManager myTxManager;
@ -168,17 +171,6 @@ public abstract class BaseTransactionProcessor {
@Autowired
private IResourceVersionSvc myResourceVersionSvc;
public static boolean isPlaceholder(IIdType theId) {
if (theId != null && theId.getValue() != null) {
return theId.getValue().startsWith("urn:oid:") || theId.getValue().startsWith("urn:uuid:");
}
return false;
}
private static String toStatusString(int theStatusCode) {
return theStatusCode + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
}
@VisibleForTesting
public void setDaoConfig(DaoConfig theDaoConfig) {
myDaoConfig = theDaoConfig;
@ -267,14 +259,16 @@ public abstract class BaseTransactionProcessor {
myVersionAdapter.populateEntryWithOperationOutcome(caughtEx, nextEntry);
}
private void handleTransactionCreateOrUpdateOutcome(Map<IIdType, IIdType> idSubstitutions, Map<IIdType, DaoMethodOutcome> idToPersistedOutcome,
private void handleTransactionCreateOrUpdateOutcome(IdSubstitutionMap idSubstitutions, Map<IIdType, DaoMethodOutcome> idToPersistedOutcome,
IIdType nextResourceId, DaoMethodOutcome outcome,
IBase newEntry, String theResourceType,
IBaseResource theRes, RequestDetails theRequestDetails) {
IIdType newId = outcome.getId().toUnqualified();
IIdType resourceId = isPlaceholder(nextResourceId) ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
if (newId.equals(resourceId) == false) {
idSubstitutions.put(resourceId, newId);
if (!nextResourceId.isEmpty()) {
idSubstitutions.put(resourceId, newId);
}
if (isPlaceholder(resourceId)) {
/*
* The correct way for substitution IDs to be is to be with no resource type, but we'll accept the qualified kind too just to be lenient.
@ -330,30 +324,6 @@ public abstract class BaseTransactionProcessor {
return theRes.getMeta().getLastUpdated();
}
private String performIdSubstitutionsInMatchUrl(Map<IIdType, IIdType> theIdSubstitutions, String theMatchUrl) {
String matchUrl = theMatchUrl;
if (isNotBlank(matchUrl)) {
for (Map.Entry<IIdType, IIdType> nextSubstitutionEntry : theIdSubstitutions.entrySet()) {
IIdType nextTemporaryId = nextSubstitutionEntry.getKey();
IIdType nextReplacementId = nextSubstitutionEntry.getValue();
String nextTemporaryIdPart = nextTemporaryId.getIdPart();
String nextReplacementIdPart = nextReplacementId.getValueAsString();
if (isUrn(nextTemporaryId) && nextTemporaryIdPart.length() > URN_PREFIX.length()) {
matchUrl = matchUrl.replace(nextTemporaryIdPart, nextReplacementIdPart);
String escapedUrlParam = UrlUtil.escapeUrlParam(nextTemporaryIdPart);
if (isNotBlank(escapedUrlParam)) {
matchUrl = matchUrl.replace(escapedUrlParam, nextReplacementIdPart);
}
}
}
}
return matchUrl;
}
private boolean isUrn(IIdType theId) {
return defaultString(theId.getValue()).startsWith(URN_PREFIX);
}
public void setDao(BaseStorageDao theDao) {
myDao = theDao;
}
@ -392,10 +362,10 @@ public abstract class BaseTransactionProcessor {
List<RetriableBundleTask> nonGetCalls = new ArrayList<>();
CountDownLatch completionLatch = new CountDownLatch(requestEntriesSize);
for (int i=0; i< requestEntriesSize ; i++ ) {
for (int i = 0; i < requestEntriesSize; i++) {
IBase nextRequestEntry = requestEntries.get(i);
RetriableBundleTask retriableBundleTask = new RetriableBundleTask(completionLatch, theRequestDetails, responseMap, i, nextRequestEntry, theNestedMode);
if (myVersionAdapter.getEntryRequestVerb(myContext, nextRequestEntry).equalsIgnoreCase("GET")) {
if (myVersionAdapter.getEntryRequestVerb(myContext, nextRequestEntry).equalsIgnoreCase("GET")) {
getCalls.add(retriableBundleTask);
} else {
nonGetCalls.add(retriableBundleTask);
@ -408,24 +378,24 @@ public abstract class BaseTransactionProcessor {
// waiting for all async tasks to be completed
AsyncUtil.awaitLatchAndIgnoreInterrupt(completionLatch, 300L, TimeUnit.SECONDS);
// Now, create the bundle response in original order
Object nextResponseEntry;
for (int i=0; i<requestEntriesSize; i++ ) {
for (int i = 0; i < requestEntriesSize; i++) {
nextResponseEntry = responseMap.get(i);
if (nextResponseEntry instanceof BaseServerResponseExceptionHolder) {
BaseServerResponseExceptionHolder caughtEx = (BaseServerResponseExceptionHolder)nextResponseEntry;
BaseServerResponseExceptionHolder caughtEx = (BaseServerResponseExceptionHolder) nextResponseEntry;
if (caughtEx.getException() != null) {
IBase nextEntry = myVersionAdapter.addEntry(response);
populateEntryWithOperationOutcome(caughtEx.getException(), nextEntry);
myVersionAdapter.setResponseStatus(nextEntry, toStatusString(caughtEx.getException().getStatusCode()));
}
}
} else {
myVersionAdapter.addEntry(response, (IBase)nextResponseEntry);
myVersionAdapter.addEntry(response, (IBase) nextResponseEntry);
}
}
long delay = System.currentTimeMillis() - start;
ourLog.info("Batch completed in {}ms", delay);
@ -631,12 +601,12 @@ public abstract class BaseTransactionProcessor {
callWriteOperationsHook(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, theRequestDetails, theTransactionDetails, writeOperationsDetails);
}
TransactionCallback<Map<IBase, IIdType>> txCallback = status -> {
TransactionCallback<EntriesToProcessMap> txCallback = status -> {
final Set<IIdType> allIds = new LinkedHashSet<>();
final Map<IIdType, IIdType> idSubstitutions = new HashMap<>();
final IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
final Map<IIdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
Map<IBase, IIdType> retVal = doTransactionWriteOperations(theRequestDetails, theActionName,
EntriesToProcessMap retVal = doTransactionWriteOperations(theRequestDetails, theActionName,
theTransactionDetails, allIds,
idSubstitutions, idToPersistedOutcome,
theResponse, theOriginalRequestOrder,
@ -645,7 +615,7 @@ public abstract class BaseTransactionProcessor {
theTransactionStopWatch.startTask("Commit writes to database");
return retVal;
};
Map<IBase, IIdType> entriesToProcess;
EntriesToProcessMap entriesToProcess;
try {
entriesToProcess = myHapiTransactionService.execute(theRequestDetails, theTransactionDetails, txCallback);
@ -838,8 +808,13 @@ public abstract class BaseTransactionProcessor {
}
}
if (nextResourceId.hasIdPart() && nextResourceId.getIdPart().matches("[a-zA-Z]+:.*") && !isPlaceholder(nextResourceId)) {
throw new InvalidRequestException("Invalid placeholder ID found: " + nextResourceId.getIdPart() + " - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'");
if (nextResourceId.hasIdPart() && !isPlaceholder(nextResourceId)) {
int colonIndex = nextResourceId.getIdPart().indexOf(':');
if (colonIndex != -1) {
if (INVALID_PLACEHOLDER_PATTERN.matcher(nextResourceId.getIdPart()).matches()) {
throw new InvalidRequestException("Invalid placeholder ID found: " + nextResourceId.getIdPart() + " - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'");
}
}
}
if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !isPlaceholder(nextResourceId)) {
@ -869,9 +844,9 @@ public abstract class BaseTransactionProcessor {
/**
* After pre-hooks have been called
*/
protected Map<IBase, IIdType> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName,
protected EntriesToProcessMap doTransactionWriteOperations(final RequestDetails theRequest, String theActionName,
TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
IdSubstitutionMap theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder,
List<IBase> theEntries, StopWatch theTransactionStopWatch) {
@ -884,7 +859,7 @@ public abstract class BaseTransactionProcessor {
try {
Set<String> deletedResources = new HashSet<>();
DeleteConflictList deleteConflicts = new DeleteConflictList();
Map<IBase, IIdType> entriesToProcess = new IdentityHashMap<>();
EntriesToProcessMap entriesToProcess = new EntriesToProcessMap();
Set<IIdType> nonUpdatedEntities = new HashSet<>();
Set<IBasePersistedResource> updatedEntities = new HashSet<>();
Map<String, IIdType> conditionalUrlToIdMap = new HashMap<>();
@ -1133,7 +1108,7 @@ public abstract class BaseTransactionProcessor {
theTransactionStopWatch.endCurrentTask();
for (IIdType next : theAllIds) {
IIdType replacement = theIdSubstitutions.get(next);
IIdType replacement = theIdSubstitutions.getForSource(next);
if (replacement != null && !replacement.equals(next)) {
ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
}
@ -1177,9 +1152,6 @@ public abstract class BaseTransactionProcessor {
/**
* After transaction processing and resolution of indexes and references, we want to validate that the resources that were stored _actually_
* match the conditional URLs that they were brought in on.
*
* @param theIdToPersistedOutcome
* @param conditionalUrlToIdMap
*/
private void validateAllInsertsMatchTheirConditionalUrls(Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, Map<String, IIdType> conditionalUrlToIdMap, RequestDetails theRequest) {
conditionalUrlToIdMap.entrySet().stream()
@ -1274,8 +1246,8 @@ public abstract class BaseTransactionProcessor {
* account for NOPs, so we block NOPs in that pass.
*/
private void resolveReferencesThenSaveAndIndexResources(RequestDetails theRequest, TransactionDetails theTransactionDetails,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
StopWatch theTransactionStopWatch, Map<IBase, IIdType> entriesToProcess,
IdSubstitutionMap theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
StopWatch theTransactionStopWatch, EntriesToProcessMap entriesToProcess,
Set<IIdType> nonUpdatedEntities, Set<IBasePersistedResource> updatedEntities) {
FhirTerser terser = myContext.newTerser();
theTransactionStopWatch.startTask("Index " + theIdToPersistedOutcome.size() + " resources");
@ -1333,8 +1305,8 @@ public abstract class BaseTransactionProcessor {
}
private void resolveReferencesThenSaveAndIndexResource(RequestDetails theRequest, TransactionDetails theTransactionDetails,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
Map<IBase, IIdType> entriesToProcess, Set<IIdType> nonUpdatedEntities,
IdSubstitutionMap theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
EntriesToProcessMap entriesToProcess, Set<IIdType> nonUpdatedEntities,
Set<IBasePersistedResource> updatedEntities, FhirTerser terser,
DaoMethodOutcome nextOutcome, IBaseResource nextResource,
Set<IBaseReference> theReferencesToAutoVersion) {
@ -1350,7 +1322,7 @@ public abstract class BaseTransactionProcessor {
if (targetId.getValue() == null || targetId.getValue().startsWith("#")) {
// This means it's a contained resource
continue;
} else if (theIdSubstitutions.containsValue(targetId)) {
} else if (theIdSubstitutions.containsTarget(targetId)) {
newId = targetId;
} else {
throw new InternalErrorException("References by resource with no reference ID are not supported in DAO layer");
@ -1359,9 +1331,9 @@ public abstract class BaseTransactionProcessor {
continue;
}
}
if (newId != null || theIdSubstitutions.containsKey(nextId)) {
if (newId != null || theIdSubstitutions.containsSource(nextId)) {
if (newId == null) {
newId = theIdSubstitutions.get(nextId);
newId = theIdSubstitutions.getForSource(nextId);
}
if (newId != null) {
ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
@ -1421,9 +1393,9 @@ public abstract class BaseTransactionProcessor {
if (nextRef instanceof IIdType) {
continue; // No substitution on the resource ID itself!
}
IIdType nextUriString = newIdType(nextRef.getValueAsString());
if (theIdSubstitutions.containsKey(nextUriString)) {
IIdType newId = theIdSubstitutions.get(nextUriString);
String nextUriString = nextRef.getValueAsString();
if (theIdSubstitutions.containsSource(nextUriString)) {
IIdType newId = theIdSubstitutions.getForSource(nextUriString);
ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
String existingValue = nextRef.getValueAsString();
@ -1458,26 +1430,17 @@ public abstract class BaseTransactionProcessor {
// Make sure we reflect the actual final version for the resource.
if (updateOutcome != null) {
IIdType newId = updateOutcome.getIdDt();
for (IIdType nextEntry : entriesToProcess.values()) {
if (nextEntry.getResourceType().equals(newId.getResourceType())) {
if (nextEntry.getIdPart().equals(newId.getIdPart())) {
if (!nextEntry.hasVersionIdPart() || !nextEntry.getVersionIdPart().equals(newId.getVersionIdPart())) {
nextEntry.setParts(nextEntry.getBaseUrl(), nextEntry.getResourceType(), nextEntry.getIdPart(), newId.getVersionIdPart());
}
}
}
IIdType entryId = entriesToProcess.getIdWithVersionlessComparison(newId);
if (entryId != null && !StringUtils.equals(entryId.getValue(), newId.getValue())) {
entryId.setValue(newId.getValue());
}
nextOutcome.setId(newId);
for (IIdType next : theIdSubstitutions.values()) {
if (next.getResourceType().equals(newId.getResourceType())) {
if (next.getIdPart().equals(newId.getIdPart())) {
if (!next.getValue().equals(newId.getValue())) {
next.setValue(newId.getValue());
}
}
}
IIdType target = theIdSubstitutions.getForSource(newId);
if (target != null) {
target.setValue(newId.getValue());
}
}
@ -1626,18 +1589,6 @@ public abstract class BaseTransactionProcessor {
return null;
}
private static class BaseServerResponseExceptionHolder {
private BaseServerResponseException myException;
public BaseServerResponseException getException() {
return myException;
}
public void setException(BaseServerResponseException myException) {
this.myException = myException;
}
}
/**
* Transaction Order, per the spec:
* <p>
@ -1808,4 +1759,99 @@ public abstract class BaseTransactionProcessor {
}
}
private static class BaseServerResponseExceptionHolder {
private BaseServerResponseException myException;
public BaseServerResponseException getException() {
return myException;
}
public void setException(BaseServerResponseException myException) {
this.myException = myException;
}
}
public static boolean isPlaceholder(IIdType theId) {
if (theId != null && theId.getValue() != null) {
return theId.getValue().startsWith("urn:oid:") || theId.getValue().startsWith("urn:uuid:");
}
return false;
}
private static String toStatusString(int theStatusCode) {
return theStatusCode + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
}
/**
* Given a match URL containing
*
* @param theIdSubstitutions
* @param theMatchUrl
* @return
*/
static String performIdSubstitutionsInMatchUrl(IdSubstitutionMap theIdSubstitutions, String theMatchUrl) {
String matchUrl = theMatchUrl;
if (isNotBlank(matchUrl) && !theIdSubstitutions.isEmpty()) {
int startIdx = matchUrl.indexOf('?');
while (startIdx != -1) {
int endIdx = matchUrl.indexOf('&', startIdx + 1);
if (endIdx == -1) {
endIdx = matchUrl.length();
}
int equalsIdx = matchUrl.indexOf('=', startIdx + 1);
int searchFrom;
if (equalsIdx == -1) {
searchFrom = matchUrl.length();
} else if (equalsIdx >= endIdx) {
// First equals we found is from a subsequent parameter
searchFrom = matchUrl.length();
} else {
String paramValue = matchUrl.substring(equalsIdx + 1, endIdx);
boolean isUrn = isUrn(paramValue);
boolean isUrnEscaped = !isUrn && isUrnEscaped(paramValue);
if (isUrn || isUrnEscaped) {
if (isUrnEscaped) {
paramValue = UrlUtil.unescape(paramValue);
}
IIdType replacement = theIdSubstitutions.getForSource(paramValue);
if (replacement != null) {
String replacementValue;
if (replacement.hasVersionIdPart()) {
replacementValue = replacement.toVersionless().getValue();
} else {
replacementValue = replacement.getValue();
}
matchUrl = matchUrl.substring(0, equalsIdx + 1) + replacementValue + matchUrl.substring(endIdx);
searchFrom = equalsIdx + 1 + replacementValue.length();
} else {
searchFrom = endIdx;
}
} else {
searchFrom = endIdx;
}
}
if (searchFrom >= matchUrl.length()) {
break;
}
startIdx = matchUrl.indexOf('&', searchFrom);
}
}
return matchUrl;
}
private static boolean isUrn(@Nonnull String theId) {
return theId.startsWith(URN_PREFIX);
}
private static boolean isUrnEscaped(@Nonnull String theId) {
return theId.startsWith(URN_PREFIX_ESCAPED);
}
}

50
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/EntriesToProcessMap.java Normal file
View File

@ -0,0 +1,50 @@
package ca.uhn.fhir.jpa.dao;
/*-
* #%L
* HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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 org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.HashMap;
import java.util.IdentityHashMap;
import java.util.Map;
import java.util.Set;
import static ca.uhn.fhir.jpa.dao.IdSubstitutionMap.toVersionlessValue;
public class EntriesToProcessMap {
private final IdentityHashMap<IBase, IIdType> myEntriesToProcess = new IdentityHashMap<>();
private final Map<String, IIdType> myVersionlessIdToVersionedId = new HashMap<>();
public void put(IBase theBundleEntry, IIdType theId) {
myEntriesToProcess.put(theBundleEntry, theId);
myVersionlessIdToVersionedId.put(toVersionlessValue(theId), theId);
}
public IIdType getIdWithVersionlessComparison(IIdType theId) {
return myVersionlessIdToVersionedId.get(toVersionlessValue(theId));
}
public Set<Map.Entry<IBase, IIdType>> entrySet() {
return myEntriesToProcess.entrySet();
}
}

141
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/IdSubstitutionMap.java Normal file
View File

@ -0,0 +1,141 @@
package ca.uhn.fhir.jpa.dao;
/*-
* #%L
* HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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 com.google.common.collect.Multimap;
import com.google.common.collect.MultimapBuilder;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IIdType;
import javax.annotation.Nonnull;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
public class IdSubstitutionMap {
private final Map<Entry, Entry> myMap = new HashMap<>();
private final Multimap<Entry, Entry> myReverseMap = MultimapBuilder.hashKeys().arrayListValues().build();
public boolean containsSource(IIdType theId) {
if (theId.isLocal()) {
return false;
}
return myMap.containsKey(new Entry(theId));
}
public boolean containsSource(String theId) {
return myMap.containsKey(new Entry(theId));
}
public boolean containsTarget(IIdType theId) {
return myReverseMap.containsKey(new Entry(theId));
}
public boolean containsTarget(String theId) {
return myReverseMap.containsKey(new Entry(theId));
}
public IIdType getForSource(IIdType theId) {
Entry target = myMap.get(new Entry(theId));
if (target != null) {
assert target.myId != null;
return target.myId;
}
return null;
}
public IIdType getForSource(String theId) {
Entry target = myMap.get(new Entry(theId));
if (target != null) {
assert target.myId != null;
return target.myId;
}
return null;
}
public List<Pair<IIdType, IIdType>> entrySet() {
return myMap
.entrySet()
.stream()
.map(t->Pair.of(t.getKey().myId, t.getValue().myId))
.collect(Collectors.toList());
}
public void put(IIdType theSource, IIdType theTarget) {
myMap.put(new Entry(theSource), new Entry(theTarget));
myReverseMap.put(new Entry(theTarget), new Entry(theSource));
}
public boolean isEmpty() {
return myMap.isEmpty();
}
private static class Entry {
private final String myUnversionedId;
private final IIdType myId;
private Entry(String theId) {
myId = null;
myUnversionedId = theId;
}
private Entry(IIdType theId) {
String unversionedId = toVersionlessValue(theId);
myUnversionedId = unversionedId;
myId = theId;
}
@Override
public boolean equals(Object theOther) {
if (theOther instanceof Entry) {
String otherUnversionedId = ((Entry) theOther).myUnversionedId;
if (myUnversionedId.equals(otherUnversionedId)) {
return true;
}
}
return false;
}
@Override
public int hashCode() {
return myUnversionedId.hashCode();
}
}
static String toVersionlessValue(IIdType theId) {
boolean isPlaceholder = theId.getValue().startsWith("urn:");
String unversionedId;
if (isPlaceholder || (!theId.hasBaseUrl() && !theId.hasVersionIdPart()) || !theId.hasResourceType()) {
unversionedId = theId.getValue();
} else {
unversionedId = theId.toUnqualifiedVersionless().getValue();
}
return unversionedId;
}
}

2
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/MatchResourceUrlService.java
View File

@ -185,7 +185,7 @@ public class MatchResourceUrlService {
@Nullable
public ResourcePersistentId processMatchUrlUsingCacheOnly(String theResourceType, String theMatchUrl) {
ResourcePersistentId existing = null;
if (myDaoConfig.getMatchUrlCache()) {
if (myDaoConfig.isMatchUrlCacheEnabled()) {
String matchUrl = massageForStorage(theResourceType, theMatchUrl);
existing = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.MATCH_URL, matchUrl);
}

25
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionCanonicalizer.java
View File

@ -25,11 +25,14 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionMatchingStrategy;
import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscriptionChannelType;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.resource.Subscription;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.util.HapiExtensions;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseMetaType;
import org.hl7.fhir.instance.model.api.IBaseReference;
@ -43,6 +46,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@ -79,7 +83,6 @@ public class SubscriptionCanonicalizer {
private CanonicalSubscription canonicalizeDstu2(IBaseResource theSubscription) {
ca.uhn.fhir.model.dstu2.resource.Subscription subscription = (ca.uhn.fhir.model.dstu2.resource.Subscription) theSubscription;
CanonicalSubscription retVal = new CanonicalSubscription();
try {
retVal.setStatus(org.hl7.fhir.r4.model.Subscription.SubscriptionStatus.fromCode(subscription.getStatus()));
@ -90,12 +93,28 @@ public class SubscriptionCanonicalizer {
retVal.setChannelExtensions(extractExtension(subscription));
retVal.setIdElement(subscription.getIdElement());
retVal.setPayloadString(subscription.getChannel().getPayload());
retVal.setTags(extractTags(subscription));
} catch (FHIRException theE) {
throw new InternalErrorException(theE);
}
return retVal;
}
/**
* Extract the meta tags from the subscription and convert them to a simple string map.
* @param theSubscription The subscription to extract the tags from
* @return A map of tags System:Code
*/
private Map<String, String> extractTags(IBaseResource theSubscription) {
return theSubscription.getMeta().getTag()
.stream()
.filter(t -> t.getSystem() != null && t.getCode() != null)
.collect(Collectors.toMap(
IBaseCoding::getSystem,
IBaseCoding::getCode
));
}
private CanonicalSubscription canonicalizeDstu3(IBaseResource theSubscription) {
org.hl7.fhir.dstu3.model.Subscription subscription = (org.hl7.fhir.dstu3.model.Subscription) theSubscription;
@ -113,6 +132,7 @@ public class SubscriptionCanonicalizer {
retVal.setIdElement(subscription.getIdElement());
retVal.setPayloadString(subscription.getChannel().getPayload());
retVal.setPayloadSearchCriteria(getExtensionString(subscription, HapiExtensions.EXT_SUBSCRIPTION_PAYLOAD_SEARCH_CRITERIA));
retVal.setTags(extractTags(subscription));
if (retVal.getChannelType() == CanonicalSubscriptionChannelType.EMAIL) {
String from;
@ -201,7 +221,6 @@ public class SubscriptionCanonicalizer {
private CanonicalSubscription canonicalizeR4(IBaseResource theSubscription) {
org.hl7.fhir.r4.model.Subscription subscription = (org.hl7.fhir.r4.model.Subscription) theSubscription;
CanonicalSubscription retVal = new CanonicalSubscription();
retVal.setStatus(subscription.getStatus());
retVal.setChannelType(getChannelType(theSubscription));
@ -212,6 +231,7 @@ public class SubscriptionCanonicalizer {
retVal.setIdElement(subscription.getIdElement());
retVal.setPayloadString(subscription.getChannel().getPayload());
retVal.setPayloadSearchCriteria(getExtensionString(subscription, HapiExtensions.EXT_SUBSCRIPTION_PAYLOAD_SEARCH_CRITERIA));
retVal.setTags(extractTags(subscription));
if (retVal.getChannelType() == CanonicalSubscriptionChannelType.EMAIL) {
String from;
@ -266,6 +286,7 @@ public class SubscriptionCanonicalizer {
retVal.setIdElement(subscription.getIdElement());
retVal.setPayloadString(subscription.getContentType());
retVal.setPayloadSearchCriteria(getExtensionString(subscription, HapiExtensions.EXT_SUBSCRIPTION_PAYLOAD_SEARCH_CRITERIA));
retVal.setTags(extractTags(subscription));
if (retVal.getChannelType() == CanonicalSubscriptionChannelType.EMAIL) {
String from;

11
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/model/CanonicalSubscription.java
View File

@ -68,6 +68,8 @@ public class CanonicalSubscription implements Serializable, Cloneable, IModelJso
private RestHookDetails myRestHookDetails;
@JsonProperty("extensions")
private Map<String, List<String>> myChannelExtensions;
@JsonProperty("tags")
private Map<String, String> myTags;
@JsonProperty("payloadSearchCriteria")
private String myPayloadSearchCriteria;
@ -139,6 +141,15 @@ public class CanonicalSubscription implements Serializable, Cloneable, IModelJso
}
}
public Map<String, String> getTags() {
return myTags;
}
public void setTags(Map<String, String> theTags) {
this.myTags = theTags;
}
public void setHeaders(String theHeaders) {
myHeaders = new ArrayList<>();
if (isNotBlank(theHeaders)) {

20
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/model/ChannelRetryConfiguration.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.subscription.model;
/*-
* #%L
* HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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%
*/
public class ChannelRetryConfiguration {
/**
* Number of times to retry a failed message.

11
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/model/ResourceModifiedJsonMessage.java
View File

@ -24,6 +24,8 @@ import ca.uhn.fhir.rest.server.messaging.json.BaseJsonMessage;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
import javax.annotation.Nullable;
public class ResourceModifiedJsonMessage extends BaseJsonMessage<ResourceModifiedMessage> {
@JsonProperty("payload")
@ -52,6 +54,15 @@ public class ResourceModifiedJsonMessage extends BaseJsonMessage<ResourceModifie
myPayload = thePayload;
}
@Override
@Nullable
public String getMessageKeyOrNull() {
if (myPayload == null) {
return null;
}
return myPayload.getMessageKeyOrNull();
}
@Override
public String toString() {
return new ToStringBuilder(this)

5
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/model/ResourceModifiedMessage.java
View File

@ -27,6 +27,8 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import javax.annotation.Nullable;
/**
* Most of this class has been moved to ResourceModifiedMessage in the hapi-fhir-server project, for a reusable channel ResourceModifiedMessage
* that doesn't require knowledge of subscriptions.
@ -40,6 +42,8 @@ public class ResourceModifiedMessage extends BaseResourceModifiedMessage {
@JsonProperty(value = "subscriptionId", required = false)
private String mySubscriptionId;
/**
* Constructor
*/
@ -64,6 +68,7 @@ public class ResourceModifiedMessage extends BaseResourceModifiedMessage {
mySubscriptionId = theSubscriptionId;
}
@Override
public String toString() {
return new ToStringBuilder(this)

83
hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessorTest.java Normal file
View File

@ -0,0 +1,83 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.r4.model.IdType;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
public class BaseTransactionProcessorTest {
@Test
void testPerformIdSubstitutionsInMatchUrl_MatchAtStart() {
IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType("Patient/123"));
String outcome = BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(idSubstitutions, "Patient?foo=urn:uuid:1234&bar=baz");
assertEquals("Patient?foo=Patient/123&bar=baz", outcome);
}
/**
* Make sure versioned targets get the version stripped
*/
@Test
void testPerformIdSubstitutionsInMatchUrl_MatchAtEnd() {
IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
idSubstitutions.put(new IdType("urn:uuid:7ea4f3a6-d2a3-4105-9f31-374d525085d4"), new IdType("Patient/123/_history/1"));
String outcome = BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(idSubstitutions, "Patient?name=FAMILY1&organization=urn%3Auuid%3A7ea4f3a6-d2a3-4105-9f31-374d525085d4");
assertEquals("Patient?name=FAMILY1&organization=Patient/123", outcome);
}
@Test
void testPerformIdSubstitutionsInMatchUrl_MatchEscapedParam() {
IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType("Patient/123"));
String outcome = BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(idSubstitutions, "Patient?foo=" + UrlUtil.escapeUrlParam("urn:uuid:1234") + "&bar=baz");
assertEquals("Patient?foo=Patient/123&bar=baz", outcome);
}
@Test
void testPerformIdSubstitutionsInMatchUrl_MatchInParamNameShouldntBeReplaced() {
IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType("Patient/123"));
String outcome = BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(idSubstitutions, "Patient?urn:uuid:1234=foo&bar=baz");
assertEquals("Patient?urn:uuid:1234=foo&bar=baz", outcome);
}
@Test
void testPerformIdSubstitutionsInMatchUrl_NoParams() {
IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType("Patient/123"));
String input = "Patient";
String outcome = BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(idSubstitutions, input);
assertEquals(input, outcome);
}
@Test
void testPerformIdSubstitutionsInMatchUrl_UnterminatedParams() {
IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType("Patient/123"));
String input = "Patient?foo&bar=&baz";
String outcome = BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(idSubstitutions, input);
assertEquals(input, outcome);
}
@Test
void testPerformIdSubstitutionsInMatchUrl_ReplaceMultiple() {
IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
idSubstitutions.put(new IdType("urn:uuid:1234"), new IdType("Patient/abcdefghijklmnopqrstuvwxyz0123456789"));
String input = "Patient?foo=urn:uuid:1234&bar=urn:uuid:1234&baz=urn:uuid:1234";
String outcome = BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(idSubstitutions, input);
String expected = "Patient?foo=Patient/abcdefghijklmnopqrstuvwxyz0123456789&bar=Patient/abcdefghijklmnopqrstuvwxyz0123456789&baz=Patient/abcdefghijklmnopqrstuvwxyz0123456789";
assertEquals(expected, outcome);
}
@Test
void testPerformIdSubstitutionsInMatchUrl_NonUrnSubstitution() {
IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
idSubstitutions.put(new IdType("Patient/123"), new IdType("Patient/456"));
String input = "Patient?foo=Patient/123";
String outcome = BaseTransactionProcessor.performIdSubstitutionsInMatchUrl(idSubstitutions, input);
assertEquals(input, outcome);
}
}

2
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -2338,7 +2338,7 @@ public class JsonParserDstu3Test {
ourCtx.newJsonParser().parseResource(Bundle.class, bundle);
fail();
} catch (DataFormatException e) {
assertEquals("Failed to parse JSON encoded FHIR content: Unexpected close marker '}': expected ']' (for root starting at [Source: UNKNOWN; line: 1, column: 0])\n" +
assertEquals("Failed to parse JSON encoded FHIR content: Unexpected close marker '}': expected ']' (for root starting at [Source: UNKNOWN; line: 1])\n" +
" at [Source: UNKNOWN; line: 4, column: 3]", e.getMessage());
}
}

25
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
View File

@ -38,6 +38,7 @@ import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.Type;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
@ -80,6 +81,11 @@ public class JsonParserR4Test extends BaseTest {
return b;
}
@AfterEach
public void afterEach() {
ourCtx.getParserOptions().setAutoContainReferenceTargetsWithNoId(true);
}
@Test
public void testEntitiesNotConverted() throws IOException {
Device input = loadResource(ourCtx, Device.class, "/entities-from-cerner.json");
@ -198,6 +204,25 @@ public class JsonParserR4Test extends BaseTest {
}
@Test
public void testContainedResourcesNotAutoContainedWhenConfiguredNotToDoSo() {
MedicationDispense md = new MedicationDispense();
md.addIdentifier().setValue("DISPENSE");
Medication med = new Medication();
med.getCode().setText("MED");
md.setMedication(new Reference(med));
ourCtx.getParserOptions().setAutoContainReferenceTargetsWithNoId(false);
String encoded = ourCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(md);
assertEquals("{\"resourceType\":\"MedicationDispense\",\"identifier\":[{\"value\":\"DISPENSE\"}],\"medicationReference\":{}}", encoded);
ourCtx.getParserOptions().setAutoContainReferenceTargetsWithNoId(true);
encoded = ourCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(md);
assertEquals("{\"resourceType\":\"MedicationDispense\",\"contained\":[{\"resourceType\":\"Medication\",\"id\":\"1\",\"code\":{\"text\":\"MED\"}}],\"identifier\":[{\"value\":\"DISPENSE\"}],\"medicationReference\":{\"reference\":\"#1\"}}", encoded);
}
@Test
public void testParseBundleWithMultipleNestedContainedResources() throws Exception {
String text = loadResource("/bundle-with-two-patient-resources.json");

5
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/jsonlike/JsonLikeParserTest.java
View File

@ -28,6 +28,7 @@ import java.math.BigDecimal;
import java.math.BigInteger;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
@ -537,8 +538,8 @@ public class JsonLikeParserTest {
}
@Override
public Set<String> keySet() {
return nativeObject.keySet();
public Iterator<String> keyIterator() {
return nativeObject.keySet().iterator();
}
@Override

15
hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/BatchJobHelper.java
View File

@ -62,10 +62,11 @@ public class BatchJobHelper {
public List<JobExecution> awaitAllBulkJobCompletions(boolean theFailIfNotJobsFound, String... theJobNames) {
assert theJobNames.length > 0;
List<JobInstance> matchingJobInstances = new ArrayList<>();
for (String nextName : theJobNames) {
matchingJobInstances.addAll(myJobExplorer.findJobInstancesByJobName(nextName, 0, 100));
if (theFailIfNotJobsFound) {
await().until(() -> !getJobInstances(theJobNames).isEmpty());
}
List<JobInstance> matchingJobInstances = getJobInstances(theJobNames);
if (theFailIfNotJobsFound) {
if (matchingJobInstances.isEmpty()) {
List<String> wantNames = Arrays.asList(theJobNames);
@ -81,6 +82,14 @@ public class BatchJobHelper {
return matchingExecutions;
}
private List<JobInstance> getJobInstances(String[] theJobNames) {
List<JobInstance> matchingJobInstances = new ArrayList<>();
for (String nextName : theJobNames) {
matchingJobInstances.addAll(myJobExplorer.findJobInstancesByJobName(nextName, 0, 100));
}
return matchingJobInstances;
}
public JobExecution awaitJobExecution(Long theJobExecutionId) {
JobExecution jobExecution = myJobExplorer.getJobExecution(theJobExecutionId);
awaitJobCompletion(jobExecution);

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/RemoteTerminologyServiceValidationSupport.java
View File

@ -49,6 +49,11 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
super(theFhirContext);
}
public RemoteTerminologyServiceValidationSupport(FhirContext theFhirContext, String theBaseUrl) {
super(theFhirContext);
myBaseUrl = theBaseUrl;
}
@Override
public CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
return invokeRemoteValidateCode(theCodeSystem, theCode, theDisplay, theValueSetUrl, null);

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