honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Improve loading performance (#3197) 

* Synthea perf work

* Cleanup

* Work on performance

* Ongoing perf work

* More perf work

* Perf work

* Test fixes

* Updates

* Test fix

* Test fixes

* Clean up tests

* Test cleanup

* Cleanup

* Add test

* One more perf tweak

* Fixes

* Add changelog

* Add changelog

* License header update

* License header updates
This commit is contained in:
James Agnew 2021-11-28 10:47:30 -05:00 committed by GitHub
parent 7ef1d159ee
commit aae53d6ec7
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
39 changed files with 1225 additions and 361 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

78
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));
public boolean isAutoContainReferenceTargetsWithNoId() {
return myAutoContainReferenceTargetsWithNoId;
}
return this;
/**
* 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

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) {

4
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
@ -49,7 +49,7 @@ public abstract class JsonLikeObject extends JsonLikeValue {
return null;
}
public abstract Set<String> keySet ();
public abstract Iterator<String> keyIterator();
public abstract JsonLikeValue get(String key);

55
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);
return new JacksonJsonValue(child);
}
jsonLikeMap.put(key, result);
}
return result;
return null;
}
}
@ -300,20 +283,29 @@ public class JacksonStructure implements JsonLikeStructure {
@Override
public ValueType getJsonType() {
if (null == nativeValue || nativeValue.isNull()) {
if (null == nativeValue) {
return ValueType.NULL;
}
if (nativeValue.isObject()) {
switch (nativeValue.getNodeType()) {
case NULL:
case MISSING:
return ValueType.NULL;
case OBJECT:
return ValueType.OBJECT;
}
if (nativeValue.isArray()) {
case ARRAY:
return ValueType.ARRAY;
case POJO:
case BINARY:
case STRING:
case NUMBER:
case BOOLEAN:
default:
break;
}
if (nativeValue.isValueNode()) {
return ValueType.SCALAR;
}
return null;
}
@Override
public ScalarType getDataType() {
@ -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);

43
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;
@ -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

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)."

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;

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;
}
}
}

29
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());
@ -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
@ -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);

86
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;
@ -196,11 +185,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
@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;
@ -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);
@ -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);
@ -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));
}
}
}
}
}

20
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/broker/MdmMessageKeySvc.java
View File

@ -1,5 +1,25 @@
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;

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();

98
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.
@ -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);
};
}

50
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);
}
}
}
}
@ -112,13 +119,40 @@ public class ReadOnlySearchParamCache {
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);
}
}

20
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) {
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"));
}
}

20
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/api/ISubscriptionMessageKeySvc.java
View File

@ -1,5 +1,25 @@
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;

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 {
/**

212
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;
@ -273,14 +265,16 @@ 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) {
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.
@ -336,30 +330,6 @@ 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;
}
@ -637,12 +607,12 @@ 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,
@ -651,7 +621,7 @@ 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);
@ -844,9 +814,14 @@ public abstract class BaseTransactionProcessor {
}
}
if (nextResourceId.hasIdPart() && nextResourceId.getIdPart().matches("[a-zA-Z]+:.*") && !isPlaceholder(nextResourceId)) {
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)) {
nextResourceId = newIdType(toResourceName(theBaseResource.getClass()), nextResourceId.getIdPart());
@ -875,9 +850,9 @@ 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) {
@ -890,7 +865,7 @@ 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<>();
@ -1139,7 +1114,7 @@ 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);
}
@ -1183,9 +1158,6 @@ 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()
@ -1280,8 +1252,8 @@ 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");
@ -1339,8 +1311,8 @@ 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) {
@ -1356,7 +1328,7 @@ 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");
@ -1365,9 +1337,9 @@ 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);
@ -1427,9 +1399,9 @@ 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();
@ -1464,26 +1436,17 @@ 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());
}
}
@ -1632,18 +1595,6 @@ 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>
@ -1814,4 +1765,93 @@ 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) {
matchUrl = matchUrl.substring(0, equalsIdx + 1) + replacement.getValue() + matchUrl.substring(endIdx);
searchFrom = equalsIdx + 1 + replacement.getValue().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);
}

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.

80
hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessorTest.java Normal file
View File

@ -0,0 +1,80 @@
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);
}
@Test
void testPerformIdSubstitutionsInMatchUrl_MatchAtEnd() {
IdSubstitutionMap idSubstitutions = new IdSubstitutionMap();
idSubstitutions.put(new IdType("urn:uuid:7ea4f3a6-d2a3-4105-9f31-374d525085d4"), new IdType("Patient/123"));
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

2
pom.xml
View File

@ -818,7 +818,7 @@
<hibernate_validator_version>6.1.5.Final</hibernate_validator_version>
<httpcore_version>4.4.13</httpcore_version>
<httpclient_version>4.5.13</httpclient_version>
<jackson_version>2.12.3</jackson_version>
<jackson_version>2.13.0</jackson_version>
<jackson_databind_version>${jackson_version}</jackson_databind_version>
<maven_assembly_plugin_version>3.3.0</maven_assembly_plugin_version>
<maven_license_plugin_version>1.8</maven_license_plugin_version>