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Working in-place bundle sort

This commit is contained in:
Tadgh 2021-04-20 17:48:55 -04:00
parent ff2690b74e
commit 3dee0c8ab6
2 changed files with 149 additions and 80 deletions
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189
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleUtil.java
View File

@ -20,12 +20,14 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@ -186,13 +188,47 @@ public class BundleUtil {
static int GRAY = 2;
static int BLACK = 3;
public static List<BundleEntryParts> topologicalSort(FhirContext theContext, IBaseBundle theBundle, RequestTypeEnum theRequestTypeEnum) {
public static void sortEntriesIntoProcessingOrder(FhirContext theContext, IBaseBundle theBundle) {
Map<BundleEntryParts, IBase> partsToIBaseMap = getPartsToIBaseMap(theContext, theBundle);
LinkedHashSet<IBase> retVal = new LinkedHashSet<>();
//Get all deletions.
LinkedHashSet<IBase> deleteParts = sortEntriesIntoProcessingOrder(theContext, theBundle, RequestTypeEnum.DELETE, partsToIBaseMap);
if (deleteParts == null) {
throw new IllegalStateException("Cycle!");
} else {
retVal.addAll(deleteParts);
}
//Get all Creations
LinkedHashSet<IBase> createParts= sortEntriesIntoProcessingOrder(theContext, theBundle, RequestTypeEnum.POST, partsToIBaseMap);
if (createParts== null) {
throw new IllegalStateException("Cycle!");
} else {
retVal.addAll(createParts);
}
// Get all Updates
LinkedHashSet<IBase> updateParts= sortEntriesIntoProcessingOrder(theContext, theBundle, RequestTypeEnum.PUT, partsToIBaseMap);
if (updateParts == null) {
throw new IllegalStateException("Cycle!");
} else {
retVal.addAll(updateParts);
}
//Once we are done adding all DELETE, POST, PUT operations, add everything else.
retVal.addAll(partsToIBaseMap.values());
//Blow away the entries and reset them in the right order.
TerserUtil.clearField(theContext, "entry", theBundle);
TerserUtil.setField(theContext, "entry", theBundle, retVal.toArray(new IBase[0]));
}
public static LinkedHashSet<IBase> sortEntriesIntoProcessingOrder(FhirContext theContext, IBaseBundle theBundle, RequestTypeEnum theRequestTypeEnum, Map<BundleEntryParts, IBase> thePartsToIBaseMap) {
SortLegality legality = new SortLegality();
HashMap<String, Integer> color = new HashMap<String, Integer>();
HashMap<String, Integer> color = new HashMap<>();
HashMap<String, List<String>> adjList = new HashMap<>();
List<String> topologicalOrder = new ArrayList<>();
List<BundleEntryParts> bundleEntryParts = toListOfEntries(theContext, theBundle);
bundleEntryParts.removeIf(bep -> !bep.getRequestType().equals(theRequestTypeEnum));
Set<BundleEntryParts> bundleEntryParts = thePartsToIBaseMap.keySet().stream().filter(part -> part.getRequestType().equals(theRequestTypeEnum)).collect(Collectors.toSet());
HashMap<String, BundleEntryParts> resourceIdToBundleEntryMap = new HashMap<>();
for (BundleEntryParts bundleEntryPart : bundleEntryParts) {
@ -204,7 +240,9 @@ public class BundleUtil {
resourceId = bundleEntryPart.getFullUrl();
}
}
color.put(resourceId, WHITE);
}
for (BundleEntryParts bundleEntryPart : bundleEntryParts) {
@ -229,30 +267,33 @@ public class BundleUtil {
}
});
}
//All nodes are now white
//Adjacency List has been built.
for (Map.Entry<String, Integer> entry:color.entrySet()) {
if (entry.getValue() == WHITE) {
depthFirstSearch(entry.getKey(), color, adjList, topologicalOrder, legality);
}
}
if (legality.isLegal()) {
if (ourLog.isDebugEnabled()) {
ourLog.debug("Topological order is: {}", String.join(",", topologicalOrder));
}
List<BundleEntryParts> beps = new ArrayList<>();
for (int i = 0;i < topologicalOrder.size(); i++) {
BundleEntryParts bep = resourceIdToBundleEntryMap.get(topologicalOrder.get(i));
beps.add(bep);
LinkedHashSet<IBase> orderedEntries = new LinkedHashSet<>();
for (int i = 0; i < topologicalOrder.size(); i++) {
BundleEntryParts bep;
if (theRequestTypeEnum.equals(RequestTypeEnum.DELETE)) {
int index = topologicalOrder.size() - i - 1;
bep = resourceIdToBundleEntryMap.get(topologicalOrder.get(index));
} else {
bep = resourceIdToBundleEntryMap.get(topologicalOrder.get(i));
}
IBase base = thePartsToIBaseMap.get(bep);
orderedEntries.add(base);
}
//In case of delete, we want to delete child elements LAST.
if (theRequestTypeEnum.equals(RequestTypeEnum.DELETE)) {
Collections.reverse(beps);
}
return beps;
return orderedEntries;
} else {
return null;
}
@ -295,15 +336,38 @@ public class BundleUtil {
theTopologicalOrder.add(theResourceId);
}
private static Map<BundleEntryParts, IBase> getPartsToIBaseMap(FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition bundleDef = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChildDef = bundleDef.getChildByName("entry");
List<IBase> entries = entryChildDef.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition<?> entryChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) entryChildDef.getChildByName("entry");
BaseRuntimeChildDefinition fullUrlChildDef = entryChildContentsDef.getChildByName("fullUrl");
BaseRuntimeChildDefinition resourceChildDef = entryChildContentsDef.getChildByName("resource");
BaseRuntimeChildDefinition requestChildDef = entryChildContentsDef.getChildByName("request");
BaseRuntimeElementCompositeDefinition<?> requestChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) requestChildDef.getChildByName("request");
BaseRuntimeChildDefinition requestUrlChildDef = requestChildContentsDef.getChildByName("url");
BaseRuntimeChildDefinition requestIfNoneExistChildDef = requestChildContentsDef.getChildByName("ifNoneExist");
BaseRuntimeChildDefinition methodChildDef = requestChildContentsDef.getChildByName("method");
Map<BundleEntryParts, IBase> map = new HashMap<>();
for (IBase nextEntry : entries) {
BundleEntryParts parts = getBundleEntryParts(fullUrlChildDef, resourceChildDef, requestChildDef, requestUrlChildDef, requestIfNoneExistChildDef, methodChildDef, nextEntry);
/*
* All 3 might be null - That's ok because we still want to know the
* order in the original bundle.
*/
map.put(parts, nextEntry);
}
return map;
}
public static void processEntries(FhirContext theContext, IBaseBundle theBundle, Consumer<ModifiableBundleEntry> theProcessor) {
RuntimeResourceDefinition bundleDef = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChildDef = bundleDef.getChildByName("entry");
List<IBase> entries = entryChildDef.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition<?> entryChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) entryChildDef.getChildByName("entry");
BaseRuntimeChildDefinition fullUrlChildDef = entryChildContentsDef.getChildByName("fullUrl");
BaseRuntimeChildDefinition resourceChildDef = entryChildContentsDef.getChildByName("resource");
BaseRuntimeChildDefinition requestChildDef = entryChildContentsDef.getChildByName("request");
BaseRuntimeElementCompositeDefinition<?> requestChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) requestChildDef.getChildByName("request");
@ -312,57 +376,62 @@ public class BundleUtil {
BaseRuntimeChildDefinition methodChildDef = requestChildContentsDef.getChildByName("method");
for (IBase nextEntry : entries) {
IBaseResource resource = null;
String url = null;
RequestTypeEnum requestType = null;
String conditionalUrl = null;
String fullUrl = fullUrlChildDef
.getAccessor()
.getFirstValueOrNull(nextEntry)
.map(t->((IPrimitiveType<?>)t).getValueAsString())
.orElse(null);
for (IBase nextResource : resourceChildDef.getAccessor().getValues(nextEntry)) {
resource = (IBaseResource) nextResource;
}
for (IBase nextRequest : requestChildDef.getAccessor().getValues(nextEntry)) {
for (IBase nextUrl : requestUrlChildDef.getAccessor().getValues(nextRequest)) {
url = ((IPrimitiveType<?>) nextUrl).getValueAsString();
}
for (IBase nextMethod : methodChildDef.getAccessor().getValues(nextRequest)) {
String methodString = ((IPrimitiveType<?>) nextMethod).getValueAsString();
if (isNotBlank(methodString)) {
requestType = RequestTypeEnum.valueOf(methodString);
}
}
if (requestType != null) {
//noinspection EnumSwitchStatementWhichMissesCases
switch (requestType) {
case PUT:
conditionalUrl = url != null && url.contains("?") ? url : null;
break;
case POST:
List<IBase> ifNoneExistReps = requestIfNoneExistChildDef.getAccessor().getValues(nextRequest);
if (ifNoneExistReps.size() > 0) {
IPrimitiveType<?> ifNoneExist = (IPrimitiveType<?>) ifNoneExistReps.get(0);
conditionalUrl = ifNoneExist.getValueAsString();
}
break;
}
}
}
BundleEntryParts parts = getBundleEntryParts(fullUrlChildDef, resourceChildDef, requestChildDef, requestUrlChildDef, requestIfNoneExistChildDef, methodChildDef, nextEntry);
/*
* All 3 might be null - That's ok because we still want to know the
* order in the original bundle.
*/
BundleEntryMutator mutator = new BundleEntryMutator(theContext, nextEntry, requestChildDef, requestChildContentsDef, entryChildContentsDef);
ModifiableBundleEntry entry = new ModifiableBundleEntry(new BundleEntryParts(fullUrl, requestType, url, resource, conditionalUrl), mutator);
ModifiableBundleEntry entry = new ModifiableBundleEntry(parts, mutator);
theProcessor.accept(entry);
}
}
private static BundleEntryParts getBundleEntryParts(BaseRuntimeChildDefinition fullUrlChildDef, BaseRuntimeChildDefinition resourceChildDef, BaseRuntimeChildDefinition requestChildDef, BaseRuntimeChildDefinition requestUrlChildDef, BaseRuntimeChildDefinition requestIfNoneExistChildDef, BaseRuntimeChildDefinition methodChildDef, IBase nextEntry) {
IBaseResource resource = null;
String url = null;
RequestTypeEnum requestType = null;
String conditionalUrl = null;
String fullUrl = fullUrlChildDef
.getAccessor()
.getFirstValueOrNull(nextEntry)
.map(t->((IPrimitiveType<?>)t).getValueAsString())
.orElse(null);
for (IBase nextResource : resourceChildDef.getAccessor().getValues(nextEntry)) {
resource = (IBaseResource) nextResource;
}
for (IBase nextRequest : requestChildDef.getAccessor().getValues(nextEntry)) {
for (IBase nextUrl : requestUrlChildDef.getAccessor().getValues(nextRequest)) {
url = ((IPrimitiveType<?>) nextUrl).getValueAsString();
}
for (IBase nextMethod : methodChildDef.getAccessor().getValues(nextRequest)) {
String methodString = ((IPrimitiveType<?>) nextMethod).getValueAsString();
if (isNotBlank(methodString)) {
requestType = RequestTypeEnum.valueOf(methodString);
}
}
if (requestType != null) {
//noinspection EnumSwitchStatementWhichMissesCases
switch (requestType) {
case PUT:
conditionalUrl = url != null && url.contains("?") ? url : null;
break;
case POST:
List<IBase> ifNoneExistReps = requestIfNoneExistChildDef.getAccessor().getValues(nextRequest);
if (ifNoneExistReps.size() > 0) {
IPrimitiveType<?> ifNoneExist = (IPrimitiveType<?>) ifNoneExistReps.get(0);
conditionalUrl = ifNoneExist.getValueAsString();
}
break;
}
}
}
BundleEntryParts parts = new BundleEntryParts(fullUrl, requestType, url, resource, conditionalUrl);
return parts;
}
/**
* Extract all of the resources from a given bundle
*/

40
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/TransactionHookTest.java
View File

@ -4,12 +4,10 @@ import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.server.storage.DeferredInterceptorBroadcasts;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.bundle.BundleEntryParts;
import ca.uhn.test.concurrency.PointcutLatch;
import com.google.common.collect.ListMultimap;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -33,10 +31,8 @@ import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.matchesPattern;
import static org.hamcrest.Matchers.nullValue;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.hamcrest.Matchers.is;
public class TransactionHookTest extends BaseJpaR4SystemTest {
@ -92,13 +88,14 @@ public class TransactionHookTest extends BaseJpaR4SystemTest {
organizationComponent.setResource(org1);
organizationComponent.getRequest().setMethod(Bundle.HTTPVerb.POST).setUrl("Patient");
List<BundleEntryParts> postBundleEntries = BundleUtil.topologicalSort(myFhirCtx, b, RequestTypeEnum.POST);
BundleUtil.sortEntriesIntoProcessingOrder(myFhirCtx, b);
assertThat(postBundleEntries, hasSize(4));
assertThat(b.getEntry(), hasSize(4));
int observationIndex = getIndexOfEntryWithId("Observation/O1", postBundleEntries);
int patientIndex = getIndexOfEntryWithId("Patient/P1", postBundleEntries);
int organizationIndex = getIndexOfEntryWithId("Organization/Org1", postBundleEntries);
List<Bundle.BundleEntryComponent> entry = b.getEntry();
int observationIndex = getIndexOfEntryWithId("Observation/O1", b);
int patientIndex = getIndexOfEntryWithId("Patient/P1", b);
int organizationIndex = getIndexOfEntryWithId("Organization/Org1", b);
assertTrue(organizationIndex < patientIndex);
assertTrue(patientIndex < observationIndex);
@ -125,10 +122,12 @@ public class TransactionHookTest extends BaseJpaR4SystemTest {
obs2.setHasMember(Collections.singletonList(new Reference("Observation/O1")));
bundleEntryComponent.setResource(obs2);
bundleEntryComponent.getRequest().setMethod(Bundle.HTTPVerb.POST).setUrl("Observation");
List<BundleEntryParts> postBundleEntries = BundleUtil.topologicalSort(myFhirCtx, b, RequestTypeEnum.POST);
try {
BundleUtil.sortEntriesIntoProcessingOrder(myFhirCtx, b);
fail();
} catch (IllegalStateException e ) {
//Null value indicates that we hit a cycle, and could not process the deletions in order
assertThat(postBundleEntries, is(nullValue()));
}
}
@Test
@ -164,21 +163,22 @@ public class TransactionHookTest extends BaseJpaR4SystemTest {
organizationComponent.setResource(org1);
organizationComponent.getRequest().setMethod(Bundle.HTTPVerb.DELETE).setUrl("Organization");
List<BundleEntryParts> postBundleEntries = BundleUtil.topologicalSort(myFhirCtx, b, RequestTypeEnum.DELETE);
BundleUtil.sortEntriesIntoProcessingOrder(myFhirCtx, b);
assertThat(postBundleEntries, hasSize(4));
assertThat(b.getEntry(), hasSize(4));
int observationIndex = getIndexOfEntryWithId("Observation/O1", postBundleEntries);
int patientIndex = getIndexOfEntryWithId("Patient/P1", postBundleEntries);
int organizationIndex = getIndexOfEntryWithId("Organization/Org1", postBundleEntries);
int observationIndex = getIndexOfEntryWithId("Observation/O1", b);
int patientIndex = getIndexOfEntryWithId("Patient/P1", b);
int organizationIndex = getIndexOfEntryWithId("Organization/Org1", b);
assertTrue(patientIndex < organizationIndex);
assertTrue(observationIndex < patientIndex);
}
private int getIndexOfEntryWithId(String theResourceId, List<BundleEntryParts> theBundleEntryParts) {
for (int i = 0; i < theBundleEntryParts.size(); i++) {
String id = theBundleEntryParts.get(i).getResource().getIdElement().toUnqualifiedVersionless().toString();
private int getIndexOfEntryWithId(String theResourceId, Bundle theBundle) {
List<Bundle.BundleEntryComponent> entries = theBundle.getEntry();
for (int i = 0; i < entries.size(); i++) {
String id = entries.get(i).getResource().getIdElement().toUnqualifiedVersionless().toString();
if (id.equals(theResourceId)) {
return i;
}