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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
jamesagnew 2018-03-04 11:04:07 -05:00
parent 07290ae8a0 928cf23b4c
commit 8bdca012d6
22 changed files with 436 additions and 173 deletions
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2
appveyor.yml
View File

@ -4,4 +4,4 @@ cache:
- C:\maven\
- C:\Users\appveyor\.m2\repository
build_script:
- cmd: mvn -P MINPARALLEL,ALLMODULES,ERRORPRONE_JDK8 install
- cmd: mvn -P MINPARALLEL,ALLMODULES clean install

32
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.parser;
* 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.
@ -38,6 +38,7 @@ import java.util.*;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@SuppressWarnings("WeakerAccess")
public abstract class BaseParser implements IParser {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
@ -156,7 +157,6 @@ public abstract class BaseParser implements IParser {
}
private void containResourcesForEncoding(ContainedResources theContained, IBaseResource theResource, IBaseResource theTarget) {
Set<String> allIds = new HashSet<String>();
Map<String, IBaseResource> existingIdToContainedResource = null;
if (theTarget instanceof IResource) {
@ -167,9 +167,8 @@ public abstract class BaseParser implements IParser {
if (!nextId.startsWith("#")) {
nextId = '#' + nextId;
}
allIds.add(nextId);
if (existingIdToContainedResource == null) {
existingIdToContainedResource = new HashMap<String, IBaseResource>();
existingIdToContainedResource = new HashMap<>();
}
existingIdToContainedResource.put(nextId, next);
}
@ -182,9 +181,8 @@ public abstract class BaseParser implements IParser {
if (!nextId.startsWith("#")) {
nextId = '#' + nextId;
}
allIds.add(nextId);
if (existingIdToContainedResource == null) {
existingIdToContainedResource = new HashMap<String, IBaseResource>();
existingIdToContainedResource = new HashMap<>();
}
existingIdToContainedResource.put(nextId, next);
}
@ -480,7 +478,7 @@ public abstract class BaseParser implements IParser {
@Override
public void setPreferTypes(List<Class<? extends IBaseResource>> thePreferTypes) {
if (thePreferTypes != null) {
ArrayList<Class<? extends IBaseResource>> types = new ArrayList<Class<? extends IBaseResource>>();
ArrayList<Class<? extends IBaseResource>> types = new ArrayList<>();
for (Class<? extends IBaseResource> next : thePreferTypes) {
if (Modifier.isAbstract(next.getModifiers()) == false) {
types.add(next);
@ -516,8 +514,7 @@ public abstract class BaseParser implements IParser {
}
}
List<T> newList = new ArrayList<T>();
newList.addAll(theProfiles);
List<T> newList = new ArrayList<>(theProfiles);
BaseRuntimeElementDefinition<?> idElement = myContext.getElementDefinition("id");
@SuppressWarnings("unchecked")
@ -1183,8 +1180,10 @@ public abstract class BaseParser implements IParser {
}
public void addContained(IIdType theId, IBaseResource theResource) {
myResourceToId.put(theResource, theId);
myResources.add(theResource);
if (!hasId(theId)) {
myResourceToId.put(theResource, theId);
myResources.add(theResource);
}
}
public List<IBaseResource> getContainedResources() {
@ -1195,6 +1194,15 @@ public abstract class BaseParser implements IParser {
return myResourceToId.get(theNext);
}
public boolean hasId(IIdType theId) {
for (IIdType next : myResourceToId.values()) {
if (Objects.equals(next.getValue(), theId.getValue())) {
return true;
}
}
return false;
}
public boolean isEmpty() {
return myResourceToId.isEmpty();
}

16
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/api/IHttpResponse.java
View File

@ -65,31 +65,31 @@ public interface IHttpResponse {
/**
* Close the response
*/
public void close();
void close();
/**
* Returna reader for the response entity
*/
public Reader createReader() throws IOException;
Reader createReader() throws IOException;
/**
* Get map of the response headers and corresponding string values.
*
* @return response headers as a map header keys and they values.
*/
public Map<String, List<String>> getAllHeaders();
Map<String, List<String>> getAllHeaders();
/**
* Return all headers in the response with the given type
*/
public List<String> getHeaders(String theName);
List<String> getHeaders(String theName);
/**
* Extracts {@code Content-Type} value from the response exactly as
* specified by the {@code Content-Type} header. Returns {@code null}
* if not specified.
*/
public String getMimeType();
String getMimeType();
/**
* @return the native response, depending on the client library used
@ -101,18 +101,18 @@ public interface IHttpResponse {
*
* @return the response status code.
*/
public int getStatus();
int getStatus();
/**
* Get the response status information reason phrase associated with the response.
*
* @return the reason phrase.
*/
public String getStatusInfo();
String getStatusInfo();
/**
* Read the message entity input stream as an InputStream.
*/
public InputStream readEntity() throws IOException;
InputStream readEntity() throws IOException;
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/BaseParamWithPrefix.java
View File

@ -107,5 +107,4 @@ public abstract class BaseParamWithPrefix<T extends BaseParam> extends BaseParam
myPrefix = thePrefix;
return (T) this;
}
}

47
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateParam.java
View File

@ -20,21 +20,26 @@ package ca.uhn.fhir.rest.param;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.primitive.BaseDateTimeDt;
import ca.uhn.fhir.model.primitive.DateDt;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.primitive.*;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ValidateUtil;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class DateParam extends BaseParamWithPrefix<DateParam> implements /*IQueryParameterType , */IQueryParameterOr<DateParam> {
@ -222,6 +227,23 @@ public class DateParam extends BaseParamWithPrefix<DateParam> implements /*IQuer
}
@Override
public boolean equals(Object obj) {
if (obj == this) {
return true;
}
if (!(obj instanceof DateParam)) {
return false;
}
DateParam other = (DateParam) obj;
return Objects.equals(getValue(), other.getValue()) &&
Objects.equals(getPrefix(), other.getPrefix());
}
@Override
public int hashCode() {
return Objects.hash(getValue(), getPrefix());
}
@Override
public String toString() {
@ -241,8 +263,5 @@ public class DateParam extends BaseParamWithPrefix<DateParam> implements /*IQuer
protected boolean isPrecisionAllowed(TemporalPrecisionEnum thePrecision) {
return true;
}
}
}

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java
View File

@ -413,6 +413,24 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
}
@Override
public boolean equals(Object obj) {
if (obj == this) {
return true;
}
if (!(obj instanceof DateRangeParam)) {
return false;
}
DateRangeParam other = (DateRangeParam) obj;
return Objects.equals(myLowerBound, other.myLowerBound) &&
Objects.equals(myUpperBound, other.myUpperBound);
}
@Override
public int hashCode() {
return Objects.hash(myLowerBound, myUpperBound);
}
@Override
public String toString() {
StringBuilder b = new StringBuilder();
@ -484,7 +502,5 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
throw new DataFormatException("Upper bound comparator must be < or <=, can not be " + myUpperBound.getPrefix().getValue());
}
}
}
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java
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@ -463,7 +463,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
}
if (idSubstitutions.containsKey(nextId)) {
IdDt newId = idSubstitutions.get(nextId);
ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
nextRef.setReference(newId);
} else {
ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
@ -479,7 +479,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
IdDt nextUriString = new IdDt(nextRef.getValueAsString());
if (idSubstitutions.containsKey(nextUriString)) {
IdDt newId = idSubstitutions.get(nextUriString);
ourLog.info(" * Replacing resource ref {} with {}", nextUriString, newId);
ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
nextRef.setValue(newId.getValue());
} else {
ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
@ -522,7 +522,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
if (replacement.equals(next)) {
continue;
}
ourLog.info("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
}
/*

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
View File

@ -770,12 +770,11 @@ public class SearchBuilder implements ISearchBuilder {
return;
}
List<Predicate> codePredicates = new ArrayList<Predicate>();
List<Predicate> codePredicates = new ArrayList<>();
for (IQueryParameterType nextOr : theList) {
IQueryParameterType params = nextOr;
if (params instanceof UriParam) {
UriParam param = (UriParam) params;
if (nextOr instanceof UriParam) {
UriParam param = (UriParam) nextOr;
String value = param.getValue();
if (value == null) {
@ -820,7 +819,7 @@ public class SearchBuilder implements ISearchBuilder {
}
codePredicates.add(predicate);
} else {
throw new IllegalArgumentException("Invalid URI type: " + params.getClass());
throw new IllegalArgumentException("Invalid URI type: " + nextOr.getClass());
}
}
@ -1340,7 +1339,7 @@ public class SearchBuilder implements ISearchBuilder {
}
myPredicates = new ArrayList<Predicate>();
myPredicates = new ArrayList<>();
if (myParams.getEverythingMode() != null) {
Join<ResourceTable, ResourceLink> join = myResourceTableRoot.join("myResourceLinks", JoinType.LEFT);
@ -1349,7 +1348,7 @@ public class SearchBuilder implements ISearchBuilder {
StringParam idParm = (StringParam) myParams.get(BaseResource.SP_RES_ID).get(0).get(0);
Long pid = BaseHapiFhirDao.translateForcedIdToPid(myResourceName, idParm.getValue(), myForcedIdDao);
if (myAlsoIncludePids == null) {
myAlsoIncludePids = new ArrayList<Long>(1);
myAlsoIncludePids = new ArrayList<>(1);
}
myAlsoIncludePids.add(pid);
myPredicates.add(myBuilder.equal(join.get("myTargetResourcePid").as(Long.class), pid));

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java
View File

@ -505,7 +505,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
if (theIdSubstitutions.containsKey(nextId)) {
IdType newId = theIdSubstitutions.get(nextId);
ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
nextRef.setReference(newId.getValue());
} else if (nextId.getValue().startsWith("urn:")) {
throw new InvalidRequestException("Unable to satisfy placeholder ID: " + nextId.getValue());
@ -523,7 +523,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
IdType nextUriString = new IdType(nextRef.getValueAsString());
if (theIdSubstitutions.containsKey(nextUriString)) {
IdType newId = theIdSubstitutions.get(nextUriString);
ourLog.info(" * Replacing resource ref {} with {}", nextUriString, newId);
ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
nextRef.setValue(newId.getValue());
} else {
ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
@ -544,7 +544,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
StopWatch sw = new StopWatch();
myEntityManager.flush();
ourLog.info("Session flush took {}ms for {} inserts and {} updates", sw.getMillis(), insertionCount, updateCount);
ourLog.debug("Session flush took {}ms for {} inserts and {} updates", sw.getMillis(), insertionCount, updateCount);
/*
* Double check we didn't allow any duplicates we shouldn't have
@ -570,7 +570,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
if (replacement.equals(next)) {
continue;
}
ourLog.info("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
}
return entriesToProcess;
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4.java
View File

@ -514,7 +514,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
if (theIdSubstitutions.containsKey(nextId)) {
IdType newId = theIdSubstitutions.get(nextId);
ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
nextRef.setReference(newId.getValue());
} else if (nextId.getValue().startsWith("urn:")) {
throw new InvalidRequestException("Unable to satisfy placeholder ID: " + nextId.getValue());
@ -532,7 +532,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
IdType nextUriString = new IdType(nextRef.getValueAsString());
if (theIdSubstitutions.containsKey(nextUriString)) {
IdType newId = theIdSubstitutions.get(nextUriString);
ourLog.info(" * Replacing resource ref {} with {}", nextUriString, newId);
ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
nextRef.setValue(newId.getValue());
} else {
ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
@ -548,6 +548,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
myEntityManager.flush();
ourLog.debug("Session flush took {}ms for {} inserts and {} updates", sw.getMillis(), insertionCount, updateCount);
/*
* Double check we didn't allow any duplicates we shouldn't have
@ -573,7 +574,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
if (replacement.equals(next)) {
continue;
}
ourLog.info("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
}
return entriesToProcess;
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionDeliverySubscriber.java
View File

@ -44,8 +44,13 @@ public abstract class BaseSubscriptionDeliverySubscriber extends BaseSubscriptio
ourLog.warn("Unexpected payload type: {}", theMessage.getPayload());
return;
}
String subscriptionId = "(unknown?)";
try {
ResourceDeliveryMessage msg = (ResourceDeliveryMessage) theMessage.getPayload();
subscriptionId = msg.getPayload(getContext()).getIdElement().getValue();
if (!subscriptionTypeApplies(getContext(), msg.getSubscription().getBackingSubscription(getContext()))) {
return;
}
@ -77,8 +82,9 @@ public abstract class BaseSubscriptionDeliverySubscriber extends BaseSubscriptio
handleMessage(msg);
} catch (Exception e) {
ourLog.error("Failure handling subscription payload", e);
throw new MessagingException(theMessage, "Failure handling subscription payload", e);
String msg = "Failure handling subscription payload for subscription: " + subscriptionId;
ourLog.error(msg, e);
throw new MessagingException(theMessage, msg, e);
}
}

90
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/StopWatch.java
View File

@ -1,8 +1,10 @@
package ca.uhn.fhir.jpa.util;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.time.DateUtils;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.Date;
import java.util.concurrent.TimeUnit;
@ -15,9 +17,9 @@ import java.util.concurrent.TimeUnit;
* 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.
@ -28,7 +30,10 @@ import java.util.concurrent.TimeUnit;
public class StopWatch {
private long myStarted = System.currentTimeMillis();
private static final NumberFormat DAY_FORMAT = new DecimalFormat("0.0");
private static final NumberFormat TEN_DAY_FORMAT = new DecimalFormat("0");
private static Long ourNowForUnitTest;
private long myStarted = now();
/**
* Constructor
@ -46,17 +51,42 @@ public class StopWatch {
myStarted = theStart.getTime();
}
public long getMillis() {
long now = System.currentTimeMillis();
return now - myStarted;
public String formatThroughput(int theNumOperations, TimeUnit theUnit) {
double throughput = getThroughput(theNumOperations, theUnit);
return new DecimalFormat("0.0").format(throughput);
}
/**
* Given an amount of something completed so far, and a total amount, calculates how long it will take for something to complete
*
* @param theCompleteToDate The amount so far
* @param theTotal The total (must be higher than theCompleteToDate
* @return A formatted amount of time
*/
public String getEstimatedTimeRemaining(double theCompleteToDate, double theTotal) {
double completeSoFar = theCompleteToDate / theTotal;
double remaining;
if (completeSoFar > 0.5) {
remaining = (1.0 - completeSoFar);
} else {
remaining = (1.0 / completeSoFar);
}
double millis = getMillis();
long millisRemaining = (long) (millis * remaining);
return formatMillis(millisRemaining);
}
public long getMillis(Date theNow) {
return theNow.getTime() - myStarted;
}
public long getMillis() {
long now = now();
return now - myStarted;
}
public long getMillisAndRestart() {
long now = System.currentTimeMillis();
long now = now();
long retVal = now - myStarted;
myStarted = now;
return retVal;
@ -82,18 +112,13 @@ public class StopWatch {
long periodMillis = theUnit.toMillis(1);
double numerator = theNumOperations;
double denominator = ((double)millisElapsed)/((double)periodMillis);
double denominator = ((double) millisElapsed) / ((double) periodMillis);
return numerator / denominator;
}
public String formatThroughput(int theNumOperations, TimeUnit theUnit) {
double throughput = getThroughput(theNumOperations, theUnit);
return new DecimalFormat("0.0").format(throughput);
}
public void restart() {
myStarted = System.currentTimeMillis();
myStarted = now();
}
/**
@ -124,21 +149,38 @@ public class StopWatch {
static public String formatMillis(long val) {
StringBuilder buf = new StringBuilder(20);
if (val >= DateUtils.MILLIS_PER_DAY) {
long days = val / DateUtils.MILLIS_PER_DAY;
append(buf, "", 1, days);
if (days > 1) {
buf.append(" days ");
} else if (days == 1) {
buf.append(" day ");
double days = (double) val / DateUtils.MILLIS_PER_DAY;
if (days >= 10) {
buf.append(TEN_DAY_FORMAT.format(days));
buf.append(" days");
} else if (days != 1.0f) {
buf.append(DAY_FORMAT.format(days));
buf.append(" days");
} else {
buf.append(DAY_FORMAT.format(days));
buf.append(" day");
}
append(buf, "", 2, ((val % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
} else {
append(buf, "", 2, ((val % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
append(buf, ":", 2, ((val % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
append(buf, ":", 2, ((val % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
if (val <= DateUtils.MILLIS_PER_MINUTE) {
append(buf, ".", 3, (val % DateUtils.MILLIS_PER_SECOND));
}
}
append(buf, ":", 2, ((val % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
append(buf, ":", 2, ((val % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
append(buf, ".", 3, (val % DateUtils.MILLIS_PER_SECOND));
return buf.toString();
}
private static long now() {
if (ourNowForUnitTest != null) {
return ourNowForUnitTest;
}
return System.currentTimeMillis();
}
@VisibleForTesting
static void setNowForUnitTestForUnitTest(Long theNowForUnitTest) {
ourNowForUnitTest = theNowForUnitTest;
}
}

21
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -681,6 +681,27 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(actual, contains(id));
}
@Test
public void testReturnOnlyCorrectResourceType() {
ValueSet vsRes = new ValueSet();
vsRes.setUrl("http://foo");
String vsId = myValueSetDao.create(vsRes).getId().toUnqualifiedVersionless().getValue();
CodeSystem csRes = new CodeSystem();
csRes.setUrl("http://bar");
String csId = myCodeSystemDao.create(csRes).getId().toUnqualifiedVersionless().getValue();
SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true);
map.add(ValueSet.SP_URL, new UriParam("http://foo"));
List<String> actual = toUnqualifiedVersionlessIdValues(myValueSetDao.search(map));
assertThat(actual, contains(vsId));
map = new SearchParameterMap().setLoadSynchronous(true);
map.add(ValueSet.SP_URL, new UriParam("http://bar"));
actual = toUnqualifiedVersionlessIdValues(myCodeSystemDao.search(map));
assertThat(actual, contains(csId));
}
/**
* #454
*/

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
View File

@ -1569,7 +1569,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
* See #872
*/
@Test
public void testExtensionUrlWithHl7UrlPost() throws IOException {
public void testValidateExtensionUrlWithHl7UrlPost() throws IOException {
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
FhirInstanceValidator val = new FhirInstanceValidator(myValidationSupport);
interceptor.addValidatorModule(val);
@ -1578,14 +1578,15 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
try {
String input = IOUtils.toString(ResourceProviderR4Test.class.getResourceAsStream("/bug872-ext-with-hl7-url.json"), Charsets.UTF_8);
HttpPost post = new HttpPost(ourServerBase + "/Patient/aaa");
HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
post.setEntity(new StringEntity(input, ContentType.APPLICATION_JSON));
CloseableHttpResponse resp = ourHttpClient.execute(post);
try {
String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
ourLog.info(respString);
assertEquals(400, resp.getStatusLine().getStatusCode());
assertThat(respString, containsString("Unknown extension http://hl7.org/fhir/ValueSet/v3-ActInvoiceGroupCode"));
assertEquals(200, resp.getStatusLine().getStatusCode());
} finally {
IOUtils.closeQuietly(resp);
}
@ -1611,14 +1612,11 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
HttpGet get = new HttpGet(ourServerBase + "/Observation?_content=systolic&_pretty=true");
CloseableHttpResponse response = ourHttpClient.execute(get);
try {
try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
assertEquals(200, response.getStatusLine().getStatusCode());
String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(responseString);
assertThat(responseString, containsString(id1.getIdPart()));
} finally {
response.close();
}
}

176
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/util/StopWatchTest.java
View File

@ -1,20 +1,118 @@
package ca.uhn.fhir.jpa.util;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import org.apache.commons.lang3.time.DateUtils;
import org.hamcrest.Matchers;
import org.junit.After;
import org.junit.Test;
import java.util.Date;
import java.util.concurrent.TimeUnit;
import org.apache.commons.lang3.time.DateUtils;
import org.hamcrest.Matchers;
import org.junit.Test;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
public class StopWatchTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StopWatchTest.class);
@After
public void after() {
StopWatch.setNowForUnitTestForUnitTest(null);
}
private double calculateThroughput(int theMinutesElapsed, int theNumOperations) {
StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -theMinutesElapsed));
double throughput = sw.getThroughput(theNumOperations, TimeUnit.MINUTES);
ourLog.info("{} operations in {}ms = {} ops / second", theNumOperations, sw.getMillis(), throughput);
return throughput;
}
@Test
public void testEstimatedTimeRemaining() {
StopWatch.setNowForUnitTestForUnitTest(777777777L);
StopWatch sw = new StopWatch();
StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
assertEquals("00:00:00.600", sw.getEstimatedTimeRemaining(0.99, 1.0));
StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
assertEquals("00:10:00", sw.getEstimatedTimeRemaining(0.1, 1.0));
StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE + 100);
assertEquals("00:10:01", sw.getEstimatedTimeRemaining(0.1, 1.0));
StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
assertEquals("00:20:00", sw.getEstimatedTimeRemaining(0.05, 1.0));
StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
assertEquals("00:40:00", sw.getEstimatedTimeRemaining(0.025, 1.0));
StopWatch.setNowForUnitTestForUnitTest(777777777L + DateUtils.MILLIS_PER_MINUTE);
assertEquals("01:40:00", sw.getEstimatedTimeRemaining(0.01, 1.0));
}
@Test
public void testFormatMillis() {
assertEquals("00:00:01.000", StopWatch.formatMillis(DateUtils.MILLIS_PER_SECOND));
assertEquals("00:01:00.000", StopWatch.formatMillis(DateUtils.MILLIS_PER_MINUTE));
assertEquals("00:01:01", StopWatch.formatMillis(DateUtils.MILLIS_PER_MINUTE + DateUtils.MILLIS_PER_SECOND));
assertEquals("01:00:00", StopWatch.formatMillis(DateUtils.MILLIS_PER_HOUR));
assertEquals("1.0 day", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY));
assertEquals("2.0 days", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY * 2));
assertEquals("2.0 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 2) + 1));
assertEquals("2.4 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 2) + (10 * DateUtils.MILLIS_PER_HOUR)));
assertEquals("11 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 11) + (10 * DateUtils.MILLIS_PER_HOUR)));
}
@Test
public void testFormatThroughput60Ops4Min() {
StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -4));
String throughput = sw.formatThroughput(60, TimeUnit.MINUTES);
ourLog.info("{} operations in {}ms = {} ops / second", 60, sw.getMillis(), throughput);
assertThat(throughput, oneOf("14.9", "15.0", "15.1", "14,9", "15,0", "15,1"));
}
@Test
public void testMillisPerOperation() {
int minutes = 60;
StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -minutes));
int numOperations = 60;
int millis = sw.getMillisPerOperation(numOperations);
ourLog.info("{} operations in {}ms = {}ms / operation", numOperations, minutes * DateUtils.MILLIS_PER_MINUTE, millis);
assertThat(millis, Matchers.lessThan(62000));
assertThat(millis, Matchers.greaterThan(58000));
}
@Test
public void testOperationThroughput30Ops1Min() {
double throughput = calculateThroughput(1, 30);
assertThat(throughput, greaterThan(29.0));
assertThat(throughput, lessThan(31.0));
}
@Test
public void testOperationThroughput60Ops1Min() {
double throughput = calculateThroughput(1, 60);
assertThat(throughput, greaterThan(59.0));
assertThat(throughput, lessThan(61.0));
}
@Test
public void testOperationThroughput60Ops4Min() {
double throughput = calculateThroughput(4, 60);
assertThat(throughput, greaterThan(14.0));
assertThat(throughput, lessThan(16.0));
}
@Test
public void testRestart() throws InterruptedException {
StopWatch sw = new StopWatch();
Thread.sleep(500);
sw.restart();
assertThat(sw.getMillis(), lessThan(100L));
}
@Test
public void testStopwatch() throws Exception {
StopWatch sw = new StopWatch();
@ -37,62 +135,6 @@ public class StopWatchTest {
assertThat(sw.getStartedDate().getTime(), lessThan(System.currentTimeMillis()));
}
@Test
public void testRestart() throws InterruptedException {
StopWatch sw = new StopWatch();
Thread.sleep(500);
sw.restart();
assertThat(sw.getMillis(), lessThan(100L));
}
@Test
public void testMillisPerOperation() {
int minutes = 60;
StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -minutes));
int numOperations = 60;
int millis = sw.getMillisPerOperation(numOperations);
ourLog.info("{} operations in {}ms = {}ms / operation", numOperations, minutes*DateUtils.MILLIS_PER_MINUTE, millis);
assertThat(millis, Matchers.lessThan(62000));
assertThat(millis, Matchers.greaterThan(58000));
}
@Test
public void testOperationThroughput60Ops1Min() {
double throughput = calculateThroughput(1, 60);
assertThat(throughput, greaterThan(59.0));
assertThat(throughput, lessThan(61.0));
}
@Test
public void testOperationThroughput30Ops1Min() {
double throughput = calculateThroughput(1, 30);
assertThat(throughput, greaterThan(29.0));
assertThat(throughput, lessThan(31.0));
}
@Test
public void testOperationThroughput60Ops4Min() {
double throughput = calculateThroughput(4, 60);
assertThat(throughput, greaterThan(14.0));
assertThat(throughput, lessThan(16.0));
}
@Test
public void testFormatThroughput60Ops4Min() {
StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -4));
String throughput = sw.formatThroughput(60, TimeUnit.MINUTES);
ourLog.info("{} operations in {}ms = {} ops / second", 60, sw.getMillis(), throughput);
assertThat(throughput, oneOf("14.9", "15.0", "15.1", "14,9", "15,0", "15,1"));
}
private double calculateThroughput(int theMinutesElapsed, int theNumOperations) {
StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -theMinutesElapsed));
double throughput = sw.getThroughput(theNumOperations, TimeUnit.MINUTES);
ourLog.info("{} operations in {}ms = {} ops / second", theNumOperations, sw.getMillis(), throughput);
return throughput;
}
@Test
public void testToString() throws Exception {
StopWatch sw = new StopWatch();
@ -104,14 +146,4 @@ public class StopWatchTest {
assertThat(string, startsWith("00:00"));
}
@Test
public void testFormatMillis() throws Exception {
assertEquals("00:00:01.000", StopWatch.formatMillis(DateUtils.MILLIS_PER_SECOND));
assertEquals("00:01:00.000", StopWatch.formatMillis(DateUtils.MILLIS_PER_MINUTE));
assertEquals("01:00:00.000", StopWatch.formatMillis(DateUtils.MILLIS_PER_HOUR));
assertEquals("1 day 00:00:00.000", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY));
assertEquals("2 days 00:00:00.000", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY*2));
assertEquals("2 days 00:00:00.001", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY*2)+1));
}
}

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

@ -172,7 +172,11 @@
<artifactId>guava</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava-testlib</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>

38
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/param/DateParamTest.java
View File

@ -1,18 +1,23 @@
package ca.uhn.fhir.rest.param;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import com.google.common.testing.EqualsTester;
import org.junit.Test;
import java.util.Date;
import java.util.TimeZone;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.APPROXIMATE;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.EQUAL;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.NOT_EQUAL;
import static java.util.concurrent.TimeUnit.SECONDS;
import static org.hamcrest.Matchers.endsWith;
import static org.hamcrest.Matchers.startsWith;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import java.util.Date;
import java.util.TimeZone;
import org.junit.Test;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.InstantDt;
public class DateParamTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DateParamTest.class);
@ -105,6 +110,21 @@ public class DateParamTest {
assertEquals(ParamPrefixEnum.LESSTHAN, new DateParam("lt2012").getPrefix());
assertEquals(ParamPrefixEnum.LESSTHAN_OR_EQUALS, new DateParam("le2012").getPrefix());
}
@Test()
public void testEqualsAndHashCode() {
Date now = new Date();
Date later = new Date(now.getTime() + SECONDS.toMillis(666));
new EqualsTester()
.addEqualityGroup(new DateParam(),
new DateParam(null))
.addEqualityGroup(new DateParam(NOT_EQUAL, now),
new DateParam(NOT_EQUAL, now.getTime()))
.addEqualityGroup(new DateParam(EQUAL, now),
new DateParam(EQUAL, now.getTime()))
.addEqualityGroup(new DateParam(EQUAL, later),
new DateParam(EQUAL, later.getTime()))
.addEqualityGroup(new DateParam(APPROXIMATE, "2011-11-11T11:11:11.111-11:11"))
.testEquals();
}
}

6
hapi-fhir-structures-dstu3/pom.xml
View File

@ -261,7 +261,11 @@
<artifactId>guava</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava-testlib</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>

38
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/param/DateRangeParamTest.java
View File

@ -1,12 +1,28 @@
package ca.uhn.fhir.rest.param;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.APPROXIMATE;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.EQUAL;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN_OR_EQUALS;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN_OR_EQUALS;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.NOT_EQUAL;
import static com.google.common.collect.Lists.newArrayList;
import static java.lang.System.currentTimeMillis;
import static java.util.concurrent.TimeUnit.SECONDS;
import static org.hamcrest.core.Is.is;
import static org.hamcrest.core.IsEqual.equalTo;
import static org.hamcrest.core.IsNot.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertThat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.concurrent.TimeUnit;
import com.google.common.testing.EqualsTester;
import org.junit.AfterClass;
import org.junit.Test;
@ -183,7 +199,26 @@ public class DateRangeParamTest {
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Test()
public void testEqualsAndHashCode() {
Date lowerBound = new Date(currentTimeMillis());
Date upperBound = new Date(lowerBound.getTime() + SECONDS.toMillis(1));
new EqualsTester()
.addEqualityGroup(new DateRangeParam(),
new DateRangeParam((Date) null, (Date) null))
.addEqualityGroup(new DateRangeParam(lowerBound, upperBound),
new DateRangeParam(new DateParam(GREATERTHAN_OR_EQUALS, lowerBound), new DateParam(LESSTHAN_OR_EQUALS, upperBound)))
.addEqualityGroup(new DateRangeParam(new DateParam(EQUAL, lowerBound)),
new DateRangeParam(new DateParam(null, lowerBound)),
new DateRangeParam(new DateParam(EQUAL, lowerBound), new DateParam(EQUAL, lowerBound)))
.addEqualityGroup(new DateRangeParam(lowerBound, null),
new DateRangeParam(new DateParam(GREATERTHAN_OR_EQUALS, lowerBound), null))
.addEqualityGroup(new DateRangeParam(null, upperBound),
new DateRangeParam(null, new DateParam(LESSTHAN_OR_EQUALS, upperBound)))
.testEquals();
}
private static DateRangeParam create(String theLower, String theUpper) throws InvalidRequestException {
DateRangeParam p = new DateRangeParam();
List<QualifiedParamList> tokens = new ArrayList<QualifiedParamList>();
@ -202,5 +237,4 @@ public class DateRangeParamTest {
public static Date parseM1(String theString) throws ParseException {
return new Date(ourFmt.parse(theString).getTime() - 1L);
}
}

33
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
View File

@ -88,6 +88,39 @@ public class JsonParserR4Test {
}
/*
* See #814
*/
@Test
public void testDuplicateContainedResourcesNotOutputtedTwiceWithManualIdsAndManualAddition() {
MedicationDispense md = new MedicationDispense();
MedicationRequest mr = new MedicationRequest();
mr.setId("#MR");
md.addAuthorizingPrescription().setResource(mr);
Medication med = new Medication();
med.setId("#MED");
Reference medRef = new Reference();
medRef.setReference("#MED");
md.setMedication(medRef);
mr.setMedication(medRef);
md.getContained().add(mr);
md.getContained().add(med);
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(md);
ourLog.info(encoded);
int idx = encoded.indexOf("\"Medication\"");
assertNotEquals(-1, idx);
idx = encoded.indexOf("\"Medication\"", idx + 1);
assertEquals(-1, idx);
}
@Test
public void testEncodeAndParseUnicodeCharacterInNarrative() {
Patient p = new Patient();

9
pom.xml
View File

@ -386,6 +386,10 @@
<id>darktyko</id>
<name>Kyle Meadows</name>
</developer>
<developer>
<id>Tastelezz</id>
<name>Gaetano Gallo</name>
</developer>
</developers>
@ -510,6 +514,11 @@
<artifactId>guava</artifactId>
<version>23.0</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava-testlib</artifactId>
<version>23.0</version>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-schematron</artifactId>

18
src/changes/changes.xml
View File

@ -176,6 +176,24 @@
cam be useful for tests or for static servers with small amounts
of data.
</action>
<action type="fix" issue="872">
An issue in the JPA server was corrected where searching using
URI search parameters would sometimes not include the resource type in the
criteria. This meant, for example, that a search for
<![CDATA[<code>ValueSet?url=http://foo</code>]]> would also
match any CodeSystem resource that happened to also have
that URL as the value for the "url" search parameter. Thanks
to Josh Mandel for reporting and supplying a test case!
</action>
<action type="add" issue="868">
DateParam class now has equals() and hashCode() implementations. Thanks
to Gaetano Gallo for the pull request!
</action>
<action type="fix" issue="814">
Fix a bug where under certain circumstances, duplicate contained resources
could be output by the parser's encode methods. Thanks to
Frank Tao for supplying a test case!
</action>
</release>
<release version="3.2.0" date="2018-01-13">
<action type="add">