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hapi-fhir
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Work on repopulating

This commit is contained in:
James 2017-02-06 21:57:23 -05:00
parent a760f1df7c
commit 116cb1c8f7
10 changed files with 302 additions and 130 deletions
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2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java
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@ -22,6 +22,7 @@ package ca.uhn.fhir.util;
import java.util.Collection;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseParameters;
@ -84,6 +85,7 @@ public class ParametersUtil {
}
public static IBaseParameters newInstance(FhirContext theContext) {
Validate.notNull(theContext, "theContext must not be null");
return (IBaseParameters) theContext.getResourceDefinition("Parameters").newInstance();
}
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java
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@ -101,6 +101,7 @@ public class BaseDstu2Config extends BaseConfig {
public ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 systemProviderDstu2() {
ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 retVal = new ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2();
retVal.setDao(systemDaoDstu2());
retVal.setContext(fhirContextDstu2());
return retVal;
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptParentChildLinkDao.java
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@ -1,5 +1,7 @@
package ca.uhn.fhir.jpa.dao.data;
import java.util.Collection;
/*
* #%L
* HAPI FHIR JPA Server
@ -33,4 +35,7 @@ public interface ITermConceptParentChildLinkDao extends JpaRepository<TermConcep
@Modifying
void deleteByCodeSystemVersion(@Param("cs_pid") Long thePid);
@Query("SELECT t FROM TermConceptParentChildLink t WHERE t.myChildPid = :child_pid")
Collection<TermConceptParentChildLink> findAllWithChild(@Param("child_pid") Long theConceptPid);
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -233,6 +233,7 @@ public class TermConcept implements Serializable {
@PreUpdate
@PrePersist
public void prePersist() {
if (myParentPids == null) {
Set<Long> parentPids = new HashSet<Long>();
TermConcept entity = this;
parentPids(entity, parentPids);
@ -240,6 +241,7 @@ public class TermConcept implements Serializable {
ourLog.trace("Code {}/{} has parents {}", entity.getId(), entity.getCode(), entity.getParentPidsAsString());
}
}
public void setCode(String theCode) {
myCode = theCode;
@ -280,6 +282,10 @@ public class TermConcept implements Serializable {
myParentPids = b.toString();
}
public void setParentPids(String theParentPids) {
myParentPids = theParentPids;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE).append("code", myCode).append("display", myDisplay).build();

110
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
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@ -44,6 +44,9 @@ public class TermConceptParentChildLink implements Serializable {
@JoinColumn(name = "CHILD_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CHILD"))
private TermConcept myChild;
@Column(name = "CHILD_PID", insertable = false, updatable = false)
private Long myChildPid;
@ManyToOne()
@JoinColumn(name = "CODESYSTEM_PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CS"))
private TermCodeSystemVersion myCodeSystem;
@ -52,6 +55,9 @@ public class TermConceptParentChildLink implements Serializable {
@JoinColumn(name = "PARENT_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_PARENT"))
private TermConcept myParent;
@Column(name = "PARENT_PID", insertable = false, updatable = false)
private Long myParentPid;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_PC_PID", sequenceName = "SEQ_CONCEPT_PC_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PC_PID")
@ -62,51 +68,6 @@ public class TermConceptParentChildLink implements Serializable {
@Column(name = "REL_TYPE", length = 5, nullable = true)
private RelationshipTypeEnum myRelationshipType;
public TermConcept getChild() {
return myChild;
}
public RelationshipTypeEnum getRelationshipType() {
return myRelationshipType;
}
public TermCodeSystemVersion getCodeSystem() {
return myCodeSystem;
}
public TermConcept getParent() {
return myParent;
}
public void setChild(TermConcept theChild) {
myChild = theChild;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
}
public void setParent(TermConcept theParent) {
myParent = theParent;
}
public void setRelationshipType(RelationshipTypeEnum theRelationshipType) {
myRelationshipType = theRelationshipType;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((myChild == null) ? 0 : myChild.hashCode());
result = prime * result + ((myCodeSystem == null) ? 0 : myCodeSystem.hashCode());
result = prime * result + ((myParent == null) ? 0 : myParent.hashCode());
result = prime * result + ((myRelationshipType == null) ? 0 : myRelationshipType.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
@ -136,15 +97,64 @@ public class TermConceptParentChildLink implements Serializable {
return true;
}
public TermConcept getChild() {
return myChild;
}
public Long getChildPid() {
return myChildPid;
}
public TermCodeSystemVersion getCodeSystem() {
return myCodeSystem;
}
public Long getId() {
return myPid;
}
public TermConcept getParent() {
return myParent;
}
public Long getParentPid() {
return myParentPid;
}
public RelationshipTypeEnum getRelationshipType() {
return myRelationshipType;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((myChild == null) ? 0 : myChild.hashCode());
result = prime * result + ((myCodeSystem == null) ? 0 : myCodeSystem.hashCode());
result = prime * result + ((myParent == null) ? 0 : myParent.hashCode());
result = prime * result + ((myRelationshipType == null) ? 0 : myRelationshipType.hashCode());
return result;
}
public void setChild(TermConcept theChild) {
myChild = theChild;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
}
public void setParent(TermConcept theParent) {
myParent = theParent;
}
public void setRelationshipType(RelationshipTypeEnum theRelationshipType) {
myRelationshipType = theRelationshipType;
}
public enum RelationshipTypeEnum {
// ********************************************
// IF YOU ADD HERE MAKE SURE ORDER IS PRESERVED
ISA
}
public Long getId() {
return myPid;
}
}

64
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvc.java
View File

@ -23,9 +23,11 @@ package ca.uhn.fhir.jpa.term;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.TimeUnit;
@ -33,6 +35,7 @@ import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
@ -47,6 +50,8 @@ import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Stopwatch;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimaps;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
@ -305,6 +310,8 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
}
}
private ArrayListMultimap<Long, Long> myChildToParentPidCache;
private void processReindexing() {
if (System.currentTimeMillis() < myNextReindexPass && !ourForceSaveDeferredAlwaysForUnitTest) {
return;
@ -316,23 +323,60 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
int maxResult = 1000;
Page<TermConcept> resources = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
if (resources.hasContent() == false) {
Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
if (concepts.hasContent() == false) {
myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
myChildToParentPidCache = null;
return;
}
ourLog.info("Indexing {} / {} concepts", resources.getContent().size(), resources.getTotalElements());
if (myChildToParentPidCache == null) {
myChildToParentPidCache = ArrayListMultimap.create();
}
ourLog.info("Indexing {} / {} concepts", concepts.getContent().size(), concepts.getTotalElements());
int count = 0;
StopWatch stopwatch = new StopWatch();
for (TermConcept resourceTable : resources) {
saveConcept(resourceTable);
for (TermConcept nextConcept : concepts) {
StringBuilder parentsBuilder = new StringBuilder();
createParentsString(parentsBuilder, nextConcept.getId());
nextConcept.setParentPids(parentsBuilder.toString());
saveConcept(nextConcept);
count++;
}
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, resources.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
}
private void createParentsString(StringBuilder theParentsBuilder, Long theConceptPid) {
Validate.notNull(theConceptPid, "theConceptPid must not be null");
List<Long> parents = myChildToParentPidCache.get(theConceptPid);
if (parents.contains(-1L)) {
return;
} else if (parents.isEmpty()) {
Collection<TermConceptParentChildLink> parentLinks = myConceptParentChildLinkDao.findAllWithChild(theConceptPid);
if (parentLinks.isEmpty()) {
myChildToParentPidCache.put(theConceptPid, -1L);
return;
} else {
for (TermConceptParentChildLink next : parentLinks) {
myChildToParentPidCache.put(theConceptPid, next.getParentPid());
}
}
}
for (Long nextParent : parents) {
if (theParentsBuilder.length() > 0) {
theParentsBuilder.append(' ');
}
theParentsBuilder.append(nextParent);
createParentsString(theParentsBuilder, nextParent);
}
}
});
@ -340,7 +384,15 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
private int saveConcept(TermConcept theConcept) {
int retVal = 0;
/*
* If the concept has an ID, we're reindexing, so there's no need to
* save parent concepts first (it's way too slow to do that)
*/
if (theConcept.getId() == null) {
retVal += ensureParentsSaved(theConcept.getParents());
}
if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
retVal++;
theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.term;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@ -64,6 +65,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -159,7 +161,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
}
private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
//@formatter:off
Query textQuery = qb
.phrase()
.withSlop(2)
@ -169,7 +170,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
// .andField("myDisplayPhonetic").boostedTo(0.5f)
.sentence(nextFilter.getValue().toLowerCase()).createQuery();
bool.must(textQuery);
//@formatter:on
}
@Override
@ -216,10 +216,18 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
for (ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
if (isNotBlank(nextFilter.getValue())) {
if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
continue;
}
if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
}
if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == FilterOperator.EQUAL) {
addDisplayFilterExact(qb, bool, nextFilter);
} else if (nextFilter.getProperty().equals("display") && nextFilter.getOp() == FilterOperator.EQUAL) {
} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == FilterOperator.EQUAL) {
if (nextFilter.getValue().trim().contains(" ")) {
addDisplayFilterExact(qb, bool, nextFilter);
} else {
@ -237,14 +245,18 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
}
}
}
Query luceneQuery = bool.createQuery();
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
jpaQuery.setMaxResults(1000);
StopWatch sw = new StopWatch();
@SuppressWarnings("unchecked")
List<TermConcept> result = jpaQuery.getResultList();
ourLog.info("Expansion completed in {}ms", sw.getMillis());
for (TermConcept nextConcept : result) {
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
}
@ -259,7 +271,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
}
}
return retVal;
}

71
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -26,7 +26,9 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
@ -34,6 +36,8 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
@ -52,6 +56,8 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
@After
public void after() {
myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
}
@Before
@ -318,6 +324,71 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
}
@Test
public void testExpandWithIsAInExternalValueSet() {
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setOp(FilterOperator.ISA).setValue("childAA").setProperty("concept");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
}
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
@Test
public void testExpandWithIsAInExternalValueSetReindex() {
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
createExternalCsAndLocalVs();
mySystemDao.markAllResourcesForReindexing();
mySystemDao.performReindexingPass(100);
mySystemDao.performReindexingPass(100);
myHapiTerminologySvc.saveDeferred();
myHapiTerminologySvc.saveDeferred();
myHapiTerminologySvc.saveDeferred();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setOp(FilterOperator.ISA).setValue("childAA").setProperty("concept");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
}
@Test
public void testExpandInvalid() {
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter();
include.addFilter().setOp(FilterOperator.ISA).setValue("childAA");
try {
myValueSetDao.expand(vs, null);
fail();
} catch (InvalidRequestException e) {
assertEquals("Invalid filter, must have fields populated: property op value", e.getMessage());
}
}
@Test
public void testExpandWithSystemAndCodesInExternalValueSet() {
createExternalCsAndLocalVs();

40
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu2Test.java
View File

@ -10,6 +10,7 @@ import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.IOUtils;
@ -139,7 +140,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
get.addHeader("Accept", "application/xml, text/html");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent());
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, (containsString("_format=json")));
assertEquals(200, http.getStatusLine().getStatusCode());
@ -167,7 +168,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
get.addHeader("Accept", "application/xml+fhir");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent());
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, not(containsString("_format")));
assertEquals(200, http.getStatusLine().getStatusCode());
@ -216,7 +217,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
assertEquals(200, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
Parameters parameters = ourCtx.newXmlParser().parseResource(Parameters.class, output);
@ -246,7 +247,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'context' must be provided"));
} finally {
@ -257,7 +258,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'searchParam' must be provided"));
} finally {
@ -268,7 +269,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'text' must be provided"));
} finally {
@ -286,7 +287,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
@Test
public void testTransactionFromBundle() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
}
@ -295,7 +296,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
public void testTransactionFromBundle2() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
@ -311,7 +312,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
*/
bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
bundle = IOUtils.toString(bundleRes);
bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
@ -335,7 +336,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
public void testTransactionFromBundle3() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/grahame-transaction.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
}
@ -343,7 +344,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
@Test
public void testTransactionFromBundle4() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
Bundle bundleResp = ourCtx.newXmlParser().parseResource(Bundle.class, response);
@ -358,7 +359,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
@Test
public void testTransactionFromBundle5() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle2.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
try {
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
fail();
@ -372,7 +373,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
@Test
public void testTransactionFromBundle6() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle3.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
// try {
// fail();
@ -427,5 +428,18 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
assertEquals(0, respSub.getEntry().size());
}
@Test
public void testMarkResourcesForReindexing() throws Exception {
HttpGet get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertEquals(200, http.getStatusLine().getStatusCode());
} finally {
IOUtils.closeQuietly(http);;
}
}
}

34
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderDstu3Test.java
View File

@ -129,7 +129,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent());
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
assertThat(encoded, containsString("transaction-response"));
@ -162,7 +162,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent());
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
assertThat(encoded, containsString("transaction-response"));
@ -271,14 +271,14 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
try {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/questionnaire-sdc-profile-example-ussg-fht.xml");
String bundleStr = IOUtils.toString(bundleRes);
String bundleStr = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
HttpPost req = new HttpPost(ourServerBase);
req.setEntity(new StringEntity(bundleStr, ContentType.parse(Constants.CT_FHIR_XML + "; charset=utf-8")));
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent());
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
//@formatter:off
@ -314,7 +314,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent());
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, containsString("_format=json"));
assertEquals(200, http.getStatusLine().getStatusCode());
@ -342,7 +342,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
get.addHeader("Accept", "application/xml+fhir");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent());
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, not(containsString("_format")));
assertEquals(200, http.getStatusLine().getStatusCode());
@ -373,7 +373,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
HttpGet get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertEquals(200, http.getStatusLine().getStatusCode());
} finally {
@ -404,7 +404,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
assertEquals(200, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
Parameters parameters = ourCtx.newXmlParser().parseResource(Parameters.class, output);
@ -434,7 +434,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'context' must be provided"));
} finally {
@ -445,7 +445,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'searchParam' must be provided"));
} finally {
@ -456,7 +456,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'text' must be provided"));
} finally {
@ -500,7 +500,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
public void testTransactionFromBundle2() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
@ -516,7 +516,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
*/
bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
bundle = IOUtils.toString(bundleRes);
bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
@ -540,7 +540,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
public void testTransactionFromBundle3() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/grahame-transaction.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
}
@ -548,7 +548,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
@Test
public void testTransactionFromBundle4() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/simone_bundle.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
Bundle bundleResp = ourCtx.newXmlParser().parseResource(Bundle.class, response);
@ -563,7 +563,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
@Test
public void testTransactionFromBundle5() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/simone_bundle2.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
try {
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
fail();
@ -577,7 +577,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
@Test
public void testTransactionFromBundle6() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/simone_bundle3.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
// try {
// fail();