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Work on everything fixes

This commit is contained in:
James Agnew 2017-06-19 06:16:27 -04:00
parent e6cb973f5f
commit 55a67ae055
4 changed files with 263 additions and 17 deletions
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64
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
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@ -44,6 +44,7 @@ import org.hl7.fhir.instance.model.api.*;
import com.google.common.collect.*;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.jpa.dao.SearchBuilder.IncludesIterator;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
import ca.uhn.fhir.jpa.entity.*;
@ -71,6 +72,7 @@ import ca.uhn.fhir.util.UrlUtil;
*/
public class SearchBuilder implements ISearchBuilder {
private static Long NO_MORE = Long.valueOf(-1);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchBuilder.class);
private List<Long> myAlsoIncludePids;
private CriteriaBuilder myBuilder;
@ -90,7 +92,6 @@ public class SearchBuilder implements ISearchBuilder {
private ISearchParamRegistry mySearchParamRegistry;
private String mySearchUuid;
private IHapiTerminologySvc myTerminologySvc;
/**
* Constructor
*/
@ -1629,12 +1630,6 @@ public class SearchBuilder implements ISearchBuilder {
List<ResourceLink> results = q.getResultList();
for (ResourceLink resourceLink : results) {
if (theReverseMode) {
// if (theEverythingModeEnum.isEncounter()) {
// if (resourceLink.getSourcePath().equals("Encounter.subject") ||
// resourceLink.getSourcePath().equals("Encounter.patient")) {
// nextRoundOmit.add(resourceLink.getSourceResourcePid());
// }
// }
pidsToInclude.add(resourceLink.getSourceResourcePid());
} else {
pidsToInclude.add(resourceLink.getTargetResourcePid());
@ -1973,6 +1968,34 @@ public class SearchBuilder implements ISearchBuilder {
return thePredicates.toArray(new Predicate[thePredicates.size()]);
}
public class IncludesIterator implements Iterator<Long>{
private Long myNext;
@Override
public boolean hasNext() {
fetchNext();
return myNext != NO_MORE;
}
@Override
public Long next() {
fetchNext();
Long retVal = myNext;
myNext = null;
return retVal;
}
private void fetchNext() {
if (myNext == null) {
}
}
}
private enum JoinEnum {
DATE, NUMBER, QUANTITY, REFERENCE, STRING, TOKEN, URI
@ -2007,16 +2030,24 @@ public class SearchBuilder implements ISearchBuilder {
}
private final class QueryIterator implements Iterator<Long> {
private boolean myFirst = true;
private IncludesIterator myIncludesIterator;
private Long myNext;
private final Set<Long> myPidSet = new HashSet<Long>();
private Iterator<Long> myPreResultsIterator;
private Iterator<Long> myResultsIterator;
private SortSpec mySort;
private boolean myStillNeedToFetchIncludes;
private StopWatch myStopwatch = null;
private QueryIterator() {
mySort = myParams.getSort();
// Includes are processed inline for $everything query
if (myParams.getEverythingMode() != null) {
myStillNeedToFetchIncludes = true;
}
}
private void fetchNext() {
@ -2060,9 +2091,26 @@ public class SearchBuilder implements ISearchBuilder {
}
}
if (myNext == null) {
if (myStillNeedToFetchIncludes) {
myIncludesIterator = new IncludesIterator();
myStillNeedToFetchIncludes = false;
}
if (myIncludesIterator != null) {
while (myIncludesIterator.hasNext()) {
Long next = myIncludesIterator.next();
if (next != null && myPidSet.add(next)) {
myNext = next;
break;
}
}
if (myNext == null) {
myNext = NO_MORE;
}
} else {
myNext = NO_MORE;
}
}
} // if we need to fetch the next result
@ -2070,9 +2118,11 @@ public class SearchBuilder implements ISearchBuilder {
ourLog.info("Initial query result returned in {}ms for query {}", myStopwatch.getMillis(), mySearchUuid);
myFirst = false;
}
if (myNext == NO_MORE) {
ourLog.info("Query found {} matches in {}ms for query {}", myPidSet.size(), myStopwatch.getMillis(), mySearchUuid);
}
}
@Override

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
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@ -241,8 +241,8 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
Set<Long> includedPids = new HashSet<Long>();
if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) {
includedPids.addAll(sb.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated()));
}
includedPids.addAll(sb.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));
}
// Execute the query and make sure we return distinct results
List<IBaseResource> resources = new ArrayList<IBaseResource>();

195
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/PatientEverythingDstu3Test.java Normal file
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@ -0,0 +1,195 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsInRelativeOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.lessThan;
import static org.hamcrest.Matchers.lessThanOrEqualTo;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.startsWith;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.*;
import java.net.*;
import java.nio.charset.StandardCharsets;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.client.methods.*;
import org.apache.http.entity.*;
import org.apache.http.message.BasicNameValuePair;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.Encounter.EncounterLocationComponent;
import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
import org.hl7.fhir.instance.model.Encounter.EncounterState;
import org.hl7.fhir.instance.model.api.*;
import org.junit.*;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(PatientEverythingDstu3Test.class);
private String orgId;
private String patId;
private String encId1;
private String encId2;
private ArrayList<String> myObsIds;
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Override
@After
public void after() throws Exception {
super.after();
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
}
@Override
public void before() throws Exception {
super.before();
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myDaoConfig.setAllowMultipleDelete(true);
Organization org = new Organization();
org.setName("an org");
orgId = ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless().getValue();
Patient patient = new Patient();
patient.getManagingOrganization().setReference(orgId);
patId = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless().getValue();
Patient patient2 = new Patient();
patient2.getManagingOrganization().setReference(orgId);
ourClient.create().resource(patient2).execute().getId().toUnqualifiedVersionless().getValue();
Encounter enc1 = new Encounter();
enc1.setStatus(EncounterStatus.CANCELLED);
enc1.getServiceProvider().setReference(orgId);
encId1 = ourClient.create().resource(enc1).execute().getId().toUnqualifiedVersionless().getValue();
Encounter enc2 = new Encounter();
enc2.setStatus(EncounterStatus.ARRIVED);
enc2.getServiceProvider().setReference(orgId);
encId2 = ourClient.create().resource(enc2).execute().getId().toUnqualifiedVersionless().getValue();
myObsIds = new ArrayList<String>();
for (int i = 0; i < 20; i++) {
Observation obs = new Observation();
obs.getSubject().setReference(patId);
obs.setStatus(ObservationStatus.FINAL);
String obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless().getValue();
myObsIds.add(obsId);
}
}
/**
* See #674
*/
@Test
public void testEverythingPagesWithCorrectEncodingJson() throws Exception {
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=json&_count=1", EncodingEnum.JSON);
assertNotNull(bundle.getLink("next").getUrl());
assertThat(bundle.getLink("next").getUrl(), containsString("_format=json"));
bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.JSON);
assertNotNull(bundle.getLink("next").getUrl());
assertThat(bundle.getLink("next").getUrl(), containsString("_format=json"));
bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.JSON);
}
/**
* See #674
*/
@Test
public void testEverythingPagesWithCorrectEncodingXml() throws Exception {
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=xml&_count=1", EncodingEnum.XML);
assertNotNull(bundle.getLink("next").getUrl());
ourLog.info("Next link: {}", bundle.getLink("next").getUrl());
assertThat(bundle.getLink("next").getUrl(), containsString("_format=xml"));
bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.XML);
assertNotNull(bundle.getLink("next").getUrl());
ourLog.info("Next link: {}", bundle.getLink("next").getUrl());
assertThat(bundle.getLink("next").getUrl(), containsString("_format=xml"));
bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.XML);
}
private Bundle fetchBundle(String theUrl, EncodingEnum theEncoding) throws IOException, ClientProtocolException {
Bundle bundle;
HttpGet get = new HttpGet(theUrl);
CloseableHttpResponse resp = ourHttpClient.execute(get);
try {
assertEquals(theEncoding.getResourceContentTypeNonLegacy(), resp.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue().replaceAll(";.*", ""));
bundle = theEncoding.newParser(myFhirCtx).parseResource(Bundle.class, IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8));
} finally {
IOUtils.closeQuietly(resp);
}
return bundle;
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
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@ -47,6 +47,7 @@ import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
import org.hl7.fhir.instance.model.Encounter.EncounterState;
import org.hl7.fhir.instance.model.api.*;
import org.junit.*;
import org.springframework.transaction.TransactionStatus;