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Fixes to loinc mapping

This commit is contained in:
James Agnew 2018-04-10 21:19:00 -04:00
parent 260aa9e9fa
commit b3a9ea263f
5 changed files with 23 additions and 27 deletions
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21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
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@ -815,7 +815,7 @@ public class SearchBuilder implements ISearchBuilder {
continue; continue;
} }
predicate = join.<Object>get("myUri").as(String.class).in(toFind); predicate = join.get("myUri").as(String.class).in(toFind);
} else if (param.getQualifier() == UriParamQualifierEnum.BELOW) { } else if (param.getQualifier() == UriParamQualifierEnum.BELOW) {
predicate = myBuilder.like(join.get("myUri").as(String.class), createLeftMatchLikeExpression(value)); predicate = myBuilder.like(join.get("myUri").as(String.class), createLeftMatchLikeExpression(value));
@ -953,8 +953,8 @@ public class SearchBuilder implements ISearchBuilder {
Predicate lb = null; Predicate lb = null;
if (lowerBound != null) { if (lowerBound != null) {
Predicate gt = theBuilder.greaterThanOrEqualTo(theFrom.<Date>get("myValueLow"), lowerBound); Predicate gt = theBuilder.greaterThanOrEqualTo(theFrom.get("myValueLow"), lowerBound);
Predicate lt = theBuilder.greaterThanOrEqualTo(theFrom.<Date>get("myValueHigh"), lowerBound); Predicate lt = theBuilder.greaterThanOrEqualTo(theFrom.get("myValueHigh"), lowerBound);
if (theRange.getLowerBound().getPrefix() == ParamPrefixEnum.STARTS_AFTER || theRange.getLowerBound().getPrefix() == ParamPrefixEnum.EQUAL) { if (theRange.getLowerBound().getPrefix() == ParamPrefixEnum.STARTS_AFTER || theRange.getLowerBound().getPrefix() == ParamPrefixEnum.EQUAL) {
lb = gt; lb = gt;
} else { } else {
@ -964,8 +964,8 @@ public class SearchBuilder implements ISearchBuilder {
Predicate ub = null; Predicate ub = null;
if (upperBound != null) { if (upperBound != null) {
Predicate gt = theBuilder.lessThanOrEqualTo(theFrom.<Date>get("myValueLow"), upperBound); Predicate gt = theBuilder.lessThanOrEqualTo(theFrom.get("myValueLow"), upperBound);
Predicate lt = theBuilder.lessThanOrEqualTo(theFrom.<Date>get("myValueHigh"), upperBound); Predicate lt = theBuilder.lessThanOrEqualTo(theFrom.get("myValueHigh"), upperBound);
if (theRange.getUpperBound().getPrefix() == ParamPrefixEnum.ENDS_BEFORE || theRange.getUpperBound().getPrefix() == ParamPrefixEnum.EQUAL) { if (theRange.getUpperBound().getPrefix() == ParamPrefixEnum.ENDS_BEFORE || theRange.getUpperBound().getPrefix() == ParamPrefixEnum.EQUAL) {
ub = lt; ub = lt;
} else { } else {
@ -2008,15 +2008,15 @@ public class SearchBuilder implements ISearchBuilder {
} }
private static List<Predicate> createLastUpdatedPredicates(final DateRangeParam theLastUpdated, CriteriaBuilder builder, From<?, ResourceTable> from) { private static List<Predicate> createLastUpdatedPredicates(final DateRangeParam theLastUpdated, CriteriaBuilder builder, From<?, ResourceTable> from) {
List<Predicate> lastUpdatedPredicates = new ArrayList<Predicate>(); List<Predicate> lastUpdatedPredicates = new ArrayList<>();
if (theLastUpdated != null) { if (theLastUpdated != null) {
if (theLastUpdated.getLowerBoundAsInstant() != null) { if (theLastUpdated.getLowerBoundAsInstant() != null) {
ourLog.debug("LastUpdated lower bound: {}", new InstantDt(theLastUpdated.getLowerBoundAsInstant())); ourLog.debug("LastUpdated lower bound: {}", new InstantDt(theLastUpdated.getLowerBoundAsInstant()));
Predicate predicateLower = builder.greaterThanOrEqualTo(from.<Date>get("myUpdated"), theLastUpdated.getLowerBoundAsInstant()); Predicate predicateLower = builder.greaterThanOrEqualTo(from.get("myUpdated"), theLastUpdated.getLowerBoundAsInstant());
lastUpdatedPredicates.add(predicateLower); lastUpdatedPredicates.add(predicateLower);
} }
if (theLastUpdated.getUpperBoundAsInstant() != null) { if (theLastUpdated.getUpperBoundAsInstant() != null) {
Predicate predicateUpper = builder.lessThanOrEqualTo(from.<Date>get("myUpdated"), theLastUpdated.getUpperBoundAsInstant()); Predicate predicateUpper = builder.lessThanOrEqualTo(from.get("myUpdated"), theLastUpdated.getUpperBoundAsInstant());
lastUpdatedPredicates.add(predicateUpper); lastUpdatedPredicates.add(predicateUpper);
} }
} }
@ -2262,10 +2262,7 @@ public class SearchBuilder implements ISearchBuilder {
if (myNext == null) { if (myNext == null) {
fetchNext(); fetchNext();
} }
if (myNext == NO_MORE) { return myNext != NO_MORE;
return false;
}
return true;
} }
@Override @Override

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -758,8 +758,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
// Grab the existing versions so we can delete them later // Grab the existing versions so we can delete them later
List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystemResourcePid); List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystemResourcePid);
verifyNoDuplicates(theCodeSystemVersion.getConcepts(), new HashSet<String>());
/* /*
* For now we always delete old versions.. At some point it would be nice to allow configuration to keep old versions * For now we always delete old versions.. At some point it would be nice to allow configuration to keep old versions
*/ */
@ -808,8 +806,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
ourLog.info("Validating all codes in CodeSystem for storage (this can take some time for large sets)"); ourLog.info("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
// Validate the code system // Validate the code system
ArrayList<String> conceptsStack = new ArrayList<String>(); ArrayList<String> conceptsStack = new ArrayList<>();
IdentityHashMap<TermConcept, Object> allConcepts = new IdentityHashMap<TermConcept, Object>(); IdentityHashMap<TermConcept, Object> allConcepts = new IdentityHashMap<>();
int totalCodeCount = 0; int totalCodeCount = 0;
for (TermConcept next : theCodeSystemVersion.getConcepts()) { for (TermConcept next : theCodeSystemVersion.getConcepts()) {
totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack, allConcepts); totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack, allConcepts);
@ -911,15 +909,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
return retVal; return retVal;
} }
private void verifyNoDuplicates(Collection<TermConcept> theConcepts, Set<String> theCodes) {
for (TermConcept next : theConcepts) {
if (!theCodes.add(next.getCode())) {
throw new InvalidRequestException("Duplicate code " + next.getCode() + " found in codesystem after checking " + theCodes.size() + " codes");
}
verifyNoDuplicates(next.getChildren().stream().map(TermConceptParentChildLink::getChild).collect(Collectors.toList()), theCodes);
}
}
/** /**
* This method is present only for unit tests, do not call from client code * This method is present only for unit tests, do not call from client code
*/ */

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
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@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor; import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum; import ca.uhn.fhir.validation.ResultSeverityEnum;
import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder; import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder;
import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder; import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource; import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.jpa.HibernatePersistenceProvider; import org.hibernate.jpa.HibernatePersistenceProvider;
@ -104,7 +105,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
DataSource dataSource = ProxyDataSourceBuilder DataSource dataSource = ProxyDataSourceBuilder
.create(retVal) .create(retVal)
// .logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL") .logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
.logSlowQueryBySlf4j(10, TimeUnit.SECONDS) .logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
.countQuery(new ThreadQueryCountHolder()) .countQuery(new ThreadQueryCountHolder())
.build(); .build();

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
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@ -182,6 +182,15 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
return ids; return ids;
} }
@Test
@Ignore
public void test() throws IOException {
HttpGet get = new HttpGet(ourServerBase + "/QuestionnaireResponse?_count=50&status=completed&questionnaire=ARIncenterAbsRecord&_lastUpdated=%3E"+UrlUtil.escapeUrlParam("=2018-01-01")+"&context.organization=O3435");
ourLog.info("*** MAKING QUERY");
ourHttpClient.execute(get);
System.exit(0);
}
@Test @Test
public void testBundleCreate() throws Exception { public void testBundleCreate() throws Exception {
IGenericClient client = myClient; IGenericClient client = myClient;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
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@ -205,7 +205,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
ValueSet outcome = myTermSvc.expandValueSet(vs); ValueSet outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains()); codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("ParentA", "childAAA", "childAAB", "childAA", "childAB", "ParentB")); assertThat(codes, containsInAnyOrder("ParentWithNoChildrenA", "ParentWithNoChildrenB", "ParentWithNoChildrenC", "ParentA", "childAAA", "childAAB", "childAA", "childAB", "ParentB"));
} }
@Test @Test