mirror of
https://github.com/hapifhir/hapi-fhir.git
synced 2025-02-16 18:05:19 +00:00
Back out changes relating to validate operations. Cleanup of code
This commit is contained in:
ianmarshall
parent
92313cd770
commit
3fef8f7bef
@ -88,7 +88,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
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}
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@Nonnull
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@Override
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@Override
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public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
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return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
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}
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@ -85,7 +85,7 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
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@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
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@OperationParam(name = "codingA", min = 0, max = 1) Coding theCodingA,
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@OperationParam(name = "codingB", min = 0, max = 1) Coding theCodingB,
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@OperationParam(name="version", min=0, max=1) org.hl7.fhir.r4.model.StringType theVersion,
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@OperationParam(name="version", min=0, max=1) StringType theVersion,
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RequestDetails theRequestDetails
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) {
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@ -85,7 +85,7 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
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@OperationParam(name="system", min=0, max=1) UriType theSystem,
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@OperationParam(name="codingA", min=0, max=1) Coding theCodingA,
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@OperationParam(name="codingB", min=0, max=1) Coding theCodingB,
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@OperationParam(name="version", min=0, max=1) org.hl7.fhir.r4.model.StringType theVersion,
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@OperationParam(name="version", min=0, max=1) StringType theVersion,
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RequestDetails theRequestDetails
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) {
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@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.term;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.support.ConceptValidationOptions;
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import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
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import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.context.support.ValidationSupportContext;
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import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
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@ -126,7 +125,6 @@ import org.hl7.fhir.r4.model.IntegerType;
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import org.hl7.fhir.r4.model.StringType;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
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import org.hl7.fhir.utilities.validation.ValidationOptions;
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import org.quartz.JobExecutionContext;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.context.ApplicationContext;
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@ -174,7 +172,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNoneBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.apache.commons.lang3.StringUtils.isNotEmpty;
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public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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public static final int DEFAULT_FETCH_SIZE = 250;
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@ -237,14 +234,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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private ITermCodeSystemStorageSvc myConceptStorageSvc;
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@Autowired
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private ApplicationContext myApplicationContext;
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@Autowired
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private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
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private volatile IValidationSupport myJpaValidationSupport;
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private volatile IValidationSupport myValidationSupport;
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@Override
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public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
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TermCodeSystemVersion cs = getCurrentCodeSystemVersionForVersion(theSystem,null);
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TermCodeSystemVersion cs = getCurrentCodeSystemVersion(theSystem,null);
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return cs != null;
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}
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@ -616,7 +611,6 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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private Boolean expandValueSetHandleIncludeOrExclude(@Nullable ValueSetExpansionOptions theExpansionOptions, IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theIncludeOrExclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex, VersionIndependentConcept theWantConceptOrNull) {
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String system = theIncludeOrExclude.getSystem();
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String systemVersion = theIncludeOrExclude.getVersion();
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boolean hasSystem = isNotBlank(system);
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boolean hasValueSet = theIncludeOrExclude.getValueSet().size() > 0;
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@ -631,7 +625,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
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if (cs != null) {
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return expandValueSetHandleIncludeOrExcludeUsingDatabase(theValueSetCodeAccumulator, theAddedCodes, theIncludeOrExclude, theAdd, theCodeCounter, theQueryIndex, theWantConceptOrNull, system, cs, systemVersion);
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return expandValueSetHandleIncludeOrExcludeUsingDatabase(theValueSetCodeAccumulator, theAddedCodes, theIncludeOrExclude, theAdd, theCodeCounter, theQueryIndex, theWantConceptOrNull, system, cs);
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} else {
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@ -672,7 +666,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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nextSystem = system;
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}
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LookupCodeResult lookup = myValidationSupport.lookupCode(new ValidationSupportContext(provideValidationSupport()), nextSystem, next.getCode(), systemVersion);
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LookupCodeResult lookup = myValidationSupport.lookupCode(new ValidationSupportContext(provideValidationSupport()), nextSystem, next.getCode());
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if (lookup != null && lookup.isFound()) {
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addOrRemoveCode(theValueSetCodeAccumulator, theAddedCodes, theAdd, nextSystem, next.getCode(), lookup.getCodeDisplay());
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foundCount++;
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@ -766,7 +760,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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@Nonnull
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private Boolean expandValueSetHandleIncludeOrExcludeUsingDatabase(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theIncludeOrExclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex, VersionIndependentConcept theWantConceptOrNull, String theSystem, TermCodeSystem theCs, String theSystemVersion) {
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private Boolean expandValueSetHandleIncludeOrExcludeUsingDatabase(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theIncludeOrExclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex, VersionIndependentConcept theWantConceptOrNull, String theSystem, TermCodeSystem theCs) {
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TermCodeSystemVersion csv = theCs.getCurrentVersion();
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FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
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@ -794,7 +788,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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/*
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* Filters
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*/
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handleFilters(bool, theSystem, qb, theIncludeOrExclude, theSystemVersion);
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handleFilters(bool, theSystem, qb, theIncludeOrExclude);
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Query luceneQuery = bool.createQuery();
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@ -903,15 +897,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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}
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private void handleFilters(BooleanJunction<?> theBool, String theSystem, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude, String theSystemVersion) {
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private void handleFilters(BooleanJunction<?> theBool, String theSystem, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude) {
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if (theIncludeOrExclude.getFilter().size() > 0) {
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for (ValueSet.ConceptSetFilterComponent nextFilter : theIncludeOrExclude.getFilter()) {
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handleFilter(theSystem, theQb, theBool, nextFilter, theSystemVersion);
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handleFilter(theSystem, theQb, theBool, nextFilter);
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}
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}
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}
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private void handleFilter(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
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private void handleFilter(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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if (isBlank(theFilter.getValue()) && theFilter.getOp() == null && isBlank(theFilter.getProperty())) {
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return;
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}
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@ -927,24 +921,24 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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break;
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case "concept":
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case "code":
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handleFilterConceptAndCode(theSystem, theQb, theBool, theFilter, theSystemVersion);
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handleFilterConceptAndCode(theSystem, theQb, theBool, theFilter);
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break;
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case "parent":
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case "child":
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isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
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handleFilterLoincParentChild(theQb, theBool, theFilter);
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handleFilterLoincParentChild(theBool, theFilter);
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break;
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case "ancestor":
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isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
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handleFilterLoincAncestor(theSystem, theQb, theBool, theFilter, theSystemVersion);
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handleFilterLoincAncestor(theSystem, theBool, theFilter);
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break;
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case "descendant":
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isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
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handleFilterLoincDescendant(theSystem, theQb, theBool, theFilter, theSystemVersion);
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handleFilterLoincDescendant(theSystem, theBool, theFilter);
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break;
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case "copyright":
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isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
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handleFilterLoincCopyright(theQb, theBool, theFilter);
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handleFilterLoincCopyright(theBool, theFilter);
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break;
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default:
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handleFilterRegex(theBool, theFilter);
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@ -952,11 +946,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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}
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private boolean isCodeSystemLoingOrThrowInvalidRequestException(String theSystem, String theProperty) {
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private void isCodeSystemLoingOrThrowInvalidRequestException(String theSystem, String theProperty) {
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if (!isCodeSystemLoinc(theSystem)) {
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throw new InvalidRequestException("Invalid filter, property " + theProperty + " is LOINC-specific and cannot be used with system: " + theSystem);
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}
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return true;
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}
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private boolean isCodeSystemLoinc(String theSystem) {
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@ -991,8 +984,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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bool.must(textQuery);
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}
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private void handleFilterConceptAndCode(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
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TermConcept code = findCode(theSystem, theFilter.getValue(), theSystemVersion)
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private void handleFilterConceptAndCode(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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TermConcept code = findCode(theSystem, theFilter.getValue())
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.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theFilter.getValue()));
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if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
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@ -1004,7 +997,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
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private void handleFilterLoincParentChild(QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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private void handleFilterLoincParentChild(BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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switch (theFilter.getOp()) {
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case EQUAL:
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addLoincFilterParentChildEqual(theBool, theFilter.getProperty(), theFilter.getValue());
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@ -1037,41 +1030,41 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
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private void handleFilterLoincAncestor(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
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private void handleFilterLoincAncestor(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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switch (theFilter.getOp()) {
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case EQUAL:
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addLoincFilterAncestorEqual(theSystem, theQb, theBool, theFilter, theSystemVersion);
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addLoincFilterAncestorEqual(theSystem, theBool, theFilter);
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break;
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case IN:
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addLoincFilterAncestorIn(theSystem, theQb, theBool, theFilter, theSystemVersion);
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addLoincFilterAncestorIn(theSystem, theBool, theFilter);
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break;
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default:
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throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
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}
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}
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private void addLoincFilterAncestorEqual(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
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addLoincFilterAncestorEqual(theSystem, theQb, theBool, theFilter.getProperty(), theFilter.getValue(), theSystemVersion);
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private void addLoincFilterAncestorEqual(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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addLoincFilterAncestorEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue());
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}
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private void addLoincFilterAncestorEqual(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, String theProperty, String theValue, String theSystemVersion) {
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List<Term> terms = getAncestorTerms(theSystem, theProperty, theValue, theSystemVersion);
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private void addLoincFilterAncestorEqual(String theSystem, BooleanJunction<?> theBool, String theProperty, String theValue) {
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List<Term> terms = getAncestorTerms(theSystem, theProperty, theValue);
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theBool.must(new TermsQuery(terms));
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}
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private void addLoincFilterAncestorIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
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private void addLoincFilterAncestorIn(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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String[] values = theFilter.getValue().split(",");
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List<Term> terms = new ArrayList<>();
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for (String value : values) {
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terms.addAll(getAncestorTerms(theSystem, theFilter.getProperty(), value, theSystemVersion));
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terms.addAll(getAncestorTerms(theSystem, theFilter.getProperty(), value));
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}
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theBool.must(new TermsQuery(terms));
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}
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private List<Term> getAncestorTerms(String theSystem, String theProperty, String theValue, String theSystemVersion) {
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private List<Term> getAncestorTerms(String theSystem, String theProperty, String theValue) {
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List<Term> retVal = new ArrayList<>();
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TermConcept code = findCode(theSystem, theValue, theSystemVersion)
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TermConcept code = findCode(theSystem, theValue)
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.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));
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retVal.add(new Term("myParentPids", "" + code.getId()));
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@ -1081,41 +1074,41 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
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private void handleFilterLoincDescendant(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
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private void handleFilterLoincDescendant(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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switch (theFilter.getOp()) {
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case EQUAL:
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addLoincFilterDescendantEqual(theSystem, theBool, theFilter, theSystemVersion);
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addLoincFilterDescendantEqual(theSystem, theBool, theFilter);
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break;
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case IN:
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addLoincFilterDescendantIn(theSystem, theQb, theBool, theFilter, theSystemVersion);
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addLoincFilterDescendantIn(theSystem, theBool, theFilter);
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break;
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default:
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throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
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}
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}
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private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
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addLoincFilterDescendantEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue(), theSystemVersion);
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private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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addLoincFilterDescendantEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue());
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}
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private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, String theProperty, String theValue, String theSystemVersion) {
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List<Term> terms = getDescendantTerms(theSystem, theProperty, theValue, theSystemVersion);
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private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, String theProperty, String theValue) {
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List<Term> terms = getDescendantTerms(theSystem, theProperty, theValue);
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theBool.must(new TermsQuery(terms));
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}
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private void addLoincFilterDescendantIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter, String theSystemVersion) {
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private void addLoincFilterDescendantIn(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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String[] values = theFilter.getValue().split(",");
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List<Term> terms = new ArrayList<>();
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for (String value : values) {
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terms.addAll(getDescendantTerms(theSystem, theFilter.getProperty(), value, theSystemVersion));
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terms.addAll(getDescendantTerms(theSystem, theFilter.getProperty(), value));
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}
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theBool.must(new TermsQuery(terms));
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}
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private List<Term> getDescendantTerms(String theSystem, String theProperty, String theValue, String theSystemVersion) {
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private List<Term> getDescendantTerms(String theSystem, String theProperty, String theValue) {
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List<Term> retVal = new ArrayList<>();
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TermConcept code = findCode(theSystem, theValue, theSystemVersion)
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TermConcept code = findCode(theSystem, theValue)
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.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));
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String[] parentPids = code.getParentPidsAsString().split(" ");
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@ -1127,7 +1120,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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return retVal;
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}
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private void handleFilterLoincCopyright(QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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private void handleFilterLoincCopyright(BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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if (theFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
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String copyrightFilterValue = defaultString(theFilter.getValue()).toLowerCase();
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@ -1365,7 +1358,6 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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@Override
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public Optional<TermConcept> findCode(String theCodeSystem, String theCode) {
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return findCode(theCodeSystem, theCode, null);
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}
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@Override
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@ -1378,7 +1370,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
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txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_MANDATORY);
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return txTemplate.execute(t -> {
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TermCodeSystemVersion csv = getCurrentCodeSystemVersionForVersion(theCodeSystem, theVersion);
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TermCodeSystemVersion csv = getCurrentCodeSystemVersion(theCodeSystem, theVersion);
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if (csv == null) {
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return Optional.empty();
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}
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@ -1387,8 +1379,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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@Nullable
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private TermCodeSystemVersion getCurrentCodeSystemVersionForVersion(String theUri, String theVersion) {
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StringBuffer key = new StringBuffer(theUri);
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private TermCodeSystemVersion getCurrentCodeSystemVersion(String theUri, String theVersion) {
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StringBuilder key = new StringBuilder(theUri);
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if (theVersion != null) {
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key.append("_").append(theVersion);
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}
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@ -1820,16 +1812,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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|
||||
@Override
|
||||
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB,
|
||||
IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
|
||||
IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
|
||||
return subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, null, null, null);
|
||||
}
|
||||
|
||||
@Override
|
||||
@Transactional
|
||||
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB,
|
||||
IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB,
|
||||
IPrimitiveType<String> theSystemVersion, String theCodingAVersion,
|
||||
String theCodingBVersion) {
|
||||
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB, IPrimitiveType<String> theSystemVersion, String theCodingAVersion, String theCodingBVersion) {
|
||||
VersionIndependentConceptWithSystemVersion conceptA = toConcept(theCodeA, theSystem, theCodingA, theSystemVersion, theCodingAVersion);
|
||||
VersionIndependentConceptWithSystemVersion conceptB = toConcept(theCodeB, theSystem, theCodingB, theSystemVersion, theCodingBVersion);
|
||||
|
||||
@ -2085,6 +2074,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
||||
|
||||
while (scrollableResultsIterator.hasNext()) {
|
||||
TermConceptMapGroupElement nextElement = scrollableResultsIterator.next();
|
||||
// TODO: The invocation of the size() below does not seem to be necessary but for some reason, removing it causes tests in TerminologySvcImplR4Test to fail.
|
||||
nextElement.getConceptMapGroupElementTargets().size();
|
||||
myEntityManager.detach(nextElement);
|
||||
|
||||
@ -2138,11 +2128,6 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
||||
@CoverageIgnore
|
||||
@Override
|
||||
public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
|
||||
return validateCode(theValidationSupportContext, theOptions, theCodeSystem, theCode, theDisplay, theValueSetUrl, null);
|
||||
}
|
||||
|
||||
@Override
|
||||
public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl, String theSystemVersion) {
|
||||
invokeRunnableForUnitTest();
|
||||
|
||||
if (isNotBlank(theValueSetUrl)) {
|
||||
@ -2151,7 +2136,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
||||
|
||||
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
|
||||
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
|
||||
Optional<VersionIndependentConcept> codeOpt = txTemplate.execute(t -> findCode(theCodeSystem, theCode, theSystemVersion).map(c -> new VersionIndependentConcept(theCodeSystem, c.getCode())));
|
||||
Optional<VersionIndependentConcept> codeOpt = txTemplate.execute(t -> findCode(theCodeSystem, theCode).map(c -> new VersionIndependentConcept(theCodeSystem, c.getCode())));
|
||||
|
||||
if (codeOpt != null && codeOpt.isPresent()) {
|
||||
VersionIndependentConcept code = codeOpt.get();
|
||||
@ -2182,7 +2167,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
||||
}
|
||||
}
|
||||
|
||||
CodeValidationResult retVal = null;
|
||||
CodeValidationResult retVal;
|
||||
if (valueSet != null) {
|
||||
retVal = new InMemoryTerminologyServerValidationSupport(myContext).validateCodeInValueSet(theValidationSupportContext, theValidationOptions, theCodeSystem, theCode, theDisplay, valueSet);
|
||||
} else {
|
||||
@ -2415,9 +2400,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
||||
}
|
||||
|
||||
@NotNull
|
||||
private VersionIndependentConceptWithSystemVersion toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theSystemType,
|
||||
IBaseCoding theCodingType, IPrimitiveType<String> theSystemVersionType,
|
||||
String theCodingVersionType) {
|
||||
private VersionIndependentConceptWithSystemVersion toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theSystemType, IBaseCoding theCodingType, IPrimitiveType<String> theSystemVersionType, String theCodingVersionType) {
|
||||
String code = theCodeType != null ? theCodeType.getValueAsString() : null;
|
||||
String system = theSystemType != null ? theSystemType.getValueAsString() : null;
|
||||
String systemVersion = theSystemVersionType != null ? theSystemVersionType.getValueAsString() : null;
|
||||
|
||||
@ -234,10 +234,12 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
||||
@Override
|
||||
@Transactional(propagation = Propagation.NEVER)
|
||||
public void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
|
||||
TermCodeSystem termCodeSystem = theCodeSystemVersion.getCodeSystem();
|
||||
// Delete TermCodeSystemVersion
|
||||
ourLog.info(" * Deleting code system version {}", theCodeSystemVersion.getCodeSystemVersionId());
|
||||
deleteCodeSystemVersion(theCodeSystemVersion.getPid());
|
||||
|
||||
// Check if the version deleted is the current version. If so, delete TermCodeSystem as well.
|
||||
TermCodeSystem termCodeSystem = theCodeSystemVersion.getCodeSystem();
|
||||
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
|
||||
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
|
||||
txTemplate.executeWithoutResult(t -> {
|
||||
@ -312,8 +314,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
||||
if (termCodeSystem != null) {
|
||||
TermCodeSystemVersion codeSystemVersion = getExistingTermCodeSystemVersion(termCodeSystem.getPid(), theCodeSystem.getVersion());
|
||||
if (codeSystemVersion != null) {
|
||||
TermCodeSystem myCodeSystemEntity = getOrCreateTermCodeSystem(codeSystemResourcePid, theCodeSystem.getUrl(), theCodeSystem.getUrl(), theResourceEntity);
|
||||
validateCodeSystemVersionUpdate(myCodeSystemEntity,theCodeSystem.getUrl(), theCodeSystem.getVersion(), theResourceEntity);
|
||||
TermCodeSystem myCodeSystemEntity = getOrCreateDistinctTermCodeSystem(codeSystemResourcePid, theCodeSystem.getUrl(), theCodeSystem.getUrl(), theCodeSystem.getVersion(), theResourceEntity);
|
||||
return;
|
||||
}
|
||||
}
|
||||
@ -370,8 +371,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
||||
/*
|
||||
* Get CodeSystem and validate CodeSystemVersion
|
||||
*/
|
||||
TermCodeSystem codeSystem = getOrCreateTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theCodeSystemResourceTable);
|
||||
validateCodeSystemVersionUpdate(codeSystem, theSystemUri, theSystemVersionId, theCodeSystemResourceTable);
|
||||
TermCodeSystem codeSystem = getOrCreateDistinctTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theSystemVersionId, theCodeSystemResourceTable);
|
||||
|
||||
/*
|
||||
* Delete version being replaced.
|
||||
@ -691,7 +691,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
private TermCodeSystem getOrCreateTermCodeSystem(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, ResourceTable theCodeSystemResourceTable) {
|
||||
private TermCodeSystem getOrCreateDistinctTermCodeSystem(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
|
||||
TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
|
||||
if (codeSystem == null) {
|
||||
codeSystem = myCodeSystemDao.findByResourcePid(theCodeSystemResourcePid.getIdAsLong());
|
||||
@ -704,10 +704,11 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
||||
codeSystem.setCodeSystemUri(theSystemUri);
|
||||
codeSystem.setName(theSystemName);
|
||||
codeSystem = myCodeSystemDao.save(codeSystem);
|
||||
checkForCodeSystemVersionDuplicate(codeSystem,theSystemUri, theSystemVersionId, theCodeSystemResourceTable);
|
||||
return codeSystem;
|
||||
}
|
||||
|
||||
private void validateCodeSystemVersionUpdate(TermCodeSystem theCodeSystem, String theSystemUri, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
|
||||
private void checkForCodeSystemVersionDuplicate(TermCodeSystem theCodeSystem, String theSystemUri, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
|
||||
// Check if CodeSystemVersion entity already exists.
|
||||
TermCodeSystemVersion codeSystemVersionEntity;
|
||||
String msg = null;
|
||||
|
||||
@ -416,51 +416,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByValueSetWithFilter() throws IOException {
|
||||
loadAndPersistCodeSystem();
|
||||
|
||||
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "valueSet", toExpand)
|
||||
.andParameter("filter", new StringType("blood"))
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
assertThat(resp, stringContainsInOrder(
|
||||
"<code value=\"11378-7\"/>",
|
||||
"<display value=\"Systolic blood pressure at First encounter\"/>"));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrlWithFilter() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("filter", new StringType("first"))
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
assertThat(resp, stringContainsInOrder(
|
||||
"<code value=\"11378-7\"/>",
|
||||
"<display value=\"Systolic blood pressure at First encounter\"/>"));
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testExpandByValueSetWithPreExpansion() throws IOException {
|
||||
myDaoConfig.setPreExpandValueSets(true);
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user