Implement both a copyright property and a copyright filter for LOINC. #1451
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678d58ab90
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@ -199,6 +199,20 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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}
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}
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private void addCopyrightFilter3rdParty(BooleanJunction<?> bool) {
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// FIXME: DM 2019-09-13 - This feels hacky but it works until we have a better way for filtering TermConcept based on TermConceptProperty.
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Term term = new Term(TermConceptPropertyFieldBridge.CONCEPT_FIELD_PROPERTY_PREFIX + "EXTERNAL_COPYRIGHT_NOTICE", ".*");
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RegexpQuery query = new RegexpQuery(term);
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bool.must(query);
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}
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private void addCopyrightFilterLoinc(BooleanJunction<?> bool) {
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// FIXME: DM 2019-09-13 - This feels hacky but it works until we have a better way for filtering TermConcept based on TermConceptProperty.
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Term term = new Term(TermConceptPropertyFieldBridge.CONCEPT_FIELD_PROPERTY_PREFIX + "EXTERNAL_COPYRIGHT_NOTICE", ".*");
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RegexpQuery query = new RegexpQuery(term);
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bool.must(query).not();
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}
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private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ValueSet.ConceptSetFilterComponent nextFilter) {
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bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
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}
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@ -728,74 +742,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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*/
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if (theInclude.getFilter().size() > 0) {
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for (ValueSet.ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
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if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
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continue;
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}
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if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
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throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
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}
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if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
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addDisplayFilterExact(qb, bool, nextFilter);
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} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
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if (nextFilter.getValue().trim().contains(" ")) {
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addDisplayFilterExact(qb, bool, nextFilter);
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} else {
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addDisplayFilterInexact(qb, bool, nextFilter);
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}
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} else if (nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) {
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TermConcept code = findCode(system, nextFilter.getValue())
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.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue()));
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if (nextFilter.getOp() == ValueSet.FilterOperator.ISA) {
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ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
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bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
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} else {
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throw new InvalidRequestException("Don't know how to handle op=" + nextFilter.getOp() + " on property " + nextFilter.getProperty());
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}
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} else {
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if (nextFilter.getOp() == ValueSet.FilterOperator.REGEX) {
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/*
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* We treat the regex filter as a match on the regex
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* anywhere in the property string. The spec does not
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* say whether or not this is the right behaviour, but
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* there are examples that seem to suggest that it is.
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*/
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String value = nextFilter.getValue();
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if (value.endsWith("$")) {
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value = value.substring(0, value.length() - 1);
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} else if (!value.endsWith(".*")) {
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value = value + ".*";
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}
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if (!value.startsWith("^") && !value.startsWith(".*")) {
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value = ".*" + value;
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} else if (value.startsWith("^")) {
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value = value.substring(1);
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}
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Term term = new Term(TermConceptPropertyFieldBridge.CONCEPT_FIELD_PROPERTY_PREFIX + nextFilter.getProperty(), value);
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RegexpQuery query = new RegexpQuery(term);
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bool.must(query);
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} else {
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String value = nextFilter.getValue();
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Term term = new Term(TermConceptPropertyFieldBridge.CONCEPT_FIELD_PROPERTY_PREFIX + nextFilter.getProperty(), value);
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bool.must(new TermsQuery(term));
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}
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}
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handleFilter(system, qb, bool, nextFilter);
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}
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}
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Query luceneQuery = bool.createQuery();
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@ -925,6 +874,106 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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}
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private void handleFilter(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent nextFilter) {
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if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
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return;
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}
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if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
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throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
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}
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if (nextFilter.getProperty().equals("display:exact") || nextFilter.getProperty().equals("display")) {
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handleDisplayFilter(theQb, theBool, nextFilter);
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} else if (nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) {
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handleConceptAndCodeFilter(theSystem, theQb, theBool, nextFilter);
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} else if (nextFilter.getProperty().equals("copyright")) {
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handleLoincCopyrightFilter(theQb, theBool, nextFilter);
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} else {
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handleRegexFilter(theBool, nextFilter);
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}
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}
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private void handleDisplayFilter(QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent nextFilter) {
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if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
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addDisplayFilterExact(theQb, theBool, nextFilter);
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} else if (nextFilter.getProperty().equals("display") && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
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if (nextFilter.getValue().trim().contains(" ")) {
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addDisplayFilterExact(theQb, theBool, nextFilter);
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} else {
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addDisplayFilterInexact(theQb, theBool, nextFilter);
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}
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}
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}
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private void handleConceptAndCodeFilter(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent nextFilter) {
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TermConcept code = findCode(theSystem, nextFilter.getValue())
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.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + theSystem + "}" + nextFilter.getValue()));
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if (nextFilter.getOp() == ValueSet.FilterOperator.ISA) {
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ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
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theBool.must(theQb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
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} else {
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throw new InvalidRequestException("Don't know how to handle op=" + nextFilter.getOp() + " on property " + nextFilter.getProperty());
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}
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}
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private void handleLoincCopyrightFilter(QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent nextFilter) {
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if (nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
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String copyrightFilterValue = defaultString(nextFilter.getValue()).toLowerCase();
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switch (copyrightFilterValue) {
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case "loinc":
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ourLog.info(" * Filtering with value=" + nextFilter.getValue() + " on property " + nextFilter.getProperty());
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addCopyrightFilterLoinc(theBool);
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break;
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case "3rdparty":
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ourLog.info(" * Filtering with value=" + nextFilter.getValue() + " on property " + nextFilter.getProperty());
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addCopyrightFilter3rdParty(theBool);
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break;
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default:
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throw new InvalidRequestException("Don't know how to handle value=" + nextFilter.getValue() + " on property " + nextFilter.getProperty());
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}
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} else {
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throw new InvalidRequestException("Don't know how to handle op=" + nextFilter.getOp() + " on property " + nextFilter.getProperty());
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}
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}
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private void handleRegexFilter(BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent nextFilter) {
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if (nextFilter.getOp() == ValueSet.FilterOperator.REGEX) {
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/*
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* We treat the regex filter as a match on the regex
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* anywhere in the property string. The spec does not
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* say whether or not this is the right behaviour, but
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* there are examples that seem to suggest that it is.
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*/
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String value = nextFilter.getValue();
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if (value.endsWith("$")) {
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value = value.substring(0, value.length() - 1);
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} else if (!value.endsWith(".*")) {
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value = value + ".*";
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}
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if (!value.startsWith("^") && !value.startsWith(".*")) {
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value = ".*" + value;
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} else if (value.startsWith("^")) {
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value = value.substring(1);
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}
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Term term = new Term(TermConceptPropertyFieldBridge.CONCEPT_FIELD_PROPERTY_PREFIX + nextFilter.getProperty(), value);
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RegexpQuery query = new RegexpQuery(term);
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theBool.must(query);
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} else {
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String value = nextFilter.getValue();
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Term term = new Term(TermConceptPropertyFieldBridge.CONCEPT_FIELD_PROPERTY_PREFIX + nextFilter.getProperty(), value);
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theBool.must(new TermsQuery(term));
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}
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}
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private void expandWithoutHibernateSearch(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
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ourLog.trace("Hibernate search is not enabled");
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if (theValueSetCodeAccumulator instanceof ValueSetExpansionComponentWithConceptAccumulator) {
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@ -148,6 +148,11 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
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code.addPropertyString("HELLO", "12345-2");
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cs.getConcepts().add(code);
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code = new TermConcept(cs, "47239-9");
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code.addPropertyString("SYSTEM", "^Patient");
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code.addPropertyString("EXTERNAL_COPYRIGHT_NOTICE", "Copyright © 2006 World Health Organization...");
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cs.getConcepts().add(code);
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myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION" , cs);
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});
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}
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@ -273,6 +278,218 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
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}
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@Test
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public void testExpandValueSetPropertyFilterCopyrightWithExclude3rdParty() {
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createLoincSystemWithSomeCodes();
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List<String> codes;
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ValueSet vs;
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ValueSet outcome;
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ValueSet.ConceptSetComponent exclude;
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// Include
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vs = new ValueSet();
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vs.getCompose()
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.addInclude()
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.setSystem(CS_URL);
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// Exclude
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exclude = vs.getCompose().addExclude();
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exclude.setSystem(CS_URL);
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exclude
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.EQUAL)
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.setValue("3rdParty");
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outcome = myTermSvc.expandValueSet(vs);
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codes = toCodesContains(outcome.getExpansion().getContains());
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assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4"));
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// Include
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vs = new ValueSet();
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vs.getCompose()
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.addInclude()
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.setSystem(CS_URL);
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// Exclude
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exclude = vs.getCompose().addExclude();
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exclude.setSystem(CS_URL);
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exclude
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.EQUAL)
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.setValue("3rdparty");
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outcome = myTermSvc.expandValueSet(vs);
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codes = toCodesContains(outcome.getExpansion().getContains());
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assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4"));
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}
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@Test
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public void testExpandValueSetPropertyFilterCopyrightWithExcludeLoinc() {
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createLoincSystemWithSomeCodes();
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List<String> codes;
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ValueSet vs;
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ValueSet outcome;
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ValueSet.ConceptSetComponent exclude;
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// Include
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vs = new ValueSet();
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vs.getCompose()
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.addInclude()
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.setSystem(CS_URL);
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// Exclude
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exclude = vs.getCompose().addExclude();
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exclude.setSystem(CS_URL);
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exclude
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.EQUAL)
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.setValue("LOINC");
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outcome = myTermSvc.expandValueSet(vs);
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codes = toCodesContains(outcome.getExpansion().getContains());
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assertThat(codes, containsInAnyOrder("47239-9"));
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// Include
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vs = new ValueSet();
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vs.getCompose()
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.addInclude()
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.setSystem(CS_URL);
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// Exclude
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exclude = vs.getCompose().addExclude();
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exclude.setSystem(CS_URL);
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exclude
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.EQUAL)
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.setValue("loinc");
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outcome = myTermSvc.expandValueSet(vs);
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codes = toCodesContains(outcome.getExpansion().getContains());
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assertThat(codes, containsInAnyOrder("47239-9"));
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}
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@Test
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public void testExpandValueSetPropertyFilterCopyrightWithInclude3rdParty() {
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createLoincSystemWithSomeCodes();
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List<String> codes;
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ValueSet vs;
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ValueSet outcome;
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ValueSet.ConceptSetComponent include;
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// Include
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vs = new ValueSet();
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include = vs.getCompose().addInclude();
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include.setSystem(CS_URL);
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include
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.EQUAL)
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.setValue("3rdParty");
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outcome = myTermSvc.expandValueSet(vs);
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codes = toCodesContains(outcome.getExpansion().getContains());
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assertThat(codes, containsInAnyOrder("47239-9"));
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// Include
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vs = new ValueSet();
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include = vs.getCompose().addInclude();
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include.setSystem(CS_URL);
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include
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.EQUAL)
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.setValue("3rdparty");
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outcome = myTermSvc.expandValueSet(vs);
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codes = toCodesContains(outcome.getExpansion().getContains());
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assertThat(codes, containsInAnyOrder("47239-9"));
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}
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@Test
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public void testExpandValueSetPropertyFilterCopyrightWithIncludeLoinc() {
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createLoincSystemWithSomeCodes();
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List<String> codes;
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ValueSet vs;
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ValueSet outcome;
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ValueSet.ConceptSetComponent include;
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// Include
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vs = new ValueSet();
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include = vs.getCompose().addInclude();
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include.setSystem(CS_URL);
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include
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.EQUAL)
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.setValue("LOINC");
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outcome = myTermSvc.expandValueSet(vs);
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codes = toCodesContains(outcome.getExpansion().getContains());
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assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4"));
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// Include
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vs = new ValueSet();
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include = vs.getCompose().addInclude();
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include.setSystem(CS_URL);
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include
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.EQUAL)
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.setValue("loinc");
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outcome = myTermSvc.expandValueSet(vs);
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codes = toCodesContains(outcome.getExpansion().getContains());
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assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4"));
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}
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@Test
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public void testExpandValueSetPropertyFilterCopyrightWithUnsupportedOp() {
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createLoincSystemWithSomeCodes();
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List<String> codes;
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ValueSet vs;
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ValueSet outcome;
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ValueSet.ConceptSetComponent include;
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// Include
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vs = new ValueSet();
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include = vs.getCompose().addInclude();
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include.setSystem(CS_URL);
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include
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.ISA)
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.setValue("LOINC");
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try {
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outcome = myTermSvc.expandValueSet(vs);
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} catch (InvalidRequestException e) {
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assertEquals(400, e.getStatusCode());
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assertEquals("Don't know how to handle op=ISA on property copyright", e.getMessage());
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}
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}
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@Test
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public void testExpandValueSetPropertyFilterCopyrightWithUnsupportedValue() {
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createLoincSystemWithSomeCodes();
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List<String> codes;
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ValueSet vs;
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ValueSet outcome;
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ValueSet.ConceptSetComponent include;
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// Include
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vs = new ValueSet();
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include = vs.getCompose().addInclude();
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include.setSystem(CS_URL);
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include
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.addFilter()
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.setProperty("copyright")
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.setOp(ValueSet.FilterOperator.EQUAL)
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.setValue("bogus");
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try {
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outcome = myTermSvc.expandValueSet(vs);
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} catch (InvalidRequestException e) {
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assertEquals(400, e.getStatusCode());
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assertEquals("Don't know how to handle value=bogus on property copyright", e.getMessage());
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}
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}
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@Test
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public void testExpandValueSetPropertySearchWithRegexExclude() {
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createLoincSystemWithSomeCodes();
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@ -297,7 +514,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
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.setValue(".*\\^Donor$");
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outcome = myTermSvc.expandValueSet(vs);
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codes = toCodesContains(outcome.getExpansion().getContains());
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assertThat(codes, containsInAnyOrder("43343-3", "43343-4"));
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assertThat(codes, containsInAnyOrder("43343-3", "43343-4", "47239-9"));
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}
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@Test
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@ -324,7 +541,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
|
|||
.setValue("12345-1|12345-2");
|
||||
outcome = myTermSvc.expandValueSet(vs);
|
||||
codes = toCodesContains(outcome.getExpansion().getContains());
|
||||
assertThat(codes, containsInAnyOrder("50015-7"));
|
||||
assertThat(codes, containsInAnyOrder("50015-7", "47239-9"));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
Loading…
Reference in New Issue