support validation against code system fragments
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bcde2d2f46
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4cbf328e54
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@ -112,10 +112,17 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
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if (system == null && !code.hasDisplay()) { // dealing with just a plain code (enum)
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system = systemForCodeInValueSet(code.getCode());
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}
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if (!code.hasSystem())
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if (!code.hasSystem()) {
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if (options.isGuessSystem() && system == null && Utilities.isAbsoluteUrl(code.getCode())) {
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system = "urn:ietf:rfc:3986"; // this arises when using URIs bound to value sets
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}
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code.setSystem(system);
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}
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inExpansion = checkExpansion(code);
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CodeSystem cs = context.fetchCodeSystem(system);
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if (cs == null) {
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cs = findSpecialCodeSystem(system);
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}
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if (cs == null) {
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warningMessage = "Unable to resolve system "+system+" - system is not specified or implicit";
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if (!inExpansion)
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@ -123,7 +130,7 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
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}
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if (cs!=null && cs.getContent() != CodeSystemContentMode.COMPLETE) {
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warningMessage = "Unable to resolve system "+system+" - system is not complete";
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if (!inExpansion)
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if (!inExpansion && cs.getContent() != CodeSystemContentMode.FRAGMENT) // we're going to give it a go if it's a fragment
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throw new FHIRException(warningMessage);
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}
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@ -147,6 +154,17 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
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return res;
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}
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private CodeSystem findSpecialCodeSystem(String system) {
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if ("urn:ietf:rfc:3986".equals(system)) {
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CodeSystem cs = new CodeSystem();
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cs.setUrl(system);
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cs.setUserData("tx.cs.special", new URICodeSystem());
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cs.setContent(CodeSystemContentMode.COMPLETE);
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return cs;
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}
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return null;
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}
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boolean checkExpansion(Coding code) {
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if (valueset==null || !valueset.hasExpansion())
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return false;
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@ -164,9 +182,14 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
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}
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private ValidationResult validateCode(Coding code, CodeSystem cs) {
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ConceptDefinitionComponent cc = findCodeInConcept(cs.getConcept(), code.getCode());
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if (cc == null)
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ConceptDefinitionComponent cc = cs.hasUserData("tx.cs.special") ? ((SpecialCodeSystem) cs.getUserData("tx.cs.special")).findConcept(code) : findCodeInConcept(cs.getConcept(), code.getCode());
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if (cc == null) {
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if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
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return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_FRAGMENT, gen(code), cs.getUrl()));
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} else {
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return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_, gen(code), cs.getUrl()));
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}
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}
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if (code.getDisplay() == null)
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return new ValidationResult(cc);
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CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
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@ -419,6 +419,7 @@ public class I18nConstants {
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public final static String UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__ = "Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__";
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public final static String DISPLAY_NAME_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF_ = "Display_Name_for__should_be_one_of__instead_of_";
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public final static String UNKNOWN_CODE__IN_ = "Unknown_Code__in_";
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public final static String UNKNOWN_CODE__IN_FRAGMENT = "UNKNOWN_CODE__IN_FRAGMENT";
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public final static String CODE_FOUND_IN_EXPANSION_HOWEVER_ = "Code_found_in_expansion_however_";
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public final static String NONE_OF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_ = "None_of_the_provided_codes_are_in_the_value_set_";
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public final static String CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE = "Coding_has_no_system__cannot_validate";
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@ -419,6 +419,7 @@ Error_parsing_ = Error parsing {0}:{1}
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Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__ = Unable to connect to terminology server. Use parameter ''-tx n/a'' tun run without using terminology services to validate LOINC, SNOMED, ICD-X etc. Error = {0}
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Display_Name_for__should_be_one_of__instead_of_ = Display Name for {0}#{1} should be one of ''{2}'' instead of ''{3}''
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Unknown_Code__in_ = Unknown Code {0} in {1}
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UNKNOWN_CODE__IN_FRAGMENT = Unknown Code {0} in {1} - note that the code system is labelled as a fragment, so the code may be valid in some other fragment
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Code_found_in_expansion_however_ = Code found in expansion, however: {0}
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None_of_the_provided_codes_are_in_the_value_set_ = None of the provided codes are in the value set {0}
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Coding_has_no_system__cannot_validate = Coding has no system - cannot validate
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