fix R4 compilation error and update pr for R5
This commit is contained in:
Oliver Egger
parent
1c73a3771e
commit
f659b67307
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@ -80,9 +80,8 @@ public class FHIRMappingLanguageTests implements ITransformerServices {
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@BeforeClass
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static public void setUp() throws Exception {
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if (context == null) {
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context = new SimpleWorkerContext();
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PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
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context.loadFromPackage(pcm.loadPackageCacheLatest("hl7.fhir.core"), null, "StructureDefinition");
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context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
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jsonParser = new JsonParser();
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jsonParser.setOutputStyle(OutputStyle.PRETTY);
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}
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@ -1170,13 +1170,15 @@ public class StructureMapUtilities {
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target.addListMode(StructureMapTargetListMode.SHARE);
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lexer.next();
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target.setListRuleId(lexer.take());
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} else if (lexer.getCurrent().equals("first"))
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} else {
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if (lexer.getCurrent().equals("first"))
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target.addListMode(StructureMapTargetListMode.FIRST);
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else
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target.addListMode(StructureMapTargetListMode.LAST);
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lexer.next();
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}
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}
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}
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private void parseParameter(StructureMapGroupRuleTargetComponent target, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
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@ -1219,7 +1221,7 @@ public class StructureMapUtilities {
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}
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public enum VariableMode {
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INPUT, OUTPUT
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INPUT, OUTPUT, SHARED
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}
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public class Variable {
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@ -1280,13 +1282,22 @@ public class StructureMapUtilities {
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public String summary() {
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CommaSeparatedStringBuilder s = new CommaSeparatedStringBuilder();
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CommaSeparatedStringBuilder t = new CommaSeparatedStringBuilder();
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CommaSeparatedStringBuilder sh = new CommaSeparatedStringBuilder();
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for (Variable v : list)
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if (v.mode == VariableMode.INPUT)
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switch(v.mode) {
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case INPUT:
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s.append(v.summary());
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else
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break;
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case OUTPUT:
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t.append(v.summary());
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return "source variables ["+s.toString()+"], target variables ["+t.toString()+"]";
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break;
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case SHARED:
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sh.append(v.summary());
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break;
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}
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return "source variables ["+s.toString()+"], target variables ["+t.toString()+"], shared variables ["+sh.toString()+"]";
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}
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}
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public class TransformContext {
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@ -1379,7 +1390,7 @@ public class StructureMapUtilities {
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if (source != null) {
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for (Variables v : source) {
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for (StructureMapGroupRuleTargetComponent t : rule.getTarget()) {
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processTarget(rule.getName(), context, v, map, group, t, rule.getSource().size() == 1 ? rule.getSourceFirstRep().getVariable() : null, atRoot);
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processTarget(rule.getName(), context, v, map, group, t, rule.getSource().size() == 1 ? rule.getSourceFirstRep().getVariable() : null, atRoot, vars);
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}
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if (rule.hasRule()) {
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for (StructureMapGroupRuleComponent childrule : rule.getRule()) {
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@ -1781,7 +1792,7 @@ public class StructureMapUtilities {
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return false;
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}
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private void processTarget(String ruleId, TransformContext context, Variables vars, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, String srcVar, boolean atRoot) throws FHIRException {
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private void processTarget(String ruleId, TransformContext context, Variables vars, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, String srcVar, boolean atRoot, Variables sharedVars) throws FHIRException {
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Base dest = null;
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if (tgt.hasContext()) {
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dest = vars.get(VariableMode.OUTPUT, tgt.getContext());
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@ -1795,8 +1806,17 @@ public class StructureMapUtilities {
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v = runTransform(ruleId, context, map, group, tgt, vars, dest, tgt.getElement(), srcVar, atRoot);
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if (v != null && dest != null)
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v = dest.setProperty(tgt.getElement().hashCode(), tgt.getElement(), v); // reset v because some implementations may have to rewrite v when setting the value
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} else if (dest != null)
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} else if (dest != null) {
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if (tgt.hasListMode(StructureMapTargetListMode.SHARE)) {
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v = sharedVars.get(VariableMode.SHARED, tgt.getListRuleId());
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if (v == null) {
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v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
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sharedVars.add(VariableMode.SHARED, tgt.getListRuleId(), v);
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}
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} else {
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v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
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}
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}
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if (tgt.hasVariable() && v != null)
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vars.add(VariableMode.OUTPUT, tgt.getVariable(), v);
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}
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@ -0,0 +1 @@
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*.out
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@ -0,0 +1,6 @@
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<fml-tests>
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<test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patassignment" source="qr.json" map="qr2pat-assignment.map" output="qr2pat-assignment-res.json" />
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<test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patgender" source="qr.json" map="qr2pat-gender.map" output="qr2pat-gender-res.json" />
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<test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannametwice" source="qr.json" map="qr2pat-humannametwice.map" output="qr2pat-humannametwice-res.json" />
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<test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannameshared" source="qr.json" map="qr2pat-humannameshared.map" output="qr2pat-humannameshared-res.json" />
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</fml-tests>
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@ -0,0 +1,39 @@
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{
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"resourceType": "QuestionnaireResponse",
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"status": "in-progress",
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"item": [
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{
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"linkId": "patient",
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"text": "Patient",
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"item": [
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{
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"linkId": "patient.lastname",
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"text": "Name",
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"answer": [
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{
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"valueString": "Brönnimann-Bertholet"
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}
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]
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},
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{
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"linkId": "patient.firstname",
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"text": "Vorname",
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"answer": [
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{
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"valueString": "Elisabeth"
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}
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]
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},
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{
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"linkId": "patient.sex",
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"text": "Geschlecht",
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"answer": [
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{
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"valueString": "female"
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}
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]
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}
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]
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}
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]
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}
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@ -0,0 +1,4 @@
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{
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"resourceType" : "Patient",
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"gender" : "female"
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}
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@ -0,0 +1,8 @@
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map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patassignment" = "qr2patassignment"
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uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
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uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
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group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
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src -> tgt.gender = 'female' "Simple Assignment";
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}
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@ -0,0 +1,4 @@
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{
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"resourceType" : "Patient",
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"gender" : "female"
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}
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@ -0,0 +1,12 @@
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map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patgender" = "qr2patgender"
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uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
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uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
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group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
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src.item as item -> tgt as patient then item(item, patient);
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}
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group item(source src, target tgt: Patient) {
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src.item as item where linkId.value in ('patient.sex') -> tgt.gender = (item.answer.valueString);
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}
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@ -0,0 +1,8 @@
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{
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"resourceType" : "Patient",
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"name" : [{
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"family" : "Brönnimann-Bertholet",
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"given" : ["Elisabeth"]
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}],
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"gender" : "female"
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}
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@ -0,0 +1,26 @@
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map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannameshared" = "qr2pathumannametwice"
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uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
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uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
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group entry(source src : QuestionnaireResponse, target tgt : Patient) {
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src.item as item then item(item, tgt);
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}
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group item(source src, target tgt) {
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src.item as item then item(item, tgt);
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src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name share patientName then humanNameFamily(item, name);
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src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name share patientName then humanNameGiven(item, name);
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src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
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}
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group humanNameFamily(source src, target tgt: HumanName) {
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src.answer as answer -> tgt.family = (answer.valueString);
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}
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group humanNameGiven(source src, target tgt: HumanName) {
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src.answer as answer -> tgt.given = (answer.valueString);
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}
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group administrativeGender(source src, target tgt: code) {
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src.answer as answer -> tgt = (answer.valueString);
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}
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@ -0,0 +1,10 @@
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{
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"resourceType" : "Patient",
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"name" : [{
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"family" : "Brönnimann-Bertholet"
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},
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{
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"given" : ["Elisabeth"]
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}],
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"gender" : "female"
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}
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@ -0,0 +1,26 @@
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map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannametwice" = "qr2pathumannametwice"
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uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
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uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
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group entry(source src : QuestionnaireResponse, target tgt : Patient) {
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src.item as item then item(item, tgt);
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}
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group item(source src, target tgt) {
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src.item as item then item(item, tgt);
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src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name then humanNameFamily(item, name);
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src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name then humanNameGiven(item, name);
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src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
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}
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group humanNameFamily(source src, target tgt: HumanName) {
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src.answer as answer -> tgt.family = (answer.valueString);
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}
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group humanNameGiven(source src, target tgt: HumanName) {
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src.answer as answer -> tgt.given = (answer.valueString);
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}
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group administrativeGender(source src, target tgt: code) {
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src.answer as answer -> tgt = (answer.valueString);
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}
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@ -0,0 +1,167 @@
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package org.hl7.fhir.r5.test;
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import static org.junit.Assert.assertTrue;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import javax.xml.parsers.ParserConfigurationException;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r5.context.SimpleWorkerContext;
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import org.hl7.fhir.r5.elementmodel.Manager;
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import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
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import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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import org.hl7.fhir.r5.formats.JsonParser;
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import org.hl7.fhir.r5.model.Base;
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import org.hl7.fhir.r5.model.Coding;
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import org.hl7.fhir.r5.model.Resource;
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import org.hl7.fhir.r5.model.ResourceFactory;
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import org.hl7.fhir.r5.model.StructureDefinition;
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import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
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import org.hl7.fhir.r5.model.StructureMap;
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import org.hl7.fhir.r5.terminologies.ConceptMapEngine;
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import org.hl7.fhir.r5.test.utils.TestingUtilities;
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import org.hl7.fhir.r5.utils.StructureMapUtilities;
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import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.cache.PackageCacheManager;
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import org.hl7.fhir.utilities.cache.ToolsVersion;
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import org.hl7.fhir.utilities.xml.XMLUtil;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import org.junit.runners.Parameterized;
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import org.junit.runners.Parameterized.Parameters;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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import org.xml.sax.SAXException;
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@RunWith(Parameterized.class)
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public class FHIRMappingLanguageTests implements ITransformerServices {
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private List<Resource> outputs = new ArrayList<Resource>();
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static private SimpleWorkerContext context;
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static private JsonParser jsonParser;
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@Parameters(name = "{index}: {0}")
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public static Iterable<Object[]> data()
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throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
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Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("fml", "manifest.xml"));
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Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
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List<Object[]> objects = new ArrayList<Object[]>();
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while (test != null && test.getNodeName().equals("test")) {
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objects.add(new Object[] { test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
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test.getAttribute("output") });
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test = XMLUtil.getNextSibling(test);
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}
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return objects;
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}
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private final String name;
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private String source;
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private String output;
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private String map;
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public FHIRMappingLanguageTests(String name, String source, String map, String output) {
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this.name = name;
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this.source = source;
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this.output = output;
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this.map = map;
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}
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@BeforeClass
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static public void setUp() throws Exception {
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if (context == null) {
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PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
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context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
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jsonParser = new JsonParser();
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jsonParser.setOutputStyle(OutputStyle.PRETTY);
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}
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}
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@Test
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public void test() throws Exception {
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String fileSource = TestingUtilities.resourceNameToFile("fml", source);
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String fileMap = TestingUtilities.resourceNameToFile("fml", map);
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String fileOutput = TestingUtilities.resourceNameToFile("fml", output);
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String fileOutputRes = TestingUtilities.resourceNameToFile("fml", output)+".out";
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outputs.clear();
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boolean ok = false;
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String msg = null;
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Resource resource = null;
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try {
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StructureMapUtilities scu = new StructureMapUtilities(context, this);
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org.hl7.fhir.r5.elementmodel.Element src = Manager.parse(context,
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new ByteArrayInputStream(TextFile.fileToBytes(fileSource)), FhirFormat.JSON);
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StructureMap structureMap = scu.parse(TextFile.fileToString(fileMap), name);
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String typeName = scu.getTargetType(structureMap).getType();
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resource = ResourceFactory.createResource(typeName);
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scu.transform(null, src, structureMap, resource);
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ok = true;
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} catch (Exception e) {
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ok = false;
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msg = e.getMessage();
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}
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if (ok) {
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ByteArrayOutputStream boas = new ByteArrayOutputStream();
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jsonParser.compose(boas, resource);
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log(boas.toString());
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TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
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msg = TestingUtilities.checkJsonIsSame(fileOutputRes,fileOutput);
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assertTrue(msg, Utilities.noString(msg));
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} else
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assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
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}
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@Override
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public void log(String message) {
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System.out.println(message);
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}
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@Override
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public Base createType(Object appInfo, String name) throws FHIRException {
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StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
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if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
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return Manager.build(context, sd);
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} else {
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if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
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name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
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return ResourceFactory.createResourceOrType(name);
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}
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}
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@Override
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public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
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if (atRootofTransform)
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outputs.add((Resource) res);
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return res;
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}
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@Override
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public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
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ConceptMapEngine cme = new ConceptMapEngine(context);
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return cme.translate(source, conceptMapUrl);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Base resolveReference(Object appContext, String url) throws FHIRException {
|
||||
throw new FHIRException("resolveReference is not supported yet");
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<Base> performSearch(Object appContext, String url) throws FHIRException {
|
||||
throw new FHIRException("performSearch is not supported yet");
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue