Merge pull request #3 from ahdis/oliveregger-fml
[GF#20324] FML support for share in Target Transform
This commit is contained in:
Grahame Grieve
GitHub
commit
a9363a5923
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@ -34,11 +34,6 @@ import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang3.NotImplementedException;
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import org.hl7.fhir.exceptions.DefinitionException;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.FHIRFormatError;
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import org.hl7.fhir.exceptions.PathEngineException;
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import org.hl7.fhir.r4.conformance.ProfileUtilities;
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import org.hl7.fhir.r4.conformance.ProfileUtilities.ProfileKnowledgeProvider;
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import org.hl7.fhir.r4.context.IWorkerContext;
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@ -91,10 +86,10 @@ import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleTargetComponent;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleTargetParameterComponent;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupTypeMode;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapInputMode;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapModelMode;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapSourceListMode;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapStructureComponent;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapTargetListMode;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapModelMode;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapStructureComponent;
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import org.hl7.fhir.r4.model.StructureMap.StructureMapTransform;
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import org.hl7.fhir.r4.model.Type;
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import org.hl7.fhir.r4.model.TypeDetails;
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@ -105,6 +100,11 @@ import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
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import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
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import org.hl7.fhir.r4.utils.FHIRLexer.FHIRLexerException;
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import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
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import org.apache.commons.lang3.NotImplementedException;
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import org.hl7.fhir.exceptions.DefinitionException;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.FHIRFormatError;
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import org.hl7.fhir.exceptions.PathEngineException;
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import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.validation.ValidationMessage;
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@ -1170,11 +1170,13 @@ 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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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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} 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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@ -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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@ -1277,16 +1279,25 @@ public class StructureMapUtilities {
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return null;
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}
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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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for (Variable v : list)
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if (v.mode == VariableMode.INPUT)
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s.append(v.summary());
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else
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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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}
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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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switch(v.mode) {
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case INPUT:
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s.append(v.summary());
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break;
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case OUTPUT:
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t.append(v.summary());
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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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v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
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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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@ -18,7 +18,8 @@ import org.junit.runners.Suite.SuiteClasses;
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NarrativeGeneratorTests.class,
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ShexGeneratorTests.class,
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BaseDateTimeTypeTest.class,
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SnapShotGenerationTests.class})
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SnapShotGenerationTests.class,
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FHIRMappingLanguageTests.class})
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public class AllTests {
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}
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@ -0,0 +1,167 @@
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package org.hl7.fhir.r4.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.r4.context.SimpleWorkerContext;
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import org.hl7.fhir.r4.elementmodel.Manager;
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import org.hl7.fhir.r4.elementmodel.Manager.FhirFormat;
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import org.hl7.fhir.r4.formats.IParser.OutputStyle;
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import org.hl7.fhir.r4.formats.JsonParser;
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import org.hl7.fhir.r4.model.Base;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.Resource;
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import org.hl7.fhir.r4.model.ResourceFactory;
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import org.hl7.fhir.r4.model.StructureDefinition;
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import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
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import org.hl7.fhir.r4.model.StructureMap;
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import org.hl7.fhir.r4.terminologies.ConceptMapEngine;
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import org.hl7.fhir.r4.test.utils.TestingUtilities;
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import org.hl7.fhir.r4.utils.StructureMapUtilities;
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import org.hl7.fhir.r4.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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||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void test() throws Exception {
|
||||
|
||||
String fileSource = TestingUtilities.resourceNameToFile("fml", source);
|
||||
String fileMap = TestingUtilities.resourceNameToFile("fml", map);
|
||||
String fileOutput = TestingUtilities.resourceNameToFile("fml", output);
|
||||
String fileOutputRes = TestingUtilities.resourceNameToFile("fml", output)+".out";
|
||||
|
||||
outputs.clear();
|
||||
|
||||
boolean ok = false;
|
||||
String msg = null;
|
||||
Resource resource = null;
|
||||
try {
|
||||
StructureMapUtilities scu = new StructureMapUtilities(context, this);
|
||||
org.hl7.fhir.r4.elementmodel.Element src = Manager.parse(context,
|
||||
new ByteArrayInputStream(TextFile.fileToBytes(fileSource)), FhirFormat.JSON);
|
||||
StructureMap structureMap = scu.parse(TextFile.fileToString(fileMap), name);
|
||||
String typeName = scu.getTargetType(structureMap).getType();
|
||||
resource = ResourceFactory.createResource(typeName);
|
||||
scu.transform(null, src, structureMap, resource);
|
||||
ok = true;
|
||||
} catch (Exception e) {
|
||||
ok = false;
|
||||
msg = e.getMessage();
|
||||
}
|
||||
if (ok) {
|
||||
ByteArrayOutputStream boas = new ByteArrayOutputStream();
|
||||
jsonParser.compose(boas, resource);
|
||||
log(boas.toString());
|
||||
TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
|
||||
msg = TestingUtilities.checkJsonIsSame(fileOutputRes,fileOutput);
|
||||
assertTrue(msg, Utilities.noString(msg));
|
||||
} else
|
||||
assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
|
||||
}
|
||||
|
||||
@Override
|
||||
public void log(String message) {
|
||||
System.out.println(message);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Base createType(Object appInfo, String name) throws FHIRException {
|
||||
StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
|
||||
if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
|
||||
return Manager.build(context, sd);
|
||||
} else {
|
||||
if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
|
||||
name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
|
||||
return ResourceFactory.createResourceOrType(name);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
|
||||
if (atRootofTransform)
|
||||
outputs.add((Resource) res);
|
||||
return res;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
|
||||
ConceptMapEngine cme = new ConceptMapEngine(context);
|
||||
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");
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1170,11 +1170,13 @@ public class StructureMapUtilities {
|
|||
target.addListMode(StructureMapTargetListMode.SHARE);
|
||||
lexer.next();
|
||||
target.setListRuleId(lexer.take());
|
||||
} else if (lexer.getCurrent().equals("first"))
|
||||
target.addListMode(StructureMapTargetListMode.FIRST);
|
||||
else
|
||||
target.addListMode(StructureMapTargetListMode.LAST);
|
||||
lexer.next();
|
||||
} else {
|
||||
if (lexer.getCurrent().equals("first"))
|
||||
target.addListMode(StructureMapTargetListMode.FIRST);
|
||||
else
|
||||
target.addListMode(StructureMapTargetListMode.LAST);
|
||||
lexer.next();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -1219,7 +1221,7 @@ public class StructureMapUtilities {
|
|||
}
|
||||
|
||||
public enum VariableMode {
|
||||
INPUT, OUTPUT
|
||||
INPUT, OUTPUT, SHARED
|
||||
}
|
||||
|
||||
public class Variable {
|
||||
|
|
@ -1277,16 +1279,25 @@ public class StructureMapUtilities {
|
|||
return null;
|
||||
}
|
||||
|
||||
public String summary() {
|
||||
CommaSeparatedStringBuilder s = new CommaSeparatedStringBuilder();
|
||||
CommaSeparatedStringBuilder t = new CommaSeparatedStringBuilder();
|
||||
for (Variable v : list)
|
||||
if (v.mode == VariableMode.INPUT)
|
||||
s.append(v.summary());
|
||||
else
|
||||
t.append(v.summary());
|
||||
return "source variables ["+s.toString()+"], target variables ["+t.toString()+"]";
|
||||
}
|
||||
public String summary() {
|
||||
CommaSeparatedStringBuilder s = new CommaSeparatedStringBuilder();
|
||||
CommaSeparatedStringBuilder t = new CommaSeparatedStringBuilder();
|
||||
CommaSeparatedStringBuilder sh = new CommaSeparatedStringBuilder();
|
||||
for (Variable v : list)
|
||||
switch(v.mode) {
|
||||
case INPUT:
|
||||
s.append(v.summary());
|
||||
break;
|
||||
case OUTPUT:
|
||||
t.append(v.summary());
|
||||
break;
|
||||
case SHARED:
|
||||
sh.append(v.summary());
|
||||
break;
|
||||
}
|
||||
return "source variables ["+s.toString()+"], target variables ["+t.toString()+"], shared variables ["+sh.toString()+"]";
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class TransformContext {
|
||||
|
|
@ -1379,7 +1390,7 @@ public class StructureMapUtilities {
|
|||
if (source != null) {
|
||||
for (Variables v : source) {
|
||||
for (StructureMapGroupRuleTargetComponent t : rule.getTarget()) {
|
||||
processTarget(rule.getName(), context, v, map, group, t, rule.getSource().size() == 1 ? rule.getSourceFirstRep().getVariable() : null, atRoot);
|
||||
processTarget(rule.getName(), context, v, map, group, t, rule.getSource().size() == 1 ? rule.getSourceFirstRep().getVariable() : null, atRoot, vars);
|
||||
}
|
||||
if (rule.hasRule()) {
|
||||
for (StructureMapGroupRuleComponent childrule : rule.getRule()) {
|
||||
|
|
@ -1781,7 +1792,7 @@ public class StructureMapUtilities {
|
|||
return false;
|
||||
}
|
||||
|
||||
private void processTarget(String ruleId, TransformContext context, Variables vars, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, String srcVar, boolean atRoot) throws FHIRException {
|
||||
private void processTarget(String ruleId, TransformContext context, Variables vars, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, String srcVar, boolean atRoot, Variables sharedVars) throws FHIRException {
|
||||
Base dest = null;
|
||||
if (tgt.hasContext()) {
|
||||
dest = vars.get(VariableMode.OUTPUT, tgt.getContext());
|
||||
|
|
@ -1795,8 +1806,17 @@ public class StructureMapUtilities {
|
|||
v = runTransform(ruleId, context, map, group, tgt, vars, dest, tgt.getElement(), srcVar, atRoot);
|
||||
if (v != null && dest != null)
|
||||
v = dest.setProperty(tgt.getElement().hashCode(), tgt.getElement(), v); // reset v because some implementations may have to rewrite v when setting the value
|
||||
} else if (dest != null)
|
||||
v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
|
||||
} else if (dest != null) {
|
||||
if (tgt.hasListMode(StructureMapTargetListMode.SHARE)) {
|
||||
v = sharedVars.get(VariableMode.SHARED, tgt.getListRuleId());
|
||||
if (v == null) {
|
||||
v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
|
||||
sharedVars.add(VariableMode.SHARED, tgt.getListRuleId(), v);
|
||||
}
|
||||
} else {
|
||||
v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
|
||||
}
|
||||
}
|
||||
if (tgt.hasVariable() && v != null)
|
||||
vars.add(VariableMode.OUTPUT, tgt.getVariable(), v);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
*.out
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
<fml-tests>
|
||||
<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" />
|
||||
<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" />
|
||||
<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" />
|
||||
<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" />
|
||||
</fml-tests>
|
||||
|
|
@ -0,0 +1,39 @@
|
|||
{
|
||||
"resourceType": "QuestionnaireResponse",
|
||||
"status": "in-progress",
|
||||
"item": [
|
||||
{
|
||||
"linkId": "patient",
|
||||
"text": "Patient",
|
||||
"item": [
|
||||
{
|
||||
"linkId": "patient.lastname",
|
||||
"text": "Name",
|
||||
"answer": [
|
||||
{
|
||||
"valueString": "Brönnimann-Bertholet"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"linkId": "patient.firstname",
|
||||
"text": "Vorname",
|
||||
"answer": [
|
||||
{
|
||||
"valueString": "Elisabeth"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"linkId": "patient.sex",
|
||||
"text": "Geschlecht",
|
||||
"answer": [
|
||||
{
|
||||
"valueString": "female"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -0,0 +1,4 @@
|
|||
{
|
||||
"resourceType" : "Patient",
|
||||
"gender" : "female"
|
||||
}
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patassignment" = "qr2patassignment"
|
||||
|
||||
uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
|
||||
uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
|
||||
|
||||
group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
|
||||
src -> tgt.gender = 'female' "Simple Assignment";
|
||||
}
|
||||
|
|
@ -0,0 +1,4 @@
|
|||
{
|
||||
"resourceType" : "Patient",
|
||||
"gender" : "female"
|
||||
}
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patgender" = "qr2patgender"
|
||||
|
||||
uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
|
||||
uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
|
||||
|
||||
group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
|
||||
src.item as item -> tgt as patient then item(item, patient);
|
||||
}
|
||||
|
||||
group item(source src, target tgt: Patient) {
|
||||
src.item as item where linkId.value in ('patient.sex') -> tgt.gender = (item.answer.valueString);
|
||||
}
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
{
|
||||
"resourceType" : "Patient",
|
||||
"name" : [{
|
||||
"family" : "Brönnimann-Bertholet",
|
||||
"given" : ["Elisabeth"]
|
||||
}],
|
||||
"gender" : "female"
|
||||
}
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannameshared" = "qr2pathumannametwice"
|
||||
|
||||
uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
|
||||
uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
|
||||
|
||||
group entry(source src : QuestionnaireResponse, target tgt : Patient) {
|
||||
src.item as item then item(item, tgt);
|
||||
}
|
||||
|
||||
group item(source src, target tgt) {
|
||||
src.item as item then item(item, tgt);
|
||||
src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name share patientName then humanNameFamily(item, name);
|
||||
src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name share patientName then humanNameGiven(item, name);
|
||||
src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
|
||||
}
|
||||
|
||||
group humanNameFamily(source src, target tgt: HumanName) {
|
||||
src.answer as answer -> tgt.family = (answer.valueString);
|
||||
}
|
||||
group humanNameGiven(source src, target tgt: HumanName) {
|
||||
src.answer as answer -> tgt.given = (answer.valueString);
|
||||
}
|
||||
|
||||
group administrativeGender(source src, target tgt: code) {
|
||||
src.answer as answer -> tgt = (answer.valueString);
|
||||
}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
{
|
||||
"resourceType" : "Patient",
|
||||
"name" : [{
|
||||
"family" : "Brönnimann-Bertholet"
|
||||
},
|
||||
{
|
||||
"given" : ["Elisabeth"]
|
||||
}],
|
||||
"gender" : "female"
|
||||
}
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannametwice" = "qr2pathumannametwice"
|
||||
|
||||
uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
|
||||
uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
|
||||
|
||||
group entry(source src : QuestionnaireResponse, target tgt : Patient) {
|
||||
src.item as item then item(item, tgt);
|
||||
}
|
||||
|
||||
group item(source src, target tgt) {
|
||||
src.item as item then item(item, tgt);
|
||||
src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name then humanNameFamily(item, name);
|
||||
src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name then humanNameGiven(item, name);
|
||||
src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
|
||||
}
|
||||
|
||||
group humanNameFamily(source src, target tgt: HumanName) {
|
||||
src.answer as answer -> tgt.family = (answer.valueString);
|
||||
}
|
||||
group humanNameGiven(source src, target tgt: HumanName) {
|
||||
src.answer as answer -> tgt.given = (answer.valueString);
|
||||
}
|
||||
|
||||
group administrativeGender(source src, target tgt: code) {
|
||||
src.answer as answer -> tgt = (answer.valueString);
|
||||
}
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
package org.hl7.fhir.r5.test;
|
||||
|
||||
import static org.junit.Assert.assertTrue;
|
||||
|
||||
import java.io.ByteArrayInputStream;
|
||||
import java.io.ByteArrayOutputStream;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import javax.xml.parsers.ParserConfigurationException;
|
||||
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.elementmodel.Manager;
|
||||
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
|
||||
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
|
||||
import org.hl7.fhir.r5.formats.JsonParser;
|
||||
import org.hl7.fhir.r5.model.Base;
|
||||
import org.hl7.fhir.r5.model.Coding;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.model.ResourceFactory;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
|
||||
import org.hl7.fhir.r5.model.StructureMap;
|
||||
import org.hl7.fhir.r5.terminologies.ConceptMapEngine;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.StructureMapUtilities;
|
||||
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.cache.PackageCacheManager;
|
||||
import org.hl7.fhir.utilities.cache.ToolsVersion;
|
||||
import org.hl7.fhir.utilities.xml.XMLUtil;
|
||||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
import org.junit.runner.RunWith;
|
||||
import org.junit.runners.Parameterized;
|
||||
import org.junit.runners.Parameterized.Parameters;
|
||||
import org.w3c.dom.Document;
|
||||
import org.w3c.dom.Element;
|
||||
import org.xml.sax.SAXException;
|
||||
|
||||
@RunWith(Parameterized.class)
|
||||
|
||||
public class FHIRMappingLanguageTests implements ITransformerServices {
|
||||
|
||||
private List<Resource> outputs = new ArrayList<Resource>();
|
||||
|
||||
static private SimpleWorkerContext context;
|
||||
static private JsonParser jsonParser;
|
||||
|
||||
@Parameters(name = "{index}: {0}")
|
||||
public static Iterable<Object[]> data()
|
||||
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
|
||||
Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("fml", "manifest.xml"));
|
||||
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
|
||||
List<Object[]> objects = new ArrayList<Object[]>();
|
||||
while (test != null && test.getNodeName().equals("test")) {
|
||||
objects.add(new Object[] { test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
|
||||
test.getAttribute("output") });
|
||||
test = XMLUtil.getNextSibling(test);
|
||||
}
|
||||
return objects;
|
||||
}
|
||||
|
||||
private final String name;
|
||||
private String source;
|
||||
private String output;
|
||||
private String map;
|
||||
|
||||
public FHIRMappingLanguageTests(String name, String source, String map, String output) {
|
||||
this.name = name;
|
||||
this.source = source;
|
||||
this.output = output;
|
||||
this.map = map;
|
||||
}
|
||||
|
||||
@BeforeClass
|
||||
static public void setUp() throws Exception {
|
||||
if (context == null) {
|
||||
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
|
||||
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
|
||||
jsonParser = new JsonParser();
|
||||
jsonParser.setOutputStyle(OutputStyle.PRETTY);
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void test() throws Exception {
|
||||
|
||||
String fileSource = TestingUtilities.resourceNameToFile("fml", source);
|
||||
String fileMap = TestingUtilities.resourceNameToFile("fml", map);
|
||||
String fileOutput = TestingUtilities.resourceNameToFile("fml", output);
|
||||
String fileOutputRes = TestingUtilities.resourceNameToFile("fml", output)+".out";
|
||||
|
||||
outputs.clear();
|
||||
|
||||
boolean ok = false;
|
||||
String msg = null;
|
||||
Resource resource = null;
|
||||
try {
|
||||
StructureMapUtilities scu = new StructureMapUtilities(context, this);
|
||||
org.hl7.fhir.r5.elementmodel.Element src = Manager.parse(context,
|
||||
new ByteArrayInputStream(TextFile.fileToBytes(fileSource)), FhirFormat.JSON);
|
||||
StructureMap structureMap = scu.parse(TextFile.fileToString(fileMap), name);
|
||||
String typeName = scu.getTargetType(structureMap).getType();
|
||||
resource = ResourceFactory.createResource(typeName);
|
||||
scu.transform(null, src, structureMap, resource);
|
||||
ok = true;
|
||||
} catch (Exception e) {
|
||||
ok = false;
|
||||
msg = e.getMessage();
|
||||
}
|
||||
if (ok) {
|
||||
ByteArrayOutputStream boas = new ByteArrayOutputStream();
|
||||
jsonParser.compose(boas, resource);
|
||||
log(boas.toString());
|
||||
TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
|
||||
msg = TestingUtilities.checkJsonIsSame(fileOutputRes,fileOutput);
|
||||
assertTrue(msg, Utilities.noString(msg));
|
||||
} else
|
||||
assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
|
||||
}
|
||||
|
||||
@Override
|
||||
public void log(String message) {
|
||||
System.out.println(message);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Base createType(Object appInfo, String name) throws FHIRException {
|
||||
StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
|
||||
if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
|
||||
return Manager.build(context, sd);
|
||||
} else {
|
||||
if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
|
||||
name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
|
||||
return ResourceFactory.createResourceOrType(name);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
|
||||
if (atRootofTransform)
|
||||
outputs.add((Resource) res);
|
||||
return res;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
|
||||
ConceptMapEngine cme = new ConceptMapEngine(context);
|
||||
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