fix issues with R3R4MapTester
This commit is contained in:
Grahame Grieve
parent
27598a382d
commit
413cbb115a
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@ -115,6 +115,7 @@ public class StructureMapUtilities {
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private ValidationOptions terminologyServiceOptions = new ValidationOptions();
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private final ProfileUtilities profileUtilities;
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private boolean exceptionsForChecks = true;
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private boolean debug;
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public StructureMapUtilities(IWorkerContext worker, ITransformerServices services, ProfileKnowledgeProvider pkp) {
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super();
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@ -1217,10 +1218,12 @@ public class StructureMapUtilities {
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}
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private void log(String cnt) {
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if (getServices() != null)
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getServices().log(cnt);
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else
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System.out.println(cnt);
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if (debug) {
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if (getServices() != null)
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getServices().log(cnt);
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else
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System.out.println(cnt);
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}
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}
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/**
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@ -1308,7 +1311,7 @@ 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, vars);
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processTarget(map.getName()+"|"+group.getName()+"|"+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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@ -1320,7 +1323,9 @@ public class StructureMapUtilities {
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}
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} else if (rule.getSource().size() == 1 && rule.getSourceFirstRep().hasVariable() && rule.getTarget().size() == 1 && rule.getTargetFirstRep().hasVariable() && rule.getTargetFirstRep().getTransform() == StructureMapTransform.CREATE && !rule.getTargetFirstRep().hasParameter()) {
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// simple inferred, map by type
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System.out.println(v.summary());
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if (debug) {
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log(v.summary());
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}
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Base src = v.get(VariableMode.INPUT, rule.getSourceFirstRep().getVariable());
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Base tgt = v.get(VariableMode.OUTPUT, rule.getTargetFirstRep().getVariable());
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String srcType = src.fhirType();
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@ -1702,18 +1707,18 @@ public class StructureMapUtilities {
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return type.equals(item.fhirType());
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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, Variables sharedVars) throws FHIRException {
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private void processTarget(String rulePath, 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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if (dest == null)
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throw new FHIRException("Rule \"" + ruleId + "\": target context not known: " + tgt.getContext());
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throw new FHIRException("Rule \"" + rulePath + "\": target context not known: " + tgt.getContext());
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if (!tgt.hasElement())
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throw new FHIRException("Rule \"" + ruleId + "\": Not supported yet");
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throw new FHIRException("Rule \"" + rulePath + "\": Not supported yet");
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}
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Base v = null;
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if (tgt.hasTransform()) {
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v = runTransform(ruleId, context, map, group, tgt, vars, dest, tgt.getElement(), srcVar, atRoot);
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v = runTransform(rulePath, 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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@ -1731,7 +1736,7 @@ public class StructureMapUtilities {
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vars.add(VariableMode.OUTPUT, tgt.getVariable(), v);
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}
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private Base runTransform(String ruleId, TransformContext context, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, Variables vars, Base dest, String element, String srcVar, boolean root) throws FHIRException {
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private Base runTransform(String rulePath, TransformContext context, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, Variables vars, Base dest, String element, String srcVar, boolean root) throws FHIRException {
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try {
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switch (tgt.getTransform()) {
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case CREATE:
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@ -1755,7 +1760,7 @@ public class StructureMapUtilities {
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}
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}
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}
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Base res = services != null ? services.createType(context.getAppInfo(), tn) : ResourceFactory.createResourceOrType(tn);
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Base res = services != null ? services.createType(context.getAppInfo(), tn) : typeFactory(tn);
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if (res.isResource() && !res.fhirType().equals("Parameters")) {
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// res.setIdBase(tgt.getParameter().size() > 1 ? getParamString(vars, tgt.getParameter().get(0)) : UUID.randomUUID().toString().toLowerCase());
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if (services != null)
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@ -1776,7 +1781,7 @@ public class StructureMapUtilities {
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if (v.size() == 0)
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return null;
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else if (v.size() != 1)
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throw new FHIRException("Rule \"" + ruleId + "\": Evaluation of " + expr.toString() + " returned " + v.size() + " objects");
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throw new FHIRException("Rule \"" + rulePath+ "\": Evaluation of " + expr.toString() + " returned " + v.size() + " objects");
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else
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return v.get(0);
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@ -1790,7 +1795,7 @@ public class StructureMapUtilities {
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}
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return new StringType(src);
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case ESCAPE:
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throw new Error("Rule \"" + ruleId + "\": Transform " + tgt.getTransform().toCode() + " not supported yet");
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throw new Error("Rule \"" + rulePath + "\": Transform " + tgt.getTransform().toCode() + " not supported yet");
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case CAST:
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src = getParamString(vars, tgt.getParameter().get(0));
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if (tgt.getParameter().size() == 1)
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@ -1849,9 +1854,9 @@ public class StructureMapUtilities {
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case REFERENCE:
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Base b = getParam(vars, tgt.getParameter().get(0));
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if (b == null)
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throw new FHIRException("Rule \"" + ruleId + "\": Unable to find parameter " + ((IdType) tgt.getParameter().get(0).getValue()).asStringValue());
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throw new FHIRException("Rule \"" + rulePath + "\": Unable to find parameter " + ((IdType) tgt.getParameter().get(0).getValue()).asStringValue());
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if (!b.isResource())
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throw new FHIRException("Rule \"" + ruleId + "\": Transform engine cannot point at an element of type " + b.fhirType());
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throw new FHIRException("Rule \"" + rulePath + "\": Transform engine cannot point at an element of type " + b.fhirType());
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else {
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String id = b.getIdBase();
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if (id == null) {
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@ -1861,7 +1866,7 @@ public class StructureMapUtilities {
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return new StringType(b.fhirType() + "/" + id);
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}
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case DATEOP:
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throw new Error("Rule \"" + ruleId + "\": Transform " + tgt.getTransform().toCode() + " not supported yet");
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throw new Error("Rule \"" + rulePath + "\": Transform " + tgt.getTransform().toCode() + " not supported yet");
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case UUID:
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return new IdType(UUID.randomUUID().toString());
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case POINTER:
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@ -1869,7 +1874,7 @@ public class StructureMapUtilities {
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if (b instanceof Resource)
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return new UriType("urn:uuid:" + ((Resource) b).getId());
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else
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throw new FHIRException("Rule \"" + ruleId + "\": Transform engine cannot point at an element of type " + b.fhirType());
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throw new FHIRException("Rule \"" + rulePath + "\": Transform engine cannot point at an element of type " + b.fhirType());
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case CC:
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CodeableConcept cc = new CodeableConcept();
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cc.addCoding(buildCoding(getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString()), getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString())));
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@ -1878,10 +1883,28 @@ public class StructureMapUtilities {
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Coding c = buildCoding(getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString()), getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString()));
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return c;
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default:
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throw new Error("Rule \"" + ruleId + "\": Transform Unknown: " + tgt.getTransform().toCode());
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throw new Error("Rule \"" + rulePath + "\": Transform Unknown: " + tgt.getTransform().toCode());
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}
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} catch (Exception e) {
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throw new FHIRException("Exception executing transform " + tgt.toString() + " on Rule \"" + ruleId + "\": " + e.getMessage(), e);
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throw new FHIRException("Exception executing transform " + tgt.toString() + " on Rule \"" + rulePath + "\": " + e.getMessage(), e);
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}
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}
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private Base typeFactory(String tn) {
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if (Utilities.isAbsoluteUrl(tn) && !tn.startsWith("http://hl7.org/fhir/StructureDefinition")) {
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StructureDefinition sd = worker.fetchTypeDefinition(tn);
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if (sd == null) {
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if (Utilities.existsInList(tn, "http://hl7.org/fhirpath/System.String")) {
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sd = worker.fetchTypeDefinition("string");
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}
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}
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if (sd == null) {
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throw new FHIRException("Unable to create type "+tn);
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} else {
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return Manager.build(worker, sd);
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}
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} else {
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return ResourceFactory.createResourceOrType(tn);
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}
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}
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@ -2787,4 +2810,12 @@ public class StructureMapUtilities {
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}
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}
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public boolean isDebug() {
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return debug;
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}
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public void setDebug(boolean debug) {
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this.debug = debug;
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}
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}
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@ -850,6 +850,7 @@ public class I18nConstants {
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public static final String CONCEPTMAP_GROUP_SOURCE_INCOMPLETE = "CONCEPTMAP_GROUP_SOURCE_INCOMPLETE";
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public static final String CONCEPTMAP_GROUP_TARGET_INCOMPLETE = "CONCEPTMAP_GROUP_TARGET_INCOMPLETE";
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public static final String UNABLE_TO_RESOLVE_SYSTEM_SYSTEM_IS_INDETERMINATE = "UNABLE_TO_RESOLVE_SYSTEM_SYSTEM_IS_INDETERMINATE";
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public static final String SD_NO_TYPE_CODE_ON_CODE = "SD_NO_TYPE_CODE_ON_CODE";
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}
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@ -837,4 +837,8 @@ public class ValidationMessage implements Comparator<ValidationMessage>, Compara
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}
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return this;
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}
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public boolean isError() {
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return level == IssueSeverity.ERROR || level == IssueSeverity.FATAL;
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}
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}
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@ -899,4 +899,7 @@ CONCEPTMAP_GROUP_TARGET_PROPERTY_CODE_INVALID = The code {0} is invalid in the s
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CONCEPTMAP_GROUP_TARGET_PROPERTY_TYPE_UNKNOWN_SYSTEM = The system {0} is unknown, so code values can''t be checked
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SM_DEPENDENT_PARAM_TYPE_MISMATCH_DUPLICATE = The group {0} has alr
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CONCEPTMAP_GROUP_SOURCE_INCOMPLETE = Source Code System {0} doesn''t have all content (content = {1}), so the source codes cannot be checked
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CONCEPTMAP_GROUP_TARGET_INCOMPLETE = Target Code System {0} doesn''t have all content (content = {1}), so the source codes cannot be checked
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CONCEPTMAP_GROUP_TARGET_INCOMPLETE = Target Code System {0} doesn''t have all content (content = {1}), so the source codes cannot be checked
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SD_NO_TYPE_CODE_ON_CODE = Snapshot for {1} element {0} has type.code without a value
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@ -1,12 +1,15 @@
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package org.hl7.fhir.validation;
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import java.io.File;
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import java.io.IOException;
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import java.net.Authenticator;
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import java.net.PasswordAuthentication;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Locale;
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import org.hl7.fhir.convertors.loaders.loaderR5.R4BToR5Loader;
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/*
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Copyright (c) 2011+, HL7, Inc.
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All rights reserved.
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@ -72,6 +75,7 @@ import org.hl7.fhir.utilities.FileFormat;
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import org.hl7.fhir.utilities.TimeTracker;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.VersionUtilities;
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import org.hl7.fhir.utilities.json.JsonException;
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import org.hl7.fhir.utilities.npm.CommonPackages;
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import org.hl7.fhir.validation.cli.model.CliContext;
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import org.hl7.fhir.validation.cli.services.ComparisonService;
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@ -79,6 +83,7 @@ import org.hl7.fhir.validation.cli.services.ValidationService;
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import org.hl7.fhir.validation.cli.utils.Display;
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import org.hl7.fhir.validation.cli.utils.EngineMode;
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import org.hl7.fhir.validation.cli.utils.Params;
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import org.hl7.fhir.validation.special.R4R5MapTester;
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import org.hl7.fhir.validation.testexecutor.TestExecutor;
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import org.hl7.fhir.validation.testexecutor.TestExecutorParams;
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@ -132,13 +137,28 @@ public class ValidatorCli {
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}
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} else if (Params.hasParam(args, Params.TEST)) {
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parseTestParamsAndExecute(args);
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}
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else {
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} else if (Params.hasParam(args, Params.SPECIAL)) {
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executeSpecial(args);
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} else {
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Display.printCliArgumentsAndInfo(args);
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doValidation(tt, tts, cliContext);
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}
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}
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private static void executeSpecial(String[] args) throws JsonException, IOException {
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String specialMode = Params.getParam(args, Params.SPECIAL);
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if ("r4r5tests".equals(specialMode)) {
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final String target = Params.getParam(args, Params.TARGET);
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final String source = Params.getParam(args, Params.SOURCE);
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final String filter = Params.getParam(args, Params.FILTER);
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if (new File(target).exists()) {
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new R4R5MapTester().testMaps(target, source, filter);
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}
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} else {
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System.out.println("Unknown SpecialMode "+specialMode);
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}
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}
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private static void setJavaSystemProxyParamsFromParams(String[] args) {
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setJavaSystemProxyHostFromParams(args, Params.PROXY, HTTP_PROXY_HOST, HTTP_PROXY_PORT);
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@ -83,6 +83,10 @@ public class Params {
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public static final String TEST_MODULES = "-test-modules";
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public static final String TEST_NAME_FILTER = "-test-classname-filter";
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public static final String SPECIAL = "-special";
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public static final String TARGET = "-target";
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public static final String SOURCE = "-source";
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public static final String FILTER = "-filter";
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/**
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* Checks the list of passed in params to see if it contains the passed in param.
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@ -169,7 +169,7 @@ public class StructureDefinitionValidator extends BaseValidator {
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}
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if (Utilities.noString(tc) && type.hasChild("code")) {
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if (VersionUtilities.isR4Plus(context.getVersion())) {
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throw new Error("Snapshot for " + sd.getId() +" element " + path + " has type.code without a value ");
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rule(errors, "2023-03-16", IssueType.INVALID, stack.getLiteralPath(), false, I18nConstants.SD_NO_TYPE_CODE_ON_CODE, path, sd.getId());
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}
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}
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if (!Utilities.noString(tc)) {
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@ -2,14 +2,24 @@ package org.hl7.fhir.validation.special;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.net.URISyntaxException;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Locale;
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import java.util.Set;
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import org.hl7.fhir.r5.model.CanonicalResource;
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import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
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import org.hl7.fhir.r5.model.Parameters;
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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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@ -18,17 +28,19 @@ import org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader;
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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.r4.formats.IParser.OutputStyle;
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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.test.utils.TestingUtilities;
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import org.hl7.fhir.r5.context.SimpleWorkerContext;
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import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
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import org.hl7.fhir.r5.context.SimpleWorkerContext.SimpleWorkerContextBuilder;
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import org.hl7.fhir.r5.elementmodel.Element;
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import org.hl7.fhir.r5.elementmodel.Manager;
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import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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import org.hl7.fhir.r5.utils.structuremap.ResolvedGroup;
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import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
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import org.hl7.fhir.r5.utils.structuremap.VariableMode;
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import org.hl7.fhir.r5.utils.validation.IResourceValidator;
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import org.hl7.fhir.r5.utils.validation.IValidatorResourceFetcher;
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import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
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import org.hl7.fhir.r5.utils.validation.constants.IdStatus;
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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.VersionUtilities;
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@ -39,11 +51,13 @@ import org.hl7.fhir.utilities.json.model.JsonProperty;
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import org.hl7.fhir.utilities.json.parser.JsonParser;
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import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.npm.NpmPackage;
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import org.hl7.fhir.utilities.validation.ValidationMessage;
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import org.hl7.fhir.validation.IgLoader;
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import org.hl7.fhir.validation.ValidatorUtils;
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import org.hl7.fhir.validation.instance.InstanceValidator;
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import org.hl7.fhir.validation.special.R4R5MapTester.Stats;
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public class R4R5MapTester {
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public class R4R5MapTester implements IValidatorResourceFetcher {
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public class Stats {
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@ -51,6 +65,9 @@ public class R4R5MapTester {
|
|||
private int total;
|
||||
private int parsed;
|
||||
private int forward;
|
||||
private int validated;
|
||||
private int error;
|
||||
private int back;
|
||||
|
||||
public void example() {
|
||||
total++;
|
||||
|
|
@ -76,6 +93,22 @@ public class R4R5MapTester {
|
|||
return parsed;
|
||||
}
|
||||
|
||||
public int forwardCount() {
|
||||
return forward;
|
||||
}
|
||||
|
||||
public int validatedCount() {
|
||||
return validated;
|
||||
}
|
||||
|
||||
public int errorCount() {
|
||||
return error;
|
||||
}
|
||||
|
||||
public int backCount() {
|
||||
return back;
|
||||
}
|
||||
|
||||
public String summary() {
|
||||
if (errors.size() == 0) {
|
||||
return "All OK";
|
||||
|
|
@ -87,22 +120,36 @@ public class R4R5MapTester {
|
|||
public boolean ok() {
|
||||
return errors.size() == 0;
|
||||
}
|
||||
|
||||
public void valid(boolean valid) {
|
||||
validated++;
|
||||
if (!valid) {
|
||||
error++;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public void back() {
|
||||
back++;
|
||||
}
|
||||
}
|
||||
|
||||
private boolean saveProcess = false;
|
||||
private boolean saveProcess = true;
|
||||
|
||||
private SimpleWorkerContext context;
|
||||
private FilesystemPackageCacheManager pcm;
|
||||
private StructureMapUtilities utils;
|
||||
private List<StructureMap> allMaps;
|
||||
|
||||
private InstanceValidator validator;
|
||||
|
||||
public static void main(String[] args) throws JsonException, IOException {
|
||||
|
||||
// arg[0] is the location of the fhir-extensions repo
|
||||
new R4R5MapTester().testMaps(args[0]);
|
||||
new R4R5MapTester().testMaps(args[0], args[1], args[2]);
|
||||
}
|
||||
|
||||
public void testMaps(String src) throws JsonException, IOException {
|
||||
public void testMaps(String src, String maps, String filter) throws JsonException, IOException {
|
||||
log("Load Test Outcomes");
|
||||
JsonObject json = JsonParser.parseObjectFromFile(Utilities.path(src, "input", "_data", "conversions.json"));
|
||||
log("Load R5");
|
||||
|
|
@ -111,17 +158,37 @@ public class R4R5MapTester {
|
|||
log("Load Maps");
|
||||
// context.loadFromPackage(pcm.loadPackage(), null);
|
||||
|
||||
loadPackage("hl7.fhir.uv.extensions#dev");
|
||||
loadPackage("hl7.fhir.r4.core#4.0.1");
|
||||
loadPackage("hl7.fhir.r4b.core#4.3.0");
|
||||
loadPackage("hl7.terminology.r5#5.0.0", false);
|
||||
utils = new StructureMapUtilities(context);
|
||||
utils.setDebug(false);
|
||||
|
||||
loadPackage("hl7.fhir.uv.extensions#dev", maps == null);
|
||||
if (maps != null) {
|
||||
loadFromFolder(Utilities.path(maps, "r4-2-r5"));
|
||||
loadFromFolder(Utilities.path(maps, "r4b-2-r5"));
|
||||
loadFromFolder(Utilities.path(maps, "r5-2-r4"));
|
||||
loadFromFolder(Utilities.path(maps, "r5-2-r4b"));
|
||||
}
|
||||
loadPackage("hl7.fhir.r4.core#4.0.1", false);
|
||||
loadPackage("hl7.fhir.r4b.core#4.3.0", false);
|
||||
|
||||
validator = new InstanceValidator(context, null, null);
|
||||
validator.setSuppressLoincSnomedMessages(true);
|
||||
validator.setResourceIdRule(IdStatus.REQUIRED);
|
||||
validator.setBestPracticeWarningLevel(BestPracticeWarningLevel.Warning);
|
||||
validator.getExtensionDomains().add("http://hl7.org/fhir/us");
|
||||
validator.setFetcher(this);
|
||||
validator.setAllowExamples(true);
|
||||
validator.setDebug(false);
|
||||
validator.setForPublication(true);
|
||||
validator.setNoTerminologyChecks(true);
|
||||
context.setExpansionProfile(new Parameters());
|
||||
|
||||
log("Load R4 Examples");
|
||||
NpmPackage r4Examples = pcm.loadPackage("hl7.fhir.r4.examples");
|
||||
log("Load R4B Examples");
|
||||
NpmPackage r4bExamples = pcm.loadPackage("hl7.fhir.r4b.examples");
|
||||
|
||||
|
||||
utils = new StructureMapUtilities(context);
|
||||
allMaps = context.fetchResourcesByType(StructureMap.class);
|
||||
|
||||
log("Go. "+context.getResourceNames().size()+" types of resources");
|
||||
|
|
@ -129,17 +196,19 @@ public class R4R5MapTester {
|
|||
boolean changed = false;
|
||||
for (JsonProperty jp : json.getProperties()) {
|
||||
String rn = jp.getName();
|
||||
log(" "+rn);
|
||||
JsonObject o = json.getJsonObject(rn);
|
||||
StructureDefinition sd = context.fetchTypeDefinition(rn);
|
||||
List<StructureMap> mapSrc = utils.getMapsForUrl(allMaps, sd.getUrl(), StructureMapInputMode.SOURCE);
|
||||
List<StructureMap> mapTgt = utils.getMapsForUrl(allMaps, sd.getUrl(), StructureMapInputMode.TARGET);
|
||||
changed = checkMaps(sd, o.getJsonObject("r4"), "http://hl7.org/fhir/4.0", mapSrc, mapTgt, r4Examples) || changed;
|
||||
changed = checkMaps(sd, o.getJsonObject("r4b"), "http://hl7.org/fhir/4.3", mapSrc, mapTgt, r4bExamples) || changed;
|
||||
}
|
||||
if (changed) {
|
||||
JsonParser.compose(json, new FileOutputStream(Utilities.path(src, "input", "_data", "conversions.json")), true);
|
||||
if ("*".equals(filter) || rn.equals(filter)) {
|
||||
log(" "+rn);
|
||||
JsonObject o = json.getJsonObject(rn);
|
||||
StructureDefinition sd = context.fetchTypeDefinition(rn);
|
||||
List<StructureMap> mapSrc = utils.getMapsForUrl(allMaps, sd.getUrl(), StructureMapInputMode.SOURCE);
|
||||
List<StructureMap> mapTgt = utils.getMapsForUrl(allMaps, sd.getUrl(), StructureMapInputMode.TARGET);
|
||||
changed = checkMaps(sd, o.getJsonObject("r4"), "r4", "http://hl7.org/fhir/4.0", mapSrc, mapTgt, r4Examples) || changed;
|
||||
changed = checkMaps(sd, o.getJsonObject("r4b"), "r4b", "http://hl7.org/fhir/4.3", mapSrc, mapTgt, r4bExamples) || changed;
|
||||
JsonParser.compose(json, new FileOutputStream(Utilities.path(src, "input", "_data", "conversions.json")), true);
|
||||
System.out.println(" .. done");
|
||||
}
|
||||
}
|
||||
log("Done!");
|
||||
// load R4
|
||||
// load R4B
|
||||
// load the maps
|
||||
|
|
@ -157,15 +226,31 @@ public class R4R5MapTester {
|
|||
|
||||
}
|
||||
|
||||
private void loadPackage(String pid) throws FHIRException, IOException {
|
||||
private void loadFromFolder(String path) throws FHIRFormatError, FHIRException, FileNotFoundException, IOException {
|
||||
log("Load "+path);
|
||||
for (File f : new File(path).listFiles()) {
|
||||
if (f.getName().endsWith(".json")) {
|
||||
context.cacheResource(new org.hl7.fhir.r5.formats.JsonParser().parse(new FileInputStream(f)));
|
||||
}
|
||||
if (f.getName().endsWith(".fml")) {
|
||||
context.cacheResource(utils.parse(TextFile.fileToString(f), f.getName()));
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private void loadPackage(String pid, boolean loadMaps) throws FHIRException, IOException {
|
||||
log("Load "+pid);
|
||||
NpmPackage npm = pcm.loadPackage(pid);
|
||||
IContextResourceLoader loader = ValidatorUtils.loaderForVersion(npm.fhirVersion());
|
||||
if (!loadMaps && loader.getTypes().contains("StructureMap")) {
|
||||
loader.getTypes().remove("StructureMap");
|
||||
}
|
||||
loader.setPatchUrls(VersionUtilities.isCorePackage(npm.id()));
|
||||
int count = context.loadFromPackage(npm, loader);
|
||||
context.loadFromPackage(npm, loader);
|
||||
}
|
||||
|
||||
private boolean checkMaps(StructureDefinition sd, JsonObject json, String ns, List<StructureMap> mapSrc, List<StructureMap> mapTgt, NpmPackage examples) throws IOException {
|
||||
private boolean checkMaps(StructureDefinition sd, JsonObject json, String code, String ns, List<StructureMap> mapSrc, List<StructureMap> mapTgt, NpmPackage examples) throws IOException {
|
||||
List<StructureMap> src = utils.getMapsForUrlPrefix(mapSrc, ns, StructureMapInputMode.TARGET);
|
||||
List<StructureMap> tgt = utils.getMapsForUrlPrefix(mapTgt, ns, StructureMapInputMode.SOURCE);
|
||||
if (src.size() + tgt.size() == 0) {
|
||||
|
|
@ -199,7 +284,7 @@ public class R4R5MapTester {
|
|||
if (tsd == null) {
|
||||
json.set("testMessage", "Undefined type "+srcU);
|
||||
} else {
|
||||
testRoundTrips(sd, json, tgtG, srcG, tsd, examples);
|
||||
testRoundTrips(sd, json, tgtG, srcG, tsd, examples, code);
|
||||
}
|
||||
}
|
||||
} else {
|
||||
|
|
@ -213,41 +298,85 @@ public class R4R5MapTester {
|
|||
return true;
|
||||
}
|
||||
|
||||
private void testRoundTrips(StructureDefinition sd, JsonObject json, ResolvedGroup tgtG, ResolvedGroup srcG, StructureDefinition tsd, NpmPackage examples) throws IOException {
|
||||
|
||||
private void testRoundTrips(StructureDefinition sd, JsonObject json, ResolvedGroup tgtG, ResolvedGroup srcG, StructureDefinition tsd, NpmPackage examples, String code) throws IOException {
|
||||
Stats stats = new Stats();
|
||||
for (String s : examples.listResources(tsd.getType())) {
|
||||
log(" Test "+examples.id()+"::"+s);
|
||||
try {
|
||||
testRoundTrip(sd, tsd, tgtG, srcG, stats, examples.load("package", s));
|
||||
testRoundTrip(json, sd, tsd, tgtG, srcG, stats, examples.load("package", s), code);
|
||||
} catch (Exception e) {
|
||||
log("error: "+e.getMessage());
|
||||
stats.error("Error: "+e.getMessage());
|
||||
}
|
||||
}
|
||||
json.set("total", stats.totalCount());
|
||||
json.set("parsed", stats.parseCount());
|
||||
json.set("totalInstances", stats.totalCount());
|
||||
json.set("parsedOk", stats.parseCount());
|
||||
json.set("convertToR5OK", stats.forwardCount());
|
||||
json.set("testMessage", stats.summary());
|
||||
json.set("r5validated", stats.validatedCount());
|
||||
json.set("r5InError", stats.errorCount());
|
||||
json.remove("r5validatedOK");
|
||||
json.set("convertToR4OK", stats.backCount());
|
||||
if (stats.ok()) {
|
||||
json.set("testColor", "#d4ffdf");
|
||||
}
|
||||
}
|
||||
|
||||
private void testRoundTrip(StructureDefinition sd, StructureDefinition tsd, ResolvedGroup tgtG, ResolvedGroup srcG, Stats stats, InputStream stream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
|
||||
private void testRoundTrip(JsonObject json, StructureDefinition sd, StructureDefinition tsd, ResolvedGroup tgtG, ResolvedGroup srcG, Stats stats, InputStream stream, String code) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
|
||||
stats.example();
|
||||
Element r4 = new org.hl7.fhir.r5.elementmodel.JsonParser(context).setLogical(tsd).parseSingle(stream);
|
||||
stats.parsed();
|
||||
String id = r4.getIdBase();
|
||||
checkSave(id, "src.loaded", r4);
|
||||
json.remove(id);
|
||||
checkSave(id+"."+code, "loaded", r4);
|
||||
|
||||
Resource r5 = ResourceFactory.createResource(sd.getType());
|
||||
utils.transform(context, r4, tgtG.getTargetMap(), r4);
|
||||
stats.forward();
|
||||
Resource r5 = null;
|
||||
try {
|
||||
r5 = ResourceFactory.createResource(sd.getType());
|
||||
utils.transform(context, r4, tgtG.getTargetMap(), r5);
|
||||
stats.forward();
|
||||
checkSave(id+"."+code,"converted", r5);
|
||||
} catch (Exception e) {
|
||||
json.forceObject(id).set("conversion-error", e.getMessage());
|
||||
throw e;
|
||||
}
|
||||
|
||||
try {
|
||||
List<ValidationMessage> r5validationErrors = new ArrayList<ValidationMessage>();
|
||||
validator.validate(null, r5validationErrors, r5);
|
||||
boolean valid = true;
|
||||
for (ValidationMessage vm : r5validationErrors) {
|
||||
if (vm.isError()) {
|
||||
// json.forceObject(id).forceArray("r5-errors").add(vm.summary());
|
||||
valid = false;
|
||||
}
|
||||
}
|
||||
stats.valid(valid);
|
||||
} catch (Exception e) {
|
||||
json.forceObject(id).set("validation-error", e.getMessage());
|
||||
throw e;
|
||||
}
|
||||
|
||||
try {
|
||||
Element rt4 = Manager.build(context, tsd);
|
||||
utils.transform(context, r5, srcG.getTargetMap(), rt4);
|
||||
stats.back();
|
||||
checkSave(id+"."+code, "returned", r4);
|
||||
} catch (Exception e) {
|
||||
json.forceObject(id).set("return-error", e.getMessage());
|
||||
throw e;
|
||||
}
|
||||
}
|
||||
|
||||
private void checkSave(String id, String state, Element e) {
|
||||
private void checkSave(String id, String state, Element e) throws FHIRException, FileNotFoundException, IOException {
|
||||
if (saveProcess) {
|
||||
// new org.hl7.fhir.r4.elementmodel.JsonParser(context).compose(r3, bso, OutputStyle.PRETTY, null);
|
||||
new org.hl7.fhir.r5.elementmodel.JsonParser(context).compose(e, new FileOutputStream(Utilities.path("[tmp]", "r4r5", e.fhirType()+"-"+id+"-"+state+".json")), OutputStyle.PRETTY, id);
|
||||
}
|
||||
}
|
||||
|
||||
private void checkSave(String id, String state, Resource r) throws FHIRException, FileNotFoundException, IOException {
|
||||
if (saveProcess) {
|
||||
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "r4r5", r.fhirType()+"-"+id+"-"+state+".json")), r);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -255,4 +384,35 @@ public class R4R5MapTester {
|
|||
System.out.println(msg);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Element fetch(IResourceValidator validator, Object appContext, String url) throws FHIRException, IOException {
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean resolveURL(IResourceValidator validator, Object appContext, String path, String url, String type)
|
||||
throws IOException, FHIRException {
|
||||
return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
public byte[] fetchRaw(IResourceValidator validator, String url) throws IOException {
|
||||
throw new Error("Not done yet");
|
||||
}
|
||||
|
||||
@Override
|
||||
public IValidatorResourceFetcher setLocale(Locale locale) {
|
||||
throw new Error("Not done yet");
|
||||
}
|
||||
|
||||
@Override
|
||||
public CanonicalResource fetchCanonicalResource(IResourceValidator validator, String url) throws URISyntaxException {
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean fetchesCanonicalResource(IResourceValidator validator, String url) {
|
||||
return false;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue