Fixing issues and preparing for release (#225)
* Issue #189 - improve Questionnaire error message * fix for issue #187 * more work on comparison * Fix for NamingSystem display
This commit is contained in:
Grahame Grieve
GitHub
parent
94cca87107
commit
4a4ca9a804
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@ -226,7 +226,6 @@ public class CodeSystemComparer extends CanonicalResourceComparer {
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}
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}
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private boolean hasDesignation(ConceptDefinitionDesignationComponent td, List<ConceptDefinitionDesignationComponent> designation) {
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for (ConceptDefinitionDesignationComponent t : designation) {
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if (designationsMatch(td, t)) {
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@ -303,7 +302,6 @@ public class CodeSystemComparer extends CanonicalResourceComparer {
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return null;
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}
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public XhtmlNode renderConcepts(CodeSystemComparison comparison, String id, String prefix) throws FHIRException, IOException {
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// columns: code, display (left|right), properties (left|right)
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HierarchicalTableGenerator gen = new HierarchicalTableGenerator(Utilities.path("[tmp]", "compare"), false);
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@ -0,0 +1,166 @@
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package org.hl7.fhir.r5.comparison;
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import java.awt.image.renderable.RenderContext;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.PathEngineException;
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import org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison;
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import org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison;
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import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison;
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import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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import org.hl7.fhir.r5.model.Base;
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import org.hl7.fhir.r5.model.CodeSystem;
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import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
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import org.hl7.fhir.r5.model.StringType;
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import org.hl7.fhir.r5.model.StructureDefinition;
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import org.hl7.fhir.r5.model.TypeDetails;
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import org.hl7.fhir.r5.model.ValueSet;
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import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
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import org.hl7.fhir.r5.utils.LiquidEngine;
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import org.hl7.fhir.r5.utils.LiquidEngine.LiquidDocument;
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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.xhtml.XhtmlComposer;
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public class ComparisonRenderer implements IEvaluationContext {
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private IWorkerContext context;
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private ComparisonSession session;
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private Map<String, String> templates = new HashMap<>();
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private String folder;
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public ComparisonRenderer(IWorkerContext context, String folder) {
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super();
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this.context = context;
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this.folder = folder;
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}
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public Map<String, String> getTemplates() {
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return templates;
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}
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public void render() throws IOException {
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for (String id : session.getCompares().keySet()) {
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renderComparison(id, session.getCompares().get(id));
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}
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}
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private void renderComparison(String id, ResourceComparison comp) throws IOException {
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if (comp instanceof ProfileComparison) {
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renderProfile(id, (ProfileComparison) comp);
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} else if (comp instanceof ValueSetComparison) {
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renderValueSet(id, (ValueSetComparison) comp);
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} else if (comp instanceof CodeSystemComparison) {
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renderCodeSystem(id, (CodeSystemComparison) comp);
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}
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}
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private void renderCodeSystem(String id, CodeSystemComparison comp) throws IOException {
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String template = templates.get("CodeSystem");
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Map<String, Base> vars = new HashMap<>();
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CodeSystemComparer cs = new CodeSystemComparer(session);
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vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
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vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
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vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
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String cnt = processTemplate(template, "CodeSystem", vars);
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TextFile.stringToFile(cnt, file(id+".html"));
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-union.json")), comp.getUnion());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-intersection.json")), comp.getIntersection());
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}
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private String file(String name) throws IOException {
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return Utilities.path(folder, name);
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}
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private void renderValueSet(String id, ValueSetComparison comp) throws FHIRException, IOException {
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String template = templates.get("ValueSet");
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Map<String, Base> vars = new HashMap<>();
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ValueSetComparer cs = new ValueSetComparer(session);
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vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
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vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
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vars.put("compose", new StringType(new XhtmlComposer(true).compose(cs.renderCompose(comp, "", ""))));
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vars.put("expnsion", new StringType(new XhtmlComposer(true).compose(cs.renderExpansion(comp, "", ""))));
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String cnt = processTemplate(template, "ValueSet", vars);
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TextFile.stringToFile(cnt, file(id+".html"));
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-union.json")), comp.getUnion());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-intersection.json")), comp.getIntersection());
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}
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private void renderProfile(String id, ProfileComparison comp) throws IOException {
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String template = templates.get("Profile");
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Map<String, Base> vars = new HashMap<>();
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ProfileComparer cs = new ProfileComparer(session);
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vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
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vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
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// vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
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String cnt = processTemplate(template, "CodeSystem", vars);
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TextFile.stringToFile(cnt, file(id+".html"));
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-union.json")), comp.getUnion());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-intersection.json")), comp.getIntersection());
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}
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private String processTemplate(String template, String name, Map<String, Base> vars) {
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LiquidEngine engine = new LiquidEngine(context, this);
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LiquidDocument doc = engine.parse(template, name+".template");
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return engine.evaluate(doc, null, vars);
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}
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@Override
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public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
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@SuppressWarnings("unchecked")
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Map<String, Base> vars = (Map<String, Base>) appContext;
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return vars.get(name);
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}
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@Override
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public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException {
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@SuppressWarnings("unchecked")
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Map<String, Base> vars = (Map<String, Base>) appContext;
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Base b = vars.get(name);
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return new TypeDetails(CollectionStatus.SINGLETON, b == null ? "Base" : b.fhirType());
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}
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@Override
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public boolean log(String argument, List<Base> focus) {
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return false;
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}
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@Override
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public FunctionDetails resolveFunction(String functionName) {
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return null;
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}
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@Override
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public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
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return null;
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}
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@Override
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public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> parameters) {
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return null;
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}
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@Override
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public Base resolveReference(Object appContext, String url, Base refContext) throws FHIRException {
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return null;
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}
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@Override
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public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
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return false;
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}
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@Override
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public ValueSet resolveValueSet(Object appContext, String url) {
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return null;
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}
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}
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@ -25,6 +25,7 @@ public class ComparisonSession {
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private IWorkerContext context;
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private String sessiondId;
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private int count;
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private boolean debug;
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public ComparisonSession(IWorkerContext context) {
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super();
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@ -90,6 +91,22 @@ public class ComparisonSession {
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public void identify(ResourceComparison res) {
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count++;
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res.setId(sessiondId+"-"+count);
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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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public Map<String, ResourceComparison> getCompares() {
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return compares;
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}
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}
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@ -113,6 +113,10 @@ public class ProfileComparer extends CanonicalResourceComparer {
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assert(right != null);
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assert(left.path().equals(right.path()));
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if (session.isDebug()) {
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System.out.println("Compare elements at "+path);
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}
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// not allowed to be different:
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ruleEqual(comp, res, left.current().getDefaultValue(), right.current().getDefaultValue(), "defaultValue", path);
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ruleEqual(comp, res, left.current().getMeaningWhenMissingElement(), right.current().getMeaningWhenMissingElement(), "meaningWhenMissing", path);
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@ -256,7 +260,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
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matchR.add(r);
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StructuralMatch<ElementDefinition> sm = new StructuralMatch<ElementDefinition>(l.current(), r.current());
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res.getChildren().add(sm);
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compareElements(comp, sm, l.path(), null, left, right);
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compareElements(comp, sm, l.path(), null, l, r);
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}
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}
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for (DefinitionNavigator r : rc) {
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@ -332,7 +336,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
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return "left: "+left+"; right: "+right;
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}
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private List<Coding> mergeCodings(List<Coding> left, List<Coding> right) {
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List<Coding> result = new ArrayList<Coding>();
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result.addAll(left);
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@ -347,7 +350,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
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return result;
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}
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private List<StringType> mergeStrings(List<StringType> left, List<StringType> right) {
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List<StringType> result = new ArrayList<StringType>();
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result.addAll(left);
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@ -434,7 +436,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
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return Integer.toString(defn.current().getMin())+".."+defn.current().getMax();
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}
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private Collection<? extends TypeRefComponent> unionTypes(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
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List<TypeRefComponent> result = new ArrayList<TypeRefComponent>();
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for (TypeRefComponent l : left)
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@ -514,14 +515,12 @@ public class ProfileComparer extends CanonicalResourceComparer {
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results.add(nw);
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}
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private boolean derivesFrom(StructureDefinition left, StructureDefinition right) {
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// left derives from right if it's base is the same as right
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// todo: recursive...
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return left.hasBaseDefinition() && left.getBaseDefinition().equals(right.getUrl());
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}
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private Collection<? extends TypeRefComponent> intersectTypes(ProfileComparison comp, StructuralMatch<ElementDefinition> res, ElementDefinition ed, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
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List<TypeRefComponent> result = new ArrayList<TypeRefComponent>();
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for (TypeRefComponent l : left) {
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@ -601,7 +600,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
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return b.toString();
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}
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private boolean compareBindings(ProfileComparison comp, StructuralMatch<ElementDefinition> res, ElementDefinition subset, ElementDefinition superset, String path, ElementDefinition lDef, ElementDefinition rDef) throws FHIRFormatError, DefinitionException, IOException {
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assert(lDef.hasBinding() || rDef.hasBinding());
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if (!lDef.hasBinding()) {
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@ -746,8 +744,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
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return sd;
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}
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private boolean isPreferredOrExample(ElementDefinitionBindingComponent binding) {
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return binding.getStrength() == BindingStrength.EXAMPLE || binding.getStrength() == BindingStrength.PREFERRED;
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}
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@ -231,6 +231,9 @@ public class DataRenderer {
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}
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public String display(DataType type) {
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if (type.isEmpty())
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return "";
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if (type instanceof Coding) {
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return displayCoding((Coding) type);
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} else if (type instanceof CodeableConcept) {
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@ -693,7 +696,7 @@ public class DataRenderer {
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}
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public static String displayPeriod(Period p) {
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String s = !p.hasStart() ? "?ngen-5?" : p.getStartElement().toHumanDisplay();
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String s = !p.hasStart() ? "(?)" : p.getStartElement().toHumanDisplay();
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s = s + " --> ";
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return s + (!p.hasEnd() ? "(ongoing)" : p.getEndElement().toHumanDisplay());
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}
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@ -182,7 +182,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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if (!CACHE_VERSION.equals(v)) {
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clearCache();
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ini.setStringProperty("cache", "version", CACHE_VERSION, null);
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save = true;
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ini.save();
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}
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}
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@ -99,7 +99,7 @@ Questionnaire_QR_Q_NotFound = The questionnaire "{0}" could not be resolved, so
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Questionnaire_Q_EnableWhen_After = The target of this enableWhen rule ({0}) comes after the question itself
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Questionnaire_Q_EnableWhen_IsInner = Questions with an enableWhen cannot refer to an inner question for it''s enableWhen condition
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Questionnaire_Q_EnableWhen_NoLink = Questions with an enableWhen must have a value for the question link
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Questionnaire_Q_EnableWhen_NoTarget = Unable to find target "{0}" for this question enableWhen
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Questionnaire_Q_EnableWhen_NoTarget = Unable to find an item with the linkId "{0}" which is referenced in the enableWhen for "{1}"
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Questionnaire_Q_EnableWhen_Self = Target for this question enableWhen can''t reference itself
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Reference_REF_Aggregation = Reference is {0} which isn''t supported by the specified aggregation mode(s) for the reference
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Reference_REF_BadTargetType = Invalid Resource target type. Found {0}, but expected one of ({1})
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@ -95,7 +95,7 @@ public class QuestionnaireValidator extends BaseValidator {
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Element tgt = getQuestionById(item, ql);
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if (rule(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), tgt == null, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_ISINNER)) {
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tgt = getQuestionById(questionnaire, ql);
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if (rule(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), tgt != null, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_NOTARGET, ql)) {
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if (rule(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), tgt != null, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_NOTARGET, ql, item.getChildValue("linkId"))) {
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if (rule(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), tgt != item, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_SELF)) {
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if (!isBefore(item, tgt, parents)) {
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warning(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), false, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_AFTER, ql);
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