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

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/CodeSystemComparer.java

@@ -226,7 +226,6 @@ public class CodeSystemComparer extends CanonicalResourceComparer {
     }
   }
 
-
   private boolean hasDesignation(ConceptDefinitionDesignationComponent td, List<ConceptDefinitionDesignationComponent> designation) {
     for (ConceptDefinitionDesignationComponent t : designation) {
       if (designationsMatch(td, t)) {
@@ -303,7 +302,6 @@ public class CodeSystemComparer extends CanonicalResourceComparer {
     return null;
   }
 
-
   public XhtmlNode renderConcepts(CodeSystemComparison comparison, String id, String prefix) throws FHIRException, IOException {
     // columns: code, display (left|right), properties (left|right)
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(Utilities.path("[tmp]", "compare"), false);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ComparisonRenderer.java

@@ -0,0 +1,166 @@
+package org.hl7.fhir.r5.comparison;
+
+import java.awt.image.renderable.RenderContext;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.PathEngineException;
+import org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison;
+import org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison;
+import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison;
+import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
+import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.model.Base;
+import org.hl7.fhir.r5.model.CodeSystem;
+import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
+import org.hl7.fhir.r5.model.StringType;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.TypeDetails;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
+import org.hl7.fhir.r5.utils.LiquidEngine;
+import org.hl7.fhir.r5.utils.LiquidEngine.LiquidDocument;
+import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
+
+public class ComparisonRenderer implements IEvaluationContext {
+
+  private IWorkerContext context;
+  private ComparisonSession session;
+  private Map<String, String> templates = new HashMap<>();
+  private String folder;
+
+  public ComparisonRenderer(IWorkerContext context, String folder) {
+    super();
+    this.context = context;       
+    this.folder = folder;
+  }
+
+  public Map<String, String> getTemplates() {
+    return templates;
+  }
+  
+  public void render() throws IOException {
+    for (String id : session.getCompares().keySet()) {
+      renderComparison(id, session.getCompares().get(id));      
+    }
+  }
+
+  private void renderComparison(String id, ResourceComparison comp) throws IOException {    
+    if (comp instanceof ProfileComparison) {
+      renderProfile(id, (ProfileComparison) comp);
+    } else if (comp instanceof ValueSetComparison) {
+      renderValueSet(id, (ValueSetComparison) comp);
+    } else if (comp instanceof CodeSystemComparison) {
+      renderCodeSystem(id, (CodeSystemComparison) comp);
+    }   
+  }
+
+  private void renderCodeSystem(String id, CodeSystemComparison comp) throws IOException {  
+    String template = templates.get("CodeSystem");
+    Map<String, Base> vars = new HashMap<>();
+    CodeSystemComparer cs = new CodeSystemComparer(session);
+    vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
+    vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
+    vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
+    String cnt = processTemplate(template, "CodeSystem", vars);
+    TextFile.stringToFile(cnt, file(id+".html"));
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-union.json")), comp.getUnion());
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-intersection.json")), comp.getIntersection());
+  }
+
+  private String file(String name) throws IOException {
+    return Utilities.path(folder, name);
+  }
+
+  private void renderValueSet(String id, ValueSetComparison comp) throws FHIRException, IOException {
+    String template = templates.get("ValueSet");
+    Map<String, Base> vars = new HashMap<>();
+    ValueSetComparer cs = new ValueSetComparer(session);
+    vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
+    vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
+    vars.put("compose", new StringType(new XhtmlComposer(true).compose(cs.renderCompose(comp, "", ""))));
+    vars.put("expnsion", new StringType(new XhtmlComposer(true).compose(cs.renderExpansion(comp, "", ""))));
+    String cnt = processTemplate(template, "ValueSet", vars);
+    TextFile.stringToFile(cnt, file(id+".html"));
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-union.json")), comp.getUnion());
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-intersection.json")), comp.getIntersection());
+  }
+
+  private void renderProfile(String id, ProfileComparison comp) throws IOException {
+    String template = templates.get("Profile");
+    Map<String, Base> vars = new HashMap<>();
+    ProfileComparer cs = new ProfileComparer(session);
+    vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
+    vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
+//    vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
+    String cnt = processTemplate(template, "CodeSystem", vars);
+    TextFile.stringToFile(cnt, file(id+".html"));
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-union.json")), comp.getUnion());
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", id + "-intersection.json")), comp.getIntersection());
+  }
+
+  private String processTemplate(String template, String name, Map<String, Base> vars) {
+    LiquidEngine engine = new LiquidEngine(context, this);
+    LiquidDocument doc = engine.parse(template, name+".template");
+    return engine.evaluate(doc, null, vars);
+  }
+
+  @Override
+  public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
+    @SuppressWarnings("unchecked")
+    Map<String, Base> vars = (Map<String, Base>) appContext;
+    return vars.get(name);
+  }
+
+  @Override
+  public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException {
+    @SuppressWarnings("unchecked")
+    Map<String, Base> vars = (Map<String, Base>) appContext;
+    Base b = vars.get(name);
+    return new TypeDetails(CollectionStatus.SINGLETON, b == null ? "Base" : b.fhirType());
+  }
+
+  @Override
+  public boolean log(String argument, List<Base> focus) {
+    return false;
+  }
+
+  @Override
+  public FunctionDetails resolveFunction(String functionName) {
+    return null;
+  }
+
+  @Override
+  public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
+    return null;
+  }
+
+  @Override
+  public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> parameters) {
+    return null;
+  }
+
+  @Override
+  public Base resolveReference(Object appContext, String url, Base refContext) throws FHIRException {
+    return null;
+  }
+
+  @Override
+  public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
+    return false;
+  }
+
+  @Override
+  public ValueSet resolveValueSet(Object appContext, String url) {
+    return null;
+  }
+
+}

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ComparisonSession.java

@@ -25,6 +25,7 @@ public class ComparisonSession {
   private IWorkerContext context;
   private String sessiondId;
   private int count;
+  private boolean debug;
   
   public ComparisonSession(IWorkerContext context) {
     super();
@@ -90,6 +91,22 @@ public class ComparisonSession {
   public void identify(ResourceComparison res) {
     count++;
     res.setId(sessiondId+"-"+count);
-    
   }
+
+  public boolean isDebug() {
+    return debug;
+  }
+
+  public void setDebug(boolean debug) {
+    this.debug = debug;
+  }
+
+  public Map<String, ResourceComparison> getCompares() {
+    return compares;
+  }
+  
+  
+  
+  
+  
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ProfileComparer.java

@@ -113,6 +113,10 @@ public class ProfileComparer extends CanonicalResourceComparer {
     assert(right != null);
     assert(left.path().equals(right.path()));
 
+    if (session.isDebug()) {
+      System.out.println("Compare elements at "+path);
+    }
+    
     // not allowed to be different:   
     ruleEqual(comp, res, left.current().getDefaultValue(), right.current().getDefaultValue(), "defaultValue", path);
     ruleEqual(comp, res, left.current().getMeaningWhenMissingElement(), right.current().getMeaningWhenMissingElement(), "meaningWhenMissing", path);
@@ -256,7 +260,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
         matchR.add(r);
         StructuralMatch<ElementDefinition> sm = new StructuralMatch<ElementDefinition>(l.current(), r.current());
         res.getChildren().add(sm);
-        compareElements(comp, sm, l.path(), null, left, right);
+        compareElements(comp, sm, l.path(), null, l, r);
       }
     }
     for (DefinitionNavigator r : rc) {
@@ -332,7 +336,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return "left: "+left+"; right: "+right;
   }
 
-
   private List<Coding> mergeCodings(List<Coding> left, List<Coding> right) {
     List<Coding> result = new ArrayList<Coding>();
     result.addAll(left);
@@ -347,7 +350,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return result;
   }
 
-
   private List<StringType> mergeStrings(List<StringType> left, List<StringType> right) {
     List<StringType> result = new ArrayList<StringType>();
     result.addAll(left);
@@ -434,7 +436,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return Integer.toString(defn.current().getMin())+".."+defn.current().getMax();
   }
 
-
   private Collection<? extends TypeRefComponent> unionTypes(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
     List<TypeRefComponent> result = new ArrayList<TypeRefComponent>();
     for (TypeRefComponent l : left) 
@@ -514,14 +515,12 @@ public class ProfileComparer extends CanonicalResourceComparer {
       results.add(nw);      
   }
 
-
   private boolean derivesFrom(StructureDefinition left, StructureDefinition right) {
     // left derives from right if it's base is the same as right
     // todo: recursive...
     return left.hasBaseDefinition() && left.getBaseDefinition().equals(right.getUrl());
   }
 
-
   private Collection<? extends TypeRefComponent> intersectTypes(ProfileComparison comp, StructuralMatch<ElementDefinition> res, ElementDefinition ed, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
     List<TypeRefComponent> result = new ArrayList<TypeRefComponent>();
     for (TypeRefComponent l : left) {
@@ -601,7 +600,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return b.toString();
   }
 
-
   private boolean compareBindings(ProfileComparison comp, StructuralMatch<ElementDefinition> res, ElementDefinition subset, ElementDefinition superset, String path, ElementDefinition lDef, ElementDefinition rDef) throws FHIRFormatError, DefinitionException, IOException {
     assert(lDef.hasBinding() || rDef.hasBinding());
     if (!lDef.hasBinding()) {
@@ -746,8 +744,6 @@ public class ProfileComparer extends CanonicalResourceComparer {
     return sd;
   }
 
-
-
   private boolean isPreferredOrExample(ElementDefinitionBindingComponent binding) {
     return binding.getStrength() == BindingStrength.EXAMPLE || binding.getStrength() == BindingStrength.PREFERRED;
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java

@@ -231,6 +231,9 @@ public class DataRenderer {
   }
   
   public String display(DataType type) {
+    if (type.isEmpty())
+      return "";
+    
     if (type instanceof Coding) {
       return displayCoding((Coding) type);
     } else if (type instanceof CodeableConcept) {
@@ -693,7 +696,7 @@ public class DataRenderer {
   }
 
   public static String displayPeriod(Period p) {
-    String s = !p.hasStart() ? "?ngen-5?" : p.getStartElement().toHumanDisplay();
+    String s = !p.hasStart() ? "(?)" : p.getStartElement().toHumanDisplay();
     s = s + " --> ";
     return s + (!p.hasEnd() ? "(ongoing)" : p.getEndElement().toHumanDisplay());
   }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/FilesystemPackageCacheManager.java

@@ -182,7 +182,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
     if (!CACHE_VERSION.equals(v)) {
       clearCache();
       ini.setStringProperty("cache", "version", CACHE_VERSION, null);
-      save = true;
+      ini.save();
     }
   }
 

org.hl7.fhir.utilities/src/main/resources/Messages.properties

@@ -99,7 +99,7 @@ Questionnaire_QR_Q_NotFound = The questionnaire "{0}" could not be resolved, so
 Questionnaire_Q_EnableWhen_After = The target of this enableWhen rule ({0}) comes after the question itself
 Questionnaire_Q_EnableWhen_IsInner = Questions with an enableWhen cannot refer to an inner question for it''s enableWhen condition
 Questionnaire_Q_EnableWhen_NoLink = Questions with an enableWhen must have a value for the question link
-Questionnaire_Q_EnableWhen_NoTarget = Unable to find target "{0}" for this question enableWhen
+Questionnaire_Q_EnableWhen_NoTarget = Unable to find an item with the linkId "{0}" which is referenced in the enableWhen for "{1}"
 Questionnaire_Q_EnableWhen_Self = Target for this question enableWhen can''t reference itself
 Reference_REF_Aggregation = Reference is {0} which isn''t supported by the specified aggregation mode(s) for the reference
 Reference_REF_BadTargetType = Invalid Resource target type. Found {0}, but expected one of ({1})

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/QuestionnaireValidator.java

@@ -95,7 +95,7 @@ public class QuestionnaireValidator extends BaseValidator {
           Element tgt = getQuestionById(item, ql);
           if (rule(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), tgt == null, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_ISINNER)) {
             tgt = getQuestionById(questionnaire, ql);
-            if (rule(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), tgt != null, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_NOTARGET, ql)) {
+            if (rule(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), tgt != null, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_NOTARGET, ql, item.getChildValue("linkId"))) {
               if (rule(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), tgt != item, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_SELF)) {
                 if (!isBefore(item, tgt, parents)) {
                   warning(errors, IssueType.BUSINESSRULE, ns.getLiteralPath(), false, I18nConstants.QUESTIONNAIRE_Q_ENABLEWHEN_AFTER, ql);