Merge pull request #975 from hapifhir/gg-202211-fixes

Gg 202211 fixes

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java

@@ -1238,5 +1238,18 @@ public class Element extends Base {
     }
     return "e:"+e+",w:"+w+",h:"+h;
   }
+
+  public void populatePaths(String path) {
+    if (path == null) {
+      path = fhirType();
+    }
+    setPath(path);
+    if (children != null) {
+      for (Element n : children) {
+        n.populatePaths(path+"."+n.getName());
+      }
+    }
+    
+  }
   
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java

@@ -636,6 +636,10 @@ public class JsonParser extends ParserBase {
 
   @Override
   public void compose(Element e, OutputStream stream, OutputStyle style, String identity) throws FHIRException, IOException {
+    if (e.getPath() == null) {
+      e.populatePaths(null);
+    }
+    
     OutputStreamWriter osw = new OutputStreamWriter(stream, "UTF-8");
     if (style == OutputStyle.CANONICAL)
       json = new JsonCreatorCanonical(osw);
@@ -654,6 +658,10 @@ public class JsonParser extends ParserBase {
   }
 
   public void compose(Element e, JsonCreator json) throws Exception {
+    if (e.getPath() == null) {
+      e.populatePaths(null);
+    }
+    
     this.json = json;
     json.beginObject();
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/TurtleParser.java

@@ -315,6 +315,10 @@ public class TurtleParser extends ParserBase {
 
 
   public void compose(Element e, Turtle ttl, String base) throws FHIRException {
+    if (e.getPath() == null) {
+      e.populatePaths(null);
+    }
+    
     ttl.prefix("fhir", FHIR_URI_BASE);
     ttl.prefix("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
     ttl.prefix("owl", "http://www.w3.org/2002/07/owl#");

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java

@@ -602,6 +602,9 @@ public class XmlParser extends ParserBase {
     xml.setSortAttributes(false);
     xml.setPretty(style == OutputStyle.PRETTY);
     xml.start();
+    if (e.getPath() == null) {
+      e.populatePaths(null);
+    }
     String ns = e.getProperty().getXmlNamespace();
     if (ns!=null && !"noNamespace".equals(ns)) {
       xml.setDefaultNamespace(ns);
@@ -654,6 +657,9 @@ public class XmlParser extends ParserBase {
   }
   
   public void compose(Element e, IXMLWriter xml) throws Exception {
+    if (e.getPath() == null) {
+      e.populatePaths(null);
+    }
     xml.start();
     xml.setDefaultNamespace(e.getProperty().getXmlNamespace());
     if (schemaPath != null) {

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

@@ -15,6 +15,7 @@ import java.time.format.FormatStyle;
 import java.time.format.SignStyle;
 import java.util.Currency;
 import java.util.List;
+import java.util.Set;
 
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
@@ -97,6 +98,45 @@ public class DataRenderer extends Renderer {
 
   // -- 2. Markdown support -------------------------------------------------------
   
+  public static String processRelativeUrls(String markdown, String path) {
+    if (markdown == null) {
+      return "";
+    }
+    if (!Utilities.isAbsoluteUrl(path)) {
+      return markdown;
+    }
+    String basePath = path.contains("/") ? path.substring(0, path.lastIndexOf("/")+1) : path+"/";
+    StringBuilder b = new StringBuilder();
+    int i = 0;
+    while (i < markdown.length()) {
+      if (i < markdown.length()-3 && markdown.substring(i, i+2).equals("](")) {
+        int j = i + 2;
+        while (j < markdown.length() && markdown.charAt(j) != ')')
+          j++;
+        if (j < markdown.length()) {
+          String url = markdown.substring(i+2, j);
+          if (!Utilities.isAbsoluteUrl(url) && !url.startsWith("..")) {
+            // it's relative - so it's relative to the base URL
+              b.append("](");
+              b.append(basePath);
+          } else {
+            b.append("](");
+          }
+          i = i + 1;
+        } else 
+          b.append(markdown.charAt(i));
+      } else {
+        b.append(markdown.charAt(i));
+      }
+      i++;
+    }
+    return b.toString();
+  }
+
+  protected void addMarkdown(XhtmlNode x, String text, String path) throws FHIRFormatError, IOException, DefinitionException {
+    addMarkdown(x, processRelativeUrls(text, path));
+  }
+  
   protected void addMarkdown(XhtmlNode x, String text) throws FHIRFormatError, IOException, DefinitionException {
     if (text != null) {
       // 1. custom FHIR extensions

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

@@ -68,6 +68,7 @@ import org.hl7.fhir.r5.renderers.utils.DirectWrappers;
 import org.hl7.fhir.r5.renderers.utils.DirectWrappers.BaseWrapperDirect;
 import org.hl7.fhir.r5.renderers.utils.DirectWrappers.PropertyWrapperDirect;
 import org.hl7.fhir.r5.renderers.utils.DirectWrappers.ResourceWrapperDirect;
+import org.hl7.fhir.r5.renderers.utils.ElementWrappers;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext;
 import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
 import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceWithReference;
@@ -103,7 +104,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
     boolean idDone = false;
     XhtmlNode p = x.para();
     if (context.isAddGeneratedNarrativeHeader()) {
-      p.b().tx("Generated Narrative: "+r.fhirType());
+      p.b().tx("Generated Narrative: "+r.fhirType()+(context.isContained() ? " #"+r.getId() : ""));
       if (!Utilities.noString(r.getId())) {
         p.an(r.getId());
       }
@@ -756,35 +757,50 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
     if (children.isEmpty()) {
       renderLeaf(res, e, defn, x, x, false, showCodeDetails, readDisplayHints(defn), path, indent);
     } else {
-      for (PropertyWrapper p : splitExtensions(profile, e.children())) {
+      List<PropertyWrapper> pl = splitExtensions(profile, e.children());
-        if (p.hasValues()) {
+      for (PropertyWrapper p : pl) {
-          ElementDefinition child = getElementDefinition(children, path+"."+p.getName(), p);
+        generateForProperty(res, profile, allElements, children, x, path, showCodeDetails, indent, false, p);
-          if (child == null) {
+      }
-            child = p.getElementDefinition();
+      for (PropertyWrapper p : pl) {
-          }
+        generateForProperty(res, profile, allElements, children, x, path, showCodeDetails, indent, true, p);
-          if (child != null) {
+      }
-            if (!child.getBase().hasPath() || !child.getBase().getPath().startsWith("Resource.")) {
+    }
-              generateElementByProfile(res, profile, allElements, x, path, showCodeDetails, indent, p, child);
+  }
-            }
+
-          }
+  private void generateForProperty(ResourceWrapper res, StructureDefinition profile,
+      List<ElementDefinition> allElements, List<ElementDefinition> children, XhtmlNode x, String path,
+      boolean showCodeDetails, int indent, boolean round2, PropertyWrapper p)
+      throws UnsupportedEncodingException, IOException, EOperationOutcome {
+    if (p.hasValues()) {
+      ElementDefinition child = getElementDefinition(children, path+"."+p.getName(), p);
+      if (child == null) {
+        child = p.getElementDefinition();
+      }
+      if (child != null) {
+        if (!child.getBase().hasPath() || !child.getBase().getPath().startsWith("Resource.")) {
+          generateElementByProfile(res, profile, allElements, x, path, showCodeDetails, indent, p, child, round2);
         }
       }
     }
   }
 
   public void generateElementByProfile(ResourceWrapper res, StructureDefinition profile, List<ElementDefinition> allElements, XhtmlNode x, String path,
-      boolean showCodeDetails, int indent, PropertyWrapper p, ElementDefinition child) throws UnsupportedEncodingException, IOException, EOperationOutcome {
+      boolean showCodeDetails, int indent, PropertyWrapper p, ElementDefinition child, boolean round2) throws UnsupportedEncodingException, IOException, EOperationOutcome {
     Map<String, String> displayHints = readDisplayHints(child);
     if ("DomainResource.contained".equals(child.getBase().getPath())) {
-//      for (BaseWrapper v : p.getValues()) {
+      if (round2) {
-//        x.hr();
+        for (BaseWrapper v : p.getValues()) {
-//        RenderingContext ctxt = context.clone();
+          if (!RendererFactory.hasSpecificRenderer(v.fhirType())) {
-//        ctxt.setContained(true);
+            x.hr();
-//        ResourceRenderer rnd = RendererFactory.factory(v.fhirType(), ctxt);
+            RenderingContext ctxt = context.copy();
-//        ResourceWrapper rw = new ElementWrappers.ResourceWrapperMetaElement(ctxt, (org.hl7.fhir.r5.elementmodel.Element) v.getBase());
+            ctxt.setContained(true);
-//        rnd.render(x.blockquote(), rw);
+            ResourceRenderer rnd = RendererFactory.factory(v.fhirType(), ctxt);
-//      }
+            ResourceWrapper rw = new ElementWrappers.ResourceWrapperMetaElement(ctxt, (org.hl7.fhir.r5.elementmodel.Element) v.getBase());
-    } else if (!exemptFromRendering(child)) {
+            rnd.render(x.blockquote(), rw);
+          }
+        }
+      }
+    } else if (!round2 && !exemptFromRendering(child)) {
       if (isExtension(p)) {
         hasExtensions = true;
       }

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

@@ -769,7 +769,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
       td = tr.td();
       if (cs != null) {
         String defn = CodeSystemUtilities.getCodeDefinition(cs, c.getCode());
-        addMarkdown(td, defn);
+        addMarkdown(td, defn, cs.getUserString("path"));
       }
     }
     for (String n  : Utilities.sorted(properties.keySet())) {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/SimpleHTTPClient.java

@@ -139,7 +139,9 @@ public class SimpleHTTPClient {
       u = new URL(url);
       c = (HttpURLConnection) u.openConnection();
       c.setRequestMethod("GET");
-      c.setRequestProperty("Accept", accept);
+      if (accept != null) {
+        c.setRequestProperty("Accept", accept);
+      }
       setHeaders(c);
       c.setInstanceFollowRedirects(false); 
       if (trustAll && url.startsWith("https://")) {

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java

@@ -618,6 +618,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
     if (map == null) throw new Error("Unable to find map " + mapUri + " (Known Maps = " + context.listMapUrls() + ")");
     org.hl7.fhir.r5.elementmodel.Element resource = getTargetResourceFromStructureMap(map);
     scu.transform(null, src, map, resource);
+    resource.populatePaths(null);
     return resource;
   }
 

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java

@@ -385,6 +385,7 @@ public class ValidationService {
       for (String src : cliContext.getIgs()) {
         igLoader.loadIg(validator.getIgs(), validator.getBinaries(), src, cliContext.isRecursive());
       }
+      System.out.println("  Package Summary: "+validator.getContext().loadedPackageSummary());
       System.out.print("  Get set... ");
       validator.setQuestionnaireMode(cliContext.getQuestionnaireMode());
       validator.setLevel(cliContext.getLevel());

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java

@@ -2410,12 +2410,20 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         DecimalStatus ds = Utilities.checkDecimal(e.primitiveValue(), true, false);
         if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, ds == DecimalStatus.OK || ds == DecimalStatus.RANGE, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_DECIMAL_VALID, e.primitiveValue())) {
           warning(errors, IssueType.VALUE, e.line(), e.col(), path, ds != DecimalStatus.RANGE, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_DECIMAL_RANGE, e.primitiveValue());
-          try {
+          try {            
             Decimal v = new Decimal(e.getValue());
-            ok = rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxValueDecimalType() ||
+            if (context.hasMaxValueDecimalType() && context.getMaxValueDecimalType().hasValue()) {
-                !context.getMaxValueDecimalType().hasValue() || checkDecimalMaxValue(v, context.getMaxValueDecimalType().getValue()), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_DECIMAL_GT, (context.hasMaxValueDecimalType() ? context.getMaxValueDecimalType() : "")) && ok;
+              ok = rule(errors, IssueType.INVALID, e.line(), e.col(), path, checkDecimalMaxValue(v, context.getMaxValueDecimalType().getValue()), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_DECIMAL_GT, context.getMaxValueDecimalType()) && ok;
-            ok = rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMinValueIntegerType() || 
+            } else if (context.hasMaxValueIntegerType() && context.getMaxValueIntegerType().hasValue()) {
-                !context.getMinValueIntegerType().hasValue() || checkDecimalMinValue(v, context.getMaxValueDecimalType().getValue()), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_DECIMAL_LT, (context.hasMinValueIntegerType() ? context.getMinValueIntegerType() : "")) && ok;
+              // users can also provide a max integer type. It's not clear whether that's actually valid, but we'll check for it anyway
+              ok = rule(errors, IssueType.INVALID, e.line(), e.col(), path, checkDecimalMaxValue(v, new BigDecimal(context.getMaxValueIntegerType().getValue())), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_DECIMAL_GT, context.getMaxValueIntegerType()) && ok;
+            }
+            
+            if (context.hasMinValueDecimalType() && context.getMaxValueDecimalType().hasValue()) {
+              ok = rule(errors, IssueType.INVALID, e.line(), e.col(), path, checkDecimalMinValue(v, context.getMaxValueDecimalType().getValue()), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_DECIMAL_LT, context.getMaxValueDecimalType()) && ok;
+            } else if (context.hasMinValueIntegerType() && context.getMaxValueIntegerType().hasValue()) {
+              ok = rule(errors, IssueType.INVALID, e.line(), e.col(), path, checkDecimalMinValue(v, new BigDecimal(context.getMaxValueIntegerType().getValue())), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_DECIMAL_LT, context.getMaxValueIntegerType()) && ok;
+            }
           } catch (Exception ex) {
             // should never happen?
           }

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/snomed.cache

@@ -2067,3 +2067,14 @@ v: {
   "system" : "http://snomed.info/sct"
 }
 -------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://snomed.info/sct",
+  "code" : "324689003",
+  "display" : "Nystatin 100000 unit/mL oral suspension"
+}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
+v: {
+  "display" : "Product containing precisely nystatin 100000 unit/1 milliliter conventional release oral suspension (clinical drug)",
+  "code" : "324689003",
+  "system" : "http://snomed.info/sct"
+}
+-------------------------------------------------------------------------------------