Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core

# Conflicts:
#	org.hl7.fhir.validation/src/test/resources/validation-examples/manifest.json

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Enumerations.java

@@ -10014,6 +10014,57 @@ The primary difference between a medication statement and a medication administr
           return _4_1_0;
         throw new FHIRException("Unknown FHIRVersion code '"+codeString+"'");
         }
+        
+        public static boolean isValidCode(String codeString) {
+          if (codeString == null || "".equals(codeString))
+              return false;
+      if ("0.01".equals(codeString))
+        return true;
+      if ("0.05".equals(codeString))
+        return true;
+      if ("0.06".equals(codeString))
+        return true;
+      if ("0.11".equals(codeString))
+        return true;
+      if ("0.0.80".equals(codeString))
+        return true;
+      if ("0.0.81".equals(codeString))
+        return true;
+      if ("0.0.82".equals(codeString))
+        return true;
+      if ("0.4.0".equals(codeString))
+        return true;
+      if ("0.5.0".equals(codeString))
+        return true;
+      if ("1.0.0".equals(codeString))
+        return true;
+      if ("1.0.1".equals(codeString))
+        return true;
+      if ("1.0.2".equals(codeString))
+        return true;
+      if ("1.1.0".equals(codeString))
+        return true;
+      if ("1.4.0".equals(codeString))
+        return true;
+      if ("1.6.0".equals(codeString))
+        return true;
+      if ("1.8.0".equals(codeString))
+        return true;
+      if ("3.0.0".equals(codeString))
+        return true;
+      if ("3.0.1".equals(codeString))
+        return true;
+      if ("3.3.0".equals(codeString))
+        return true;
+      if ("3.5.0".equals(codeString))
+        return true;
+      if ("4.0.0".equals(codeString))
+        return true;
+      if ("4.1.0".equals(codeString))
+        return true;
+      return false;
+      }
+
         @Override
         public String toString() {
           return toCode();

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java

@@ -4145,10 +4145,12 @@ public class FHIRPathEngine {
         List<ElementDefinition> childDefinitions = ProfileUtilities.getChildMap(sd, element);
         for (ElementDefinition t : childDefinitions) {
           if (t.getPath().endsWith(".extension") && t.hasSliceName()) {
-           sd = worker.fetchResource(StructureDefinition.class, t.getType().get(0).getProfile().get(0).getValue());
+           StructureDefinition exsd = worker.fetchResource(StructureDefinition.class, t.getType().get(0).getProfile().get(0).getValue());
-           while (sd!=null && !sd.getBaseDefinition().equals("http://hl7.org/fhir/StructureDefinition/Extension"))
+           while (exsd!=null && !exsd.getBaseDefinition().equals("http://hl7.org/fhir/StructureDefinition/Extension"))
-             sd = worker.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
+             exsd = worker.fetchResource(StructureDefinition.class, exsd.getBaseDefinition());
-           if (sd.getUrl().equals(targetUrl)) {
+           if (exsd.getUrl().equals(targetUrl)) {
+             if (ProfileUtilities.getChildMap(sd, t).isEmpty())
+               sd = exsd;
              focus = t;
              break;
            }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NPMPackageGenerator.java

@@ -25,6 +25,7 @@ import java.io.BufferedOutputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.GregorianCalendar;
 import java.util.HashSet;
@@ -85,7 +86,18 @@ public class NPMPackageGenerator {
     System.out.println("create package file at "+destFile);
     this.destFile = destFile;
     start();
-    buildPackageJson(canonical, kind, url, genDate, ig);
+    List<String> fhirVersion = new ArrayList<>();
+    for (Enumeration<FHIRVersion> v : ig.getFhirVersion())
+      fhirVersion.add(v.asStringValue());
+    buildPackageJson(canonical, kind, url, genDate, ig, fhirVersion);
+  }
+  
+  public NPMPackageGenerator(String destFile, String canonical, String url, PackageType kind, ImplementationGuide ig, String genDate, List<String> fhirVersion) throws FHIRException, IOException {
+    super();
+    System.out.println("create package file at "+destFile);
+    this.destFile = destFile;
+    start();
+    buildPackageJson(canonical, kind, url, genDate, ig, fhirVersion);
   }
   
   public NPMPackageGenerator(String destFile, JsonObject npm) throws FHIRException, IOException {
@@ -102,7 +114,7 @@ public class NPMPackageGenerator {
   }
   
   
-  private void buildPackageJson(String canonical, PackageType kind, String web, String genDate, ImplementationGuide ig) throws FHIRException, IOException {
+  private void buildPackageJson(String canonical, PackageType kind, String web, String genDate, ImplementationGuide ig, List<String> fhirVersion) throws FHIRException, IOException {
     CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
     if (!ig.hasPackageId())
       b.append("packageId");
@@ -134,8 +146,8 @@ public class NPMPackageGenerator {
     if (kind != PackageType.CORE) {
       JsonObject dep = new JsonObject();
       npm.add("dependencies", dep);
-      for (Enumeration<FHIRVersion> v : ig.getFhirVersion()) { // TODO: fix for multiple versions
+      for (String v : fhirVersion) { // TODO: fix for multiple versions
-        dep.addProperty("hl7.fhir.core", v.asStringValue());
+        dep.addProperty("hl7.fhir.core", v);
       }
       for (ImplementationGuideDependsOnComponent d : ig.getDependsOn()) {
         dep.addProperty(d.getPackageId(), d.getVersion());

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

@@ -343,5 +343,10 @@ import com.google.gson.JsonObject;
       }
     }
 
+    /** special case when playing around inside the package **/
+    public Map<String, byte[]> getContent() {
+      return content;
+    }
+
 
   }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/JSONUtil.java

@@ -1,5 +1,7 @@
 package org.hl7.fhir.utilities.json;
 
+import java.io.IOException;
+
 /*-
  * #%L
  * org.hl7.fhir.utilities
@@ -22,12 +24,13 @@ package org.hl7.fhir.utilities.json;
 
 
 import com.google.gson.JsonArray;
+import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
 
 public class JSONUtil {
 
-  public static JsonObject parse(String json) {
+  public static JsonObject parse(String json) throws IOException {
-    return (JsonObject) new com.google.gson.JsonParser().parse(json);    
+    return JsonTrackingParser.parseJson(json);    
     
   }
 
@@ -56,4 +59,13 @@ public class JSONUtil {
     return res;
   }
 
+  public static JsonObject findByStringProp(JsonArray arr, String prop, String value) {
+    for (JsonElement e : arr) {
+      JsonObject obj = (JsonObject) e;
+      if (obj.has(prop) && obj.get(prop).getAsString().equals(value)) 
+        return obj;
+    }
+    return null;
+  }
+
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java

@@ -817,8 +817,9 @@ public class ValidationEngine {
         if (refs.size() > 1)
           produceValidationSummary(outcome);
         results.addEntry().setResource(outcome);
-      } catch (Throwable e) {
+      } catch (Exception e) {
         System.out.println("Validation Infrastructure fail validating "+ref+": "+e.getMessage());
+        throw e;
       }
     }
     if (asBundle)

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java

@@ -107,7 +107,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
       
     if (ve == null || !v.equals(veVersion)) {
       if (v.equals("5.0"))
-        ve = new ValidationEngine("hl7.fhir.core#4.1.0", DEF_TX, null, FhirPublication.R5);
+        ve = new ValidationEngine("hl7.fhir.core#current", DEF_TX, null, FhirPublication.R5);
       else if (v.equals("3.0"))
         ve = new ValidationEngine("hl7.fhir.core#3.0.1", DEF_TX, null, FhirPublication.STU3);
       else if (v.equals("4.0"))

org.hl7.fhir.validation/src/test/resources/validation-examples/extension-slice-profile.xml

@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--<StructureDefinition xmlns="http://hl7.org/fhir" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hl7.org/fhir ../../../../../../FHIR/schema/fhir-single.xsd">-->
+<StructureDefinition xmlns="http://hl7.org/fhir">
+	<id value="extension-slice-profile"/>
+	<url value="http://hl7.org/fhir/StructureDefinition/extension-slice-profile"/>
+	<name value="ExtensionSliceProfile"/>
+	<status value="draft"/>
+	<description value="Test slicing by extension with fixed value"/>
+	<kind value="resource"/>
+	<abstract value="false"/>
+	<type value="Patient"/>
+	<baseDefinition value="http://hl7.org/fhir/StructureDefinition/Patient"/>
+	<derivation value="constraint"/>
+	<differential>
+		<element id="Patient">
+			<path value="Patient"/>
+		</element>
+		<element id="Patient.name">
+			<path value="Patient.name"/>
+			<slicing>
+        <discriminator>
+          <type value="value"/>
+          <path value="extension(&#39;http://hl7.org/fhir/StructureDefinition/data-absent-reason&#39;).valueCode"/>
+        </discriminator>
+        <rules value="open"/>
+      </slicing>
+		</element>
+		<element id="Patient.name:foo">
+			<path value="Patient.name"/>
+			<sliceName value="foo"/>
+			<min value="1"/>
+		</element>
+		<element id="Patient.name:foo.extension:dar">
+			<path value="Patient.name.extension"/>
+			<sliceName value="dar"/>
+			<min value="1"/>
+			<type>
+        <code value="Extension"/>
+        <profile value="http://hl7.org/fhir/StructureDefinition/data-absent-reason"/>
+      </type>
+		</element>
+		<element id="Patient.name:foo.extension:dar.valueCode">
+			<path value="Patient.name.extension.valueCode"/>
+			<fixedCode value="unknown"/>
+    </element>
+	</differential>
+</StructureDefinition>

org.hl7.fhir.validation/src/test/resources/validation-examples/extension-slice.xml

@@ -0,0 +1,13 @@
+<Patient xmlns="http://hl7.org/fhir">
+  <id value="extension-slice"/>
+  <text>
+    <status value="generated"/>
+    <div xmlns="http://www.w3.org/1999/xhtml">
+    </div>
+  </text>
+  <name>
+    <extension url="http://hl7.org/fhir/StructureDefinition/data-absent-reason">
+      <valueCode value="unknown"/>
+    </extension>
+  </name>
+</Patient>

org.hl7.fhir.validation/src/test/resources/validation-examples/manifest.json

@@ -461,11 +461,11 @@
         "questionnaire" : "questionnaire-enableWhen-test3.xml",
         "errorCount": 0
       },
-      "slice-by-polymorphic-type2.xml" : {
+      "extension-slice.xml" : {
         "errorCount": 0,
         "profile" : {
-          "source" : "slice-by-polymorphic-type2-profile.xml", 
+          "source" : "extension-slice-profile.xml", 
-          "errorCount": 0
+          "errorCount": 0          
         }
       }
 		}

release.bat

@@ -9,31 +9,10 @@ echo ===============================================================
 pause
 
 call mvn versions:set -DnewVersion=3.7.26-SNAPSHOT
-
-echo ===============================================================
-echo upgraded version number using maven
-echo next: do git commit / push
-echo ===============================================================
-pause
-
 call git commit -a -m "Release new version"
 call git push origin master
-
-echo ===============================================================
-echo done git commit / push
-echo next: replace references in java code + ivy
-echo ===============================================================
-pause
-
 call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.java" --excludeFileMask "*.dll, *.exe" --includeSubDirectories --find "3.7.25-SNAPSHOT" --replace "3.7.26-SNAPSHOT"
 call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.xml" --excludeFileMask "*.dll, *.exe" --find "3.7.25-SNAPSHOT" --replace "3.7.26-SNAPSHOT"
-
-echo ===============================================================
-echo done replacing references
-echo next: do maven release
-echo ===============================================================
-pause
-
 call mvn deploy
 
 echo ===============================================================