Merge pull request #89 from ahdis/oliveregger_cdacore20parseandtest

CDA Parsing tests with FHIRPath, ED datatype handling

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

@@ -40,6 +40,7 @@ import javax.xml.transform.sax.SAXSource;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.conformance.ProfileUtilities;
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
@@ -244,8 +245,18 @@ public class XmlParser extends ParserBase {
     if (!Utilities.noString(text)) {
     	Property property = getTextProp(properties);
     	if (property != null) {
-  	    context.getChildren().add(new Element(property.getName(), property, property.getType(), text).markLocation(line(node), col(node)));
+        if ("ED.data[x]".equals(property.getDefinition().getId())) {
-    	} else {
+          if ("B64".equals(node.getAttribute("representation"))) {
+            context.getChildren().add(new Element("dataBase64Binary", property, "base64Binary", text).markLocation(line(node), col(node)));
+          } else {
+            context.getChildren().add(new Element("dataString", property, "string", text).markLocation(line(node), col(node)));           
+          }
+        } else {
+          context.getChildren().add(
+              new Element(property.getName(), property, property.getType(), text).markLocation(line(node), col(node)));
+        }
+      } 
+    	else {
         logError(line(node), col(node), path, IssueType.STRUCTURE, "Text should not be present", IssueSeverity.ERROR);
     	}    		
     }

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java

@@ -1,5 +1,8 @@
 package org.hl7.fhir.r5.test;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
@@ -13,28 +16,119 @@ import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.elementmodel.Manager;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
+import org.hl7.fhir.r5.utils.FHIRPathEngine;
 import org.hl7.fhir.utilities.cache.PackageCacheManager;
 import org.hl7.fhir.utilities.cache.ToolsVersion;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 
 public class CDARoundTripTests {
 
   private SimpleWorkerContext context;
+  private FHIRPathEngine fp;
 
   @Before
   public void setUp() throws Exception {
     context = new SimpleWorkerContext();
     PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
-    context.loadFromPackage(pcm.loadPackage("hl7.fhir.core"), null, "StructureDefinition");
+    context.loadFromPackage(pcm.loadPackage("hl7.fhir.core", "dev"), null, "StructureDefinition");
-    context.loadFromPackage(pcm.loadPackage("hl7.fhir.cda"), null, "StructureDefinition");
+    context.loadFromPackage(pcm.loadPackage("hl7.fhir.cda", "dev"), null, "StructureDefinition");
+    fp = new FHIRPathEngine(context);
   }
   
   @Test
+  public void testCDA() throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
+    try {
+
+      String fileSource = TestingUtilities.resourceNameToFile("cda", "cda-original.xml");
+      String roundTrip = TestingUtilities.resourceNameToFile("cda", "cda-roundtrip.xml");
+      String jsonRoundTrip = TestingUtilities.resourceNameToFile("cda", "cda-roundtrip.json");
+
+      Element e = Manager.parse(context, new FileInputStream(fileSource), FhirFormat.XML);
+
+      Manager.compose(context, e, new FileOutputStream(roundTrip), FhirFormat.XML, OutputStyle.PRETTY, null);
+      Manager.compose(context, e, new FileOutputStream(jsonRoundTrip), FhirFormat.JSON, OutputStyle.PRETTY, null);
+
+//    <typeId root="2.16.840.1.113883.1.3" extension="POCD_HD000040"/>
+//      assertEquals("POCD_HD000040", fp.evaluateToString(e, "typeId.extension"));
+//      assertEquals("2.16.840.1.113883.1.3", fp.evaluateToString(e, "typeId.root"));
+//    <templateId root="2.16.840.1.113883.3.27.1776"/>
+//      assertEquals("2.16.840.1.113883.3.27.1776", fp.evaluateToString(e, "templateId.root"));
+//    <id extension="c266" root="2.16.840.1.113883.19.4"/>
+      assertEquals("2.16.840.1.113883.19.4", fp.evaluateToString(e, "id.root"));
+      assertEquals("c266", fp.evaluateToString(e, "id.extension"));
+
+//    <title>Good Health Clinic Consultation Note</title>
+      assertEquals("Good Health Clinic Consultation Note", fp.evaluateToString(e, "title.dataString"));
+//    <effectiveTime value="20000407"/>
+      assertEquals("2000-04-07", fp.evaluateToString(e, "effectiveTime.value"));
+//    <confidentialityCode code="N" codeSystem="2.16.840.1.113883.5.25"/>
+      assertEquals("N", fp.evaluateToString(e, "confidentialityCode.code"));
+      assertEquals("2.16.840.1.113883.5.25", fp.evaluateToString(e, "confidentialityCode.codeSystem"));
+//    <languageCode code="en-US"/>
+      assertEquals("en-US", fp.evaluateToString(e, "languageCode.code"));
+//    <setId extension="BB35" root="2.16.840.1.113883.19.7"/>
+      assertEquals("BB35", fp.evaluateToString(e, "setId.extension"));
+      assertEquals("2.16.840.1.113883.19.7", fp.evaluateToString(e, "setId.root"));
+//    <versionNumber value="2"/>
+      assertEquals("2", fp.evaluateToString(e, "versionNumber.value"));
+//    <recordTarget>
+//      <patientRole>
+//        <id extension="12345" root="2.16.840.1.113883.19.5"/>
+      assertEquals("12345", fp.evaluateToString(e, "recordTarget.patientRole.id.extension"));
+      assertEquals("2.16.840.1.113883.19.5", fp.evaluateToString(e, "recordTarget.patientRole.id.root"));
+//        <patient>
+//          <name>
+//            <family>Levin</family>
+      assertEquals("Levin", fp.evaluateToString(e, "recordTarget.patientRole.patient.name.family.dataString"));
+//    <given>Henry</given>
+      assertEquals("Henry", fp.evaluateToString(e, "recordTarget.patientRole.patient.name.given.dataString"));
+//            <suffix>the 7th</suffix>
+//          </name>
+//          <administrativeGenderCode code="M" codeSystem="2.16.840.1.113883.5.1"/>
+//          <birthTime value="19320924"/>
+//        </patient>
+//        <providerOrganization>
+//          <id root="2.16.840.1.113883.19.5"/>
+//        </providerOrganization>
+//      </patientRole>
+//    </recordTarget>
+      
+//      <component>
+//      <structuredBody>
+//    <component>
+//    <section>
+      
+//      <component>
+//      <section>
+//        <code code="8709-8" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC"/>
+//        <title>Skin Exam</title>
+//        <text>Erythematous rash, palmar surface, left index finger.
+//           <renderMultiMedia referencedObject="MM1"/>
+//        </text>
+
+      assertEquals("Skin Exam", fp.evaluateToString(e, "component.structuredBody.component.section.component.section.where(code.code='8709-8' and code.codeSystem='2.16.840.1.113883.6.1').title.dataString"));
+      // <div>Erythematous rash, palmar surface, left index finger.
+      // <img src="MM1"/></div>
+      String text = fp.evaluateToString(e, "component.structuredBody.component.section.component.section.where(code.code='8709-8' and code.codeSystem='2.16.840.1.113883.6.1').text");
+      assertTrue(text.contains("<img src=\"MM1\"/>"));
+    } catch (Exception e) {
+      System.out.println(e.getMessage());
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Ignore
   public void testDCI() throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
     try {
-    Element e = Manager.parse(context, new FileInputStream("C:\\work\\org.hl7.fhir.us\\ccda-to-fhir-maps\\cda\\IAT2-Discharge_Summary-DCI.xml"), FhirFormat.XML);
+      Element e = Manager.parse(context,
-    Manager.compose(context, e, new FileOutputStream("C:\\temp\\ccda.xml"), FhirFormat.XML, OutputStyle.PRETTY, null);
+          new FileInputStream("C:\\work\\org.hl7.fhir.us\\ccda-to-fhir-maps\\cda\\IAT2-Discharge_Summary-DCI.xml"),
+          FhirFormat.XML);
+
+      Manager.compose(context, e, new FileOutputStream("C:\\temp\\ccda.xml"), FhirFormat.XML, OutputStyle.PRETTY, null);
 //    Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge_Summary-DCI.out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
 //    Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge_Summary-DCI.out.ttl"), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
     } catch (Exception e) {
@@ -44,20 +138,44 @@ public class CDARoundTripTests {
     }
   }
 
-  @Test
+  @Ignore
-  public void testEpic() throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
+  public void testEpic()
-    Element e = Manager.parse(context, new FileInputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.xml"), FhirFormat.XML);
+      throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
-    Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.out.xml"), FhirFormat.XML, OutputStyle.PRETTY, null);
+    Element e = Manager.parse(context,
-    Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
+        new FileInputStream(
-    Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.out.ttl"), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
+            "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.xml"),
+        FhirFormat.XML);
+    Manager.compose(context, e,
+        new FileOutputStream(
+            "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.out.xml"),
+        FhirFormat.XML, OutputStyle.PRETTY, null);
+    Manager.compose(context, e,
+        new FileOutputStream(
+            "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.out.json"),
+        FhirFormat.JSON, OutputStyle.PRETTY, null);
+    Manager.compose(context, e,
+        new FileOutputStream(
+            "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.out.ttl"),
+        FhirFormat.TURTLE, OutputStyle.PRETTY, null);
   }
 
-  @Test
+  @Ignore
-  public void testDHIT() throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
+  public void testDHIT()
-    Element e = Manager.parse(context, new FileInputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.xml"), FhirFormat.XML);
+      throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
-    Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.xml"), FhirFormat.XML, OutputStyle.PRETTY, null);
+    Element e = Manager.parse(context,
-    Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
+        new FileInputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.xml"),
-    Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.ttl"), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
+        FhirFormat.XML);
+    Manager.compose(context, e,
+        new FileOutputStream(
+            "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.xml"),
+        FhirFormat.XML, OutputStyle.PRETTY, null);
+    Manager.compose(context, e,
+        new FileOutputStream(
+            "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.json"),
+        FhirFormat.JSON, OutputStyle.PRETTY, null);
+    Manager.compose(context, e,
+        new FileOutputStream(
+            "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.ttl"),
+        FhirFormat.TURTLE, OutputStyle.PRETTY, null);
   }
-
 }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/CDANarrativeFormat.java

@@ -187,7 +187,7 @@ public class CDANarrativeFormat {
   private void processRenderMultiMedia(Element e, XhtmlNode xn) throws FHIRException {
     XhtmlNode xc = xn.addTag("img");
     String v = e.getAttribute("referencedObject");
-    xn.attribute("src", v);
+    xc.attribute("src", v);
     processAttributes(e, xc, "ID", "language", "styleCode");
     processChildren(e, xc);
   }