[GF#20324] FML support for share in Target Transform

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/StructureMapUtilities.java

@@ -34,11 +34,6 @@ import java.util.Map;
 import java.util.Set;
 import java.util.UUID;
 
-import org.apache.commons.lang3.NotImplementedException;
-import org.hl7.fhir.exceptions.DefinitionException;
-import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.exceptions.PathEngineException;
 import org.hl7.fhir.r4.conformance.ProfileUtilities;
 import org.hl7.fhir.r4.conformance.ProfileUtilities.ProfileKnowledgeProvider;
 import org.hl7.fhir.r4.context.IWorkerContext;
@@ -91,10 +86,10 @@ import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleTargetComponent;
 import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleTargetParameterComponent;
 import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupTypeMode;
 import org.hl7.fhir.r4.model.StructureMap.StructureMapInputMode;
-import org.hl7.fhir.r4.model.StructureMap.StructureMapModelMode;
 import org.hl7.fhir.r4.model.StructureMap.StructureMapSourceListMode;
-import org.hl7.fhir.r4.model.StructureMap.StructureMapStructureComponent;
 import org.hl7.fhir.r4.model.StructureMap.StructureMapTargetListMode;
+import org.hl7.fhir.r4.model.StructureMap.StructureMapModelMode;
+import org.hl7.fhir.r4.model.StructureMap.StructureMapStructureComponent;
 import org.hl7.fhir.r4.model.StructureMap.StructureMapTransform;
 import org.hl7.fhir.r4.model.Type;
 import org.hl7.fhir.r4.model.TypeDetails;
@@ -105,6 +100,11 @@ import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
 import org.hl7.fhir.r4.utils.FHIRLexer.FHIRLexerException;
 import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
+import org.apache.commons.lang3.NotImplementedException;
+import org.hl7.fhir.exceptions.DefinitionException;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.exceptions.PathEngineException;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
@@ -1170,13 +1170,15 @@ public class StructureMapUtilities {
 				target.addListMode(StructureMapTargetListMode.SHARE);
 				lexer.next();
 				target.setListRuleId(lexer.take());
-			} else if (lexer.getCurrent().equals("first")) 
+			} else {
+				if (lexer.getCurrent().equals("first")) 
 					target.addListMode(StructureMapTargetListMode.FIRST);
 				else
 					target.addListMode(StructureMapTargetListMode.LAST);
 				lexer.next();
 			}
 		}
+	}
 
 
 	private void parseParameter(StructureMapGroupRuleTargetComponent target, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
@@ -1219,7 +1221,7 @@ public class StructureMapUtilities {
 	}
 
 	public enum VariableMode {
-		INPUT, OUTPUT
+		INPUT, OUTPUT, SHARED
 	}
 
 	public class Variable {
@@ -1280,13 +1282,22 @@ public class StructureMapUtilities {
 	    public String summary() {
 	      CommaSeparatedStringBuilder s = new CommaSeparatedStringBuilder();
 	      CommaSeparatedStringBuilder t = new CommaSeparatedStringBuilder();
+	      CommaSeparatedStringBuilder sh = new CommaSeparatedStringBuilder();
 	      for (Variable v : list)
-        if (v.mode == VariableMode.INPUT)
+	      	switch(v.mode) {
+	      	case INPUT:
 	          s.append(v.summary());
-        else
+	          break;
+	        case OUTPUT:
 	          t.append(v.summary());
-      return "source variables ["+s.toString()+"], target variables ["+t.toString()+"]";
+	          break;
+	        case SHARED:
+	          sh.append(v.summary());
+	          break;
 	      	}
+	      return "source variables ["+s.toString()+"], target variables ["+t.toString()+"], shared variables ["+sh.toString()+"]";
+	    }
+	    
 	}
 
 	public class TransformContext {
@@ -1379,7 +1390,7 @@ public class StructureMapUtilities {
 		if (source != null) {
 			for (Variables v : source) {
 				for (StructureMapGroupRuleTargetComponent t : rule.getTarget()) {
-					processTarget(rule.getName(), context, v, map, group, t, rule.getSource().size() == 1 ? rule.getSourceFirstRep().getVariable() : null, atRoot);
+					processTarget(rule.getName(), context, v, map, group, t, rule.getSource().size() == 1 ? rule.getSourceFirstRep().getVariable() : null, atRoot, vars);
 				}
 				if (rule.hasRule()) {
 					for (StructureMapGroupRuleComponent childrule : rule.getRule()) {
@@ -1781,7 +1792,7 @@ public class StructureMapUtilities {
     return false;
   }
 
-  private void processTarget(String ruleId, TransformContext context, Variables vars, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, String srcVar, boolean atRoot) throws FHIRException {
+  private void processTarget(String ruleId, TransformContext context, Variables vars, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, String srcVar, boolean atRoot, Variables sharedVars) throws FHIRException {
 	  Base dest = null;
 	  if (tgt.hasContext()) {
   		dest = vars.get(VariableMode.OUTPUT, tgt.getContext());
@@ -1795,8 +1806,17 @@ public class StructureMapUtilities {
 	    v = runTransform(ruleId, context, map, group, tgt, vars, dest, tgt.getElement(), srcVar, atRoot);
 	    if (v != null && dest != null)
 	      v = dest.setProperty(tgt.getElement().hashCode(), tgt.getElement(), v); // reset v because some implementations may have to rewrite v when setting the value
-	  } else if (dest != null) 
+	  } else if (dest != null) { 
+	  	if (tgt.hasListMode(StructureMapTargetListMode.SHARE)) {
+	  		v = sharedVars.get(VariableMode.SHARED, tgt.getListRuleId());
+	  		if (v == null) {
 	  			v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
+	  			sharedVars.add(VariableMode.SHARED, tgt.getListRuleId(), v);	  			
+	  		}
+	  	} else {
+	  		v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
+	  	}
+	  }
 	  if (tgt.hasVariable() && v != null)
 	    vars.add(VariableMode.OUTPUT, tgt.getVariable(), v);
 	}

org.hl7.fhir.r4/src/main/resources/fml/.gitignore

@@ -0,0 +1 @@
+*.out

org.hl7.fhir.r4/src/main/resources/fml/manifest.xml

@@ -0,0 +1,6 @@
+<fml-tests>
+ <test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patassignment" source="qr.json" map="qr2pat-assignment.map" output="qr2pat-assignment-res.json" />
+ <test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patgender" source="qr.json" map="qr2pat-gender.map" output="qr2pat-gender-res.json" />
+ <test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannametwice" source="qr.json" map="qr2pat-humannametwice.map" output="qr2pat-humannametwice-res.json" />
+ <test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannameshared" source="qr.json" map="qr2pat-humannameshared.map" output="qr2pat-humannameshared-res.json" />
+</fml-tests>

org.hl7.fhir.r4/src/main/resources/fml/qr.json

@@ -0,0 +1,39 @@
+{
+  "resourceType": "QuestionnaireResponse",
+  "status": "in-progress",
+  "item": [
+    {
+      "linkId": "patient",
+      "text": "Patient",
+      "item": [
+        {
+          "linkId": "patient.lastname",
+          "text": "Name",
+          "answer": [
+            {
+              "valueString": "Brönnimann-Bertholet"
+            }
+          ]
+        },
+        {
+          "linkId": "patient.firstname",
+          "text": "Vorname",
+          "answer": [
+            {
+              "valueString": "Elisabeth"
+            }
+          ]
+        },
+        {
+          "linkId": "patient.sex",
+          "text": "Geschlecht",
+          "answer": [
+            {
+              "valueString": "female"
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}

org.hl7.fhir.r4/src/main/resources/fml/qr2pat-assignment-res.json

@@ -0,0 +1,4 @@
+{
+  "resourceType" : "Patient",
+  "gender" : "female"
+}

org.hl7.fhir.r4/src/main/resources/fml/qr2pat-assignment.map

@@ -0,0 +1,8 @@
+map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patassignment" = "qr2patassignment"
+
+uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
+uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
+
+group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
+  src -> tgt.gender = 'female' "Simple Assignment";
+}

org.hl7.fhir.r4/src/main/resources/fml/qr2pat-gender-res.json

@@ -0,0 +1,4 @@
+{
+  "resourceType" : "Patient",
+  "gender" : "female"
+}

org.hl7.fhir.r4/src/main/resources/fml/qr2pat-gender.map

@@ -0,0 +1,12 @@
+map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patgender" = "qr2patgender"
+
+uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
+uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
+
+group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
+  src.item as item -> tgt as patient then item(item, patient);
+}
+
+group item(source src, target tgt: Patient) {
+  src.item as item where linkId.value in ('patient.sex') -> tgt.gender = (item.answer.valueString);
+}

org.hl7.fhir.r4/src/main/resources/fml/qr2pat-humannameshared-res.json

@@ -0,0 +1,8 @@
+{
+  "resourceType" : "Patient",
+  "name" : [{
+    "family" : "Brönnimann-Bertholet",
+    "given" : ["Elisabeth"]
+  }],
+  "gender" : "female"
+}

org.hl7.fhir.r4/src/main/resources/fml/qr2pat-humannameshared.map

@@ -0,0 +1,26 @@
+map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannameshared" = "qr2pathumannametwice"
+
+uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
+uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
+
+group entry(source src : QuestionnaireResponse, target tgt : Patient) {
+  src.item as item then item(item, tgt);
+}
+
+group item(source src, target tgt) {
+  src.item as item then item(item, tgt);
+  src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name share patientName then humanNameFamily(item, name);
+  src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name share patientName then humanNameGiven(item, name);
+  src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
+}
+
+group humanNameFamily(source src, target tgt: HumanName) {
+  src.answer as answer -> tgt.family = (answer.valueString);
+}
+group humanNameGiven(source src, target tgt: HumanName) {
+  src.answer as answer -> tgt.given = (answer.valueString);
+}
+
+group administrativeGender(source src, target tgt: code) {
+  src.answer as answer -> tgt = (answer.valueString);
+}

org.hl7.fhir.r4/src/main/resources/fml/qr2pat-humannametwice-res.json

@@ -0,0 +1,10 @@
+{
+  "resourceType" : "Patient",
+  "name" : [{
+    "family" : "Brönnimann-Bertholet"
+  },
+  {
+    "given" : ["Elisabeth"]
+  }],
+  "gender" : "female"
+}

org.hl7.fhir.r4/src/main/resources/fml/qr2pat-humannametwice.map

@@ -0,0 +1,26 @@
+map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannametwice" = "qr2pathumannametwice"
+
+uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
+uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
+
+group entry(source src : QuestionnaireResponse, target tgt : Patient) {
+  src.item as item then item(item, tgt);
+}
+
+group item(source src, target tgt) {
+  src.item as item then item(item, tgt);
+  src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name then humanNameFamily(item, name);
+  src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name then humanNameGiven(item, name);
+  src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
+}
+
+group humanNameFamily(source src, target tgt: HumanName) {
+  src.answer as answer -> tgt.family = (answer.valueString);
+}
+group humanNameGiven(source src, target tgt: HumanName) {
+  src.answer as answer -> tgt.given = (answer.valueString);
+}
+
+group administrativeGender(source src, target tgt: code) {
+  src.answer as answer -> tgt = (answer.valueString);
+}

org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/AllTests.java

@@ -18,7 +18,8 @@ import org.junit.runners.Suite.SuiteClasses;
     NarrativeGeneratorTests.class,
     ShexGeneratorTests.class,
     BaseDateTimeTypeTest.class,
-    SnapShotGenerationTests.class})
+    SnapShotGenerationTests.class,
+    FHIRMappingLanguageTests.class})
 public class AllTests {
 
 }

org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/FHIRMappingLanguageTests.java

@@ -0,0 +1,168 @@
+package org.hl7.fhir.r4.test;
+
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r4.context.SimpleWorkerContext;
+import org.hl7.fhir.r4.elementmodel.Manager;
+import org.hl7.fhir.r4.elementmodel.Manager.FhirFormat;
+import org.hl7.fhir.r4.formats.IParser.OutputStyle;
+import org.hl7.fhir.r4.formats.JsonParser;
+import org.hl7.fhir.r4.model.Base;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Resource;
+import org.hl7.fhir.r4.model.ResourceFactory;
+import org.hl7.fhir.r4.model.StructureDefinition;
+import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
+import org.hl7.fhir.r4.model.StructureMap;
+import org.hl7.fhir.r4.terminologies.ConceptMapEngine;
+import org.hl7.fhir.r4.test.utils.TestingUtilities;
+import org.hl7.fhir.r4.utils.StructureMapUtilities;
+import org.hl7.fhir.r4.utils.StructureMapUtilities.ITransformerServices;
+import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.cache.PackageCacheManager;
+import org.hl7.fhir.utilities.cache.ToolsVersion;
+import org.hl7.fhir.utilities.xml.XMLUtil;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.SAXException;
+
+@RunWith(Parameterized.class)
+
+public class FHIRMappingLanguageTests implements ITransformerServices {
+
+	private List<Resource> outputs = new ArrayList<Resource>();
+
+	static private SimpleWorkerContext context;
+	static private JsonParser jsonParser;
+
+	@Parameters(name = "{index}: {0}")
+	public static Iterable<Object[]> data()
+			throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
+		Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("fml", "manifest.xml"));
+		Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
+		List<Object[]> objects = new ArrayList<Object[]>();
+		while (test != null && test.getNodeName().equals("test")) {
+			objects.add(new Object[] { test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
+					test.getAttribute("output") });
+			test = XMLUtil.getNextSibling(test);
+		}
+		return objects;
+	}
+
+	private final String name;
+	private String source;
+	private String output;
+	private String map;
+
+	public FHIRMappingLanguageTests(String name, String source, String map, String output) {
+		this.name = name;
+		this.source = source;
+		this.output = output;
+		this.map = map;
+	}
+
+	@BeforeClass
+	static public void setUp() throws Exception {
+		if (context == null) {
+			context = new SimpleWorkerContext();
+			PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
+			context.loadFromPackage(pcm.loadPackageCacheLatest("hl7.fhir.core"), null, "StructureDefinition");
+			jsonParser = new JsonParser();
+			jsonParser.setOutputStyle(OutputStyle.PRETTY);
+		}
+	}
+
+	@Test
+	public void test() throws Exception {
+
+		String fileSource = TestingUtilities.resourceNameToFile("fml", source);
+		String fileMap = TestingUtilities.resourceNameToFile("fml", map);
+		String fileOutput = TestingUtilities.resourceNameToFile("fml", output);
+		String fileOutputRes = TestingUtilities.resourceNameToFile("fml", output)+".out";
+
+		outputs.clear();
+
+		boolean ok = false;
+		String msg = null;
+		Resource resource = null;
+		try {
+			StructureMapUtilities scu = new StructureMapUtilities(context, this);
+			org.hl7.fhir.r4.elementmodel.Element src = Manager.parse(context,
+					new ByteArrayInputStream(TextFile.fileToBytes(fileSource)), FhirFormat.JSON);
+			StructureMap structureMap = scu.parse(TextFile.fileToString(fileMap), name);
+			String typeName = scu.getTargetType(structureMap).getType();
+			resource = ResourceFactory.createResource(typeName);
+			scu.transform(null, src, structureMap, resource);
+			ok = true;
+		} catch (Exception e) {
+			ok = false;
+			msg = e.getMessage();
+		}
+		if (ok) {
+			ByteArrayOutputStream boas = new ByteArrayOutputStream();
+			jsonParser.compose(boas, resource);
+			log(boas.toString());
+			TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
+			msg = TestingUtilities.checkJsonIsSame(fileOutputRes,fileOutput);
+			assertTrue(msg, Utilities.noString(msg));
+		} else
+			assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
+	}
+
+	@Override
+	public void log(String message) {
+		System.out.println(message);
+	}
+
+	@Override
+	public Base createType(Object appInfo, String name) throws FHIRException {
+		StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
+		if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
+			return Manager.build(context, sd);
+		} else {
+			if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
+				name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
+			return ResourceFactory.createResourceOrType(name);
+		}
+	}
+
+	@Override
+	public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
+		if (atRootofTransform)
+			outputs.add((Resource) res);
+		return res;
+	}
+
+	@Override
+	public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
+		ConceptMapEngine cme = new ConceptMapEngine(context);
+		return cme.translate(source, conceptMapUrl);
+	}
+
+	@Override
+	public Base resolveReference(Object appContext, String url) throws FHIRException {
+		throw new FHIRException("resolveReference is not supported yet");
+	}
+
+	@Override
+	public List<Base> performSearch(Object appContext, String url) throws FHIRException {
+		throw new FHIRException("performSearch is not supported yet");
+	}
+
+}