Merge pull request #104 from ahdis/oliveregger_fmltests
FML updates for tests and validator
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commit
9b64f03a3e
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@ -389,7 +389,9 @@ public class ExpressionNode {
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b.append(")");
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}
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if (inner != null) {
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b.append(".");
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if (!((ExpressionNode.Kind.Function == inner.getKind()) && (ExpressionNode.Function.Item == inner.getFunction()))) {
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b.append(".");
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}
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b.append(inner.toString());
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}
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if (operation != null) {
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@ -248,11 +248,13 @@ public class FHIRPathEngine {
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public FHIRPathEngine(IWorkerContext worker) {
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super();
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this.worker = worker;
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for (StructureDefinition sd : worker.allStructures()) {
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if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() != StructureDefinitionKind.LOGICAL)
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allTypes.put(sd.getName(), sd);
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if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
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primitiveTypes.add(sd.getName());
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if (this.worker!=null) {
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for (StructureDefinition sd : worker.allStructures()) {
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if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() != StructureDefinitionKind.LOGICAL)
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allTypes.put(sd.getName(), sd);
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if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
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primitiveTypes.add(sd.getName());
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}
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}
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}
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}
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@ -1078,6 +1080,7 @@ public class FHIRPathEngine {
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case Lower: return checkParamCount(lexer, location, exp, 0);
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case Upper: return checkParamCount(lexer, location, exp, 0);
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case ToChars: return checkParamCount(lexer, location, exp, 0);
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case IndexOf : return checkParamCount(lexer, location, exp, 1);
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case Substring: return checkParamCount(lexer, location, exp, 1, 2);
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case StartsWith: return checkParamCount(lexer, location, exp, 1);
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case EndsWith: return checkParamCount(lexer, location, exp, 1);
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@ -390,7 +390,9 @@ public class ExpressionNode {
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b.append(")");
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}
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if (inner != null) {
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b.append(".");
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if (!((ExpressionNode.Kind.Function == inner.getKind()) && (ExpressionNode.Function.Item == inner.getFunction()))) {
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b.append(".");
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}
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b.append(inner.toString());
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}
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if (operation != null) {
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@ -82,7 +82,7 @@ public class FHIRMappingLanguageTests implements ITransformerServices {
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static public void setUp() throws Exception {
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if (context == null) {
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PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
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context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
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context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.1"));
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jsonParser = new JsonParser();
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jsonParser.setOutputStyle(OutputStyle.PRETTY);
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}
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@ -93,7 +93,7 @@ public class FHIRMappingLanguageTests implements ITransformerServices {
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InputStream fileSource = TestingUtilities.loadTestResourceStream("r5", "fml", source);
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InputStream fileMap = TestingUtilities.loadTestResourceStream("r5", "fml", map);
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String fileOutput = TestingUtilities.tempFile("fml", output);
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String outputJson = TestingUtilities.loadTestResource("r5","fml", output);
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String fileOutputRes = TestingUtilities.tempFile("fml", output)+".out";
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outputs.clear();
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@ -117,9 +117,10 @@ public class FHIRMappingLanguageTests implements ITransformerServices {
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if (ok) {
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ByteArrayOutputStream boas = new ByteArrayOutputStream();
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jsonParser.compose(boas, resource);
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log(boas.toString());
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String result = boas.toString();
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log(result);
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TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
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msg = TestingUtilities.checkJsonIsSame(fileOutputRes,fileOutput);
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msg = TestingUtilities.checkJsonSrcIsSame(result, outputJson);
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assertTrue(msg, Utilities.noString(msg));
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} else
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assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
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@ -293,7 +293,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
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}
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}
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private SimpleWorkerContext context;
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// private FHIRPathEngine fpe;
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private Map<String, byte[]> binaries = new HashMap<String, byte[]>();
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@ -754,7 +754,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
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return FhirFormat.TEXT;
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return checkIsResource(TextFile.fileToBytes(path), path);
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}
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}
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public void connectToTSServer(String url, String log, FhirPublication version) throws URISyntaxException, FHIRException {
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context.setTlogging(false);
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@ -770,7 +770,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
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throw e;
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}
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}
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}
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}
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public void loadProfile(String src) throws Exception {
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if (context.hasResource(StructureDefinition.class, src))
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@ -809,10 +809,10 @@ public class ValidationEngine implements IValidatorResourceFetcher {
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}
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}
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}
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}
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}
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if (canonical != null)
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grabNatives(source, canonical);
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}
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}
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public Resource loadFileWithErrorChecking(String version, Entry<String, byte[]> t, String fn) {
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if (debug)
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@ -908,10 +908,10 @@ public class ValidationEngine implements IValidatorResourceFetcher {
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if (e.getKey().endsWith(".zip"))
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binaries.put(prefix+"#"+e.getKey(), e.getValue());
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}
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}
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}
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public void setQuestionnaires(List<String> questionnaires) {
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}
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}
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public void setNative(boolean doNative) {
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this.doNative = doNative;
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@ -1168,12 +1168,12 @@ public class ValidationEngine implements IValidatorResourceFetcher {
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private void validateSHEX(String location, List<ValidationMessage> messages) {
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messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.INFORMATIONAL, location, "SHEX Validation is not done yet", IssueSeverity.INFORMATION));
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}
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}
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private void validateXmlSchema(String location, List<ValidationMessage> messages) throws FileNotFoundException, IOException, SAXException {
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XmlValidator xml = new XmlValidator(messages, loadSchemas(), loadTransforms());
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messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.INFORMATIONAL, location, "XML Schema Validation is not done yet", IssueSeverity.INFORMATION));
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}
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}
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private Map<String, byte[]> loadSchemas() throws IOException {
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Map<String, byte[]> res = new HashMap<String, byte[]>();
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@ -1197,7 +1197,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
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private void validateJsonSchema(String location, List<ValidationMessage> messages) {
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messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.INFORMATIONAL, location, "JSON Schema Validation is not done yet", IssueSeverity.INFORMATION));
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}
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}
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private List<ValidationMessage> filterMessages(List<ValidationMessage> messages) {
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List<ValidationMessage> filteredValidation = new ArrayList<ValidationMessage>();
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@ -1229,7 +1229,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
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}
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new NarrativeGenerator("", "", context).generate(null, op);
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return op;
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}
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}
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public static String issueSummary (OperationOutcomeIssueComponent issue) {
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String source = ToolingExtensions.readStringExtension(issue, ToolingExtensions.EXT_ISSUE_SOURCE);
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