use of org.hl7.fhir.r5.model.Narrative in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerator method generateDocumentNarrative.
public XhtmlNode generateDocumentNarrative(Bundle feed) {
/*
When the document is presented for human consumption, applications must present the collated narrative portions of the following resources in order:
* The Composition resource
* The Subject resource
* Resources referenced in the section.content
*/
XhtmlNode root = new XhtmlNode(NodeType.Element, "div");
Composition comp = (Composition) feed.getEntry().get(0).getResource();
root.getChildNodes().add(comp.getText().getDiv());
Resource subject = ResourceUtilities.getById(feed, null, comp.getSubject().getReference());
if (subject != null && subject instanceof DomainResource) {
root.hr();
root.getChildNodes().add(((DomainResource) subject).getText().getDiv());
}
List<SectionComponent> sections = comp.getSection();
renderSections(feed, root, sections, 1);
return root;
}
use of org.hl7.fhir.r5.model.Narrative in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerator method generateByProfile.
private boolean generateByProfile(ResourceContext rc, StructureDefinition profile, boolean showCodeDetails) {
XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
x.para().b().tx("Generated Narrative" + (showCodeDetails ? " with Details" : ""));
try {
generateByProfile(rc.resourceResource, profile, rc.resourceResource, profile.getSnapshot().getElement(), profile.getSnapshot().getElement().get(0), getChildrenForPath(profile.getSnapshot().getElement(), rc.resourceResource.getResourceType().toString()), x, rc.resourceResource.getResourceType().toString(), showCodeDetails, rc);
} catch (Exception e) {
e.printStackTrace();
x.para().b().setAttribute("style", "color: maroon").tx("Exception generating Narrative: " + e.getMessage());
}
inject(rc.resourceResource, x, NarrativeStatus.GENERATED);
return true;
}
use of org.hl7.fhir.r5.model.Narrative in project org.hl7.fhir.core by hapifhir.
the class QuestionnaireBuilder method processDataType.
private void processDataType(StructureDefinition profile, QuestionnaireItemComponent group, ElementDefinition element, String path, TypeRefComponent t, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> answerGroups, List<ElementDefinition> parents) throws FHIRException {
String tc = t.getWorkingCode();
if (tc.equals("code"))
addCodeQuestions(group, element, path, answerGroups);
else if (Utilities.existsInList(tc, "string", "id", "oid", "uuid", "markdown"))
addStringQuestions(group, element, path, answerGroups);
else if (Utilities.existsInList(tc, "uri", "url", "canonical"))
addUriQuestions(group, element, path, answerGroups);
else if (tc.equals("boolean"))
addBooleanQuestions(group, element, path, answerGroups);
else if (tc.equals("decimal"))
addDecimalQuestions(group, element, path, answerGroups);
else if (tc.equals("dateTime") || tc.equals("date"))
addDateTimeQuestions(group, element, path, answerGroups);
else if (tc.equals("instant"))
addInstantQuestions(group, element, path, answerGroups);
else if (tc.equals("time"))
addTimeQuestions(group, element, path, answerGroups);
else if (tc.equals("CodeableConcept"))
addCodeableConceptQuestions(group, element, path, answerGroups);
else if (tc.equals("Period"))
addPeriodQuestions(group, element, path, answerGroups);
else if (tc.equals("Ratio"))
addRatioQuestions(group, element, path, answerGroups);
else if (tc.equals("HumanName"))
addHumanNameQuestions(group, element, path, answerGroups);
else if (tc.equals("Address"))
addAddressQuestions(group, element, path, answerGroups);
else if (tc.equals("ContactPoint"))
addContactPointQuestions(group, element, path, answerGroups);
else if (tc.equals("Identifier"))
addIdentifierQuestions(group, element, path, answerGroups);
else if (tc.equals("integer") || tc.equals("positiveInt") || tc.equals("unsignedInt"))
addIntegerQuestions(group, element, path, answerGroups);
else if (tc.equals("Coding"))
addCodingQuestions(group, element, path, answerGroups);
else if (Utilities.existsInList(tc, "Quantity", "Count", "Age", "Duration", "Distance", "Money"))
addQuantityQuestions(group, element, path, answerGroups);
else if (tc.equals("Money"))
addMoneyQuestions(group, element, path, answerGroups);
else if (tc.equals("Reference"))
addReferenceQuestions(group, element, path, t.getTargetProfile(), answerGroups);
else if (tc.equals("Duration"))
addDurationQuestions(group, element, path, answerGroups);
else if (tc.equals("base64Binary"))
addBinaryQuestions(group, element, path, answerGroups);
else if (tc.equals("Attachment"))
addAttachmentQuestions(group, element, path, answerGroups);
else if (tc.equals("Age"))
addAgeQuestions(group, element, path, answerGroups);
else if (tc.equals("Range"))
addRangeQuestions(group, element, path, answerGroups);
else if (tc.equals("Timing"))
addTimingQuestions(group, element, path, answerGroups);
else if (tc.equals("Annotation"))
addAnnotationQuestions(group, element, path, answerGroups);
else if (tc.equals("SampledData"))
addSampledDataQuestions(group, element, path, answerGroups);
else if (tc.equals("Extension")) {
if (t.hasProfile())
addExtensionQuestions(profile, group, element, path, t.getProfile().get(0).getValue(), answerGroups, parents);
} else if (tc.equals("SampledData"))
addSampledDataQuestions(group, element, path, answerGroups);
else if (!tc.equals("Narrative") && !tc.equals("Resource") && !tc.equals("Meta") && !tc.equals("Signature")) {
StructureDefinition sd = context.fetchTypeDefinition(tc);
if (sd == null)
throw new NotImplementedException("Unhandled Data Type: " + tc + " on element " + element.getPath());
buildGroup(group, sd, sd.getSnapshot().getElementFirstRep(), parents, answerGroups);
}
}
use of org.hl7.fhir.r5.model.Narrative in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerationTests method test.
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String id, TestDetails test) throws Exception {
RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
rc.setDestDir("");
rc.setHeader(test.isHeader());
rc.setDefinitionsTarget("test.html");
rc.setTerminologyServiceOptions(TerminologyServiceOptions.defaults());
rc.setParser(new TestTypeParser());
// getting timezones correct (well, at least consistent, so tests pass on any computer)
rc.setLocale(new java.util.Locale("en", "AU"));
rc.setTimeZoneId(ZoneId.of("Australia/Sydney"));
rc.setDateTimeFormatString("yyyy-MM-dd'T'HH:mm:ssZZZZZ");
rc.setDateFormatString("yyyy-MM-dd");
rc.setMode(test.technical ? ResourceRendererMode.TECHNICAL : ResourceRendererMode.END_USER);
Resource source;
if (TestingUtilities.findTestResource("r5", "narrative", test.getId() + ".json")) {
source = (Resource) new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".json"));
} else {
source = (Resource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".xml"));
}
XhtmlNode x = RendererFactory.factory(source, rc).build(source);
String expected = TextFile.streamToString(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".html"));
String actual = HEADER + new XhtmlComposer(true, true).compose(x) + FOOTER;
String expectedFileName = CompareUtilities.tempFile("narrative", test.getId() + ".expected.html");
String actualFileName = CompareUtilities.tempFile("narrative", test.getId() + ".actual.html");
TextFile.stringToFile(expected, expectedFileName);
TextFile.stringToFile(actual, actualFileName);
String msg = CompareUtilities.checkXMLIsSame(expectedFileName, actualFileName);
Assertions.assertTrue(msg == null, "Output does not match expected: " + msg);
if (test.isMeta()) {
org.hl7.fhir.r5.elementmodel.Element e = Manager.parseSingle(context, TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".xml"), FhirFormat.XML);
x = RendererFactory.factory(source, rc).render(new ElementWrappers.ResourceWrapperMetaElement(rc, e));
expected = TextFile.streamToString(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + "-meta.html"));
actual = HEADER + new XhtmlComposer(true, true).compose(x) + FOOTER;
actualFileName = CompareUtilities.tempFile("narrative", test.getId() + "-meta.actual.html");
TextFile.stringToFile(actual, actualFileName);
msg = CompareUtilities.checkXMLIsSame(expectedFileName, actualFileName);
Assertions.assertTrue(msg == null, "Meta output does not match expected: " + msg);
}
}
use of org.hl7.fhir.r5.model.Narrative in project org.hl7.fhir.core by hapifhir.
the class Params method loadCliContext.
/**
* TODO Don't do this all in one for loop. Use the above methods.
*/
public static CliContext loadCliContext(String[] args) throws Exception {
CliContext cliContext = new CliContext();
// load the parameters - so order doesn't matter
for (int i = 0; i < args.length; i++) {
if (args[i].equals(VERSION)) {
cliContext.setSv(VersionUtilities.getCurrentPackageVersion(args[++i]));
} else if (args[i].equals(OUTPUT)) {
if (i + 1 == args.length)
throw new Error("Specified -output without indicating output file");
else
cliContext.setOutput(args[++i]);
} else if (args[i].equals(HTML_OUTPUT)) {
if (i + 1 == args.length)
throw new Error("Specified -html-output without indicating output file");
else
cliContext.setHtmlOutput(args[++i]);
} else if (args[i].equals(PROXY)) {
// ignore next parameter
i++;
} else if (args[i].equals(PROXY_AUTH)) {
i++;
} else if (args[i].equals(PROFILE)) {
String p = null;
if (i + 1 == args.length) {
throw new Error("Specified -profile without indicating profile source");
} else {
p = args[++i];
cliContext.addProfile(p);
}
} else if (args[i].equals(BUNDLE)) {
String p = null;
String r = null;
if (i + 1 == args.length) {
throw new Error("Specified -profile without indicating bundle rule ");
} else {
r = args[++i];
}
if (i + 1 == args.length) {
throw new Error("Specified -profile without indicating profile source");
} else {
p = args[++i];
}
cliContext.getBundleValidationRules().add(new BundleValidationRule(r, p));
} else if (args[i].equals(QUESTIONNAIRE)) {
if (i + 1 == args.length)
throw new Error("Specified -questionnaire without indicating questionnaire mode");
else {
String q = args[++i];
cliContext.setQuestionnaireMode(QuestionnaireMode.fromCode(q));
}
} else if (args[i].equals(LEVEL)) {
if (i + 1 == args.length)
throw new Error("Specified -level without indicating level mode");
else {
String q = args[++i];
cliContext.setLevel(ValidationLevel.fromCode(q));
}
} else if (args[i].equals(NATIVE)) {
cliContext.setDoNative(true);
} else if (args[i].equals(ASSUME_VALID_REST_REF)) {
cliContext.setAssumeValidRestReferences(true);
} else if (args[i].equals(DEBUG)) {
cliContext.setDoDebug(true);
} else if (args[i].equals(SCT)) {
cliContext.setSnomedCT(args[++i]);
} else if (args[i].equals(RECURSE)) {
cliContext.setRecursive(true);
} else if (args[i].equals(SHOW_MESSAGES_FROM_REFERENCES)) {
cliContext.setShowMessagesFromReferences(true);
} else if (args[i].equals(LOCALE)) {
if (i + 1 == args.length) {
throw new Error("Specified -locale without indicating locale");
} else {
cliContext.setLocale(new Locale(args[++i]));
}
} else if (args[i].equals(EXTENSIONS)) {
cliContext.getExtensions().add(args[++i]);
} else if (args[i].equals(NO_INTERNAL_CACHING)) {
cliContext.setNoInternalCaching(true);
} else if (args[i].equals(NO_EXTENSIBLE_BINDING_WARNINGS)) {
cliContext.setNoExtensibleBindingMessages(true);
} else if (args[i].equals(NO_UNICODE_BIDI_CONTROL_CHARS)) {
cliContext.setNoUnicodeBiDiControlChars(true);
} else if (args[i].equals(NO_INVARIANTS)) {
cliContext.setNoInvariants(true);
} else if (args[i].equals(WANT_INVARIANTS_IN_MESSAGES)) {
cliContext.setWantInvariantsInMessages(true);
} else if (args[i].equals(HINT_ABOUT_NON_MUST_SUPPORT)) {
cliContext.setHintAboutNonMustSupport(true);
} else if (args[i].equals(TO_VERSION)) {
cliContext.setTargetVer(args[++i]);
cliContext.setMode(EngineMode.VERSION);
} else if (args[i].equals(DO_NATIVE)) {
cliContext.setCanDoNative(true);
} else if (args[i].equals(NO_NATIVE)) {
cliContext.setCanDoNative(false);
} else if (args[i].equals(TRANSFORM)) {
cliContext.setMap(args[++i]);
cliContext.setMode(EngineMode.TRANSFORM);
} else if (args[i].equals(COMPILE)) {
cliContext.setMap(args[++i]);
cliContext.setMode(EngineMode.COMPILE);
} else if (args[i].equals(NARRATIVE)) {
cliContext.setMode(EngineMode.NARRATIVE);
} else if (args[i].equals(SPREADSHEET)) {
cliContext.setMode(EngineMode.SPREADSHEET);
} else if (args[i].equals(SNAPSHOT)) {
cliContext.setMode(EngineMode.SNAPSHOT);
} else if (args[i].equals(SECURITY_CHECKS)) {
cliContext.setSecurityChecks(true);
} else if (args[i].equals(CRUMB_TRAIL)) {
cliContext.setCrumbTrails(true);
} else if (args[i].equals(VERBOSE)) {
cliContext.setCrumbTrails(true);
} else if (args[i].equals(ALLOW_EXAMPLE_URLS)) {
String bl = args[++i];
if ("true".equals(bl)) {
cliContext.setAllowExampleUrls(true);
} else if ("false".equals(bl)) {
cliContext.setAllowExampleUrls(false);
} else {
throw new Error("Value for " + ALLOW_EXAMPLE_URLS + " not understood: " + bl);
}
} else if (args[i].equals(SHOW_TIMES)) {
cliContext.setShowTimes(true);
} else if (args[i].equals(OUTPUT_STYLE)) {
cliContext.setOutputStyle(args[++i]);
} else if (args[i].equals(SCAN)) {
cliContext.setMode(EngineMode.SCAN);
} else if (args[i].equals(TERMINOLOGY)) {
if (i + 1 == args.length)
throw new Error("Specified -tx without indicating terminology server");
else
cliContext.setTxServer("n/a".equals(args[++i]) ? null : args[i]);
} else if (args[i].equals(TERMINOLOGY_LOG)) {
if (i + 1 == args.length)
throw new Error("Specified -txLog without indicating file");
else
cliContext.setTxLog(args[++i]);
} else if (args[i].equals(TERMINOLOGY_CACHE)) {
if (i + 1 == args.length)
throw new Error("Specified -txCache without indicating file");
else
cliContext.setTxCache(args[++i]);
} else if (args[i].equals(LOG)) {
if (i + 1 == args.length)
throw new Error("Specified -log without indicating file");
else
cliContext.setMapLog(args[++i]);
} else if (args[i].equals(LANGUAGE)) {
if (i + 1 == args.length)
throw new Error("Specified -language without indicating language");
else
cliContext.setLang(args[++i]);
} else if (args[i].equals(IMPLEMENTATION_GUIDE) || args[i].equals(DEFINITION)) {
if (i + 1 == args.length)
throw new Error("Specified " + args[i] + " without indicating ig file");
else {
String s = args[++i];
String version = Common.getVersionFromIGName(null, s);
if (version == null) {
cliContext.addIg(s);
} else {
cliContext.setSv(version);
}
}
} else if (args[i].equals(MAP)) {
if (cliContext.getMap() == null) {
if (i + 1 == args.length)
throw new Error("Specified -map without indicating map file");
else
cliContext.setMap(args[++i]);
} else {
throw new Exception("Can only nominate a single -map parameter");
}
} else if (args[i].startsWith(X)) {
i++;
} else if (args[i].equals(CONVERT)) {
cliContext.setMode(EngineMode.CONVERT);
} else if (args[i].equals(FHIRPATH)) {
cliContext.setMode(EngineMode.FHIRPATH);
if (cliContext.getFhirpath() == null)
if (i + 1 == args.length)
throw new Error("Specified -fhirpath without indicating a FHIRPath expression");
else
cliContext.setFhirpath(args[++i]);
else
throw new Exception("Can only nominate a single -fhirpath parameter");
} else {
cliContext.addSource(args[i]);
}
}
return cliContext;
}
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