use of org.hl7.fhir.r4b.model.ExpressionNode.Function in project beneficiary-fhir-data by CMSgov.
the class BeneficiaryTransformerV2Test method verifyDualResourceExtension.
/**
* helper function to verify that {@link
* gov.cms.bfd.server.war.r4.providers.BeneficiaryTransformerV2} correctly handles patient Part D
* attributee.
*/
private void verifyDualResourceExtension(String dualId) {
String uri = "https://bluebutton.cms.gov/resources/variables/" + dualId;
Extension ex = TransformerTestUtilsV2.findExtensionByUrl(uri, patient.getExtension());
assertNotNull(ex);
Extension compare = new Extension(uri, new Coding(uri, "**", "Enrolled in Medicare A and/or B, but no Part D enrollment data for the beneficiary. (This status was indicated as 'XX' for 2006-2009)"));
assertTrue(compare.equalsDeep(ex));
}
use of org.hl7.fhir.r4b.model.ExpressionNode.Function in project kindling by HL7.
the class Publisher method execute.
/**
* Entry point to the publisher. This classes Java Main() calls this function
* to actually produce the specification
*
* @param folder
* @throws IOException
*/
public void execute(String folder) throws IOException {
tester = new PublisherTestSuites();
page.log("Publish FHIR in folder " + folder + " @ " + Config.DATE_FORMAT().format(page.getGenDate().getTime()), LogMessageType.Process);
if (web)
page.log("Build final copy for HL7 web site", LogMessageType.Process);
else
page.log("Build local copy", LogMessageType.Process);
if (outputdir != null) {
page.log("Create output in " + outputdir, LogMessageType.Process);
}
page.log("Detected Java version: " + System.getProperty("java.version") + " from " + System.getProperty("java.home") + " on " + System.getProperty("os.arch"), LogMessageType.Process);
try {
tester.initialTests();
page.setFolders(new FolderManager(folder, outputdir));
if (!initialize(folder))
throw new Exception("Unable to publish as preconditions aren't met");
cache = new IniFile(page.getFolders().rootDir + "temp" + File.separator + "build.cache");
loadSuppressedMessages(page.getFolders().rootDir);
boolean doAny = false;
for (String n : dates.keySet()) {
Long d = cache.getLongProperty("dates", n);
boolean b = d == null || (dates.get(n) > d);
cache.setLongProperty("dates", n, dates.get(n).longValue(), null);
buildFlags.put(n.toLowerCase(), b);
doAny = doAny || b;
}
cache.save();
if (noPartialBuild || !doAny || !(new File(page.getFolders().dstDir + "qa.html").exists()))
// nothing - build all
buildFlags.put("all", true);
if (singlePage != null) {
for (String n : buildFlags.keySet()) buildFlags.put(n, false);
buildFlags.put("page-" + singlePage.toLowerCase(), true);
} else if (singleResource != null) {
for (String n : buildFlags.keySet()) buildFlags.put(n, false);
buildFlags.put(singleResource.toLowerCase(), true);
}
if (!buildFlags.get("all")) {
if (!noSound) {
AudioUtilities.tone(1000, 10);
AudioUtilities.tone(1400, 10);
AudioUtilities.tone(1800, 10);
AudioUtilities.tone(1000, 10);
AudioUtilities.tone(1400, 10);
AudioUtilities.tone(1800, 10);
}
page.log("Partial Build (if you want a full build, just run the build again)", LogMessageType.Process);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (String n : buildFlags.keySet()) if (buildFlags.get(n))
b.append(n);
page.log(" Build: " + b.toString(), LogMessageType.Process);
} else {
if (!noSound)
AudioUtilities.tone(1200, 30);
page.log("Full Build", LogMessageType.Process);
}
if (isGenerate && page.getBuildId() == null)
page.setBuildId(getGitBuildId());
page.log("Version " + page.getVersion() + "-" + page.getBuildId(), LogMessageType.Hint);
Utilities.createDirectory(page.getFolders().dstDir);
Utilities.deleteTempFiles();
page.getBreadCrumbManager().parse(page.getFolders().srcDir + "hierarchy.xml");
page.loadSnomed();
page.loadLoinc();
page.loadUcum();
buildFeedsAndMaps();
prsr.setExternals(externals);
prsr.parse(page.getGenDate(), page.getValidationErrors());
for (String n : page.getDefinitions().sortedResourceNames()) if (!page.getBreadCrumbManager().knowsResource(n))
page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "hierarchy.xml", "Resource not found: " + n, IssueSeverity.ERROR));
for (String n : prsr.getErrors()) page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "source spreadsheets", n, IssueSeverity.ERROR));
if (web) {
page.log("Clear Directory", LogMessageType.Process);
Utilities.clearDirectory(page.getFolders().dstDir);
}
if (web || (isGenerate && buildFlags.get("all"))) {
Utilities.createDirectory(page.getFolders().dstDir + "html");
Utilities.createDirectory(page.getFolders().dstDir + "examples");
}
for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) if (!ig.isCore())
Utilities.createDirectory(page.getFolders().dstDir + ig.getCode());
if (buildFlags.get("all")) {
copyStaticContent();
}
page.makeRenderingContext();
loadValueSets1();
prsr.getRegistry().commit();
generateSCMaps();
validate();
processProfiles();
checkAllOk();
if (isGenerate) {
produceSpecification();
checkAllOk();
}
if (doValidate)
validationProcess();
page.saveSnomed();
page.getWorkerContext().saveCache();
processWarnings(false);
if (isGenerate && buildFlags.get("all"))
produceQA();
if (!buildFlags.get("all")) {
page.log("This was a Partial Build", LogMessageType.Process);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (String n : buildFlags.keySet()) if (buildFlags.get(n))
b.append(n);
page.log(" Build: " + b.toString(), LogMessageType.Process);
} else
page.log("This was a Full Build", LogMessageType.Process);
if (!noSound) {
AudioUtilities.tone(800, 10);
AudioUtilities.tone(1000, 10);
AudioUtilities.tone(1200, 10);
AudioUtilities.tone(1000, 10);
AudioUtilities.tone(800, 10);
}
page.log("Finished publishing FHIR @ " + Config.DATE_FORMAT().format(Calendar.getInstance().getTime()), LogMessageType.Process);
} catch (Exception e) {
if (!(e instanceof NullPointerException)) {
// because NullPointerException is unexpected...
try {
processWarnings(e instanceof EValidationFailed);
} catch (Exception e2) {
page.log(" ERROR: Unable to process warnings: " + e2.getMessage(), LogMessageType.Error);
e2.printStackTrace();
}
}
if (buildFlags.containsKey("all") && !buildFlags.get("all")) {
page.log("This was a Partial Build", LogMessageType.Process);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (String n : buildFlags.keySet()) if (buildFlags.get(n))
b.append(n);
page.log(" Build: " + b.toString(), LogMessageType.Process);
} else
page.log("This was a Full Build", LogMessageType.Process);
if (!noSound) {
AudioUtilities.tone(800, 20);
AudioUtilities.tone(1000, 20);
AudioUtilities.tone(1200, 20);
}
try {
Thread.sleep(50);
} catch (InterruptedException e1) {
}
if (!noSound) {
AudioUtilities.tone(800, 20);
AudioUtilities.tone(1000, 20);
AudioUtilities.tone(1200, 20);
}
try {
Thread.sleep(50);
} catch (InterruptedException e1) {
}
if (!noSound) {
AudioUtilities.tone(800, 20);
AudioUtilities.tone(1000, 20);
AudioUtilities.tone(1200, 20);
}
page.log("FHIR build failure @ " + Config.DATE_FORMAT().format(Calendar.getInstance().getTime()), LogMessageType.Process);
System.out.println("Error: " + e.getMessage());
e.printStackTrace();
TextFile.stringToFile(StringUtils.defaultString(e.getMessage()), Utilities.path(folder, "publish", "simple-error.txt"));
System.exit(1);
}
}
use of org.hl7.fhir.r4b.model.ExpressionNode.Function in project kindling by HL7.
the class PageProcessor method produceStructureDefinitionExamples.
private String produceStructureDefinitionExamples(ResourceDefn resource) throws Exception {
StringBuilder s = new StringBuilder();
s.append("<div id=\"tabs\">\r\n");
s.append("<ul>\r\n");
s.append(" <li><a href=\"#tabs-1\">Base Types</a></li>\r\n");
s.append(" <li><a href=\"#tabs-2\">Resources</a></li>\r\n");
s.append(" <li><a href=\"#tabs-3\">Constraints</a></li>\r\n");
s.append(" <li><a href=\"#tabs-4\">Extensions</a></li>\r\n");
s.append(" <li><a href=\"#tabs-5\">Examples</a></li>\r\n");
s.append("</ul>\r\n");
s.append("<div id=\"tabs-1\">\r\n");
// base types
s.append("<table class=\"list\">\r\n");
genStructureExampleCategory(s, "Abstract Types", "3");
genStructureExample(s, definitions.getElementLink(), "element.profile", "element", "Element");
genStructureExample(s, definitions.getBackboneLink(), "backboneelement.profile", "backboneelement", "BackBoneElement");
genStructureExample(s, "resource.html", "resource.profile", "resource", "Resource");
genStructureExample(s, "domainresource.html", "domainresource.profile", "domainresource", "DomainResource");
genStructureExampleCategory(s, "Primitive Types", "3");
List<String> names = new ArrayList<String>();
names.addAll(definitions.getPrimitives().keySet());
Collections.sort(names);
for (String n : names) {
DefinedCode dc = definitions.getPrimitives().get(n);
genStructureExample(s, "datatypes.html#" + dc.getCode(), dc.getCode().toLowerCase() + ".profile", dc.getCode().toLowerCase(), dc.getCode());
}
genStructureExampleCategory(s, "Data Types", "3");
names.clear();
names.addAll(definitions.getTypes().keySet());
names.addAll(definitions.getInfrastructure().keySet());
Collections.sort(names);
for (String n : names) {
org.hl7.fhir.definitions.model.TypeDefn t = definitions.getTypes().get(n);
if (t == null)
t = definitions.getInfrastructure().get(n);
genStructureExample(s, getLinkFor("", t.getName()), t.getName().toLowerCase() + ".profile", t.getName().toLowerCase(), t.getName());
}
s.append("</table>\r\n");
s.append("</div>\r\n");
s.append("<div id=\"tabs-2\">\r\n");
s.append("<table class=\"list\">\r\n");
genStructureExampleCategory(s, "Resources", "3");
for (String n : definitions.sortedResourceNames()) {
ResourceDefn r = definitions.getResources().get(n);
genStructureExample(s, r.getName().toLowerCase() + ".html", r.getName().toLowerCase() + ".profile", r.getName().toLowerCase(), r.getName());
}
s.append("</table>\r\n");
s.append("</div>\r\n");
s.append("<div id=\"tabs-3\">\r\n");
s.append("<table class=\"list\">\r\n");
Map<String, ConstraintStructure> constraints = new HashMap<String, ConstraintStructure>();
for (Profile pp : definitions.getPackList()) {
for (ConstraintStructure p : pp.getProfiles()) constraints.put(p.getId(), p);
}
for (String rn : definitions.sortedResourceNames()) for (Profile ap : definitions.getResourceByName(rn).getConformancePackages()) for (ConstraintStructure p : ap.getProfiles()) constraints.put(p.getId(), p);
names.clear();
names.addAll(constraints.keySet());
Collections.sort(names);
for (ImplementationGuideDefn ig : definitions.getSortedIgs()) {
boolean started = false;
for (String n : names) {
ConstraintStructure p = constraints.get(n);
if (ig == p.getUsage()) {
if (!started) {
started = true;
genStructureExampleCategory(s, ig.getName(), "3");
}
String prefix = ig.isCore() ? "" : ig.getCode() + "/";
genStructureExample(s, prefix + p.getId().toLowerCase() + ".html", prefix + p.getId().toLowerCase() + ".profile", p.getId().toLowerCase(), p.getTitle());
}
}
}
s.append("</table>\r\n");
s.append("</div>\r\n");
s.append("<div id=\"tabs-4\">\r\n");
s.append("<table class=\"list\">\r\n");
names.clear();
for (StructureDefinition sd : workerContext.getExtensionDefinitions()) names.add(sd.getUrl());
Collections.sort(names);
for (ImplementationGuideDefn ig : definitions.getSortedIgs()) {
boolean started = false;
for (String n : names) {
StructureDefinition ed = workerContext.fetchResource(StructureDefinition.class, n);
if (ig.getCode().equals(ToolResourceUtilities.getUsage(ed))) {
if (!started) {
started = true;
genStructureExampleCategory(s, ig.getName(), "3");
}
String prefix = ig.isCore() ? "" : ig.getCode() + "/";
genStructureExample(s, prefix + "extension-" + ed.getId().toLowerCase() + ".html", prefix + "extension-" + ed.getId().toLowerCase(), ed.getId().toLowerCase(), ed.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/") ? ed.getUrl().substring(40) : ed.getUrl(), ed.getName());
}
}
}
s.append("</table>\r\n");
s.append("</div>\r\n");
s.append("<div id=\"tabs-5\">\r\n");
s.append("<table class=\"list\">\r\n");
for (Example e : resource.getExamples()) {
if (e.isRegistered() && Utilities.noString(e.getIg()))
produceExampleListEntry(s, e, null, null);
}
for (Profile p : resource.getConformancePackages()) {
for (Example e : p.getExamples()) {
produceExampleListEntry(s, e, p, null);
}
}
for (Profile p : definitions.getPackList()) {
ImplementationGuideDefn ig = definitions.getIgs().get(p.getCategory());
for (Example e : p.getExamples()) {
String rn = e.getResourceName();
if (Utilities.noString(rn))
rn = e.getXml().getDocumentElement().getNodeName();
if (rn.equals(resource.getName()))
produceExampleListEntry(s, e, p, ig);
}
}
for (ImplementationGuideDefn ig : definitions.getSortedIgs()) {
if (ig.getIg() != null) {
for (ImplementationGuideDefinitionResourceComponent res : ig.getIg().getDefinition().getResource()) {
Example e = (Example) res.getUserData(ToolResourceUtilities.NAME_RES_EXAMPLE);
if (res.hasExample() && e != null && e.getResourceName().equals(resource.getName()))
produceExampleListEntry(s, res, ig);
}
}
}
s.append("</table>\r\n");
s.append("</div>\r\n");
s.append("</div>\r\n");
s.append("\r\n");
s.append("<script src=\"external/jquery/jquery.js\"> </script>\r\n");
s.append("<script src=\"jquery-ui.min.js\"> </script>\r\n");
s.append("<script>\r\n");
s.append("try {\r\n");
s.append(" var currentTabIndex = sessionStorage.getItem('fhir-sdelist-tab-index');\r\n");
s.append("}\r\n");
s.append("catch(exception){\r\n");
s.append("}\r\n");
s.append("\r\n");
s.append("if (!currentTabIndex)\r\n");
s.append(" currentTabIndex = '0';\r\n");
s.append(" \r\n");
s.append("$( '#tabs' ).tabs({\r\n");
s.append(" active: currentTabIndex,\r\n");
s.append(" activate: function( event, ui ) {\r\n");
s.append(" var active = $('.selector').tabs('option', 'active');\r\n");
s.append(" currentTabIndex = ui.newTab.index();\r\n");
s.append(" document.activeElement.blur();\r\n");
s.append(" try {\r\n");
s.append(" sessionStorage.setItem('fhir-sdelist-tab-index', currentTabIndex);\r\n");
s.append(" }\r\n");
s.append(" catch(exception){\r\n");
s.append(" }\r\n");
s.append(" }\r\n");
s.append(" });\r\n");
s.append("</script>\r\n");
s.append("\r\n");
return s.toString();
}
use of org.hl7.fhir.r4b.model.ExpressionNode.Function in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7DocumentReferenceFHIRConversionTest method doc_ref_content_test.
@ParameterizedTest
@ValueSource(strings = { "MDM^T02", "MDM^T06" })
void doc_ref_content_test(String segment) {
String documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||TEXT||||201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + // Next three lines create an attachment
"OBX|1|TX|||ECHOCARDIOGRAPHIC REPORT||||||F|||202101010000|||\n" + "OBX|2|TX|||NORMAL LV CHAMBER SIZE WITH MILD CONCENTRIC LVH||||||F|||202101010000|||\n" + "OBX|3|TX|||HYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%||||||F|||202101010000|||\n";
DocumentReference report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
DocumentReference.DocumentReferenceContentComponent content = report.getContentFirstRep();
// Future TXA.3, currently always defaults to text/plain
assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
// TXA.7 date
assertThat(content.getAttachment().getCreationElement().toString()).containsPattern("2018-01-18T03:46:00");
assertThat(content.getAttachment().hasData()).isTrue();
String decodedData = new String(Base64.getDecoder().decode(content.getAttachment().getDataElement().getValueAsString()));
assertThat(decodedData).isEqualTo("ECHOCARDIOGRAPHIC REPORT\nNORMAL LV CHAMBER SIZE WITH MILD CONCENTRIC LVH\nHYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%");
// TODO: Determine if we need to look at anything other than OBX.2 when it is TX
// Leave this test in place as a reminder
documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||||||201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + // TODO: find better code for this test which is to see that OBX.2 is the fallback.
"OBX|1|SN|||||||||F";
report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
content = report.getContentFirstRep();
// Because the OBX is not TX, the content is put in an Observation
// FHIR requires a Content element, so only a minimal one is created.
// Future OBX.2 is the backup for content type, but currently always defaults to text/plain
assertThat(content.getAttachment().hasContentType()).isTrue();
// Currently always defaults to text/plain
assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
// TXA.7 date
assertThat(content.getAttachment().getCreationElement().toString()).containsPattern("2018-01-18T03:46:00");
assertThat(content.getAttachment().hasData()).isFalse();
// Test that content is created even if TXA.7 is empty
documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + // Ensure that empty TXA.7 still works
"TXA|1||||||||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + "OBX|1|SN|||||||||F";
report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
content = report.getContentFirstRep();
// Because the OBX is not TX, the content is put in an Observation
// FHIR requires a Content element, so only a minimal one is created.
// Currently always defaults to text/plain
assertThat(content.getAttachment().hasContentType()).isTrue();
// Currently always defaults to text/plain, even if not data for content
assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
// No TXA.7 date
assertThat(content.getAttachment().hasCreationElement()).isFalse();
assertThat(content.getAttachment().hasData()).isFalse();
}
use of org.hl7.fhir.r4b.model.ExpressionNode.Function in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ObservationFHIRConversionTest method testObservationSTMultiplePartsResult.
@Test
void testObservationSTMultiplePartsResult() throws IOException {
String hl7message = baseMessage + "OBX|1|ST|^Type of protein feed^L||HYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%~Fifth line, as part of a repeated field||||||F||";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
assertThat(obsResource).hasSize(1);
Observation obs = (Observation) obsResource.get(0);
assertThat(obs.getValueStringType()).isNotNull();
StringType q = obs.getValueStringType();
assertThat(q.asStringValue()).isEqualTo("HYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%. Fifth line, as part of a repeated field.");
}
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