Examples with NamingSystem org.hl7.fhir.r5.model.NamingSystem used on opensource projects

Example 1 with NamingSystem

use of org.hl7.fhir.r5.model.NamingSystem in project kindling by HL7.

the class Publisher method generateCodeSystemRegistry.

private void generateCodeSystemRegistry() throws FileNotFoundException, IOException, Exception {
    XmlParser xml = new XmlParser();
    xml.setOutputStyle(OutputStyle.PRETTY);
    Bundle bnd = (Bundle) xml.parse(new CSFileInputStream(Utilities.path(page.getFolders().srcDir, "namingsystem", "namingsystem-terminologies.xml")));
    for (BundleEntryComponent entry : bnd.getEntry()) {
        NamingSystem ns = (NamingSystem) entry.getResource();
        entry.setFullUrl("http://hl7.org/fhir/NamingSystem/" + ns.getId());
        String url = null;
        for (NamingSystemUniqueIdComponent t : ns.getUniqueId()) {
            if (t.getType() == NamingSystemIdentifierType.URI)
                url = t.getValue();
        }
        if (url != null) {
            if (url.startsWith("http://hl7.org/fhir"))
                page.getDefinitions().addNs(url, "System " + ns.getName(), "terminologies-systems.html#" + url);
            page.getDefinitions().addNs(entry.getFullUrl(), ns.getId(), "terminologies-systems.html#" + url);
        }
    }
    List<String> names = new ArrayList<String>();
    Set<String> urls = new HashSet<>();
    names.addAll(page.getCodeSystems().keys());
    Collections.sort(names);
    for (String n : names) {
        CodeSystem cs = page.getCodeSystems().get(n);
        if (cs != null && !urls.contains(cs.getUrl()) && cs.hasUrl() && !cs.getUrl().startsWith("http://terminology.hl7.org")) {
            urls.add(cs.getUrl());
            if (cs.hasName()) {
                NamingSystem ns = new NamingSystem();
                ns.setId(cs.getId());
                ns.setName(cs.getName());
                ns.setStatus(cs.getStatus());
                if (!ns.hasStatus())
                    ns.setStatus(PublicationStatus.DRAFT);
                ns.setKind(NamingSystemType.CODESYSTEM);
                ns.setPublisher(cs.getPublisher());
                for (ContactDetail c : cs.getContact()) {
                    ContactDetail nc = ns.addContact();
                    nc.setName(c.getName());
                    for (ContactPoint cc : c.getTelecom()) {
                        nc.getTelecom().add(cc);
                    }
                }
                ns.setDate(cs.getDate());
                if (!ns.hasDate())
                    ns.setDate(page.getGenDate().getTime());
                ns.setDescription(cs.getDescription());
                ns.addUniqueId().setType(NamingSystemIdentifierType.URI).setValue(cs.getUrl()).setPreferred(true);
                String oid = CodeSystemUtilities.getOID(cs);
                if (oid != null) {
                    if (oid.startsWith("urn:oid:"))
                        oid = oid.substring(8);
                    ns.addUniqueId().setType(NamingSystemIdentifierType.OID).setValue(oid).setPreferred(false);
                }
                ns.setUserData("path", cs.getUserData("path"));
                bnd.addEntry().setResource(ns).setFullUrl("http://hl7.org/fhir/" + ns.fhirType() + "/" + ns.getId());
            }
        }
    }
    xml.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.xml")), bnd);
    cloneToXhtml("namingsystem-terminologies", "Terminology Registry", false, "resource-instance:NamingSystem", "Terminology Registry", null, wg("vocab"));
    xml.setOutputStyle(OutputStyle.CANONICAL);
    xml.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.canonical.xml")), bnd);
    JsonParser json = new JsonParser();
    json.setOutputStyle(OutputStyle.PRETTY);
    json.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.json")), bnd);
    jsonToXhtml("namingsystem-terminologies", "Terminology Registry", TextFile.fileToString(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.json")), "resource-instance:NamingSystem", "Terminology Registry", null, wg("vocab"));
    json.setOutputStyle(OutputStyle.CANONICAL);
    json.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.canonical.json")), bnd);
    RdfParser rdf = new RdfParser();
    rdf.setOutputStyle(OutputStyle.PRETTY);
    rdf.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.ttl")), bnd);
    ttlToXhtml("namingsystem-terminologies", "Terminology Registry", TextFile.fileToString(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.ttl")), "resource-instance:NamingSystem", "Terminology Registry", null, wg("vocab"));
    StringBuilder b = new StringBuilder();
    b.append("<table class=\"grid\">\r\n");
    b.append(" <tr>");
    b.append("<td><b>Name</b></td>");
    b.append("<td><b>Uri</b></td>");
    b.append("<td><b>OID</b></td>");
    b.append("</tr>\r\n");
    for (BundleEntryComponent entry : bnd.getEntry()) {
        NamingSystem ns = (NamingSystem) entry.getResource();
        String uri = "";
        String oid = "";
        for (NamingSystemUniqueIdComponent id : ns.getUniqueId()) {
            if (id.getType() == NamingSystemIdentifierType.URI)
                uri = id.getValue();
            if (id.getType() == NamingSystemIdentifierType.OID)
                oid = id.getValue();
        }
        String link = "terminologies-systems.html#" + uri;
        if (ns.getUserData("path") != null)
            link = ns.getUserString("path");
        b.append(" <tr>");
        b.append("<td><a href=\"" + link + "\">" + Utilities.escapeXml(ns.getName()) + "</a></td>");
        b.append("<td>" + Utilities.escapeXml(uri) + "</td>");
        b.append("<td>" + Utilities.escapeXml(oid) + "</td>");
        b.append("</tr>\r\n");
    }
    b.append("</table>\r\n");
    String html = TextFile.fileToString(page.getFolders().templateDir + "template-example.html").replace("<%example%>", b.toString()).replace("<%example-usage%>", "");
    html = page.processPageIncludes("namingsystem-terminologies.html", html, "resource-instance:NamingSystem", null, bnd, null, "Example", null, null, page.getDefinitions().getWorkgroups().get("fhir"));
    TextFile.stringToFile(html, page.getFolders().dstDir + "namingsystem-terminologies.html");
    cachePage("namingsystem-terminologies.html", html, "Registered Code Systems", false);
}

Example 2 with NamingSystem

use of org.hl7.fhir.r5.model.NamingSystem in project kindling by HL7.

the class PageProcessor method genNSList.

private String genNSList() throws Exception {
    StringBuilder b = new StringBuilder();
    b.append("<p>Redirects on this page:</p>\r\n");
    b.append("<ul>\r\n");
    b.append(" <li>Resources</li>\r\n");
    b.append(" <li>Data Types</li>\r\n");
    b.append(" <li>Code Systems</li>\r\n");
    b.append(" <li>Value Sets</li>\r\n");
    b.append(" <li>Extensions</li>\r\n");
    b.append(" <li>Profiles</li>\r\n");
    b.append(" <li>Naming Systems</li>\r\n");
    b.append(" <li>Examples</li>\r\n");
    b.append(" <li>Compartments</li>\r\n");
    b.append(" <li>Data Elements</li>\r\n");
    b.append(" <li>Search Parameters</li>\r\n");
    b.append(" <li>Implementation Guides</li>\r\n");
    b.append(" <li>SIDs</li>\r\n");
    b.append(" <li>Others From publish.ini</li>\r\n");
    b.append("</ul>\r\n");
    b.append("<table class=\"grid\">\r\n");
    b.append(" <tr><td><b>URL</b></td><td><b>Thing</b></td><td><b>Page</b></td></tr>");
    for (String n : definitions.sortedResourceNames()) definitions.addNs("http://hl7.org/fhir/" + n, n + " Resource", n.toLowerCase() + ".html");
    for (String n : definitions.getTypes().keySet()) definitions.addNs("http://hl7.org/fhir/" + n, "Data Type " + n, definitions.getSrcFile(n) + ".html#" + n);
    for (String n : definitions.getPrimitives().keySet()) definitions.addNs("http://hl7.org/fhir/" + n, "Primitive Data Type " + n, definitions.getSrcFile(n) + ".html#" + n);
    for (String n : definitions.getConstraints().keySet()) definitions.addNs("http://hl7.org/fhir/" + n, "Data Type Profile " + n, definitions.getSrcFile(n) + ".html#" + n);
    for (String n : definitions.getInfrastructure().keySet()) definitions.addNs("http://hl7.org/fhir/" + n, "Data Type " + n, definitions.getSrcFile(n) + ".html#" + n);
    for (CodeSystem cs : getCodeSystems().getList()) if (cs != null && cs.getUrl().startsWith("http://hl7.org/fhir"))
        definitions.addNs(cs.getUrl(), "CodeSystem " + cs.getName(), cs.getUserString("path"));
    for (ValueSet vs : getValueSets().getList()) if (vs.getUrl().startsWith("http://hl7.org/fhir"))
        definitions.addNs(vs.getUrl(), "ValueSet " + vs.present(), vs.getUserString("path"));
    for (ConceptMap cm : getConceptMaps().getList()) if (cm.getUrl().startsWith("http://hl7.org/fhir"))
        definitions.addNs(cm.getUrl(), "Concept Map" + cm.getName(), cm.getUserString("path"));
    for (StructureDefinition sd : profiles.getList()) if (sd.getUrl().startsWith("http://hl7.org/fhir") && !definitions.getResourceTemplates().containsKey(sd.getName()))
        definitions.addNs(sd.getUrl(), "Profile " + sd.getName(), sd.getUserString("path"));
    for (StructureDefinition sd : workerContext.getExtensionDefinitions()) if (sd.getUrl().startsWith("http://hl7.org/fhir"))
        definitions.addNs(sd.getUrl(), "Profile " + sd.getName(), sd.getUserString("path"));
    for (NamingSystem nss : definitions.getNamingSystems()) {
        String url = null;
        definitions.addNs("http://hl7.org/fhir/NamingSystem/" + nss.getId(), "System " + nss.getName(), nss.getUserString("path"));
        for (NamingSystemUniqueIdComponent t : nss.getUniqueId()) {
            if (t.getType() == NamingSystemIdentifierType.URI)
                url = t.getValue();
        }
        if (url != null && url.startsWith("http://hl7.org/fhir"))
            definitions.addNs(url, "System " + nss.getName(), nss.getUserString("path"));
    }
    for (String n : ini.getPropertyNames("redirects")) {
        String[] parts = ini.getStringProperty("redirects", n).split("\\;");
        definitions.addNs(n, "System " + parts[0], parts[1]);
    }
    for (ImplementationGuideDefn ig : definitions.getIgs().values()) {
        if (!ig.isCore()) {
            definitions.addNs("http://hl7.org/fhir/ImplementationGuide/" + ig.getCode(), ig.getName(), ig.getHomePage());
            definitions.addNs("http://hl7.org/fhir/" + ig.getCode(), ig.getName(), ig.getHomePage());
        }
    }
    for (Compartment t : definitions.getCompartments()) {
        definitions.addNs(t.getUri(), t.getName(), "compartmentdefinition.html#" + t.getName());
    }
    List<String> list = new ArrayList<String>();
    list.addAll(definitions.getRedirectList().keySet());
    Collections.sort(list);
    for (String url : list) {
        NamespacePair p = definitions.getRedirectList().get(url);
        b.append(" <tr><td>" + Utilities.escapeXml(url) + "</td><td>" + hsplt(Utilities.escapeXml(p.desc)) + "</td><td><a href=\"" + p.page + "\">" + hsplt(Utilities.escapeXml(p.page)) + "</a></td></tr>\r\n");
    }
    b.append("</table>\r\n");
    b.append("<p>" + Integer.toString(list.size()) + " Entries</p>\r\n");
    return b.toString();
}

Example 3 with NamingSystem

use of org.hl7.fhir.r5.model.NamingSystem in project cqf-ruler by DBCG.

the class ExampleServerR4IT method testCreateAndRead.

@Test
@Order(0)
void testCreateAndRead() {
    String methodName = "testCreateAndRead";
    ourLog.info("Entering " + methodName + "()...");
    Patient pt = new Patient();
    pt.setActive(true);
    pt.getBirthDateElement().setValueAsString("2020-01-01");
    pt.addIdentifier().setSystem("http://foo").setValue("12345");
    pt.addName().setFamily(methodName);
    IIdType id = ourClient.create().resource(pt).execute().getId();
    Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
    assertEquals(methodName, pt2.getName().get(0).getFamily());
// Wait until the MDM message has been processed
// await().until(() -> {
// sleep(1000);
// return getGoldenResourcePatient() != null;
// });
// Patient goldenRecord = getGoldenResourcePatient();
// // Verify that a golden record Patient was created
// assertNotNull(goldenRecord.getMeta().getTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD"));
}

Example 4 with NamingSystem

use of org.hl7.fhir.r5.model.NamingSystem in project hapi-fhir-jpaserver-starter by hapifhir.

the class ExampleServerR4IT method testCreateAndRead.

@Test
@Order(0)
void testCreateAndRead() {
    String methodName = "testCreateAndRead";
    ourLog.info("Entering " + methodName + "()...");
    Patient pt = new Patient();
    pt.setActive(true);
    pt.getBirthDateElement().setValueAsString("2020-01-01");
    pt.addIdentifier().setSystem("http://foo").setValue("12345");
    pt.addName().setFamily(methodName);
    IIdType id = ourClient.create().resource(pt).execute().getId();
    Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
    assertEquals(methodName, pt2.getName().get(0).getFamily());
    // Wait until the MDM message has been processed
    await().atMost(1, TimeUnit.MINUTES).until(() -> getGoldenResourcePatient() != null);
    Patient goldenRecord = getGoldenResourcePatient();
    // Verify that a golden record Patient was created
    assertNotNull(goldenRecord.getMeta().getTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD"));
}

Example 5 with NamingSystem

use of org.hl7.fhir.r5.model.NamingSystem in project org.hl7.fhir.core by hapifhir.

the class PackageMaintainer method check.

private void check(String ver) throws IOException {
    System.out.println("Check " + ver);
    List<String> allIds = listResources(Utilities.path(PATH, "hl7.fhir." + ver + ".examples", "package"));
    List<String> coreIds = listResources(Utilities.path(PATH, "hl7.fhir." + ver + ".core", "package"));
    for (String s : coreIds) {
        if (!allIds.contains(s)) {
            System.out.println("Core contains " + s + " but allIds doesn't");
        }
    }
    for (String s : allIds) {
        if (!coreIds.contains(s)) {
            String c = s.substring(0, s.indexOf("-"));
            if (Utilities.existsInList(c, "CodeSystem", "ValueSet", "ConceptMap", "StructureDefinition", "StructureMap", "NamingSystem", "SearchParameter", "OperationDefinition", "CapabilityStatement", "Conformance"))
                System.out.println("Examples contains " + s + " but core doesn't");
        }
    }
    strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".core", "package")));
    strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".expansions", "package")));
    if (!ver.equals("r2b"))
        strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".elements", "package")));
}