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

Example 1 with Base

use of org.hl7.fhir.r5.model.Base in project beneficiary-fhir-data by CMSgov.

the class BeneficiaryTransformerV2Test method setup.

@BeforeEach
public void setup() {
    List<Object> parsedRecords = ServerTestUtils.parseData(Arrays.asList(StaticRifResourceGroup.SAMPLE_A.getResources()));
    // Pull out the base Beneficiary record and fix its HICN and MBI-HASH fields.
    beneficiary = parsedRecords.stream().filter(r -> r instanceof Beneficiary).map(r -> (Beneficiary) r).findFirst().get();
    beneficiary.getSkippedRifRecords().add(new SkippedRifRecord());
    beneficiary.setLastUpdated(Instant.now());
    beneficiary.setMbiHash(Optional.of("someMBIhash"));
    // Add the history records to the Beneficiary, but nill out the HICN fields.
    Set<BeneficiaryHistory> beneficiaryHistories = parsedRecords.stream().filter(r -> r instanceof BeneficiaryHistory).map(r -> (BeneficiaryHistory) r).filter(r -> beneficiary.getBeneficiaryId().equals(r.getBeneficiaryId())).collect(Collectors.toSet());
    beneficiary.getBeneficiaryHistories().addAll(beneficiaryHistories);
    // Add the MBI history records to the Beneficiary.
    Set<MedicareBeneficiaryIdHistory> beneficiaryMbis = parsedRecords.stream().filter(r -> r instanceof MedicareBeneficiaryIdHistory).map(r -> (MedicareBeneficiaryIdHistory) r).filter(r -> beneficiary.getBeneficiaryId().equals(r.getBeneficiaryId().orElse(null))).collect(Collectors.toSet());
    beneficiary.getMedicareBeneficiaryIdHistories().addAll(beneficiaryMbis);
    assertThat(beneficiary, is(notNullValue()));
    createPatient(RequestHeaders.getHeaderWrapper());
}

Example 2 with Base

use of org.hl7.fhir.r5.model.Base in project beneficiary-fhir-data by CMSgov.

the class CoverageTransformerV2Test method setup.

@BeforeEach
public void setup() {
    List<Object> parsedRecords = ServerTestUtils.parseData(Arrays.asList(StaticRifResourceGroup.SAMPLE_A.getResources()));
    // Pull out the base Beneficiary record and fix its HICN and MBI-HASH fields.
    beneficiary = parsedRecords.stream().filter(r -> r instanceof Beneficiary).map(r -> (Beneficiary) r).findFirst().get();
    Calendar calen = Calendar.getInstance();
    calen.set(2021, 3, 17);
    beneficiary.setLastUpdated(calen.getTime().toInstant());
}

Example 3 with Base

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

the class Publisher method resolve.

@Override
public javax.xml.transform.Source resolve(String href, String base) throws TransformerException {
    if (!href.startsWith("http://fhir.healthintersections.com.au/open/ValueSet/$expand"))
        return null;
    try {
        Map<String, String> params = splitQuery(new URL(href));
        ValueSet vs = page.getValueSets().get(params.get("identifier"));
        if (vs == null) {
            page.log("unable to resolve " + params.get("identifier"), LogMessageType.Process);
            return null;
        }
        vs = page.expandValueSet(vs, true);
        if (vs == null) {
            page.log("unable to expand " + params.get("identifier"), LogMessageType.Process);
            return null;
        }
        ByteArrayOutputStream bytes = new ByteArrayOutputStream();
        new XmlParser().compose(bytes, vs, false);
        bytes.close();
        return new StreamSource(new ByteArrayInputStream(bytes.toByteArray()));
    } catch (Exception e) {
        throw new TransformerException(e);
    }
}

Example 4 with Base

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

the class Publisher method produceProfile.

private void produceProfile(ResourceDefn resource, Profile pack, ConstraintStructure profile, SectionTracker st, String intro, String notes, String prefix, ImplementationGuideDefn ig) throws Exception {
    File tmp = Utilities.createTempFile("tmp", ".tmp");
    String title = profile.getId();
    int level = (ig == null || ig.isCore()) ? 0 : 1;
    // you have to validate a profile, because it has to be merged with it's
    // base resource to fill out all the missing bits
    // validateProfile(profile);
    ByteArrayOutputStream bs = new ByteArrayOutputStream();
    XmlSpecGenerator gen = new XmlSpecGenerator(bs, title + "-definitions.html", "", page, ig.isCore() ? "" : "../");
    gen.generate(profile.getResource());
    gen.close();
    String xml = new String(bs.toByteArray());
    bs = new ByteArrayOutputStream();
    JsonSpecGenerator genJ = new JsonSpecGenerator(bs, title + "-definitions.html", "", page, ig.isCore() ? "" : "../", page.getVersion().toCode());
    genJ.generate(profile.getResource());
    genJ.close();
    String json = new String(bs.toByteArray());
    XmlParser comp = new XmlParser();
    FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + prefix + title + ".profile.xml");
    comp.setOutputStyle(OutputStyle.PRETTY).compose(s, profile.getResource());
    s.close();
    Utilities.copyFile(new CSFile(page.getFolders().dstDir + prefix + title + ".profile.xml"), new CSFile(page.getFolders().dstDir + "examples" + File.separator + title + ".profile.xml"));
    JsonParser jcomp = new JsonParser();
    s = new FileOutputStream(page.getFolders().dstDir + prefix + title + ".profile.json");
    jcomp.setOutputStyle(OutputStyle.PRETTY).compose(s, profile.getResource());
    s.close();
    // String shex = new ShExGenerator(page.getWorkerContext()).generate(HTMLLinkPolicy.NONE, profile.getResource());
    // TextFile.stringToFile(shex, Utilities.changeFileExt(page.getFolders().dstDir + prefix +title + ".profile.shex", ".shex"));
    // shexToXhtml(prefix +title + ".profile", "ShEx statement for " + prefix +title, shex, "profile-instance:type:" + title, "Type");
    TerminologyNotesGenerator tgen = new TerminologyNotesGenerator(new FileOutputStream(tmp), page);
    tgen.generate(level == 0 ? "" : "../", profile);
    tgen.close();
    String tx = TextFile.fileToString(tmp.getAbsolutePath());
    String src = TextFile.fileToString(page.getFolders().templateDir + "template-profile.html");
    src = page.processProfileIncludes(profile.getId(), profile.getId(), pack, profile, xml, json, tx, src, title + ".html", (resource == null ? profile.getResource().getType() : resource.getName()) + "/" + pack.getId() + "/" + profile.getId(), intro, notes, ig, false, false);
    if (st != null)
        src = insertSectionNumbers(src, st, title + ".html", level, null);
    else if (ig != null && !ig.isCore()) {
        src = addSectionNumbers(title + ".html", title, src, null, 1, null, ig);
        st = page.getSectionTrackerCache().get(ig.getCode() + "::" + title);
    }
    page.getHTMLChecker().registerFile(prefix + title + ".html", "StructureDefinition " + profile.getResource().getName(), HTMLLinkChecker.XHTML_TYPE, false);
    TextFile.stringToFile(src, page.getFolders().dstDir + prefix + title + ".html");
    new ProfileUtilities(page.getWorkerContext(), page.getValidationErrors(), page).generateSchematrons(new FileOutputStream(page.getFolders().dstDir + prefix + title + ".sch"), profile.getResource());
    if (pack.getExamples().size() > 0) {
        src = TextFile.fileToString(page.getFolders().templateDir + "template-profile-examples.html");
        src = page.processProfileIncludes(profile.getId(), profile.getId(), pack, profile, xml, json, tx, src, title + ".html", (resource == null ? profile.getResource().getType() : resource.getName()) + "/" + pack.getId() + "/" + profile.getId(), intro, notes, ig, false, false);
        page.getHTMLChecker().registerFile(prefix + title + "-examples.html", "Examples for StructureDefinition " + profile.getResource().getName(), HTMLLinkChecker.XHTML_TYPE, true);
        TextFile.stringToFile(src, page.getFolders().dstDir + prefix + title + "-examples.html");
    }
    src = TextFile.fileToString(page.getFolders().templateDir + "template-profile-definitions.html");
    src = page.processProfileIncludes(profile.getId(), profile.getId(), pack, profile, xml, json, tx, src, title + ".html", (resource == null ? profile.getResource().getType() : resource.getName()) + "/" + pack.getId() + "/" + profile.getId(), intro, notes, ig, false, false);
    if (st != null)
        src = insertSectionNumbers(src, st, title + "-definitions.html", level, null);
    page.getHTMLChecker().registerFile(prefix + title + "-definitions.html", "Definitions for StructureDefinition " + profile.getResource().getName(), HTMLLinkChecker.XHTML_TYPE, true);
    TextFile.stringToFile(src, page.getFolders().dstDir + prefix + title + "-definitions.html");
    src = TextFile.fileToString(page.getFolders().templateDir + "template-profile-mappings.html");
    src = page.processProfileIncludes(profile.getId(), profile.getId(), pack, profile, xml, json, tx, src, title + ".html", (resource == null ? profile.getResource().getType() : resource.getName()) + "/" + pack.getId() + "/" + profile.getId(), intro, notes, ig, false, false);
    if (st != null)
        src = insertSectionNumbers(src, st, title + "-mappings.html", level, null);
    page.getHTMLChecker().registerFile(prefix + title + "-mappings.html", "Mappings for StructureDefinition " + profile.getResource().getName(), HTMLLinkChecker.XHTML_TYPE, true);
    TextFile.stringToFile(src, page.getFolders().dstDir + prefix + title + "-mappings.html");
    try {
        processQuestionnaire(resource, profile.getResource(), st, false, prefix, ig);
    } catch (Exception e) {
        e.printStackTrace();
        page.log("Questionnaire Generation Failed: " + e.getMessage(), LogMessageType.Error);
    }
    new ReviewSpreadsheetGenerator().generate(page.getFolders().dstDir + prefix + Utilities.changeFileExt((String) profile.getResource().getUserData("filename"), "-review.xls"), "Health Level Seven International", page.getGenDate(), profile.getResource(), page);
    // xml to xhtml of xml
    // first pass is to strip the xsi: stuff. seems to need double
    // processing in order to delete namespace crap
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();
    Document xdoc = builder.parse(new CSFileInputStream(page.getFolders().dstDir + prefix + title + ".profile.xml"));
    XmlGenerator xmlgen = new XmlGenerator();
    xmlgen.generate(xdoc.getDocumentElement(), tmp, "http://hl7.org/fhir", xdoc.getDocumentElement().getLocalName());
    // reload it now
    builder = factory.newDocumentBuilder();
    xdoc = builder.parse(new CSFileInputStream(tmp.getAbsolutePath()));
    XhtmlGenerator xhtml = new XhtmlGenerator(new ExampleAdorner(page.getDefinitions(), page.genlevel(level)));
    ByteArrayOutputStream b = new ByteArrayOutputStream();
    xhtml.generate(xdoc, b, "StructureDefinition", profile.getTitle(), 0, true, title + ".profile.xml.html");
    String html = TextFile.fileToString(page.getFolders().templateDir + "template-profile-example-xml.html").replace("<%example%>", b.toString());
    html = page.processProfileIncludes(title + ".profile.xml.html", profile.getId(), pack, profile, "", "", "", html, title + ".html", (resource == null ? profile.getResource().getType() : resource.getName()) + "/" + pack.getId() + "/" + profile.getId(), intro, notes, ig, false, hasNarrative(xdoc));
    TextFile.stringToFile(html, page.getFolders().dstDir + prefix + title + ".profile.xml.html");
    page.getHTMLChecker().registerFile(prefix + title + ".profile.xml.html", "StructureDefinition", HTMLLinkChecker.XHTML_TYPE, false);
    String n = prefix + title + ".profile";
    json = resource2Json(profile.getResource());
    json = "<div class=\"example\">\r\n<p>" + Utilities.escapeXml("StructureDefinition for " + profile.getResource().getDescription()) + "</p>\r\n<p><a href=\"" + title + ".profile.json\">Raw JSON</a></p>\r\n<pre class=\"json\">\r\n" + Utilities.escapeXml(json) + "\r\n</pre>\r\n</div>\r\n";
    html = TextFile.fileToString(page.getFolders().templateDir + "template-profile-example-json.html").replace("<%example%>", json);
    html = page.processProfileIncludes(title + ".profile.json.html", profile.getId(), pack, profile, "", "", "", html, title + ".html", (resource == null ? profile.getResource().getType() : resource.getName()) + "/" + pack.getId() + "/" + profile.getId(), intro, notes, ig, false, false);
    TextFile.stringToFile(html, page.getFolders().dstDir + prefix + title + ".profile.json.html");
    // page.getEpub().registerFile(n + ".json.html", description, EPubManager.XHTML_TYPE);
    page.getHTMLChecker().registerExternal(n + ".json.html");
    tmp.delete();
}

Example 5 with Base

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

the class Publisher method checkFragment.

public void checkFragment(Fragment f) {
    try {
        // System.out.println("    "+f.page+"/"+f.id);
        String xml = f.getXml();
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        factory.setNamespaceAware(true);
        DocumentBuilder builder = factory.newDocumentBuilder();
        InputSource is = new InputSource(new StringReader(xml));
        Document doc = builder.parse(is);
        org.w3c.dom.Element base = doc.getDocumentElement();
        String type = base.getAttribute("fragment");
        if (!page.getDefinitions().hasPrimitiveType(type)) {
            if (f.isJson()) {
                org.hl7.fhir.r5.elementmodel.JsonParser p = new org.hl7.fhir.r5.elementmodel.JsonParser(page.getWorkerContext());
                p.setupValidation(ValidationPolicy.QUICK, null);
                p.parse(base.getTextContent(), type);
            } else {
                org.hl7.fhir.r5.elementmodel.XmlParser p = new org.hl7.fhir.r5.elementmodel.XmlParser(page.getWorkerContext());
                p.setupValidation(ValidationPolicy.QUICK, null);
                p.parse(XMLUtil.getFirstChild(base), type);
            }
        }
    } catch (Exception e) {
        page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.STRUCTURE, f.getPage(), "Fragment Error in page " + f.getPage() + (f.id != null ? "#" + f.id : "") + ": " + e.getMessage(), IssueSeverity.ERROR));
    }
}