Examples with XmlParser org.hl7.fhir.r4.formats.XmlParser used on opensource projects

Example 1 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project kindling by HL7.

the class Publisher method produceProfiledTypeProfile.

private void produceProfiledTypeProfile(ProfiledType pt) throws Exception {
    String fn = pt.getName().toLowerCase() + ".profile.xml";
    StructureDefinition rp = pt.getProfile();
    FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + fn);
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, rp);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(fn, ".canonical.xml"));
    new XmlParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, rp);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(fn, ".json"));
    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, rp);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(fn, ".canonical.json"));
    new JsonParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, rp);
    s.close();
    Utilities.copyFile(new CSFile(page.getFolders().dstDir + fn), new CSFile(Utilities.path(page.getFolders().dstDir, "examples", fn)));
    addToResourceFeed(rp, page.getTypeBundle(), (fn));
    cloneToXhtml(pt.getName().toLowerCase() + ".profile", "StructureDefinition for " + pt.getName(), false, "profile-instance:type:" + pt.getName(), "Type", null, wg("mnm"));
    jsonToXhtml(pt.getName().toLowerCase() + ".profile", "StructureDefinition for " + pt.getName(), resource2Json(rp), "profile-instance:type:" + pt.getName(), "Type", null, wg("mnm"));
    ttlToXhtml(pt.getName().toLowerCase() + ".profile", "StructureDefinition for " + pt.getName(), resource2Ttl(rp), "profile-instance:type:" + pt.getName(), "Type", null, wg("mnm"));
    String shex = new ShExGenerator(page.getWorkerContext()).generate(HTMLLinkPolicy.NONE, rp);
    TextFile.stringToFile(shex, Utilities.changeFileExt(page.getFolders().dstDir + fn, ".shex"));
    shexToXhtml(pt.getName().toLowerCase(), "ShEx statement for " + pt.getName(), shex, "profile-instance:type:" + pt.getName(), "Type", null, wg("mnm"));
}

Example 2 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser 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 3 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser 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 4 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project kindling by HL7.

the class Publisher method generateProfile.

private StructureDefinition generateProfile(ResourceDefn root, String n, String xmlSpec, String jsonSpec, String ttlSpec, boolean gen) throws Exception, FileNotFoundException {
    StructureDefinition rp = root.getProfile();
    page.getProfiles().see(rp, page.packageInfo());
    FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + n + ".profile.xml");
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, rp);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + n + ".profile.canonical.xml");
    new XmlParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, rp);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + n + ".profile.json");
    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, rp);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + n + ".profile.canonical.json");
    new JsonParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, rp);
    s.close();
    Utilities.copyFile(new CSFile(page.getFolders().dstDir + n + ".profile.xml"), new CSFile(page.getFolders().dstDir + "examples" + File.separator + n + ".profile.xml"));
    if (buildFlags.get("all")) {
        addToResourceFeed(rp, page.getResourceBundle(), null);
    }
    if (gen) {
        saveAsPureHtml(rp, new FileOutputStream(page.getFolders().dstDir + "html" + File.separator + n + ".html"));
        cloneToXhtml(n + ".profile", "StructureDefinition for " + n, true, "profile-instance:resource:" + root.getName(), "Profile", root, root.getWg());
        jsonToXhtml(n + ".profile", "StructureDefinition for " + n, resource2Json(rp), "profile-instance:resource:" + root.getName(), "Profile", root, root.getWg());
        ttlToXhtml(n + ".profile", "StructureDefinition for " + n, resource2Ttl(rp), "profile-instance:resource:" + root.getName(), "Profile", root, root.getWg());
        String shex = new ShExGenerator(page.getWorkerContext()).generate(HTMLLinkPolicy.NONE, rp);
        TextFile.stringToFile(shex, page.getFolders().dstDir + n + ".shex");
        shexToXhtml(n, "ShEx statement for " + n, shex, "profile-instance:type:" + root.getName(), "Type", root, root.getWg());
    }
    return rp;
}

Example 5 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project kindling by HL7.

the class Publisher method stripXml.

private InputStream stripXml(InputStream source) throws Exception {
    XmlParser p = new XmlParser();
    Resource r = p.parse(source);
    minify(r);
    ByteArrayOutputStream bo = new ByteArrayOutputStream();
    p.compose(bo, r);
    bo.close();
    return new ByteArrayInputStream(bo.toByteArray());
}