Examples with ConceptMapValidator org.hl7.fhir.definitions.validation.ConceptMapValidator used on opensource projects

Example 1 with ConceptMapValidator

use of org.hl7.fhir.definitions.validation.ConceptMapValidator in project kindling by HL7.

the class Publisher method processExample.

private void processExample(Example e, ResourceDefn resn, StructureDefinition profile, Profile pack, ImplementationGuideDefn ig) throws Exception {
    if (e.getType() == ExampleType.Tool)
        return;
    long time = System.currentTimeMillis();
    int level = (ig == null || ig.isCore()) ? 0 : 1;
    String prefix = (ig == null || ig.isCore()) ? "" : ig.getCode() + File.separator;
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();
    Document xdoc;
    String narrative = null;
    String n = e.getTitle();
    if (examplesProcessed.contains(prefix + n))
        return;
    examplesProcessed.add(prefix + n);
    // strip the xsi: stuff. seems to need double processing in order to
    // delete namespace crap
    xdoc = e.getXml();
    XmlGenerator xmlgen = new XmlGenerator();
    CSFile file = new CSFile(page.getFolders().dstDir + prefix + n + ".xml");
    xmlgen.generate(xdoc.getDocumentElement(), file, "http://hl7.org/fhir", xdoc.getDocumentElement().getLocalName());
    // check the narrative. We generate auto-narrative. If the resource didn't
    // have it's own original narrative, then we save it anyway
    // n
    String rt = null;
    try {
        RenderingContext lrc = page.getRc().copy().setLocalPrefix("").setTooCostlyNoteEmpty(PageProcessor.TOO_MANY_CODES_TEXT_EMPTY).setTooCostlyNoteNotEmpty(PageProcessor.TOO_MANY_CODES_TEXT_NOT_EMPTY);
        xdoc = loadDom(new FileInputStream(file), true);
        rt = xdoc.getDocumentElement().getNodeName();
        String id = XMLUtil.getNamedChildValue(xdoc.getDocumentElement(), "id");
        if (!page.getDefinitions().getBaseResources().containsKey(rt) && !id.equals(e.getId()))
            throw new Error("Resource in " + prefix + n + ".xml needs an id of value=\"" + e.getId() + "\"");
        page.getDefinitions().addNs("http://hl7.org/fhir/" + rt + "/" + id, "Example", prefix + n + ".html");
        if (rt.equals("ValueSet") || rt.equals("CodeSystem") || rt.equals("ConceptMap") || rt.equals("CapabilityStatement") || rt.equals("Library")) {
            // for these, we use the reference implementation directly
            CanonicalResource res = (CanonicalResource) loadExample(file);
            if (res.getUrl() != null && res.getUrl().startsWith("http://hl7.org/fhir"))
                res.setVersion(page.getVersion().toCode());
            boolean wantSave = false;
            if (res instanceof CapabilityStatement) {
                ((CapabilityStatement) res).setFhirVersion(page.getVersion());
                if (res.hasText() && res.getText().hasDiv())
                    wantSave = updateVersion(((CapabilityStatement) res).getText().getDiv());
            }
            if (!res.hasText() || !res.getText().hasDiv()) {
                RendererFactory.factory(res, lrc).render(res);
                wantSave = true;
            }
            if (wantSave) {
                if (page.getVersion().isR4B()) {
                    org.hl7.fhir.r4.model.Resource r4 = new org.hl7.fhir.r4.formats.XmlParser().parse(new FileInputStream(file));
                    new org.hl7.fhir.r4.formats.XmlParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(file), r4);
                } else {
                    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(file), res);
                }
            }
            narrative = new XhtmlComposer(XhtmlComposer.HTML).compose(res.getText().getDiv());
        } else {
            if (rt.equals("Bundle")) {
                List<Element> entries = new ArrayList<Element>();
                XMLUtil.getNamedChildren(xdoc.getDocumentElement(), "entry", entries);
                boolean wantSave = false;
                for (Element entry : entries) {
                    Element ers = XMLUtil.getFirstChild(XMLUtil.getNamedChild(entry, "resource"));
                    id = XMLUtil.getNamedChildValue(ers, "id");
                    if (id != null)
                        page.getDefinitions().addNs("http://hl7.org/fhir/" + ers.getLocalName() + "/" + id, "Example", prefix + n + ".html", true);
                    if (ers != null) {
                        String ert = ers.getLocalName();
                        String s = null;
                        if (!page.getDefinitions().getBaseResources().containsKey(ert) && !ert.equals("Binary") && !ert.equals("Parameters") && !ert.equals("Bundle")) {
                            ResourceRenderer r = RendererFactory.factory(ers.getLocalName(), lrc);
                            ResourceWrapper rw = new DOMWrappers.ResourceWrapperElement(lrc, ers, page.getDefinitions().getResourceByName(ers.getLocalName()).getProfile());
                            XhtmlNode div = rw.getNarrative();
                            if (div == null || div.isEmpty()) {
                                wantSave = true;
                                r.render(rw);
                            } else
                                s = new XhtmlComposer(true).compose(div);
                            if (s != null)
                                narrative = narrative == null ? s : narrative + "<hr/>\r\n" + s;
                        }
                        if (ert.equals("NamingSystem")) {
                            ByteArrayOutputStream bs = new ByteArrayOutputStream();
                            new XmlGenerator().generate(ers, bs);
                            bs.close();
                            NamingSystem ns = (NamingSystem) new XmlParser().parse(new ByteArrayInputStream(bs.toByteArray()));
                            if (!ns.hasUrl() || ns.getUrl().startsWith("http://hl7.org/fhir"))
                                ns.setVersion(page.getVersion().toCode());
                            ns.setUserData("path", prefix + n + ".html");
                            page.getDefinitions().getNamingSystems().add(ns);
                        }
                    }
                }
                if (wantSave)
                    new XmlGenerator().generate(xdoc.getDocumentElement(), file, "http://hl7.org/fhir", xdoc.getDocumentElement().getLocalName());
            } else {
                if (!page.getDefinitions().getBaseResources().containsKey(rt) && !rt.equals("Binary") && !rt.equals("Parameters")) {
                    ResourceRenderer r = RendererFactory.factory(xdoc.getDocumentElement().getLocalName(), lrc);
                    ResourceWrapper rw = new DOMWrappers.ResourceWrapperElement(lrc, xdoc.getDocumentElement(), page.getDefinitions().getResourceByName(xdoc.getDocumentElement().getLocalName()).getProfile());
                    XhtmlNode div = rw.getNarrative();
                    if (div == null || div.isEmpty()) {
                        narrative = new XhtmlComposer(true).compose(r.render(rw));
                        new XmlGenerator().generate(xdoc.getDocumentElement(), file, "http://hl7.org/fhir", xdoc.getDocumentElement().getLocalName());
                    } else {
                        narrative = new XhtmlComposer(true).compose(div);
                    }
                }
            }
        }
    } catch (Exception ex) {
        StringWriter errors = new StringWriter();
        ex.printStackTrace();
        XhtmlNode xhtml = new XhtmlNode(NodeType.Element, "div");
        xhtml.addTag("p").setAttribute("style", "color: maroon").addText("Error processing narrative: " + ex.getMessage());
        xhtml.addTag("p").setAttribute("style", "color: maroon").addText(errors.toString());
        narrative = new XhtmlComposer(XhtmlComposer.HTML).compose(xhtml);
    }
    if (rt.equals("ValueSet")) {
        try {
            ValueSet vs = (ValueSet) loadExample(file);
            vs.setUserData("filename", Utilities.changeFileExt(file.getName(), ""));
            vs.addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType("fhir"));
            if (vs.getUrl().startsWith("http://hl7.org/fhir"))
                vs.setVersion(page.getVersion().toCode());
            page.getVsValidator().validate(page.getValidationErrors(), "Value set Example " + prefix + n, vs, false, false);
            if (vs.getUrl() == null)
                throw new Exception("Value set example " + e.getTitle() + " has no url");
            vs.setUserData("path", prefix + n + ".html");
            if (vs.getUrl().startsWith("http:"))
                page.getValueSets().see(vs, page.packageInfo());
            addToResourceFeed(vs, valueSetsFeed, file.getName());
            page.getDefinitions().getValuesets().see(vs, page.packageInfo());
        } catch (Exception ex) {
            if (page.getVersion().isR4B()) {
                System.out.println("Value set " + file.getAbsolutePath() + " couldn't be parsed - ignoring! msg = " + ex.getMessage());
            } else {
                throw new FHIRException("Unable to parse " + file.getAbsolutePath() + ": " + ex.getMessage(), ex);
            }
        }
    } else if (rt.equals("CodeSystem")) {
        CodeSystem cs = (CodeSystem) loadExample(file);
        if (cs.getUrl().startsWith("http://hl7.org/fhir"))
            cs.setVersion(page.getVersion().toCode());
        cs.setUserData("example", "true");
        cs.setUserData("filename", Utilities.changeFileExt(file.getName(), ""));
        cs.addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType("fhir"));
        cs.setUserData("path", prefix + n + ".html");
        addToResourceFeed(cs, valueSetsFeed, file.getName());
        page.getCodeSystems().see(cs, page.packageInfo());
    } else if (rt.equals("ConceptMap") && !page.getVersion().isR4B()) {
        ConceptMap cm = (ConceptMap) loadExample(file);
        new ConceptMapValidator(page.getDefinitions(), e.getTitle()).validate(cm, false);
        if (cm.getUrl() == null)
            throw new Exception("Value set example " + e.getTitle() + " has no identifier");
        if (cm.getUrl().startsWith("http://hl7.org/fhir"))
            cm.setVersion(page.getVersion().toCode());
        addToResourceFeed(cm, conceptMapsFeed, file.getName());
        page.getDefinitions().getConceptMaps().see(cm, page.packageInfo());
        cm.setUserData("path", prefix + n + ".html");
        page.getConceptMaps().see(cm, page.packageInfo());
    } else if (rt.equals("Library")) {
        try {
            Library lib = (Library) loadExample(file);
            if (lib.hasUrl() && lib.getUrl().startsWith("http://hl7.org/fhir"))
                lib.setVersion(page.getVersion().toCode());
            lib.setUserData("example", "true");
            lib.setUserData("filename", Utilities.changeFileExt(file.getName(), ""));
            lib.setUserData("path", prefix + n + ".html");
            page.getWorkerContext().cacheResource(lib);
        } catch (Exception ex) {
            System.out.println("Internal exception processing Library " + file.getName() + ": " + ex.getMessage() + ". Does the libary code need regenerating?");
            ex.printStackTrace();
        }
    }
    // queue for json and canonical XML generation processing
    e.setResourceName(resn.getName());
    String canonical = "http://hl7.org/fhir/";
    org.hl7.fhir.r5.elementmodel.Element ex = Manager.parse(page.getWorkerContext(), new CSFileInputStream(page.getFolders().dstDir + prefix + n + ".xml"), FhirFormat.XML);
    new DefinitionsUsageTracker(page.getDefinitions()).updateUsage(ex);
    Manager.compose(page.getWorkerContext(), ex, new FileOutputStream(page.getFolders().dstDir + prefix + n + ".json"), FhirFormat.JSON, OutputStyle.PRETTY, canonical);
    // Manager.compose(page.getWorkerContext(), ex, new FileOutputStream(Utilities.changeFileExt(destName, ".canonical.json")), FhirFormat.JSON, OutputStyle.CANONICAL);
    // Manager.compose(page.getWorkerContext(), ex, new FileOutputStream(Utilities.changeFileExt(destName, ".canonical.xml")), FhirFormat.XML, OutputStyle.CANONICAL);
    Manager.compose(page.getWorkerContext(), ex, new FileOutputStream(page.getFolders().dstDir + prefix + n + ".ttl"), FhirFormat.TURTLE, OutputStyle.PRETTY, resn.getName().equals("Parameters") || resn.getName().equals("OperationOutcome") ? null : canonical);
    String json = TextFile.fileToString(page.getFolders().dstDir + prefix + n + ".json");
    // String json2 = "<div class=\"example\">\r\n<p>" + Utilities.escapeXml(e.getDescription()) + "</p>\r\n<p><a href=\""+ n + ".json\">Raw JSON</a> (<a href=\""+n + ".canonical.json\">Canonical</a>)</p>\r\n<pre class=\"json\">\r\n" + Utilities.escapeXml(json)
    // + "\r\n</pre>\r\n</div>\r\n";
    json = "<div class=\"example\">\r\n<p>" + Utilities.escapeXml(e.getDescription()) + "</p>\r\n<pre class=\"json\">\r\n" + Utilities.escapeXml(json) + "\r\n</pre>\r\n</div>\r\n";
    String html = TextFile.fileToString(page.getFolders().templateDir + "template-example-json.html").replace("<%example%>", json);
    html = page.processPageIncludes(n + ".json.html", html, e.getResourceName() == null ? "profile-instance:resource:" + e.getResourceName() : "resource-instance:" + e.getResourceName(), null, null, null, "Example", null, resn, resn.getWg());
    TextFile.stringToFile(html, page.getFolders().dstDir + prefix + n + ".json.html");
    page.getHTMLChecker().registerExternal(prefix + n + ".json.html");
    String ttl = TextFile.fileToString(page.getFolders().dstDir + prefix + n + ".ttl");
    ttl = "<div class=\"example\">\r\n<p>" + Utilities.escapeXml(e.getDescription()) + "</p>\r\n<pre class=\"rdf\">\r\n" + Utilities.escapeXml(ttl) + "\r\n</pre>\r\n</div>\r\n";
    html = TextFile.fileToString(page.getFolders().templateDir + "template-example-ttl.html").replace("<%example%>", ttl);
    html = page.processPageIncludes(n + ".ttl.html", html, e.getResourceName() == null ? "profile-instance:resource:" + e.getResourceName() : "resource-instance:" + e.getResourceName(), null, null, null, "Example", null, resn, resn.getWg());
    TextFile.stringToFile(html, page.getFolders().dstDir + prefix + n + ".ttl.html");
    page.getHTMLChecker().registerExternal(prefix + n + ".ttl.html");
    // reload it now, xml to xhtml of xml
    builder = factory.newDocumentBuilder();
    xdoc = builder.parse(new CSFileInputStream(file));
    XhtmlGenerator xhtml = new XhtmlGenerator(new ExampleAdorner(page.getDefinitions(), page.genlevel(level)));
    ByteArrayOutputStream b = new ByteArrayOutputStream();
    xhtml.generate(xdoc, b, n.toUpperCase().substring(0, 1) + n.substring(1), Utilities.noString(e.getId()) ? e.getDescription() : e.getDescription() + " (id = \"" + e.getId() + "\")", 0, true, n + ".xml.html");
    html = TextFile.fileToString(page.getFolders().templateDir + "template-example-xml.html").replace("<%example%>", b.toString());
    html = page.processPageIncludes(n + ".xml.html", html, resn == null ? "profile-instance:resource:" + rt : "resource-instance:" + resn.getName(), null, n + ".xml.html", profile, null, "Example", (hasNarrative(xdoc)) ? new Boolean(true) : null, ig, resn, resn.getWg());
    TextFile.stringToFile(html, page.getFolders().dstDir + prefix + n + ".xml.html");
    XhtmlDocument d = new XhtmlParser().parse(new CSFileInputStream(page.getFolders().dstDir + prefix + n + ".xml.html"), "html");
    XhtmlNode pre = d.getElement("html").getElement("body").getElement("div");
    e.setXhtm(b.toString());
    Element root = xdoc.getDocumentElement();
    Element meta = XMLUtil.getNamedChild(root, "meta");
    if (meta == null) {
        Element id = XMLUtil.getNamedChild(root, "id");
        if (id == null)
            meta = XMLUtil.insertChild(xdoc, root, "meta", FormatUtilities.FHIR_NS, 2);
        else {
            Element pid = XMLUtil.getNextSibling(id);
            if (pid == null)
                throw new Exception("not handled - id is last child in " + n);
            else
                meta = XMLUtil.insertChild(xdoc, root, "meta", FormatUtilities.FHIR_NS, pid, 2);
        }
    }
    Element tag = XMLUtil.getNamedChild(meta, "tag");
    Element label = XMLUtil.insertChild(xdoc, meta, "security", FormatUtilities.FHIR_NS, tag, 4);
    XMLUtil.addTextTag(xdoc, label, "system", FormatUtilities.FHIR_NS, "http://terminology.hl7.org/CodeSystem/v3-ActReason", 6);
    XMLUtil.addTextTag(xdoc, label, "code", FormatUtilities.FHIR_NS, "HTEST", 6);
    XMLUtil.addTextTag(xdoc, label, "display", FormatUtilities.FHIR_NS, "test health data", 6);
    XMLUtil.spacer(xdoc, label, 4);
    XMLUtil.spacer(xdoc, meta, 2);
    String destf = (!Utilities.noString(e.getId())) ? page.getFolders().dstDir + "examples" + File.separator + n + "(" + e.getId() + ").xml" : page.getFolders().dstDir + "examples" + File.separator + n + ".xml";
    FileOutputStream fs = new FileOutputStream(destf);
    XMLUtil.saveToFile(root, fs);
    fs.close();
    // now, we create an html page from the narrative
    narrative = fixExampleReferences(e.getTitle(), narrative);
    html = TextFile.fileToString(page.getFolders().templateDir + "template-example.html").replace("<%example%>", narrative == null ? "" : narrative).replace("<%example-usage%>", genExampleUsage(e, page.genlevel(level)));
    html = page.processPageIncludes(n + ".html", html, resn == null ? "profile-instance:resource:" + rt : "resource-instance:" + resn.getName(), null, profile, null, "Example", ig, resn, resn.getWg());
    TextFile.stringToFile(html, page.getFolders().dstDir + prefix + n + ".html");
    // head =
    // "<html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\">\r\n<head>\r\n <title>"+Utilities.escapeXml(e.getDescription())+"</title>\r\n <link rel=\"Stylesheet\" href=\"fhir.css\" type=\"text/css\" media=\"screen\"/>\r\n"+
    // "</head>\r\n<body>\r\n<p>&nbsp;</p>\r\n<p>"+Utilities.escapeXml(e.getDescription())+"</p>\r\n"+
    // "<p><a href=\""+n+".xml.html\">XML</a> <a href=\""+n+".json.html\">JSON</a></p>\r\n";
    // tail = "\r\n</body>\r\n</html>\r\n";
    // TextFile.stringToFile(head+narrative+tail, page.getFolders().dstDir + n +
    // ".html");
    page.getHTMLChecker().registerExternal(prefix + n + ".html");
    page.getHTMLChecker().registerExternal(prefix + n + ".xml.html");
}