Examples with DomainResource org.hl7.fhir.r4.model.DomainResource used on opensource projects

Example 86 with DomainResource

use of org.hl7.fhir.r4.model.DomainResource in project kindling by HL7.

the class Publisher method addToResourceFeed.

private void addToResourceFeed(DomainResource resource, Bundle dest, String filename) throws Exception {
    maybeFixResourceId(resource, filename);
    if (resource.getId() == null)
        throw new Exception("Resource has no id");
    BundleEntryComponent byId = ResourceUtilities.getEntryById(dest, resource.getResourceType(), resource.getId());
    if (byId != null)
        dest.getEntry().remove(byId);
    deletefromFeed(resource.getResourceType(), resource.getId(), dest);
    ResourceUtilities.meta(resource).setLastUpdated(page.getGenDate().getTime());
    if (!resource.hasText() || !resource.getText().hasDiv()) {
        RendererFactory.factory(resource, page.getRc().copy()).render(resource);
    }
    if (resource.getText() == null || resource.getText().getDiv() == null)
        throw new Exception("Example Resource " + resource.getId() + " does not have any narrative");
    dest.getEntry().add(new BundleEntryComponent().setResource(resource).setFullUrl("http://hl7.org/fhir/" + resource.getResourceType().toString() + "/" + resource.getId()));
}

Example 87 with DomainResource

use of org.hl7.fhir.r4.model.DomainResource in project kindling by HL7.

the class Publisher method validate.

private void validate() throws Exception {
    page.log("Validating", LogMessageType.Process);
    ResourceValidator val = new ResourceValidator(page.getDefinitions(), page.getTranslations(), page.getCodeSystems(), page.getFolders().srcDir, fpUsages, page.getSuppressedMessages(), page.getWorkerContext());
    val.resolvePatterns();
    ProfileValidator valp = new ProfileValidator(page.getWorkerContext(), null);
    for (String n : page.getDefinitions().getTypes().keySet()) page.getValidationErrors().addAll(val.checkStucture(n, page.getDefinitions().getTypes().get(n)));
    val.checkSearchParams(page.getValidationErrors(), page.getDefinitions().getResourceByName("Resource"));
    val.checkSearchParams(page.getValidationErrors(), page.getDefinitions().getResourceByName("DomainResource"));
    for (String n : page.getDefinitions().sortedResourceNames()) if (hasBuildFlag("page-" + n.toLowerCase()))
        page.getValidationErrors().addAll(val.check(n, page.getDefinitions().getResources().get(n)));
    page.getValidationErrors().addAll(val.check("Parameters", page.getDefinitions().getResourceByName("Parameters")));
    for (String rname : page.getDefinitions().sortedResourceNames()) {
        ResourceDefn r = page.getDefinitions().getResources().get(rname);
        checkExampleLinks(page.getValidationErrors(), r);
    }
    for (Compartment cmp : page.getDefinitions().getCompartments()) page.getValidationErrors().addAll(val.check(cmp));
    page.setPatternFinder(val.getPatternFinder());
    val.report();
    val.summariseSearchTypes(page.getSearchTypeUsage());
    val.dumpParams();
    val.close();
    checkAllOk();
}

Example 88 with DomainResource

use of org.hl7.fhir.r4.model.DomainResource in project kindling by HL7.

the class Publisher method saveAsPureHtml.

private void saveAsPureHtml(DomainResource resource, FileOutputStream stream, boolean isPretty) throws Exception {
    XhtmlDocument html = new XhtmlDocument();
    html.setNodeType(NodeType.Document);
    html.addComment("Generated by automatically by FHIR Tooling");
    XhtmlNode doc = html.addTag("html");
    XhtmlNode head = doc.addTag("head");
    XhtmlNode work = head.addTag("title");
    work.addText("test title");
    work = head.addTag("link");
    work.setAttribute("rel", "Stylesheet");
    work.setAttribute("href", "/css/fhir.css");
    work.setAttribute("type", "text/css");
    work.setAttribute("media", "screen");
    work = doc.addTag("body");
    if ((resource.hasText()) && (resource.getText().hasDiv())) {
        work.getAttributes().putAll(resource.getText().getDiv().getAttributes());
        work.getChildNodes().addAll(resource.getText().getDiv().getChildNodes());
    }
    XhtmlComposer xml = new XhtmlComposer(XhtmlComposer.HTML, isPretty);
    xml.compose(stream, html);
    stream.close();
}

Example 89 with DomainResource

use of org.hl7.fhir.r4.model.DomainResource in project kindling by HL7.

the class PageProcessor method processPageIncludesForPrinting.

String processPageIncludesForPrinting(String file, String src, Resource resource, ImplementationGuideDefn ig) throws Exception {
    boolean even = false;
    List<String> tabs = new ArrayList<String>();
    while (src.contains("<%") || src.contains("[%")) {
        int i1 = src.indexOf("<%");
        int i2 = src.indexOf("%>");
        if (i1 == -1) {
            i1 = src.indexOf("[%");
            i2 = src.indexOf("%]");
        }
        String s1 = src.substring(0, i1);
        String s2 = src.substring(i1 + 2, i2).trim();
        String s3 = src.substring(i2 + 2);
        String name = file.substring(0, file.indexOf("."));
        String[] com = s2.split(" ");
        if (com.length == 3 && com[0].equals("edt")) {
            if (tabs != null)
                tabs.add("tabs-" + com[1]);
            src = s1 + orgDT(com[1], xmlForDt(com[1], com[2]), treeForDt(com[1]), umlForDt(com[1], com[2]), umlForDt(com[1], com[2] + "b"), profileRef(com[1]), tsForDt(com[1]), jsonForDt(com[1], com[2]), ttlForDt(com[1], com[2]), diffForDt(com[1], com[2])) + s3;
        } else if (com.length == 2 && com[0].equals("dt")) {
            if (tabs != null)
                tabs.add("tabs-" + com[1]);
            src = s1 + xmlForDt(com[1], null) + tsForDt(com[1]) + s3;
        } else if (com.length == 2 && com[0].equals("adt")) {
            if (tabs != null)
                tabs.add("tabs-" + com[1]);
            src = s1 + xmlForDt(com[1], null) + tsForDt(com[1]) + s3;
        } else if (com.length == 2 && com[0].equals("dt.constraints"))
            src = s1 + genConstraints(com[1], "") + s3;
        else if (com.length == 2 && com[0].equals("dt.restrictions"))
            src = s1 + genRestrictions(com[1]) + s3;
        else if (com.length == 2 && com[0].equals("dictionary"))
            src = s1 + dictForDt(com[1]) + s3;
        else if (Utilities.existsInList(com[0], "pageheader", "dtheader", "atheader", "mdtheader", "edheader", "mmheader", "drheader", "elheader", "belheader", "extheader", "resourcesheader", "formatsheader", "narrheader", "refheader", "extrasheader", "profilesheader", "txheader", "txheader0", "fmtheader", "igheader", "cmpheader", "atomheader", "dictheader", "ctheader", "adheader", "pdheader", "tdheader", "cdheader", "diheader", "statheader", "ordistheader", "ucheader", "rrheader"))
            src = s1 + s3;
        else if (com[0].equals("resheader"))
            src = s1 + resHeader(name, "Document", com.length > 1 ? com[1] : null) + s3;
        else if (com[0].equals("aresheader"))
            src = s1 + abstractResHeader(name, "Document", com.length > 1 ? com[1] : null) + s3;
        else if (com[0].equals("codelist"))
            src = s1 + codelist((CodeSystem) resource, com.length > 1 ? com[1] : null, false, true, file) + s3;
        else if (com[0].equals("codelist-nh"))
            src = s1 + codelist((CodeSystem) resource, com.length > 1 ? com[1] : null, false, false, file) + s3;
        else if (com[0].equals("linkcodelist"))
            src = s1 + codelist((CodeSystem) resource, com.length > 1 ? com[1] : null, true, false, file) + s3;
        else if (com[0].equals("sct-vs-list"))
            src = s1 + getSnomedCTVsList() + s3;
        else if (com[0].equals("sct-concept-list"))
            src = s1 + getSnomedCTConceptList() + s3;
        else if (com[0].equals("codetoc"))
            src = s1 + codetoc(com.length > 1 ? com[1] : null) + s3;
        else if (com[0].equals("res-category")) {
            src = s1 + resCategory(s2.substring(com[0].length() + 1)) + s3;
            even = false;
        } else if (com[0].equals("res-item")) {
            even = !even;
            src = s1 + resItem(com[1], even) + s3;
        } else if (com[0].equals("resdesc")) {
            src = s1 + resDesc(com[1]) + s3;
        } else if (com[0].equals("rescat")) {
            src = s1 + resCat(com.length == 1 ? null : s2.substring(7)) + s3;
        } else if (com[0].equals("w5"))
            src = s1 + genW5("true".equals(com[1])) + s3;
        else if (com[0].equals("vs-warning"))
            src = s1 + vsWarning((ValueSet) resource) + s3;
        else if (com[0].equals("res-status-special"))
            src = s1 + vsSpecialStatus((DomainResource) resource) + s3;
        else if (com[0].equals("file")) {
            if (new File(folders.templateDir + com[1] + ".html").exists()) {
                src = s1 + TextFile.fileToString(folders.templateDir + com[1] + ".html") + s3;
            } else {
                src = s1 + TextFile.fileToString(folders.srcDir + com[1] + ".html") + s3;
            }
        } else if (com[0].equals("conceptmaplistvs")) {
            throw new Error("Fix this");
        // BindingSpecification bs = definitions.getBindingByName(Utilities.fileTitle(file));
        // String ref;
        // if (bs == null) {
        // ref = "http://hl7.org/fhir/ValueSet/"+Utilities.fileTitle(file);
        // } else {
        // ref = bs.getReference();
        // if (ref.startsWith("valueset-"))
        // ref = ref.substring(9);
        // ref = "http://hl7.org/fhir/ValueSet/"+ref;
        // }
        // src = s1 + conceptmaplist(ref, com[1]) + s3;
        } else if (com[0].equals("dtmappings"))
            src = s1 + genDataTypeMappings(com[1]) + s3;
        else if (com[0].equals("dtusage"))
            src = s1 + genDataTypeUsage(com[1]) + s3;
        else if (com[0].equals("othertabs"))
            src = s1 + genOtherTabs(com[1], tabs) + s3;
        else if (com[0].equals("toc"))
            src = s1 + generateToc() + s3;
        else if (com.length != 1)
            throw new Exception("Instruction <%" + s2 + "%> not understood parsing page " + file);
        else if (com[0].equals("newheader"))
            src = s1 + TextFile.fileToString(folders.srcDir + "newheader.html") + s3;
        else if (com[0].equals("newheader1"))
            src = s1 + TextFile.fileToString(folders.srcDir + "newheader1.html") + s3;
        else if (com[0].equals("footer"))
            src = s1 + TextFile.fileToString(folders.srcDir + "footer.html") + s3;
        else if (com[0].equals("newfooter"))
            src = s1 + TextFile.fileToString(folders.srcDir + "newfooter.html") + s3;
        else if (com[0].equals("footer1"))
            src = s1 + TextFile.fileToString(folders.srcDir + "footer1.html") + s3;
        else if (com[0].equals("footer2"))
            src = s1 + TextFile.fileToString(folders.srcDir + "footer2.html") + s3;
        else if (com[0].equals("footer3"))
            src = s1 + TextFile.fileToString(folders.srcDir + "footer3.html") + s3;
        else if (com[0].equals("title"))
            src = s1 + Utilities.escapeXml(name.toUpperCase().substring(0, 1) + name.substring(1)) + s3;
        else if (com[0].equals("xtitle"))
            src = s1 + Utilities.escapeXml(name.toUpperCase().substring(0, 1) + name.substring(1)) + s3;
        else if (com[0].equals("name"))
            src = s1 + name + s3;
        else if (com[0].equals("version"))
            src = s1 + ini.getStringProperty("FHIR", "version") + s3;
        else if (com[0].equals("gendate"))
            src = s1 + Config.DATE_FORMAT().format(new Date()) + s3;
        else if (com[0].equals("maindiv"))
            src = s1 + s3;
        else if (com[0].equals("/maindiv"))
            src = s1 + s3;
        else if (com[0].equals("enteredInErrorTable"))
            src = s1 + enteredInErrorTable() + s3;
        else if (com[0].equals("events"))
            src = s1 + getEventsTable(file) + s3;
        else if (com[0].equals("resourcecodes"))
            src = s1 + genResCodes() + s3;
        else if (com[0].equals("datatypecodes"))
            src = s1 + genDTCodes() + s3;
        else // src = s1 + genBindingTable(false) + s3;
        if (com[0].equals("codeslist"))
            src = s1 + genCodeSystemsTable() + s3;
        else if (com[0].equals("valuesetslist"))
            src = s1 + genValueSetsTable(ig) + s3;
        else if (com[0].equals("igvaluesetslist"))
            src = s1 + genIGValueSetsTable() + s3;
        else if (com[0].equals("namespacelist"))
            src = s1 + genNSList() + s3;
        else if (com[0].equals("resimplall"))
            src = s1 + genResImplList() + s3;
        else if (com[0].equals("txurl"))
            src = s1 + "http://hl7.org/fhir/" + Utilities.fileTitle(file) + s3;
        else if (com[0].equals("vstxurl"))
            src = s1 + "http://hl7.org/fhir/ValueSet/" + Utilities.fileTitle(file) + s3;
        else if (com[0].equals("csurl")) {
            if (resource instanceof CodeSystem)
                src = s1 + ((CodeSystem) resource).getUrl() + s3;
            else
                src = s1 + ((ValueSet) resource).getUrl() + s3;
        } else if (com[0].equals("vsurl")) {
            if (resource instanceof CodeSystem)
                src = s1 + ((CodeSystem) resource).getUrl() + s3;
            else
                src = s1 + ((ValueSet) resource).getUrl() + s3;
        } else if (com[0].equals("txdef"))
            src = s1 + generateCodeDefinition(Utilities.fileTitle(file)) + s3;
        else if (com[0].equals("vsxref"))
            src = s1 + xreferencesForFhir(name) + s3;
        else if (com[0].equals("vsdef"))
            if (resource instanceof CodeSystem)
                src = s1 + Utilities.escapeXml(((CodeSystem) resource).getDescription()) + s3;
            else
                src = s1 + Utilities.escapeXml(((ValueSet) resource).getDescription()) + s3;
        else if (com[0].equals("txusage"))
            src = s1 + generateValueSetUsage((ValueSet) resource, genlevel(0), true) + s3;
        else if (com[0].equals("vsusage"))
            src = s1 + generateValueSetUsage((ValueSet) resource, genlevel(0), true) + s3;
        else if (com[0].equals("csusage"))
            src = s1 + generateCSUsage((CodeSystem) resource, genlevel(0)) + s3;
        else if (com[0].equals("vssummary"))
            src = s1 + "todo" + s3;
        else if (com[0].equals("piperesources"))
            src = s1 + pipeResources() + s3;
        else if (com[0].equals("pub-type"))
            src = s1 + publicationType + s3;
        else // src = s1 + expandValueSet(Utilities.fileTitle(file), resource == null ? null : (ValueSet) resource) + s3;
        if (com[0].equals("vsexpansionig"))
            src = s1 + expandValueSetIG((ValueSet) resource, true) + s3;
        else if (com[0].equals("pub-notice"))
            src = s1 + publicationNotice + s3;
        else if (com[0].startsWith("!"))
            src = s1 + s3;
        else if (macros.containsKey(com[0])) {
            src = s1 + macros.get(com[0]) + s3;
        } else
            throw new Exception("Instruction <%" + s2 + "%> not understood parsing page " + file);
    }
    return src;
}

Example 90 with DomainResource

use of org.hl7.fhir.r4.model.DomainResource in project redmatch by aehrc.

the class RedmatchApi method export.

/**
 * Exports the generated FHIR resources that result from running a Redmatch rules document.
 *
 * @param redmatchRulesFile The Redmatch rules document.
 * @param progressReporter An object used to report progress. Can be null.
 * @param cancelToken Used to check if the user has cancelled the operation.
 * @return List of diagnostic messages.
 */
public List<Diagnostic> export(@NotNull File redmatchRulesFile, ProgressReporter progressReporter, CancelChecker cancelToken) {
    try {
        Pair<Map<String, DomainResource>, List<Diagnostic>> data = transform(redmatchRulesFile, progressReporter, cancelToken);
        // If the resource map is empty then something went wrong or the operation was cancelled by the user
        if (data.getValue0().isEmpty()) {
            return data.getValue1();
        }
        Map<String, DomainResource> resourceMap = data.getValue0();
        // Group resources by type
        final Map<String, List<DomainResource>> grouped = new HashMap<>();
        for (String key : resourceMap.keySet()) {
            DomainResource dr = resourceMap.get(key);
            String resourceType = dr.getResourceType().toString();
            List<DomainResource> list = grouped.computeIfAbsent(resourceType, k -> new ArrayList<>());
            list.add(dr);
        }
        File baseFolder = redmatchRulesFile.toPath().getParent().toFile();
        Path outputFolder = createOutputFolder(baseFolder).toPath();
        save(grouped, outputFolder, progressReporter, cancelToken);
        return data.getValue1();
    } catch (Exception e) {
        log.error(e);
        return List.of(new Diagnostic(zeroZero, "Could not complete transformation:" + e.getLocalizedMessage(), DiagnosticSeverity.Error, "API"));
    }
}