use of org.hl7.fhir.r4b.model.CanonicalResource in project kindling by HL7.
the class PageProcessor method getProfileContext.
private String getProfileContext(CanonicalResource mr, String prefix) throws DefinitionException {
DataRenderer gen = new DataRenderer(workerContext);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (UsageContext uc : mr.getUseContext()) {
String vs = gen.display(uc.getValue());
if (vs != null)
b.append(gen.display(uc.getCode()) + ": " + vs);
}
for (CodeableConcept cc : mr.getJurisdiction()) {
b.append("Country: " + gen.displayCodeableConcept(cc));
}
if (mr.getExperimental()) {
if (isTrialUse(mr))
b.append("Not yet ready for Production use");
else
b.append("Not Intended for Production use");
}
if (b.length() == 0)
return "<a href=\"" + prefix + "metadatatypes.html#UsageContext\">Use Context</a>: Any";
else
return "<a href=\"" + prefix + "metadatatypes.html#UsageContext\">Use Context</a>: " + b.toString();
}
use of org.hl7.fhir.r4b.model.CanonicalResource in project kindling by HL7.
the class Regenerator method generateProfile.
private CanonicalResource generateProfile(String root, ResourceDefn r, Profile p, ConstraintStructure cs) throws IOException {
StructureDefinition sd = cs.getResource().copy();
sd.setSnapshot(null);
if (!Utilities.noString(cs.getSummary())) {
sd.addExtension(BuildExtensions.EXT_SUMMARY, new StringType(cs.getSummary()));
}
File fn = new File(Utilities.path(root, sd.fhirType().toLowerCase() + "-profile-" + sd.getId() + ".gen.xml"));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fn), sd);
fn.setLastModified(r.getTimestamp());
return sd;
}
use of org.hl7.fhir.r4b.model.CanonicalResource in project kindling by HL7.
the class SourceParser method loadExternal.
private void loadExternal(String n) throws Exception {
File file = new File(Utilities.path(rootDir, "vscache", "externals", Integer.toString(n.hashCode()) + ".xml"));
if (!file.exists()) {
logger.log("Fetch " + n, LogMessageType.Process);
if (n.startsWith("ftp:")) {
byte[] source = ftpFetch(n);
TextFile.bytesToFile(source, file.getAbsolutePath());
} else if (n.startsWith("http:") || n.startsWith("https:"))
throw new Exception("HTTP externals are not yet supported: " + n);
else
throw new Exception("Unknown protocol for externals: " + n);
}
String stated = ini.getStringProperty("externals", n);
if (Utilities.noString(stated))
stated = n;
Resource res = new XmlParser().parse(new FileInputStream(file));
if (res instanceof CanonicalResource) {
res.setUserData("external.url", stated);
res.setUserData("path", stated);
context.cacheResource(res);
externals.addEntry().setFullUrl("http://hl7.org/fhir/" + res.fhirType() + "/" + res.getId()).setResource(res).addLink().setRelation("via").setUrl(stated);
} else
throw new Exception("Unsupported external resource type " + res.fhirType());
}
use of org.hl7.fhir.r4b.model.CanonicalResource in project kindling by HL7.
the class SourceParser method loadResource.
private ResourceDefn loadResource(String n, Map<String, ResourceDefn> map, boolean isAbstract, boolean isTemplate, String t, boolean isInterface) throws Exception {
String folder = n;
WorkGroup wg = definitions.getWorkgroups().get(ini.getStringProperty("workgroups", n));
if (wg == null)
throw new Exception("No Workgroup found for resource " + n + ": '" + ini.getStringProperty("workgroups", n) + "'");
File f = new File(Utilities.path(srcDir, folder, n + ".svg"));
if (isTemplate) {
File spreadsheet = new CSFile((srcDir) + folder + File.separatorChar + n + "-spreadsheet.xml");
OldSpreadsheetParser sparser = new OldSpreadsheetParser("core", new CSFileInputStream(spreadsheet), spreadsheet.getName(), spreadsheet.getAbsolutePath(), definitions, srcDir, logger, registry, version, context, genDate, isAbstract, page, false, ini, wg, definitions.getProfileIds(), fpUsages, page.getConceptMaps(), exceptionIfExcelNotNormalised, page.packageInfo(), page.getRc());
ResourceDefn root;
try {
root = sparser.parseResource(isTemplate);
} catch (Exception e) {
throw new Exception("Error Parsing Resource " + n + ": " + e.getMessage(), e);
}
root.setAbstract(isAbstract);
root.setInterface(isInterface);
errors.addAll(sparser.getErrors());
setResourceProps(n, wg, root);
String sc = ini.getStringProperty("security-categorization", root.getName().toLowerCase());
if (sc != null) {
root.setSecurityCategorization(SecurityCategorization.fromCode(sc));
} else if (!Utilities.existsInList(root.getName(), "Resource", "DomainResource", "CanonicalResource", "MetadataResource", "MetadataPattern"))
throw new Exception("Must have an entry in the security-categorization section of fhir.ini for the resource " + root.getName());
for (EventDefn e : sparser.getEvents()) {
processEvent(e, root.getRoot());
}
if (map != null) {
map.put(root.getName(), root);
}
if (!isTemplate) {
definitions.getKnownResources().put(root.getName(), new DefinedCode(root.getName(), root.getRoot().getDefinition(), n));
context.getResourceNames().add(root.getName());
}
if (root.getNormativeVersion() != null || root.getNormativePackage() != null) {
root.setStatus(StandardsStatus.NORMATIVE);
}
if (f.exists()) {
parseSvgFile(f, root.getLayout(), f.getName());
}
if (map != null) {
map.put(root.getName(), root);
}
return root;
} else {
try {
new SpreadSheetReloader(context, srcDir, t, version.toCode()).process();
} catch (Exception e) {
System.out.println("Error loading spreadsheet for resource " + t + ": " + e.getMessage());
}
new SpreadSheetCreator(context, srcDir, t).generateSpreadsheet();
ResourceDefn rootNew = new ResourceParser(srcDir, definitions, context, wg, registry, version.toCode(), page.getConceptMaps()).parse(n, t);
if (f.exists()) {
parseSvgFile(f, rootNew.getLayout(), f.getName());
}
if (!isTemplate) {
definitions.getKnownResources().put(rootNew.getName(), new DefinedCode(rootNew.getName(), rootNew.getRoot().getDefinition(), n));
context.getResourceNames().add(rootNew.getName());
}
setResourceProps(n, wg, rootNew);
if (map != null) {
map.put(rootNew.getName(), rootNew);
}
return rootNew;
}
}
use of org.hl7.fhir.r4b.model.CanonicalResource 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> </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");
}
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