use of org.hl7.fhir.r5.model.Resource in project kindling by HL7.
the class Publisher method produceConceptMap.
private void produceConceptMap(ConceptMap cm, ResourceDefn rd, SectionTracker st) throws Exception {
RenderingContext lrc = page.getRc().copy().setLocalPrefix("");
RendererFactory.factory(cm, lrc).render(cm);
String n = cm.getUserString("path");
FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(n, ".xml"));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, cm);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(n, ".canonical.xml"));
new XmlParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, cm);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(n, ".json"));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, cm);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + Utilities.changeFileExt(n, ".canonical.json"));
new JsonParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, cm);
s.close();
Utilities.copyFile(new CSFile(page.getFolders().dstDir + Utilities.changeFileExt(n, ".xml")), new CSFile(page.getFolders().dstDir + "examples" + File.separator + Utilities.changeFileExt(n, ".xml")));
// saveAsPureHtml(cm, new FileOutputStream(Utilities.path(page.getFolders().dstDir, "html", n)), true);
String src = TextFile.fileToString(page.getFolders().templateDir + "template-status-map.html");
Map<String, String> others = new HashMap<String, String>();
others.put("status-map", new XhtmlComposer(XhtmlComposer.HTML).compose(cm.getText().getDiv()));
TextFile.stringToFile(insertSectionNumbers(page.processPageIncludes(n, src, "conceptmap-instance", others, null, null, "Profile", null, rd, rd.getWg()), st, n, 0, null), page.getFolders().dstDir + n);
page.getHTMLChecker().registerFile(n, cm.getTitle(), HTMLLinkChecker.XHTML_TYPE, true);
cloneToXhtml(Utilities.changeFileExt(n, ""), cm.getTitle(), true, "conceptmap-instance", "Profile", null, ((ResourceDefn) cm.getUserData("resource-definition")).getWg());
jsonToXhtml(Utilities.changeFileExt(n, ""), cm.getTitle(), resource2Json(cm), "conceptmap-instance", "Profile", null, ((ResourceDefn) cm.getUserData("resource-definition")).getWg());
ttlToXhtml(Utilities.changeFileExt(n, ""), cm.getTitle(), resource2Ttl(cm), "conceptmap-instance", "Profile", null, ((ResourceDefn) cm.getUserData("resource-definition")).getWg());
}
use of org.hl7.fhir.r5.model.Resource in project kindling by HL7.
the class Publisher method checkBundleURLs.
/**
* This is not true of bundles generally, but it is true of all the
* conformance bundles produced by the spec:
*
* all entries must have a fullUrl, and it must equal http://hl7.org/fhir/[type]/[id]
*
* @param bnd - the bundle to check
*/
private void checkBundleURLs(Bundle bnd) {
int i = 0;
for (BundleEntryComponent e : bnd.getEntry()) {
i++;
if (!e.getResource().hasUserData("external.url")) {
if (!e.hasFullUrl())
page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "Bundle " + bnd.getId(), "no Full URL on entry " + Integer.toString(i), IssueSeverity.ERROR));
else if (!e.getFullUrl().endsWith("/" + e.getResource().getResourceType().toString() + "/" + e.getResource().getId()) && e.getResource().getResourceType() != ResourceType.CodeSystem)
page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "Bundle " + bnd.getId(), "URL doesn't match resource and id on entry " + Integer.toString(i) + " : " + e.getFullUrl() + " should end with /" + e.getResource().getResourceType().toString() + "/" + e.getResource().getId(), IssueSeverity.ERROR));
else if (!e.getFullUrl().equals("http://hl7.org/fhir/" + e.getResource().getResourceType().toString() + "/" + e.getResource().getId()) && e.getResource().getResourceType() != ResourceType.CodeSystem)
page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "Bundle " + bnd.getId(), "URL is non-FHIR " + Integer.toString(i) + " : " + e.getFullUrl() + " should start with http://hl7.org/fhir/ for HL7-defined artifacts", IssueSeverity.WARNING));
if (e.getResource() instanceof CanonicalResource) {
CanonicalResource m = (CanonicalResource) e.getResource();
String url = m.getUrl();
if (url != null && url.startsWith("http://hl7.org/fhir") && !SIDUtilities.isKnownSID(url)) {
if (!page.getVersion().toCode().equals(m.getVersion()))
page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "Bundle " + bnd.getId(), "definitions in FHIR space should have the correct version (url = " + url + ", version = " + m.getVersion() + ")", IssueSeverity.ERROR));
}
}
}
}
}
use of org.hl7.fhir.r5.model.Resource in project kindling by HL7.
the class Publisher method execute.
/**
* Entry point to the publisher. This classes Java Main() calls this function
* to actually produce the specification
*
* @param folder
* @throws IOException
*/
public void execute(String folder) throws IOException {
tester = new PublisherTestSuites();
page.log("Publish FHIR in folder " + folder + " @ " + Config.DATE_FORMAT().format(page.getGenDate().getTime()), LogMessageType.Process);
if (web)
page.log("Build final copy for HL7 web site", LogMessageType.Process);
else
page.log("Build local copy", LogMessageType.Process);
if (outputdir != null) {
page.log("Create output in " + outputdir, LogMessageType.Process);
}
page.log("Detected Java version: " + System.getProperty("java.version") + " from " + System.getProperty("java.home") + " on " + System.getProperty("os.arch"), LogMessageType.Process);
try {
tester.initialTests();
page.setFolders(new FolderManager(folder, outputdir));
if (!initialize(folder))
throw new Exception("Unable to publish as preconditions aren't met");
cache = new IniFile(page.getFolders().rootDir + "temp" + File.separator + "build.cache");
loadSuppressedMessages(page.getFolders().rootDir);
boolean doAny = false;
for (String n : dates.keySet()) {
Long d = cache.getLongProperty("dates", n);
boolean b = d == null || (dates.get(n) > d);
cache.setLongProperty("dates", n, dates.get(n).longValue(), null);
buildFlags.put(n.toLowerCase(), b);
doAny = doAny || b;
}
cache.save();
if (noPartialBuild || !doAny || !(new File(page.getFolders().dstDir + "qa.html").exists()))
// nothing - build all
buildFlags.put("all", true);
if (singlePage != null) {
for (String n : buildFlags.keySet()) buildFlags.put(n, false);
buildFlags.put("page-" + singlePage.toLowerCase(), true);
} else if (singleResource != null) {
for (String n : buildFlags.keySet()) buildFlags.put(n, false);
buildFlags.put(singleResource.toLowerCase(), true);
}
if (!buildFlags.get("all")) {
if (!noSound) {
AudioUtilities.tone(1000, 10);
AudioUtilities.tone(1400, 10);
AudioUtilities.tone(1800, 10);
AudioUtilities.tone(1000, 10);
AudioUtilities.tone(1400, 10);
AudioUtilities.tone(1800, 10);
}
page.log("Partial Build (if you want a full build, just run the build again)", LogMessageType.Process);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (String n : buildFlags.keySet()) if (buildFlags.get(n))
b.append(n);
page.log(" Build: " + b.toString(), LogMessageType.Process);
} else {
if (!noSound)
AudioUtilities.tone(1200, 30);
page.log("Full Build", LogMessageType.Process);
}
if (isGenerate && page.getBuildId() == null)
page.setBuildId(getGitBuildId());
page.log("Version " + page.getVersion() + "-" + page.getBuildId(), LogMessageType.Hint);
Utilities.createDirectory(page.getFolders().dstDir);
Utilities.deleteTempFiles();
page.getBreadCrumbManager().parse(page.getFolders().srcDir + "hierarchy.xml");
page.loadSnomed();
page.loadLoinc();
page.loadUcum();
buildFeedsAndMaps();
prsr.setExternals(externals);
prsr.parse(page.getGenDate(), page.getValidationErrors());
for (String n : page.getDefinitions().sortedResourceNames()) if (!page.getBreadCrumbManager().knowsResource(n))
page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "hierarchy.xml", "Resource not found: " + n, IssueSeverity.ERROR));
for (String n : prsr.getErrors()) page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "source spreadsheets", n, IssueSeverity.ERROR));
if (web) {
page.log("Clear Directory", LogMessageType.Process);
Utilities.clearDirectory(page.getFolders().dstDir);
}
if (web || (isGenerate && buildFlags.get("all"))) {
Utilities.createDirectory(page.getFolders().dstDir + "html");
Utilities.createDirectory(page.getFolders().dstDir + "examples");
}
for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) if (!ig.isCore())
Utilities.createDirectory(page.getFolders().dstDir + ig.getCode());
if (buildFlags.get("all")) {
copyStaticContent();
}
page.makeRenderingContext();
loadValueSets1();
prsr.getRegistry().commit();
generateSCMaps();
validate();
processProfiles();
checkAllOk();
if (isGenerate) {
produceSpecification();
checkAllOk();
}
if (doValidate)
validationProcess();
page.saveSnomed();
page.getWorkerContext().saveCache();
processWarnings(false);
if (isGenerate && buildFlags.get("all"))
produceQA();
if (!buildFlags.get("all")) {
page.log("This was a Partial Build", LogMessageType.Process);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (String n : buildFlags.keySet()) if (buildFlags.get(n))
b.append(n);
page.log(" Build: " + b.toString(), LogMessageType.Process);
} else
page.log("This was a Full Build", LogMessageType.Process);
if (!noSound) {
AudioUtilities.tone(800, 10);
AudioUtilities.tone(1000, 10);
AudioUtilities.tone(1200, 10);
AudioUtilities.tone(1000, 10);
AudioUtilities.tone(800, 10);
}
page.log("Finished publishing FHIR @ " + Config.DATE_FORMAT().format(Calendar.getInstance().getTime()), LogMessageType.Process);
} catch (Exception e) {
if (!(e instanceof NullPointerException)) {
// because NullPointerException is unexpected...
try {
processWarnings(e instanceof EValidationFailed);
} catch (Exception e2) {
page.log(" ERROR: Unable to process warnings: " + e2.getMessage(), LogMessageType.Error);
e2.printStackTrace();
}
}
if (buildFlags.containsKey("all") && !buildFlags.get("all")) {
page.log("This was a Partial Build", LogMessageType.Process);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (String n : buildFlags.keySet()) if (buildFlags.get(n))
b.append(n);
page.log(" Build: " + b.toString(), LogMessageType.Process);
} else
page.log("This was a Full Build", LogMessageType.Process);
if (!noSound) {
AudioUtilities.tone(800, 20);
AudioUtilities.tone(1000, 20);
AudioUtilities.tone(1200, 20);
}
try {
Thread.sleep(50);
} catch (InterruptedException e1) {
}
if (!noSound) {
AudioUtilities.tone(800, 20);
AudioUtilities.tone(1000, 20);
AudioUtilities.tone(1200, 20);
}
try {
Thread.sleep(50);
} catch (InterruptedException e1) {
}
if (!noSound) {
AudioUtilities.tone(800, 20);
AudioUtilities.tone(1000, 20);
AudioUtilities.tone(1200, 20);
}
page.log("FHIR build failure @ " + Config.DATE_FORMAT().format(Calendar.getInstance().getTime()), LogMessageType.Process);
System.out.println("Error: " + e.getMessage());
e.printStackTrace();
TextFile.stringToFile(StringUtils.defaultString(e.getMessage()), Utilities.path(folder, "publish", "simple-error.txt"));
System.exit(1);
}
}
use of org.hl7.fhir.r5.model.Resource in project kindling by HL7.
the class Publisher method processProfiles.
@SuppressWarnings("unchecked")
private void processProfiles() throws Exception {
page.log(" ...process profiles (base)", LogMessageType.Process);
// first, for each type and resource, we build it's master profile
for (DefinedCode t : page.getDefinitions().getPrimitives().values()) {
if (t instanceof PrimitiveType)
genPrimitiveTypeProfile((PrimitiveType) t);
else
genPrimitiveTypeProfile((DefinedStringPattern) t);
}
genXhtmlProfile();
for (TypeDefn t : page.getDefinitions().getTypes().values()) genTypeProfile(t);
for (TypeDefn t : page.getDefinitions().getInfrastructure().values()) genTypeProfile(t);
page.log(" ...process profiles (resources)", LogMessageType.Process);
for (ResourceDefn r : page.getDefinitions().getBaseResources().values()) {
r.setConformancePack(makeConformancePack(r));
r.setProfile(new ProfileGenerator(page.getDefinitions(), page.getWorkerContext(), page, page.getGenDate(), page.getVersion(), dataElements, fpUsages, page.getFolders().rootDir, page.getUml(), page.getRc()).generate(r.getConformancePack(), r, "core", false));
if (page.getProfiles().has(r.getProfile().getUrl()))
throw new Exception("Duplicate Profile URL " + r.getProfile().getUrl());
page.getProfiles().see(r.getProfile(), page.packageInfo());
ResourceTableGenerator rtg = new ResourceTableGenerator(page.getFolders().dstDir, page, null, true, page.getVersion());
r.getProfile().getText().setDiv(new XhtmlNode(NodeType.Element, "div"));
r.getProfile().getText().getDiv().getChildNodes().add(rtg.generate(r, "", false));
}
for (String rn : page.getDefinitions().sortedResourceNames()) {
ResourceDefn r = page.getDefinitions().getResourceByName(rn);
r.setConformancePack(makeConformancePack(r));
r.setProfile(new ProfileGenerator(page.getDefinitions(), page.getWorkerContext(), page, page.getGenDate(), page.getVersion(), dataElements, fpUsages, page.getFolders().rootDir, page.getUml(), page.getRc()).generate(r.getConformancePack(), r, "core", false));
if (page.getProfiles().has(r.getProfile().getUrl()))
throw new Exception("Duplicate Profile URL " + r.getProfile().getUrl());
page.getProfiles().see(r.getProfile(), page.packageInfo());
ResourceTableGenerator rtg = new ResourceTableGenerator(page.getFolders().dstDir, page, null, true, page.getVersion());
r.getProfile().getText().setDiv(new XhtmlNode(NodeType.Element, "div"));
r.getProfile().getText().getDiv().getChildNodes().add(rtg.generate(r, "", false));
}
for (ResourceDefn r : page.getDefinitions().getResourceTemplates().values()) {
r.setConformancePack(makeConformancePack(r));
r.setProfile(new ProfileGenerator(page.getDefinitions(), page.getWorkerContext(), page, page.getGenDate(), page.getVersion(), dataElements, fpUsages, page.getFolders().rootDir, page.getUml(), page.getRc()).generate(r.getConformancePack(), r, "core", true));
ResourceTableGenerator rtg = new ResourceTableGenerator(page.getFolders().dstDir, page, null, true, page.getVersion());
r.getProfile().getText().setDiv(new XhtmlNode(NodeType.Element, "div"));
r.getProfile().getText().getDiv().getChildNodes().add(rtg.generate(r, "", true));
if (page.getProfiles().has(r.getProfile().getUrl()))
throw new Exception("Duplicate Profile URL " + r.getProfile().getUrl());
page.getProfiles().see(r.getProfile(), page.packageInfo());
}
for (ProfiledType pt : page.getDefinitions().getConstraints().values()) {
genProfiledTypeProfile(pt);
}
page.log(" ...process profiles (extensions)", LogMessageType.Process);
for (StructureDefinition ex : page.getWorkerContext().getExtensionDefinitions()) processExtension(ex);
for (ResourceDefn r : page.getDefinitions().getResources().values()) {
// boolean logged = false;
for (Profile ap : r.getConformancePackages()) {
// logged = true;
for (ConstraintStructure p : ap.getProfiles()) processProfile(ap, p, ap.getId(), r);
}
}
page.log(" ...process profiles (packs)", LogMessageType.Process);
// we have profiles scoped by resources, and stand alone profiles
for (Profile ap : page.getDefinitions().getPackList()) {
// page.log(" ... pack "+ap.getId(), LogMessageType.Process);
for (ConstraintStructure p : ap.getProfiles()) processProfile(ap, p, ap.getId(), null);
}
page.log(" ...process logical models", LogMessageType.Process);
for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) {
for (LogicalModel lm : ig.getLogicalModels()) {
page.log(" ...process logical model " + lm.getId(), LogMessageType.Process);
if (lm.getDefinition() == null)
lm.setDefinition(new ProfileGenerator(page.getDefinitions(), page.getWorkerContext(), page, page.getGenDate(), page.getVersion(), dataElements, fpUsages, page.getFolders().rootDir, page.getUml(), page.getRc()).generateLogicalModel(ig, lm.getResource()));
}
}
// now, validate the profiles
for (Profile ap : page.getDefinitions().getPackList()) for (ConstraintStructure p : ap.getProfiles()) validateProfile(p);
for (ResourceDefn r : page.getDefinitions().getResources().values()) for (Profile ap : r.getConformancePackages()) for (ConstraintStructure p : ap.getProfiles()) validateProfile(p);
page.log(" ...Check FHIR Path Expressions", LogMessageType.Process);
StringBuilder b = new StringBuilder();
FHIRPathEngine fp = new FHIRPathEngine(page.getWorkerContext());
fp.setHostServices(page.getExpressionResolver());
for (FHIRPathUsage p : fpUsages) {
checkExpression(b, fp, p);
}
TextFile.stringToFile(b.toString(), Utilities.path(page.getFolders().dstDir, "fhirpaths.txt"));
checkAllOk();
}
use of org.hl7.fhir.r5.model.Resource in project kindling by HL7.
the class PageProcessor method genStatusCodes.
private String genStatusCodes() throws Exception {
StringBuilder b = new StringBuilder();
b.append("<table border=\"1\">\r\n");
int colcount = 0;
for (ArrayList<String> row : definitions.getStatusCodes().values()) {
int rc = 0;
for (int i = 0; i < row.size(); i++) if (!Utilities.noString(row.get(i)))
rc = i;
if (rc > colcount)
colcount = rc;
}
// b.append("<tr>");
// b.append("<td>Path</td>");
// for (int i = 0; i < colcount; i++)
// b.append("<td>c").append(Integer.toString(i + 1)).append("</td>");
// b.append("</tr>\r\n");
List<String> names = new ArrayList<String>();
for (String n : definitions.getStatusCodes().keySet()) names.add(n);
Collections.sort(names);
ArrayList<String> row = definitions.getStatusCodes().get("@code");
b.append("<tr>");
b.append("<td><b>code</b></td>");
for (int i = 0; i < colcount; i++) b.append("<td><b><a href=\"codesystem-resource-status.html#resource-status-" + row.get(i) + "\">").append(row.get(i)).append("</a></b></td>");
b.append("</tr>\r\n");
row = definitions.getStatusCodes().get("@codes");
b.append("<tr>");
b.append("<td><b>stated codes</b></td>");
for (int i = 0; i < colcount; i++) b.append("<td>").append(i < row.size() ? row.get(i) : "").append("</td>");
b.append("</tr>\r\n");
b.append("<tr>");
b.append("<td>actual codes</td>");
for (int i = 0; i < colcount; i++) {
Set<String> codeset = new HashSet<String>();
for (String n : names) {
if (!n.startsWith("@")) {
row = definitions.getStatusCodes().get(n);
String c = row.get(i);
if (!Utilities.noString(c)) {
codeset.add(c);
}
}
}
b.append("<td>").append(separated(codeset, ", ")).append("</td>");
}
b.append("</tr>\r\n");
row = definitions.getStatusCodes().get("@issues");
b.append("<tr>");
b.append("<td><b>Issues?</b></td>");
for (int i = 0; i < colcount; i++) {
String s = i < row.size() ? row.get(i) : "";
b.append("<td").append(Utilities.noString(s) ? "" : " style=\"background-color: #ffcccc\"").append(">").append(s).append("</td>");
}
b.append("</tr>\r\n");
for (String n : names) {
if (!n.startsWith("@")) {
b.append("<tr>");
ElementDefn ed = getElementDefn(n);
if (ed == null || !ed.isModifier())
b.append("<td>").append(linkToPath(n)).append("</td>");
else
b.append("<td><b>").append(linkToPath(n)).append("</b></td>");
row = definitions.getStatusCodes().get(n);
for (int i = 0; i < colcount; i++) b.append("<td>").append(i < row.size() ? row.get(i) : "").append("</td>");
b.append("</tr>\r\n");
}
}
b.append("</table>\r\n");
CodeSystem cs = getCodeSystems().get("http://hl7.org/fhir/resource-status");
row = definitions.getStatusCodes().get("@code");
for (int i = 0; i < colcount; i++) {
String code = row.get(i);
String definition = CodeSystemUtilities.getCodeDefinition(cs, code);
Set<String> dset = new HashSet<String>();
for (String n : names) {
if (!n.startsWith("@")) {
ArrayList<String> rowN = definitions.getStatusCodes().get(n);
String c = rowN.get(i);
String d = getDefinition(n, c);
if (!Utilities.noString(d))
dset.add(d);
}
}
b.append("<hr/>\r\n");
b.append("<h4>").append(code).append("</h4>\r\n");
b.append("<p>").append(Utilities.escapeXml(definition)).append("</p>\r\n");
b.append("<p>Definitions for matching codes:</p>\r\n");
b.append("<ul>\r\n");
for (String s : sorted(dset)) b.append("<li>").append(Utilities.escapeXml(s)).append("</li>\r\n");
b.append("</ul>\r\n");
}
return b.toString();
}
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