use of org.hl7.fhir.definitions.model.ImplementationGuideDefn in project kindling by HL7.
the class Publisher method produceConformancePackage.
private void produceConformancePackage(ResourceDefn res, Profile pack, SectionTracker st) throws Exception {
String resourceName = res == null ? "" : res.getName();
if (Utilities.noString(resourceName)) {
if (pack.getProfiles().size() == 1)
if (pack.getProfiles().get(0).getDefn() != null)
resourceName = pack.getProfiles().get(0).getDefn().getName();
else
resourceName = pack.getProfiles().get(0).getResource().getType();
else if (pack.getProfiles().size() == 0) {
// throw new Exception("Unable to determine resource name - no profiles"); no, we don't complain
} else if (pack.getProfiles().get(0).getDefn() != null) {
resourceName = pack.getProfiles().get(0).getDefn().getName();
for (int i = 1; i < pack.getProfiles().size(); i++) if (!pack.getProfiles().get(i).getDefn().getName().equals(resourceName))
throw new Exception("Unable to determine resource name - profile mismatch " + resourceName + "/" + pack.getProfiles().get(i).getDefn().getName());
}
}
ImplementationGuideDefn ig = page.getDefinitions().getIgs().get(pack.getCategory());
String prefix = (ig == null || ig.isCore()) ? "" : ig.getCode() + File.separator;
String intro = pack.getIntroduction() != null ? page.loadXmlNotesFromFile(pack.getIntroduction(), false, null, null, null, null, res == null ? wg("fhir") : res.getWg()) : null;
String notes = pack.getNotes() != null ? page.loadXmlNotesFromFile(pack.getNotes(), false, null, null, null, null, res == null ? wg("fhir") : res.getWg()) : null;
if (!("profile".equals(pack.metadata("navigation")) && pack.getProfiles().size() == 1)) {
String src = TextFile.fileToString(page.getFolders().templateDir + "template-conformance-pack.html");
src = page.processConformancePackageIncludes(pack, src, intro, notes, resourceName, ig);
if (st != null)
src = insertSectionNumbers(src, st, pack.getId().toLowerCase() + ".html", 0, null);
else if (ig != null && !ig.isCore())
src = addSectionNumbers(pack.getId() + ".html", pack.getId().toLowerCase(), src, null, 1, null, ig);
page.getHTMLChecker().registerFile(prefix + pack.getId().toLowerCase() + ".html", "Profile " + pack.getId(), HTMLLinkChecker.XHTML_TYPE, true);
TextFile.stringToFile(src, page.getFolders().dstDir + prefix + pack.getId().toLowerCase() + ".html");
}
// now, we produce each profile
for (ConstraintStructure profile : pack.getProfiles()) produceProfile(res, pack, profile, st, intro, notes, prefix, ig);
for (SearchParameter sp : pack.getSearchParameters()) producePackSearchParameter(res, pack, sp, st, ig);
for (Example ex : pack.getExamples()) {
StructureDefinition sd = null;
boolean ambiguous = false;
for (ConstraintStructure sdt : pack.getProfiles()) {
if (sdt.getResource().getSnapshot().getElement().get(0).getPath().equals(resourceName))
if (sd == null)
sd = sdt.getResource();
else
ambiguous = true;
}
if (ambiguous)
processExample(ex, res, null, null, ig);
else
processExample(ex, res, sd, pack, ig);
}
// create examples here
// if (examples != null) {
// for (String en : examples.keySet()) {
// processExample(examples.get(en), null, profile.getSource());
}
use of org.hl7.fhir.definitions.model.ImplementationGuideDefn in project kindling by HL7.
the class Publisher method produceSpec.
private void produceSpec() throws Exception {
for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) {
for (LogicalModel lm : ig.getLogicalModels()) {
page.log(" ...logical model " + lm.getId(), LogMessageType.Process);
produceLogicalModel(lm, ig);
}
}
for (StructureDefinition ed : page.getWorkerContext().getExtensionDefinitions()) {
String filename = "extension-" + (ed.getUrl().startsWith("http://fhir-registry.smarthealthit.org/StructureDefinition/") ? ed.getUrl().substring(59).toLowerCase() : ed.getUrl().substring(40).toLowerCase());
ed.setUserData("filename", filename);
ImplementationGuideDefn ig = page.getDefinitions().getIgs().get(ed.getUserString(ToolResourceUtilities.NAME_RES_IG));
if (ig == null) {
ig = page.getDefinitions().getIgs().get("core");
}
ed.setUserData("path", (ig.isCore() ? "" : ig.getCode() + File.separator) + filename + ".html");
}
page.updateDiffEngineDefinitions();
loadValueSets2();
page.log(" ...extensions", LogMessageType.Process);
for (StructureDefinition ae : page.getWorkerContext().getExtensionDefinitions()) produceExtensionDefinition(ae);
checkAllOk();
page.log(" ...resource identities", LogMessageType.Process);
for (String rname : page.getDefinitions().getBaseResources().keySet()) {
ResourceDefn r = page.getDefinitions().getBaseResources().get(rname);
produceResource1(r, r.isAbstract());
}
for (String rname : page.getDefinitions().sortedResourceNames()) {
if (!rname.equals("ValueSet") && !rname.equals("CodeSystem") && wantBuild(rname)) {
ResourceDefn r = page.getDefinitions().getResources().get(rname);
produceResource1(r, false);
}
}
if (buildFlags.get("all")) {
page.log(" ...base profiles", LogMessageType.Process);
produceBaseProfile();
}
for (String rname : page.getDefinitions().getBaseResources().keySet()) {
ResourceDefn r = page.getDefinitions().getBaseResources().get(rname);
page.log(" ...resource " + r.getName(), LogMessageType.Process);
produceResource2(r, !rname.equals("Parameters"), rname.equals("Resource") ? "Meta" : null, false);
}
for (String rname : page.getDefinitions().sortedResourceNames()) {
if (!rname.equals("ValueSet") && !rname.equals("CodeSystem") && wantBuild(rname)) {
ResourceDefn r = page.getDefinitions().getResources().get(rname);
page.log(" ...resource " + r.getName(), LogMessageType.Process);
produceResource2(r, false, null, false);
}
}
for (Compartment c : page.getDefinitions().getCompartments()) {
if (buildFlags.get("all")) {
page.log(" ...compartment " + c.getName(), LogMessageType.Process);
produceCompartment(c);
}
}
Regenerator regen = new Regenerator(page.getFolders().srcDir, page.getDefinitions(), page.getWorkerContext());
regen.generate();
Bundle searchParamsFeed = new Bundle();
searchParamsFeed.setId("searchParams");
searchParamsFeed.setType(BundleType.COLLECTION);
searchParamsFeed.setMeta(new Meta().setLastUpdated(page.getResourceBundle().getMeta().getLastUpdated()));
Set<String> uris = new HashSet<String>();
for (ResourceDefn rd : page.getDefinitions().getBaseResources().values()) addSearchParams(uris, searchParamsFeed, rd);
for (String n : page.getDefinitions().sortedResourceNames()) {
ResourceDefn rd = page.getDefinitions().getResources().get(n);
addSearchParams(uris, searchParamsFeed, rd);
}
for (Profile cp : page.getDefinitions().getPackList()) {
addSearchParams(uris, searchParamsFeed, cp);
}
checkBundleURLs(searchParamsFeed);
for (String n : page.getIni().getPropertyNames("pages")) {
if (buildFlags.get("all") || buildFlags.get("page-" + n.toLowerCase())) {
page.log(" ...page " + n, LogMessageType.Process);
producePage(n, page.getIni().getStringProperty("pages", n));
}
}
for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) {
for (String n : ig.getPageList()) {
page.log(" ...ig page " + n, LogMessageType.Process);
produceIgPage(n, ig);
}
for (ImplementationGuideDefinitionPageComponent page : ig.getSpecialPages()) {
produceIgPage(ig, page);
}
for (Profile p : ig.getProfiles()) {
if (!p.getOperations().isEmpty()) {
produceIgOperations(ig, p);
}
}
}
if (page.getIni().getPropertyNames("ig-pages") != null) {
for (String n : page.getIni().getPropertyNames("ig-pages")) {
page.log(" ...page " + n, LogMessageType.Process);
for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) {
if (!ig.isCore())
produceIgPage(n, ig, page.getIni().getStringProperty("ig-pages", n));
}
}
}
for (String n : page.getDefinitions().getDictionaries().keySet()) {
if (buildFlags.get("all")) {
// || buildFlags.get("dict-" + n.toLowerCase())) {
page.log(" ...dictionary " + n, LogMessageType.Process);
produceDictionary(page.getDefinitions().getDictionaries().get(n));
}
}
int i = 0;
for (String n : page.getIni().getPropertyNames("sid")) {
page.log(" ...sid " + n, LogMessageType.Process);
produceSid(i, n, page.getIni().getStringProperty("sid", n));
i++;
}
if (buildFlags.get("all")) {
page.log(" ...check Fragments", LogMessageType.Process);
checkFragments();
for (Profile p : page.getDefinitions().getPackList()) {
// if (!n.startsWith("http://")) {
page.log(" ...Profile " + p.getId(), LogMessageType.Process);
produceConformancePackage(null, p, null);
// }
}
produceUml();
page.getVsValidator().checkDuplicates(page.getValidationErrors());
if (buildFlags.get("all")) {
// if (page.getToc().containsKey("1.1"))
// throw new Exception("Duplicate DOC Entry "+"1.1");
page.getToc().put("1.1", new TocEntry("1.1", "Table Of Contents", "toc.html", false));
page.log(" ...page toc.html", LogMessageType.Process);
producePage("toc.html", null);
}
checkAllOk();
page.log(" ...collections ", LogMessageType.Process);
com.google.gson.JsonObject diff = new com.google.gson.JsonObject();
page.getDiffEngine().getDiffAsJson(diff);
Gson gson = new GsonBuilder().setPrettyPrinting().create();
String json = gson.toJson(diff);
TextFile.stringToFile(json, Utilities.path(page.getFolders().dstDir, "fhir.diff.json"));
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = dbf.newDocumentBuilder();
Document doc = builder.newDocument();
Element element = doc.createElement("difference");
doc.appendChild(element);
page.getDiffEngine().getDiffAsXml(doc, element);
prettyPrint(doc, Utilities.path(page.getFolders().dstDir, "fhir.diff.xml"));
checkBundleURLs(page.getResourceBundle());
checkStructureDefinitions(page.getResourceBundle());
page.getResourceBundle().getEntry().sort(new ProfileBundleSorter());
FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + "profiles-resources.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, page.getResourceBundle());
s.close();
s = new FileOutputStream(page.getFolders().dstDir + "profiles-resources.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, page.getResourceBundle());
s.close();
checkBundleURLs(page.getTypeBundle());
checkStructureDefinitions(page.getTypeBundle());
page.getTypeBundle().getEntry().sort(new ProfileBundleSorter());
s = new FileOutputStream(page.getFolders().dstDir + "profiles-types.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, page.getTypeBundle());
s.close();
s = new FileOutputStream(page.getFolders().dstDir + "profiles-types.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, page.getTypeBundle());
s.close();
Bundle extensionsFeed = new Bundle();
extensionsFeed.setId("extensions");
extensionsFeed.setType(BundleType.COLLECTION);
extensionsFeed.setMeta(new Meta().setLastUpdated(page.getResourceBundle().getMeta().getLastUpdated()));
Set<String> urls = new HashSet<String>();
for (StructureDefinition ed : page.getWorkerContext().getExtensionDefinitions()) {
if (!urls.contains(ed.getUrl())) {
urls.add(ed.getUrl());
extensionsFeed.getEntry().add(new BundleEntryComponent().setResource(ed).setFullUrl("http://hl7.org/fhir/" + ed.fhirType() + "/" + ed.getId()));
}
}
checkBundleURLs(extensionsFeed);
checkStructureDefinitions(extensionsFeed);
s = new FileOutputStream(page.getFolders().dstDir + "extension-definitions.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, extensionsFeed);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + "extension-definitions.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, extensionsFeed);
s.close();
Utilities.copyFile(page.getFolders().dstDir + "extension-definitions.xml", page.getFolders().dstDir + "examples" + File.separator + "extension-definitions.xml");
s = new FileOutputStream(page.getFolders().dstDir + "search-parameters.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, searchParamsFeed);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + "search-parameters.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, searchParamsFeed);
s.close();
Utilities.copyFile(page.getFolders().dstDir + "search-parameters.xml", page.getFolders().dstDir + "examples" + File.separator + "search-parameters.xml");
for (ResourceDefn rd : page.getDefinitions().getResources().values()) addOtherProfiles(profileBundle, rd);
for (Profile cp : page.getDefinitions().getPackList()) {
addOtherProfiles(profileBundle, cp);
}
checkBundleURLs(profileBundle);
checkStructureDefinitions(profileBundle);
s = new FileOutputStream(page.getFolders().dstDir + "profiles-others.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, profileBundle);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + "profiles-others.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, profileBundle);
s.close();
Utilities.copyFile(page.getFolders().dstDir + "profiles-others.xml", page.getFolders().dstDir + "examples" + File.separator + "profiles-others.xml");
// todo-bundle - should this be checked?
// int ec = 0;
// for (Resource e : valueSetsFeed.getItem()) {
// ValueSet vs = (ValueSet) e;
// if (!vs.getUrl().equals(e.getId())) {
// ec++;
// page.log("Valueset id mismatch: atom entry has '"+e.getId()+"', but value set is '"+vs.getUrl()+"'", LogMessageType.Error);
// }
// }
// if (ec > 0)
// throw new Exception("Cannot continue due to value set mis-identification");
checkBundleURLs(dataElements);
s = new FileOutputStream(page.getFolders().dstDir + "dataelements.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, dataElements);
s.close();
Utilities.copyFile(page.getFolders().dstDir + "dataelements.xml", page.getFolders().dstDir + "examples" + File.separator + "dataelements.xml");
s = new FileOutputStream(page.getFolders().dstDir + "dataelements.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, dataElements);
s.close();
checkBundleURLs(valueSetsFeed);
s = new FileOutputStream(page.getFolders().dstDir + "valuesets.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, valueSetsFeed);
s.close();
Utilities.copyFile(page.getFolders().dstDir + "valuesets.xml", page.getFolders().dstDir + "examples" + File.separator + "valuesets.xml");
s = new FileOutputStream(page.getFolders().dstDir + "valuesets.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, valueSetsFeed);
s.close();
checkBundleURLs(conceptMapsFeed);
s = new FileOutputStream(page.getFolders().dstDir + "conceptmaps.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, conceptMapsFeed);
s.close();
Utilities.copyFile(page.getFolders().dstDir + "conceptmaps.xml", page.getFolders().dstDir + "examples" + File.separator + "conceptmaps.xml");
s = new FileOutputStream(page.getFolders().dstDir + "conceptmaps.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, conceptMapsFeed);
s.close();
checkBundleURLs(externals);
s = new FileOutputStream(page.getFolders().dstDir + "external-resources.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, externals);
s.close();
Utilities.copyFile(page.getFolders().dstDir + "external-resources.xml", page.getFolders().dstDir + "examples" + File.separator + "external-resources.xml");
s = new FileOutputStream(page.getFolders().dstDir + "external-resources.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, externals);
s.close();
ImplementationGuide expIg = new ImplementationGuide();
expIg.addFhirVersion(page.getVersion());
expIg.setPackageId(pidRoot() + ".expansions");
expIg.setVersion(page.getVersion().toCode());
expIg.setLicense(ImplementationGuide.SPDXLicense.CC01_0);
expIg.setTitle("FHIR " + page.getVersion().getDisplay() + " package : Expansions");
expIg.setDescription("Expansions for the " + page.getVersion().getDisplay() + " version of the FHIR standard");
NPMPackageGenerator npm = new NPMPackageGenerator(Utilities.path(page.getFolders().dstDir, pidRoot() + ".expansions.tgz"), "http://hl7.org/fhir", "http://hl7.org/fhir", PackageType.CORE, expIg, page.getGenDate().getTime(), true);
Bundle expansionFeed = new Bundle();
Set<String> urlset = new HashSet<>();
expansionFeed.setId("valueset-expansions");
expansionFeed.setType(BundleType.COLLECTION);
expansionFeed.setMeta(new Meta().setLastUpdated(page.getGenDate().getTime()));
expansionFeed.getFormatCommentsPre().add("This collection contains expansions for all the value sets that are used on an element of type \r\n" + "'code', to help with code generation (saves the code generator having to figure out how to \r\n" + "do the expansions or find a terminology server that supports the same version of the value sets");
for (ValueSet vs : page.getValueSets().getList()) {
if (!urlset.contains(vs.getUrl())) {
urlset.add(vs.getUrl());
if (vs.getUserData(ToolResourceUtilities.NAME_VS_USE_MARKER) != null) {
ValueSet evs = null;
if (vs.hasUserData("expansion"))
evs = (ValueSet) vs.getUserData("expansion");
else {
ValueSetExpansionOutcome vse = page.getWorkerContext().expandVS(vs, true, false);
if (vse.getValueset() != null) {
evs = vse.getValueset();
vs.setUserData("expansion", evs);
}
}
if (evs != null) {
ValueSet vsc = vs.copy();
vsc.setText(null);
vsc.setExpansion(evs.getExpansion());
expansionFeed.addEntry().setFullUrl("http://hl7.org/fhir/" + vsc.fhirType() + "/" + vsc.getId()).setResource(vsc);
npm.addFile(Category.RESOURCE, "ValueSet-" + vsc.getId() + ".json", new JsonParser().composeBytes(vsc));
}
}
}
}
npm.finish();
if (!isCIBuild) {
String id = pidRoot() + ".expansions";
new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).addPackageToCache(id, "current", new FileInputStream(Utilities.path(page.getFolders().dstDir, id + ".tgz")), Utilities.path(page.getFolders().dstDir, id + ".tgz"));
}
s = new FileOutputStream(page.getFolders().dstDir + "expansions.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, expansionFeed);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + "expansions.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, expansionFeed);
s.close();
produceComparisons();
produceSpecMap();
processRDF();
page.log("....version maps", LogMessageType.Process);
ZipGenerator zip = new ZipGenerator(page.getFolders().dstDir + "r3r4maps.zip");
zip.addFiles(Utilities.path(page.getFolders().rootDir, "implementations", "r3maps", "R3toR4", ""), "r3/", null, null);
zip.addFiles(Utilities.path(page.getFolders().rootDir, "implementations", "r3maps", "R4toR3", ""), "r4/", null, null);
zip.close();
page.log("....definitions", LogMessageType.Process);
zip = new ZipGenerator(page.getFolders().dstDir + "definitions.xml.zip");
zip.addFileName("version.info", page.getFolders().dstDir + "version.info", false);
zip.addFileName("profiles-types.xml", page.getFolders().dstDir + "profiles-types.xml", false);
zip.addFileName("profiles-resources.xml", page.getFolders().dstDir + "profiles-resources.xml", false);
zip.addFileName("profiles-others.xml", page.getFolders().dstDir + "profiles-others.xml", false);
zip.addFileName("extension-definitions.xml", page.getFolders().dstDir + "extension-definitions.xml", false);
zip.addFileName("search-parameters.xml", page.getFolders().dstDir + "search-parameters.xml", false);
zip.addFileName("valuesets.xml", page.getFolders().dstDir + "valuesets.xml", false);
zip.addFileName("conceptmaps.xml", page.getFolders().dstDir + "conceptmaps.xml", false);
zip.addFileName("dataelements.xml", page.getFolders().dstDir + "dataelements.xml", false);
zip.addFileName("fhir-all-xsd.zip", page.getFolders().dstDir + "fhir-all-xsd.zip", false);
zip.close();
zip = new ZipGenerator(page.getFolders().dstDir + "definitions.json.zip");
zip.addFileName("version.info", page.getFolders().dstDir + "version.info", false);
zip.addFileName("profiles-types.json", page.getFolders().dstDir + "profiles-types.json", false);
zip.addFileName("profiles-resources.json", page.getFolders().dstDir + "profiles-resources.json", false);
zip.addFileName("profiles-others.json", page.getFolders().dstDir + "profiles-others.json", false);
zip.addFileName("extension-definitions.json", page.getFolders().dstDir + "extension-definitions.json", false);
zip.addFileName("search-parameters.json", page.getFolders().dstDir + "search-parameters.json", false);
zip.addFileName("valuesets.json", page.getFolders().dstDir + "valuesets.json", false);
zip.addFileName("conceptmaps.json", page.getFolders().dstDir + "conceptmaps.json", false);
zip.addFileName("dataelements.json", page.getFolders().dstDir + "dataelements.json", false);
zip.addFileName("fhir.schema.json.zip", page.getFolders().dstDir + "fhir.schema.json.zip", false);
zip.close();
zip = new ZipGenerator(page.getFolders().dstDir + "definitions.xlsx.zip");
for (String rn : page.getDefinitions().sortedResourceNames()) {
zip.addFileName(rn.toLowerCase() + ".xlsx", page.getFolders().dstDir + rn.toLowerCase() + ".xlsx", false);
}
zip.close();
// this is the actual package used by the validator.
zip = new ZipGenerator(page.getFolders().dstDir + "validator.pack");
// conformance resources
zip.addFileName("profiles-types.json", page.getFolders().dstDir + "profiles-types.json", false);
zip.addFileName("profiles-resources.json", page.getFolders().dstDir + "profiles-resources.json", false);
zip.addFileName("profiles-others.json", page.getFolders().dstDir + "profiles-others.json", false);
zip.addFileName("extension-definitions.json", page.getFolders().dstDir + "extension-definitions.json", false);
zip.addFileName("valuesets.json", page.getFolders().dstDir + "valuesets.json", false);
zip.addFileName("conceptmaps.json", page.getFolders().dstDir + "conceptmaps.json", false);
// native schema
zip.addFileName("fhir-all-xsd.zip", page.getFolders().dstDir + "fhir-all-xsd.zip", false);
zip.addFileName("fhir.schema.json.zip", page.getFolders().dstDir + "fhir.schema.json.zip", false);
zip.addFileName("fhir.shex", page.getFolders().dstDir + "fhir.shex", false);
zip.close();
page.log("....dstu3 format (xml)", LogMessageType.Process);
DSTU3ValidationConvertor dstu3 = new DSTU3ValidationConvertor();
dstu3.convert(page.getFolders().dstDir + "profiles-types.xml", page.getFolders().tmpDir + "profiles-types-r3.xml");
dstu3.convert(page.getFolders().dstDir + "profiles-resources.xml", page.getFolders().tmpDir + "profiles-resources-r3.xml");
dstu3.convert(page.getFolders().dstDir + "profiles-others.xml", page.getFolders().tmpDir + "profiles-others-r3.xml");
dstu3.convert(page.getFolders().dstDir + "extension-definitions.xml", page.getFolders().tmpDir + "extension-definitions-r3.xml");
dstu3.convert(page.getFolders().dstDir + "search-parameters.xml", page.getFolders().tmpDir + "search-parameters-r3.xml");
dstu3.convert(page.getFolders().dstDir + "valuesets.xml", page.getFolders().tmpDir + "valuesets-r3.xml");
dstu3.convert(page.getFolders().dstDir + "conceptmaps.xml", page.getFolders().tmpDir + "conceptmaps-r3.xml");
dstu3.convert(page.getFolders().dstDir + "dataelements.xml", page.getFolders().tmpDir + "dataelements-r3.xml");
zip = new ZipGenerator(page.getFolders().dstDir + "definitions-r3.xml.zip");
zip.addFileName("profiles-types.xml", page.getFolders().tmpDir + "profiles-types-r3.xml", false);
zip.addFileName("profiles-resources.xml", page.getFolders().tmpDir + "profiles-resources-r3.xml", false);
zip.addFileName("profiles-others.xml", page.getFolders().tmpDir + "profiles-others-r3.xml", false);
zip.addFileName("extension-definitions.xml", page.getFolders().tmpDir + "extension-definitions-r3.xml", false);
zip.addFileName("search-parameters.xml", page.getFolders().tmpDir + "search-parameters-r3.xml", false);
zip.addFileName("valuesets.xml", page.getFolders().tmpDir + "valuesets-r3.xml", false);
zip.addFileName("conceptmaps.xml", page.getFolders().tmpDir + "conceptmaps-r3.xml", false);
zip.addFileName("dataelements.xml", page.getFolders().tmpDir + "dataelements-r3.xml", false);
zip.close();
page.log("....dstu3 format (json)", LogMessageType.Process);
dstu3.convertJ(page.getFolders().dstDir + "profiles-types.xml", page.getFolders().tmpDir + "profiles-types-r3.json");
dstu3.convertJ(page.getFolders().dstDir + "profiles-resources.xml", page.getFolders().tmpDir + "profiles-resources-r3.json");
dstu3.convertJ(page.getFolders().dstDir + "profiles-others.xml", page.getFolders().tmpDir + "profiles-others-r3.json");
dstu3.convertJ(page.getFolders().dstDir + "extension-definitions.xml", page.getFolders().tmpDir + "extension-definitions-r3.json");
dstu3.convertJ(page.getFolders().dstDir + "search-parameters.xml", page.getFolders().tmpDir + "search-parameters-r3.json");
dstu3.convertJ(page.getFolders().dstDir + "valuesets.xml", page.getFolders().tmpDir + "valuesets-r3.json");
dstu3.convertJ(page.getFolders().dstDir + "conceptmaps.xml", page.getFolders().tmpDir + "conceptmaps-r3.json");
dstu3.convertJ(page.getFolders().dstDir + "dataelements.xml", page.getFolders().tmpDir + "dataelements-r3.json");
zip = new ZipGenerator(page.getFolders().dstDir + "definitions-r3.json.zip");
zip.addFileName("profiles-types.json", page.getFolders().tmpDir + "profiles-types-r3.json", false);
zip.addFileName("profiles-resources.json", page.getFolders().tmpDir + "profiles-resources-r3.json", false);
zip.addFileName("profiles-others.json", page.getFolders().tmpDir + "profiles-others-r3.json", false);
zip.addFileName("extension-definitions.json", page.getFolders().tmpDir + "extension-definitions-r3.json", false);
zip.addFileName("search-parameters.json", page.getFolders().tmpDir + "search-parameters-r3.json", false);
zip.addFileName("valuesets.json", page.getFolders().tmpDir + "valuesets-r3.json", false);
zip.addFileName("conceptmaps.json", page.getFolders().tmpDir + "conceptmaps-r3.json", false);
zip.addFileName("dataelements.json", page.getFolders().tmpDir + "dataelements-r3.json", false);
zip.close();
System.gc();
page.log("....r4 in r5 format", LogMessageType.Process);
zip = new ZipGenerator(page.getFolders().dstDir + "definitions-r2asr3.xml.zip");
page.getDiffEngine().saveR4AsR5(zip, FhirFormat.XML);
zip.close();
zip = new ZipGenerator(page.getFolders().dstDir + "definitions-r2asr3.json.zip");
page.getDiffEngine().saveR4AsR5(zip, FhirFormat.JSON);
zip.close();
zip = new ZipGenerator(page.getFolders().dstDir + "all-valuesets.zip");
zip.addFileName("valuesets.xml", page.getFolders().dstDir + "valuesets.xml", false);
zip.addFileName("valuesets.json", page.getFolders().dstDir + "valuesets.json", false);
zip.addFileName("conceptmaps.xml", page.getFolders().dstDir + "conceptmaps.xml", false);
zip.addFileName("conceptmaps.json", page.getFolders().dstDir + "conceptmaps.json", false);
zip.close();
page.log("....IG Builder Resources", LogMessageType.Process);
zip = new ZipGenerator(page.getFolders().tmpDir + "ig-template.zip");
zip.addFolder(Utilities.path(page.getFolders().rootDir, "tools", "ig"), "", false, null);
zip.close();
zip = new ZipGenerator(page.getFolders().dstDir + "igpack.zip");
zip.addFileName("fhir.css", page.getFolders().dstDir + "fhir.css", false);
zip.addFileName("spec.internals", page.getFolders().dstDir + "spec.internals", false);
zip.addFileName("profiles-types.xml", page.getFolders().dstDir + "profiles-types.xml", false);
zip.addFileName("profiles-resources.xml", page.getFolders().dstDir + "profiles-resources.xml", false);
zip.addFileName("profiles-others.xml", page.getFolders().dstDir + "profiles-others.xml", false);
zip.addFileName("extension-definitions.xml", page.getFolders().dstDir + "extension-definitions.xml", false);
zip.addFileName("search-parameters.xml", page.getFolders().dstDir + "search-parameters.xml", false);
zip.addFileName("valuesets.xml", page.getFolders().dstDir + "valuesets.xml", false);
zip.addFileName("conceptmaps.xml", page.getFolders().dstDir + "conceptmaps.xml", false);
zip.addFileName("dataelements.xml", page.getFolders().dstDir + "dataelements.xml", false);
zip.addFileName("version.info", page.getFolders().dstDir + "version.info", false);
zip.addFileName("mappingSpaces.details", page.getFolders().srcDir + "mappingSpaces.xml", false);
zip.addFileName("redirect.asp.template", page.getFolders().srcDir + "redirect.asp", false);
zip.addFileName("redirect.cgi.template", page.getFolders().srcDir + "redirect.cgi", false);
zip.addFileName("redirect.php.template", page.getFolders().srcDir + "redirect.php", false);
zip.addFileName("ig-template.zip", Utilities.path(page.getFolders().tmpDir, "ig-template.zip"), false);
zip.addFiles(Utilities.path(page.getFolders().rootDir, "publish", ""), "", ".png", null);
zip.addFiles(Utilities.path(page.getFolders().rootDir, "publish", ""), "", ".gif", null);
zip.close();
page.log("....IG Builder (2)", LogMessageType.Process);
SpecNPMPackageGenerator self = new SpecNPMPackageGenerator();
self.generate(page.getFolders().dstDir, page.getBaseURL(), false, page.getGenDate().getTime(), pidRoot());
if (!isCIBuild) {
new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).addPackageToCache(pidRoot() + ".core", "current", new FileInputStream(Utilities.path(page.getFolders().dstDir, pidRoot() + ".core.tgz")), Utilities.path(page.getFolders().dstDir, pidRoot() + ".core.tgz"));
}
page.log(" ...zips", LogMessageType.Process);
zip = new ZipGenerator(page.getFolders().dstDir + "examples.zip");
zip.addFiles(page.getFolders().dstDir + "examples" + File.separator, "", null, "expansions.xml");
zip.close();
zip = new ZipGenerator(page.getFolders().dstDir + "examples-json.zip");
gson = new GsonBuilder().setPrettyPrinting().create();
File f = new CSFile(page.getFolders().dstDir);
File[] files = f.listFiles();
String[] noExt = new String[] { ".schema.json", ".canonical.json", ".diff.json", "expansions.json", "package.json", "choice-elements.json", "backbone-elements.json" };
for (int fi = 0; fi < files.length; fi++) {
if (files[fi].isFile() && (files[fi].getName().endsWith(".json"))) {
boolean ok = true;
for (String n : noExt) {
ok = ok && !files[fi].getName().endsWith(n);
}
if (ok) {
JsonObject jr = JSONUtil.parse(TextFile.fileToString(files[fi]));
if (!jr.has("url")) {
JsonObject meta = JSONUtil.forceObject(jr, "meta");
JsonArray labels = JSONUtil.forceArray(meta, "tag");
JsonObject label = JSONUtil.addObj(labels);
label.addProperty("system", "http://terminology.hl7.org/CodeSystem/v3-ActReason");
label.addProperty("code", "HTEST");
label.addProperty("display", "test health data");
}
String jrs = gson.toJson(jr);
zip.addBytes(files[fi].getName(), jrs.getBytes(Charsets.UTF_8), true);
}
}
}
zip.close();
NDJsonWriter ndjson = new NDJsonWriter(page.getFolders().dstDir + "examples-ndjson.zip", page.getFolders().tmpDir);
ndjson.addFilesFiltered(page.getFolders().dstDir, ".json", new String[] { ".schema.json", ".canonical.json", ".diff.json", "expansions.json", "package.json" });
ndjson.close();
zip = new ZipGenerator(page.getFolders().dstDir + "examples-ttl.zip");
zip.addFilesFiltered(page.getFolders().dstDir, "", ".ttl", new String[0]);
zip.close();
page.log("Check HTML Links", LogMessageType.Process);
page.getHTMLChecker().produce();
checkAllOk();
} else
page.log("Partial Build - terminating now", LogMessageType.Error);
}
use of org.hl7.fhir.definitions.model.ImplementationGuideDefn in project kindling by HL7.
the class Publisher method processQuestionnaire.
private void processQuestionnaire(ResourceDefn res, StructureDefinition profile, SectionTracker st, boolean isResource, String prefix, ImplementationGuideDefn ig) throws Exception {
QuestionnaireBuilder qb = new QuestionnaireBuilder(page.getWorkerContext());
qb.setProfile(profile);
qb.build();
Questionnaire q = qb.getQuestionnaire();
FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + prefix + profile.getId().toLowerCase() + "-questionnaire.json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, q);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + prefix + profile.getId().toLowerCase() + "-questionnaire.canonical.json");
new JsonParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, q);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + prefix + profile.getId().toLowerCase() + "-questionnaire.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, q);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + prefix + profile.getId().toLowerCase() + "-questionnaire.canonical.xml");
new XmlParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, q);
s.close();
String json = "<div class=\"example\">\r\n<p>Generated Questionnaire for " + profile.getId() + "</p>\r\n<pre class=\"json\">\r\n" + Utilities.escapeXml(new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(q)) + "\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(prefix + profile.getId().toLowerCase() + "-questionnaire.json.html", html, (isResource ? "resource-questionnaire:" : "profile-questionnaire:") + profile.getId(), null, null, null, "Questionnaire", ig, res, res == null ? wg("fhir") : res.getWg());
TextFile.stringToFile(html, page.getFolders().dstDir + prefix + profile.getId().toLowerCase() + "-questionnaire.json.html");
String xml = "<div class=\"example\">\r\n<p>Generated Questionnaire for " + profile.getId() + "</p>\r\n<pre class=\"json\">\r\n" + Utilities.escapeXml(new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeString(q)) + "\r\n</pre>\r\n</div>\r\n";
html = TextFile.fileToString(page.getFolders().templateDir + "template-example-xml.html").replace("<%example%>", xml);
html = page.processPageIncludes(prefix + profile.getId().toLowerCase() + "-questionnaire.xml.html", html, (isResource ? "resource-questionnaire:" : "profile-questionnaire:") + profile.getId(), null, null, null, "Questionnaire", ig, res, res == null ? wg("fhir") : res.getWg());
TextFile.stringToFile(html, page.getFolders().dstDir + prefix + profile.getId().toLowerCase() + "-questionnaire.xml.html");
if (false) {
File tmpTransform = Utilities.createTempFile("tmp", ".html");
// if (web) {
HashMap<String, String> params = new HashMap<String, String>();
params.put("suppressWarnings", "true");
XsltUtilities.saxonTransform(// directory for xslt references
Utilities.path(page.getFolders().rootDir, "implementations", "xmltools"), // source to run xslt on
page.getFolders().dstDir + prefix + profile.getId().toLowerCase() + "-questionnaire.xml", // xslt file to run
Utilities.path(page.getFolders().rootDir, "implementations", "xmltools", "QuestionnaireToHTML.xslt"), // file to produce
tmpTransform.getAbsolutePath(), // handle to self to implement URI resolver for terminology fetching
this, params);
// } else
// TextFile.stringToFile("test", tmpTransform.getAbsolutePath());
// now, generate the form
html = TextFile.fileToString(page.getFolders().templateDir + (isResource ? "template-questionnaire.html" : "template-profile-questionnaire.html")).replace("<%questionnaire%>", loadHtmlForm(tmpTransform.getAbsolutePath()));
} else
html = "<html><p>Not generated in this build</p></html>";
html = page.processPageIncludes(profile.getId().toLowerCase() + "-questionnaire.html", html, (isResource ? "resource-questionnaire:" : "profile-questionnaire:") + profile.getId(), null, profile, null, "Questionnaire", ig, res, res == null ? wg("fhir") : res.getWg());
int level = (ig == null || ig.isCore()) ? 0 : 1;
if (st != null)
html = insertSectionNumbers(html, st, profile.getId().toLowerCase() + "-questionnaire.html", level, null);
TextFile.stringToFile(html, page.getFolders().dstDir + prefix + profile.getId().toLowerCase() + "-questionnaire.html");
page.getHTMLChecker().registerExternal(prefix + profile.getId().toLowerCase() + "-questionnaire.html");
page.getHTMLChecker().registerExternal(prefix + profile.getId().toLowerCase() + "-questionnaire.json.html");
page.getHTMLChecker().registerExternal(prefix + profile.getId().toLowerCase() + "-questionnaire.xml.html");
}
use of org.hl7.fhir.definitions.model.ImplementationGuideDefn in project kindling by HL7.
the class Publisher method produceExtensionDefinition.
private void produceExtensionDefinition(StructureDefinition ed) throws FileNotFoundException, Exception {
if (!ped.contains(ed)) {
ped.add(ed);
ImplementationGuideDefn ig = page.getDefinitions().getIgs().get(ed.getUserString(ToolResourceUtilities.NAME_RES_IG));
String prefix = ig.isCore() ? "" : ig.getCode() + File.separator;
String filename = ed.getUserString("filename");
FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + prefix + filename + ".xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, ed);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + prefix + filename + ".canonical.xml");
new XmlParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, ed);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + prefix + filename + ".json");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, ed);
s.close();
s = new FileOutputStream(page.getFolders().dstDir + prefix + filename + ".canonical.json");
new JsonParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, ed);
s.close();
cloneToXhtml(prefix + filename, ed.getName(), false, "summary-instance", ed.getUrl(), null, wg(ed));
jsonToXhtml(prefix + filename, ed.getName(), resource2Json(ed), "extension", ed.getUrl(), null, wg(ed));
ttlToXhtml(prefix + filename, ed.getName(), resource2Ttl(ed), "extension", ed.getUrl(), null, wg(ed));
ByteArrayOutputStream bytes = new ByteArrayOutputStream();
XmlSpecGenerator gen = new XmlSpecGenerator(bytes, filename + "-definitions.html", null, /*"http://hl7.org/fhir/"*/
page, page.genlevel(ig.isCore() ? 0 : 1));
gen.generateExtension(ed);
gen.close();
String xml = bytes.toString();
bytes = new ByteArrayOutputStream();
JsonSpecGenerator genj = new JsonSpecGenerator(bytes, filename + "-definitions.html", null, /*"http://hl7.org/fhir/"*/
page, page.genlevel(ig.isCore() ? 0 : 1), page.getVersion().toCode());
genj.generateExtension(ed);
genj.close();
String json = bytes.toString();
bytes = new ByteArrayOutputStream();
TurtleSpecGenerator gent = new TurtleSpecGenerator(bytes, filename + "-definitions.html", null, /*"http://hl7.org/fhir/"*/
page, page.genlevel(ig.isCore() ? 0 : 1), page.getVersion().toCode());
gent.generateExtension(ed);
gent.close();
String ttl = bytes.toString();
bytes = new ByteArrayOutputStream();
TerminologyNotesGenerator tgen = new TerminologyNotesGenerator(bytes, page);
tgen.generateExtension("", ed);
tgen.close();
String tx = bytes.toString();
String src = TextFile.fileToString(page.getFolders().templateDir + "template-extension-mappings.html");
src = page.processExtensionIncludes(filename, ed, xml, json, ttl, tx, src, filename + ".html", ig);
page.getHTMLChecker().registerFile(prefix + filename + "-mappings.html", "Mappings for Extension " + ed.getName(), HTMLLinkChecker.XHTML_TYPE, true);
TextFile.stringToFile(src, page.getFolders().dstDir + prefix + filename + "-mappings.html");
src = TextFile.fileToString(page.getFolders().templateDir + "template-extension-definitions.html");
src = page.processExtensionIncludes(filename, ed, xml, json, ttl, tx, src, filename + ".html", ig);
page.getHTMLChecker().registerFile(prefix + filename + "-definitions.html", "Definitions for Extension " + ed.getName(), HTMLLinkChecker.XHTML_TYPE, true);
TextFile.stringToFile(src, page.getFolders().dstDir + prefix + filename + "-definitions.html");
src = TextFile.fileToString(page.getFolders().templateDir + "template-extension.html");
src = page.processExtensionIncludes(filename, ed, xml, json, ttl, tx, src, filename + ".html", ig);
page.getHTMLChecker().registerFile(prefix + filename + ".html", "Extension " + ed.getName(), HTMLLinkChecker.XHTML_TYPE, true);
TextFile.stringToFile(src, page.getFolders().dstDir + prefix + filename + ".html");
}
}
use of org.hl7.fhir.definitions.model.ImplementationGuideDefn in project kindling by HL7.
the class Publisher method generateValueSetPart2.
private void generateValueSetPart2(ValueSet vs) throws Exception {
String n = vs.getUserString("filename");
if (n == null)
n = "valueset-" + vs.getId();
ImplementationGuideDefn ig = (ImplementationGuideDefn) vs.getUserData(ToolResourceUtilities.NAME_RES_IG);
if (ig != null)
n = ig.getCode() + File.separator + n;
if (!vs.hasText() || (vs.getText().getDiv().allChildrenAreText() && (Utilities.noString(vs.getText().getDiv().allText()) || !vs.getText().getDiv().allText().matches(".*\\w.*")))) {
RenderingContext lrc = page.getRc().copy().setLocalPrefix(ig != null ? "../" : "").setTooCostlyNoteEmpty(PageProcessor.TOO_MANY_CODES_TEXT_EMPTY).setTooCostlyNoteNotEmpty(PageProcessor.TOO_MANY_CODES_TEXT_NOT_EMPTY);
RendererFactory.factory(vs, lrc).render(vs);
}
page.getVsValidator().validate(page.getValidationErrors(), n, vs, true, false);
if (isGenerate) {
// page.log(" ... "+n, LogMessageType.Process);
addToResourceFeed(vs, valueSetsFeed, null);
if (vs.getUserData("path") == null)
vs.setUserData("path", n + ".html");
page.setId(vs.getId());
String sf;
try {
sf = page.processPageIncludes(n + ".html", TextFile.fileToString(page.getFolders().templateDir + "template-vs.html"), "valueSet", null, n + ".html", vs, null, "Value Set", ig, null, wg(vs, "vocab"));
} catch (Exception e) {
throw new Exception("Error processing " + n + ".html: " + e.getMessage(), e);
}
sf = addSectionNumbers(n + ".html", "template-valueset", sf, vsCounter(), ig == null ? 0 : 1, null, ig);
TextFile.stringToFile(sf, page.getFolders().dstDir + n + ".html");
try {
String src = page.processPageIncludesForBook(n + ".html", TextFile.fileToString(page.getFolders().templateDir + "template-vs-book.html"), "valueSet", vs, ig, null);
cachePage(n + ".html", src, "Value Set " + n, false);
page.setId(null);
} catch (Exception e) {
throw new Exception("Error processing " + n + ".html: " + e.getMessage(), e);
}
IParser json = new JsonParser().setOutputStyle(OutputStyle.PRETTY);
FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + n + ".json");
json.compose(s, vs);
s.close();
json = new JsonParser().setOutputStyle(OutputStyle.CANONICAL);
s = new FileOutputStream(page.getFolders().dstDir + n + ".canonical.json");
json.compose(s, vs);
s.close();
IParser xml = new XmlParser().setOutputStyle(OutputStyle.PRETTY);
s = new FileOutputStream(page.getFolders().dstDir + n + ".xml");
xml.compose(s, vs);
s.close();
xml = new XmlParser().setOutputStyle(OutputStyle.CANONICAL);
s = new FileOutputStream(page.getFolders().dstDir + n + ".canonical.xml");
xml.compose(s, vs);
s.close();
// System.out.println(vs.getUrl());
cloneToXhtml(n, "Definition for Value Set" + vs.present(), false, "valueset-instance", "Value Set", null, wg("vocab"));
jsonToXhtml(n, "Definition for Value Set" + vs.present(), resource2Json(vs), "valueset-instance", "Value Set", null, wg("vocab"));
ttlToXhtml(n, "Definition for Value Set" + vs.present(), resource2Ttl(vs), "valueset-instance", "Value Set", null, wg("vocab"));
}
}
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