Examples with LogicalModel org.hl7.fhir.definitions.model.LogicalModel used on opensource projects

Example 16 with LogicalModel

use of org.hl7.fhir.definitions.model.LogicalModel in project kindling by HL7.

the class PageProcessor method loadXmlNotes.

public String loadXmlNotes(String name, String suffix, boolean checkHeaders, String definition, ResourceDefn resource, List<String> tabs, ImplementationGuideDefn ig, WorkGroup wg) throws Exception {
    String filename;
    if (definitions.hasLogicalModel(name)) {
        LogicalModel lm = definitions.getLogicalModel(name);
        filename = Utilities.changeFileExt(lm.getSource(), "-" + suffix + ".xml");
    } else
        filename = folders.srcDir + name + File.separatorChar + name + "-" + suffix + ".xml";
    return loadXmlNotesFromFile(filename, checkHeaders, definition, resource, tabs, ig, wg);
}

Example 17 with LogicalModel

use of org.hl7.fhir.definitions.model.LogicalModel in project kindling by HL7.

the class IgParser method load.

public void load(String rootDir, ImplementationGuideDefn igd, List<ValidationMessage> issues, Set<String> loadedIgs) throws Exception {
    logger.log(" ..." + igd.getName(), LogMessageType.Process);
    // first: parse the IG, then use it
    String myRoot = Utilities.path(rootDir, "guides", igd.getCode());
    CSFile file = new CSFile(Utilities.path(rootDir, igd.getSource()));
    ImplementationGuide ig = (ImplementationGuide) new XmlParser().parse(new FileInputStream(file));
    if (// for things published in the hl7.org/fhir namespace...
    !ig.getUrl().startsWith("http://hl7.org/fhir/"))
        throw new Exception("Illegal namespace");
    if (!ig.getUrl().equals("http://hl7.org/fhir/" + ig.getId()))
        throw new Exception("Illegal URL");
    if (!ig.hasName())
        throw new Exception("no name on IG");
    ig.setDateElement(new DateTimeType(genDate));
    igd.setName(ig.getName());
    igd.setIg(ig);
    Map<String, Resource> resources = new HashMap<String, Resource>();
    for (ImplementationGuideDependsOnComponent d : ig.getDependsOn()) {
        if (!loadedIgs.contains(d.getUri()))
            throw new Exception("Dependency on " + ig.getName() + " not satisfied: " + d.getUri());
    }
    loadedIgs.add(ig.getUrl());
    // for (UriType bin : ig.getBinary()) {
    // if (!new File(Utilities.path(myRoot, bin.getValue())).exists())
    // throw new Exception("Binary dependency in "+ig.getName()+" not found: "+bin.getValue());
    // igd.getImageList().add(bin.getValue());
    // }
    processPage(ig.getDefinition().getPage(), igd);
    List<Example> exr = new ArrayList<Example>();
    // first pass - verify the resources can be loaded
    for (ImplementationGuideDefinitionResourceComponent r : ig.getDefinition().getResource()) {
        if (!r.hasReference())
            throw new Exception("no source on resource in IG " + ig.getName());
        CSFile fn = new CSFile(Utilities.path(myRoot, r.getReference().getReference()));
        if (!fn.exists())
            throw new Exception("Source " + r.getReference().getReference() + " resource in IG " + ig.getName() + " could not be located @ " + fn.getAbsolutePath());
        String id = Utilities.changeFileExt(fn.getName(), "");
        // we're going to try and load the resource directly.
        // if that fails, then we'll treat it as an example.
        boolean isExample = r.hasExample();
        ResourceType rt = null;
        try {
            rt = new XmlParser().parse(new FileInputStream(fn)).getResourceType();
        } catch (Exception e) {
            rt = null;
            isExample = true;
        }
        if (isExample) {
            if (// which means that non conformance resources must be named
            !r.hasName())
                throw new Exception("no name on resource in IG " + ig.getName());
            Example example = new Example(r.getName(), id, r.getDescription(), fn, false, ExampleType.XmlFile, false);
            example.setIg(igd.getCode());
            if (r.hasExampleCanonicalType()) {
                example.setExampleFor(r.getExampleCanonicalType().asStringValue());
                example.setRegistered(true);
                exr.add(example);
            }
            igd.getExamples().add(example);
            r.setUserData(ToolResourceUtilities.NAME_RES_EXAMPLE, example);
            r.setReference(new Reference(example.getId() + ".html"));
        } else if (rt == ResourceType.ValueSet) {
            ValueSet vs = (ValueSet) new XmlParser().parse(new FileInputStream(fn));
            if (id.startsWith("valueset-"))
                id = id.substring(9);
            vs.setId(id);
            if (vs.getUrl() == null) {
                // Asserting this all the time causes issues for non-HL7 URL value sets
                vs.setUrl("http://hl7.org/fhir/ValueSet/" + id);
            }
            vs.setUserData(ToolResourceUtilities.NAME_RES_IG, igd);
            vs.setUserData("path", igd.getPath() + "valueset-" + id + ".html");
            vs.setUserData("filename", "valueset-" + id);
            if (committee != null) {
                if (!vs.hasExtension(ToolingExtensions.EXT_WORKGROUP)) {
                    vs.addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType(committee.getCode()));
                } else {
                    String ec = ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_WORKGROUP);
                    if (!ec.equals(committee.getCode()))
                        System.out.println("ValueSet " + vs.getUrl() + " WG mismatch 2: is " + ec + ", want to set to " + committee);
                }
            }
            new CodeSystemConvertor(codeSystems).convert(new XmlParser(), vs, fn.getAbsolutePath(), packageInfo);
            // if (id.contains(File.separator))
            igd.getValueSets().add(vs);
            if (!r.hasName())
                r.setName(vs.getName());
            if (!r.hasDescription())
                r.setDescription(vs.getDescription());
            r.setUserData(ToolResourceUtilities.RES_ACTUAL_RESOURCE, vs);
            r.setReference(new Reference(fn.getName()));
        } else if (rt == ResourceType.StructureDefinition) {
            StructureDefinition sd;
            sd = (StructureDefinition) new XmlParser().parse(new CSFileInputStream(fn));
            new ProfileUtilities(context, null, pkp).setIds(sd, false);
            if (sd.getKind() == StructureDefinitionKind.LOGICAL) {
                fn = new CSFile(Utilities.path(myRoot, r.getReference().getReference()));
                LogicalModel lm = new LogicalModel(sd);
                lm.setSource(fn.getAbsolutePath());
                lm.setId(sd.getId());
                igd.getLogicalModels().add(lm);
            } else if ("Extension".equals(sd.getType())) {
                sd.setId(tail(sd.getUrl()));
                sd.setUserData(ToolResourceUtilities.NAME_RES_IG, igd.getCode());
                ToolResourceUtilities.updateUsage(sd, igd.getCode());
                this.context.cacheResource(sd);
            } else {
                Profile pr = new Profile(igd.getCode());
                pr.setSource(fn.getAbsolutePath());
                pr.setTitle(sd.getName());
                if (!sd.hasId())
                    sd.setId(tail(sd.getUrl()));
                // Lloyd: This causes issues for profiles & extensions defined outside of HL7
                // sd.setUrl("http://hl7.org/fhir/StructureDefinition/"+sd.getId());
                pr.forceMetadata("id", sd.getId() + "-profile");
                pr.setSourceType(ConformancePackageSourceType.StructureDefinition);
                ConstraintStructure cs = new ConstraintStructure(sd, igd, wg(sd), fmm(sd), sd.getExperimental());
                pr.getProfiles().add(cs);
                igd.getProfiles().add(pr);
            }
        } else if (rt == ResourceType.Bundle) {
            Dictionary d = new Dictionary(id, r.getName(), igd.getCode(), fn.getAbsolutePath(), igd);
            igd.getDictionaries().add(d);
        } else
            logger.log("Implementation Guides do not yet support " + rt.toString(), LogMessageType.Process);
    // throw new Error("Not implemented yet - type = "+rt.toString());
    // if (r.hasExampleFor()) {
    // if (!resources.containsKey(r.getExampleFor().getReference()))
    // throw new Exception("Unable to resolve example-for reference to "+r.getExampleFor().getReference());
    // }
    }
    // second pass: load the spreadsheets
    for (ImplementationGuideDefinitionGroupingComponent p : ig.getDefinition().getGrouping()) {
        if (!p.hasName())
            throw new Exception("no name on package in IG " + ig.getName());
        for (Extension ex : p.getExtension()) {
            if (ex.getUrl().equals(ToolResourceUtilities.EXT_PROFILE_SPREADSHEET)) {
                String s = ((UriType) ex.getValue()).getValue();
                File fn = new File(Utilities.path(myRoot, s));
                if (!fn.exists())
                    throw new Exception("Spreadsheet " + s + " in package " + p.getName() + " in IG " + ig.getName() + " could not be located");
                Profile pr = new Profile(igd.getCode());
                ex.setUserData(ToolResourceUtilities.NAME_RES_PROFILE, pr);
                pr.setSource(fn.getAbsolutePath());
                pr.setSourceType(ConformancePackageSourceType.Spreadsheet);
                OldSpreadsheetParser sparser = new OldSpreadsheetParser(pr.getCategory(), new CSFileInputStream(pr.getSource()), Utilities.noString(pr.getId()) ? pr.getSource() : pr.getId(), pr.getSource(), igd, rootDir, logger, registry, FHIRVersion.fromCode(context.getVersion()), context, genDate, false, pkp, false, committee, mappings, profileIds, codeSystems, maps, workgroups, exceptionIfExcelNotNormalised);
                sparser.getBindings().putAll(commonBindings);
                sparser.setFolder(Utilities.getDirectoryForFile(pr.getSource()));
                sparser.parseConformancePackage(pr, null, Utilities.getDirectoryForFile(pr.getSource()), pr.getCategory(), issues, null);
                // System.out.println("load "+pr.getId()+" from "+s);
                igd.getProfiles().add(pr);
                // what remains to be done now is to update the package with the loaded resources, but we need to wait for all the profiles to generated, so we'll do that later
                for (BindingSpecification bs : sparser.getBindings().values()) {
                    if (!commonBindings.containsValue(bs) && bs.getValueSet() != null) {
                        ValueSet vs = bs.getValueSet();
                        String path = vs.getUserString("path");
                        path = path.substring(path.lastIndexOf("/") + 1);
                        ig.getDefinition().addResource().setName(vs.getName()).setDescription(vs.getDescription()).setReference(new Reference(path)).setUserData(ToolResourceUtilities.RES_ACTUAL_RESOURCE, vs);
                    }
                }
                // now, register resources for all the things in the spreadsheet
                for (ValueSet vs : sparser.getValuesets()) ig.getDefinition().addResource().setExample(new BooleanType(false)).setName(vs.getName()).setDescription(vs.getDescription()).setReference(new Reference("valueset-" + vs.getId() + ".html")).setUserData(ToolResourceUtilities.RES_ACTUAL_RESOURCE, vs);
                for (StructureDefinition exd : pr.getExtensions()) ig.getDefinition().addResource().setExample(new BooleanType(false)).setName(exd.getName()).setDescription(exd.getDescription()).setReference(new Reference("extension-" + exd.getId().toLowerCase() + ".html")).setUserData(ToolResourceUtilities.RES_ACTUAL_RESOURCE, exd);
                for (ConstraintStructure cs : pr.getProfiles()) {
                    cs.setResourceInfo(ig.getDefinition().addResource());
                    cs.getResourceInfo().setExample(new BooleanType(false)).setName(cs.getDefn().getName()).setDescription(cs.getDefn().getDefinition()).setReference(new Reference(cs.getId().toLowerCase() + ".html"));
                }
            }
            if (ex.getUrl().equals(ToolResourceUtilities.EXT_LOGICAL_SPREADSHEET)) {
                File fn = new CSFile(Utilities.path(myRoot, ((UriType) ex.getValue()).getValue()));
                // String source = Utilities.path(file.getParent(), e.getAttribute("source"));
                String s = fn.getName();
                if (s.endsWith("-spreadsheet.xml"))
                    s = s.substring(0, s.length() - 16);
                String id = igd.getCode() + "-" + s;
                OldSpreadsheetParser sparser = new OldSpreadsheetParser(igd.getCode(), new CSFileInputStream(fn), id, fn.getAbsolutePath(), igd, rootDir, logger, registry, FHIRVersion.fromCode(context.getVersion()), context, genDate, false, pkp, false, committee, mappings, profileIds, codeSystems, maps, workgroups, exceptionIfExcelNotNormalised);
                sparser.getBindings().putAll(commonBindings);
                sparser.setFolder(Utilities.getDirectoryForFile(fn.getAbsolutePath()));
                LogicalModel lm = sparser.parseLogicalModel();
                lm.setId(id);
                lm.setSource(fn.getAbsolutePath());
                lm.getResource().setName(lm.getId());
                igd.getLogicalModels().add(lm);
            }
        }
        ToolingExtensions.removeExtension(p, ToolResourceUtilities.EXT_PROFILE_SPREADSHEET);
        ToolingExtensions.removeExtension(p, ToolResourceUtilities.EXT_LOGICAL_SPREADSHEET);
    }
    for (Example ex : exr) {
        Profile tp = null;
        for (Profile pr : igd.getProfiles()) {
            if (("StructureDefinition/" + pr.getId()).equals(ex.getExampleFor())) {
                tp = pr;
                break;
            } else
                for (ConstraintStructure cc : pr.getProfiles()) {
                    if (("StructureDefinition/" + cc.getId()).equals(ex.getExampleFor())) {
                        tp = pr;
                        break;
                    }
                }
        }
        if (tp != null)
            tp.getExamples().add(ex);
        else
            throw new Exception("no profile found matching exampleFor = " + ex.getExampleFor());
    }
    igd.numberPages();
// // second, parse the old ig, and use that. This is being phased out
// CSFile file = new CSFile(Utilities.path(rootDir, igd.getSource()));
// DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
// factory.setNamespaceAware(true);
// DocumentBuilder builder = factory.newDocumentBuilder();
// Document xdoc = builder.parse(new CSFileInputStream(file));
// Element root = xdoc.getDocumentElement();
// if (!root.getNodeName().equals("ig"))
// throw new Exception("wrong base node");
// Element e = XMLUtil.getFirstChild(root);
// while (e != null) {
// if (e.getNodeName().equals("dependsOn")) {
// // we ignore this for now
// } else if (e.getNodeName().equals("publishing")) {
// //        if (e.hasAttribute("homepage"))
// //          igd.setPage(e.getAttribute("homepage"));
// } else if (e.getNodeName().equals("page")) {
// //        igd.getPageList().add(e.getAttribute("source"));
// } else if (e.getNodeName().equals("image")) {
// //        moved above igd.getImageList().add(e.getAttribute("source"));
// } else if (e.getNodeName().equals("valueset")) {
// //        XmlParser xml = new XmlParser();
// //        ValueSet vs = (ValueSet) xml.parse(new CSFileInputStream(Utilities.path(file.getParent(), e.getAttribute("source"))));
// //        String id = Utilities.changeFileExt(new File(Utilities.path(file.getParent(), e.getAttribute("source"))).getName(), "");
// //        if (id.startsWith("valueset-"))
// //          id = id.substring(9);
// //        if (!vs.hasId() || !vs.hasUrl()) {
// //          vs.setId(id);
// //          vs.setUrl("http://hl7.org/fhir/ValueSet/"+vs.getId());
// //        }
// //        vs.setUserData(ToolResourceUtilities.NAME_RES_IG, igd);
// //        vs.setUserData("path", igd.getCode()+File.separator+"valueset-"+vs.getId()+".html");
// //        vs.setUserData("filename", "valueset-"+vs.getId());
// //        vs.setUserData("committee", committee);
// //        igd.getValueSets().add(vs);
// } else if (e.getNodeName().equals("acronym")) {
// igd.getTlas().put(e.getAttribute("target"), e.getAttribute("id"));
// } else if (e.getNodeName().equals("example")) {
// //        String filename = e.getAttribute("source");
// //        File efile = new File(Utilities.path(file.getParent(), filename));
// //        Example example = new Example(e.getAttribute("name"), Utilities.changeFileExt(efile.getName(), ""), e.getAttribute("name"), efile, false, ExampleType.XmlFile, false);
// //        example.setIg(igd.getCode());
// //        igd.getExamples().add(example);
// } else if (e.getNodeName().equals("profile")) {
// //        moved above
// //        Profile p = new Profile(igd.getCode());
// //        p.setSource(Utilities.path(file.getParent(), e.getAttribute("source")));
// //        if ("spreadsheet".equals(e.getAttribute("type"))) {
// //          p.setSourceType(ConformancePackageSourceType.Spreadsheet);
// //          SpreadsheetParser sparser = new SpreadsheetParser(p.getCategory(), new CSFileInputStream(p.getSource()), Utilities.noString(p.getId()) ? p.getSource() : p.getId(), igd,
// //              rootDir, logger, null, context.getVersion(), context, genDate, false, igd.getExtensions(), pkp, false, committee, mappings);
// //          sparser.getBindings().putAll(commonBindings);
// //          sparser.setFolder(Utilities.getDirectoryForFile(p.getSource()));
// //          sparser.parseConformancePackage(p, null, Utilities.getDirectoryForFile(p.getSource()), p.getCategory(), issues);
// //          for (BindingSpecification bs : sparser.getBindings().values()) {
// //            if (!commonBindings.containsValue(bs) && bs.getValueSet() != null) {
// //              ValueSet vs  = bs.getValueSet();
// //              String path = vs.getUserString("filename")+".xml";
// //              ig.getPackage().get(0).addResource().setName(vs.getName()).setDescription(vs.getDescription()).setSource(new UriType(path)).setUserData(ToolResourceUtilities.RES_ACTUAL_RESOURCE, vs);
// //            }
// //          }
// //        } else {
// //          throw new Exception("Unknown profile type in IG : "+e.getNodeName());
// //          // parseConformanceDocument(p, p.getId(), new File(p.getSource()), p.getCategory());
// //        }
// //
// //        String id = e.getAttribute("id");
// //        if (Utilities.noString(id))
// //          id = Utilities.changeFileExt(e.getAttribute("source"), "");
// //        igd.getProfiles().add(p);
// //        Element ex = XMLUtil.getFirstChild(e);
// //        while (ex != null) {
// //          if (ex.getNodeName().equals("example")) {
// //            String filename = ex.getAttribute("source");
// //            Example example = new Example(ex.getAttribute("name"), Utilities.changeFileExt(Utilities.getFileNameForName(filename), ""), ex.getAttribute("name"), new File(Utilities.path(file.getParent(), filename)), false, ExampleType.XmlFile, false);
// //            p.getExamples().add(example);
// //          } else
// //            throw new Exception("Unknown element name in IG: "+ex.getNodeName());
// //          ex = XMLUtil.getNextSibling(ex);
// //        }
// } else if (e.getNodeName().equals("dictionary")) {
// //        Dictionary d = new Dictionary(e.getAttribute("id"), e.getAttribute("name"), igd.getCode(), Utilities.path(Utilities.path(file.getParent(), e.getAttribute("source"))), igd);
// //        igd.getDictionaries().add(d);
// } else if (e.getNodeName().equals("logicalModel")) {
// //        String source = Utilities.path(file.getParent(), e.getAttribute("source"));
// //        String id = igd.getCode()+"-"+e.getAttribute("id");
// //        SpreadsheetParser sparser = new SpreadsheetParser(igd.getCode(), new CSFileInputStream(source), id, igd, rootDir, logger, null, context.getVersion(), context, genDate, false, igd.getExtensions(), pkp, false, committee, mappings);
// //        sparser.getBindings().putAll(commonBindings);
// //        sparser.setFolder(Utilities.getDirectoryForFile(source));
// //        LogicalModel lm = sparser.parseLogicalModel(source);
// //        lm.setId(id);
// //        lm.setSource(source);
// //        lm.getResource().setName(lm.getId());
// //        igd.getLogicalModels().add(lm);
// } else
// throw new Exception("Unknown element name in IG: "+e.getNodeName());
// e = XMLUtil.getNextSibling(e);
// }
}

Example 18 with LogicalModel

use of org.hl7.fhir.definitions.model.LogicalModel in project kindling by HL7.

the class OldSpreadsheetParser method parseLogicalModel.

public LogicalModel parseLogicalModel() throws Exception {
    ResourceDefn resource = new ResourceDefn();
    isLogicalModel = true;
    Sheet sheet = loadSheet("Bindings");
    if (sheet != null)
        readBindings(sheet);
    sheet = loadSheet("Invariants");
    Map<String, Invariant> invariants = null;
    if (sheet != null)
        invariants = readInvariants(sheet, title, "Invariants");
    sheet = loadSheet("Data Elements");
    if (sheet == null)
        throw new Exception("No Sheet found for Data Elements");
    for (int row = 0; row < sheet.rows.size(); row++) {
        processLine(resource, sheet, row, invariants, false, null, row == 0);
    }
    parseMetadata(resource);
    if (invariants != null) {
        for (Invariant inv : invariants.values()) {
            if (Utilities.noString(inv.getContext()))
                throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " has no context");
            else {
                ElementDefn ed = findContext(resource.getRoot(), inv.getContext(), "Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " Context");
                if (ed.getName().endsWith("[x]") && !inv.getContext().endsWith("[x]"))
                    inv.setFixedName(inv.getContext().substring(inv.getContext().lastIndexOf(".") + 1));
                ed.getInvariants().put(inv.getId(), inv);
                if (Utilities.noString(inv.getXpath())) {
                    throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " (" + inv.getEnglish() + ") has no XPath statement");
                } else if (inv.getXpath().contains("\""))
                    throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " (" + inv.getEnglish() + ") contains a \" character");
            // if (Utilities.noString(inv.getExpression()))
            // throw new Exception("Type "+resource.getRoot().getName()+" Invariant "+inv.getId()+" ("+inv.getEnglish()+") has no Expression statement (in FHIRPath format)");
            }
        }
    }
    // EK: Future types. But those won't get there.
    if (bindings != null)
        resource.getRoot().getNestedBindings().putAll(bindings);
    scanNestedTypes(resource, resource.getRoot(), resource.getName());
    resolveElementReferences(resource, resource.getRoot());
    LogicalModel lm = new LogicalModel();
    lm.setResource(resource);
    lm.setWg(definitions.getWorkgroups().get("fhir"));
    return lm;
}

Example 19 with LogicalModel

use of org.hl7.fhir.definitions.model.LogicalModel in project kindling by HL7.

the class SourceParser method loadLogicalModel.

private LogicalModel loadLogicalModel(String n) throws Exception {
    File spreadsheet = new CSFile(Utilities.path(srcDir, n, n + "-spreadsheet.xml"));
    OldSpreadsheetParser sparser = new OldSpreadsheetParser(n, new CSFileInputStream(spreadsheet), spreadsheet.getName(), spreadsheet.getAbsolutePath(), definitions, srcDir, logger, registry, version, context, genDate, false, page, false, ini, wg("fhir"), definitions.getProfileIds(), fpUsages, page.getConceptMaps(), exceptionIfExcelNotNormalised, page.packageInfo(), page.getRc());
    sparser.setFolder(Utilities.getDirectoryForFile(spreadsheet.getAbsolutePath()));
    LogicalModel lm = sparser.parseLogicalModel();
    lm.setId(n);
    lm.setSource(spreadsheet.getAbsolutePath());
    lm.getResource().setName(lm.getId());
    lm.getResource().setFmmLevel(ini.getStringProperty("fmm", n.toLowerCase()));
    if (lm.getResource().getFmmLevel() == null)
        lm.getResource().setFmmLevel("1");
    lm.getResource().setStatus(StandardsStatus.INFORMATIVE);
    errors.addAll(sparser.getErrors());
    File f = new File(Utilities.path(srcDir, n, n + ".svg"));
    if (f.exists())
        parseSvgFile(f, lm.getLayout(), f.getName());
    return lm;
}

Example 20 with LogicalModel

use of org.hl7.fhir.definitions.model.LogicalModel 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);
}