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

Example 11 with Compartment

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

the class PageProcessor method getCompLinks.

private String getCompLinks(ResourceDefn resource, String param) {
    List<String> names = new ArrayList<String>();
    for (Compartment comp : definitions.getCompartments()) {
        if (comp.getResources().containsKey(resource) && !Utilities.noString(comp.getResources().get(resource)))
            names.add(comp.getName());
    }
    StringBuilder b = new StringBuilder();
    b.append("<a href=\"compartmentdefinition.html\">Compartments</a>: ");
    if ("n/a".equals(param))
        b.append("N/A");
    else {
        if (names.isEmpty())
            b.append("Not linked to any defined compartments");
        else {
            Collections.sort(names);
            boolean first = true;
            for (String name : names) {
                if (first)
                    first = false;
                else
                    b.append(", ");
                b.append("<a href=\"compartmentdefinition-" + name.toLowerCase() + ".html\">" + definitions.getCompartmentByName(name).getTitle() + "</a>");
            }
        }
    }
    return b.toString();
}

Example 12 with Compartment

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

the class SourceParser method loadCompartments.

private void loadCompartments() throws FileNotFoundException, Exception {
    XLSXmlParser xml = new XLSXmlParser(new CSFileInputStream(srcDir + "compartments.xml"), "compartments.xml");
    new XLSXmlNormaliser(srcDir + "compartments.xml", exceptionIfExcelNotNormalised).go();
    Sheet sheet = xml.getSheets().get("compartments");
    for (int row = 0; row < sheet.rows.size(); row++) {
        Compartment c = new Compartment();
        c.setName(sheet.getColumn(row, "Name"));
        if (!c.getName().startsWith("!")) {
            c.setTitle(sheet.getColumn(row, "Title"));
            c.setDescription(sheet.getColumn(row, "Description"));
            c.setIdentity(sheet.getColumn(row, "Identification"));
            c.setMembership(sheet.getColumn(row, "Inclusion"));
            definitions.getCompartments().add(c);
        }
    }
    sheet = xml.getSheets().get("resources");
    for (int row = 0; row < sheet.rows.size(); row++) {
        String mn = sheet.getColumn(row, "Resource");
        if (!Utilities.noString(mn) && !mn.startsWith("!")) {
            ResourceDefn r = definitions.getResourceByName(mn);
            for (Compartment c : definitions.getCompartments()) {
                c.getResources().put(r, sheet.getColumn(row, c.getName()));
            }
        }
    }
}

Example 13 with Compartment

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

the class Publisher method generateCompartmentDefinition.

private void generateCompartmentDefinition(Compartment c) throws Exception {
    CompartmentDefinition cpd = new CompartmentDefinition();
    cpd.setId(c.getName());
    cpd.setUrl("http://hl7.org/fhir/CompartmentDefinition/" + c.getName());
    cpd.setName("Base FHIR compartment definition for " + c.getTitle());
    cpd.setStatus(PublicationStatus.DRAFT);
    cpd.setDescription(c.getIdentity() + ". " + c.getDescription());
    cpd.setExperimental(true);
    cpd.setVersion(page.getVersion().toCode());
    cpd.setDate(page.getGenDate().getTime());
    cpd.setPublisher("FHIR Project Team");
    cpd.addContact().getTelecom().add(Factory.newContactPoint(ContactPointSystem.URL, "http://hl7.org/fhir"));
    cpd.setCode(CompartmentType.fromCode(c.getTitle()));
    cpd.setSearch(true);
    for (String rn : page.getDefinitions().sortedResourceNames()) {
        ResourceDefn rd = page.getDefinitions().getResourceByName(rn);
        String rules = c.getResources().get(rd);
        CompartmentDefinitionResourceComponent cc = cpd.addResource().setCode(rd.getName());
        if (!Utilities.noString(rules)) {
            for (String p : rules.split("\\|")) cc.addParam(p.trim());
        }
    }
    RenderingContext lrc = page.getRc().copy().setLocalPrefix("").setTooCostlyNoteEmpty(PageProcessor.TOO_MANY_CODES_TEXT_EMPTY).setTooCostlyNoteNotEmpty(PageProcessor.TOO_MANY_CODES_TEXT_NOT_EMPTY);
    RendererFactory.factory(cpd, lrc).render(cpd);
    FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + "compartmentdefinition-" + c.getName().toLowerCase() + ".xml");
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, cpd);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + "compartmentdefinition-" + c.getName().toLowerCase() + ".canonical.xml");
    new XmlParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, cpd);
    s.close();
    cloneToXhtml("compartmentdefinition-" + c.getName().toLowerCase(), "Compartment Definition for " + c.getName(), true, "resource-instance:CompartmentDefinition", "Compartment Definition for " + c.getName(), null, wg("fhir"));
    s = new FileOutputStream(page.getFolders().dstDir + "compartmentdefinition-" + c.getName().toLowerCase() + ".json");
    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, cpd);
    s.close();
    s = new FileOutputStream(page.getFolders().dstDir + "compartmentdefinition-" + c.getName().toLowerCase() + ".canonical.json");
    new JsonParser().setOutputStyle(OutputStyle.CANONICAL).compose(s, cpd);
    s.close();
    jsonToXhtml("compartmentdefinition-" + c.getName().toLowerCase(), "Compartment Definition for " + c.getName(), resource2Json(cpd), "resource-instance:CompartmentDefinition", "Compartment Definition for " + c.getName(), null, wg("fhir"));
    s = new FileOutputStream(page.getFolders().dstDir + "compartmentdefinition-" + c.getName().toLowerCase() + ".ttl");
    new RdfParser().setOutputStyle(OutputStyle.PRETTY).compose(s, cpd);
    s.close();
    ttlToXhtml("compartmentdefinition-" + c.getName().toLowerCase(), "Compartment Definition for " + c.getName(), resource2Ttl(cpd), "resource-instance:CompartmentDefinition", "Compartment Definition for " + c.getName(), null, wg("fhir"));
    Utilities.copyFile(new CSFile(page.getFolders().dstDir + "compartmentdefinition-" + c.getName().toLowerCase() + ".xml"), new CSFile(page.getFolders().dstDir + "examples" + File.separator + "compartmentdefinition-" + c.getName().toLowerCase() + ".xml"));
    addToResourceFeed(cpd, page.getResourceBundle());
}

Example 14 with Compartment

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

Example 15 with Compartment

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

the class Publisher method validate.

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