Examples with CURRENT org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus.CURRENT used on opensource projects

Example 96 with CURRENT

use of org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus.CURRENT in project integration-adaptor-111 by nhsconnect.

the class ListMapper method mapList.

public ListResource mapList(POCDMT000002UK01ClinicalDocument1 clinicalDocument, Encounter encounter, Collection<Resource> resourcesCreated, Reference deviceRef) {
    ListResource listResource = new ListResource();
    listResource.setIdElement(resourceUtil.newRandomUuid());
    Identifier docIdentifier = new Identifier();
    docIdentifier.setUse(USUAL);
    docIdentifier.setValue(clinicalDocument.getSetId().getRoot());
    listResource.setStatus(CURRENT).setTitle(LIST_TITLE).setMode(WORKING).setCode(createCodeConcept()).setSubject(encounter.getSubject()).setSourceTarget(encounter.getSubjectTarget()).setEncounter(resourceUtil.createReference(encounter)).setEncounterTarget(encounter).setDateElement(DateUtil.parse(clinicalDocument.getEffectiveTime().getValue())).setSource(deviceRef).setOrderedBy(createOrderByConcept());
    resourcesCreated.stream().sorted(resourceDateComparator).filter(it -> TRIAGE_RESOURCES.contains(it.getResourceType()) && it.hasId()).map(resourceUtil::createReference).map(ListResource.ListEntryComponent::new).forEach(listResource::addEntry);
    return listResource;
}

Example 97 with CURRENT

use of org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus.CURRENT in project pathling by aehrc.

the class InvocationVisitor method visitMemberInvocation.

/**
 * This method gets called when an element is on the right-hand side of the invocation expression,
 * or when an identifier is referred to as a term (e.g. "Encounter" or "type").
 *
 * @param ctx The {@link MemberInvocationContext}
 * @return A {@link FhirPath} expression
 */
@Override
@Nonnull
public FhirPath visitMemberInvocation(@Nullable final MemberInvocationContext ctx) {
    @Nullable final String fhirPath = checkNotNull(ctx).getText();
    checkNotNull(fhirPath);
    if (invoker != null) {
        // If there is an invoker, we treat this as a path traversal from the invoker.
        final PathTraversalInput pathTraversalInput = new PathTraversalInput(context, invoker, fhirPath);
        return new PathTraversalOperator().invoke(pathTraversalInput);
    } else {
        if (context.getThisContext().isEmpty()) {
            // See https://hl7.org/fhirpath/2018Sep/index.html#path-selection.
            if (fhirPath.equals(context.getInputContext().getExpression())) {
                return context.getInputContext();
            } else {
                // If the expression is not a reference to the subject resource, treat it as a path
                // traversal from the input context.
                final PathTraversalInput pathTraversalInput = new PathTraversalInput(context, context.getInputContext(), fhirPath);
                return new PathTraversalOperator().invoke(pathTraversalInput);
            }
        } else {
            // If we're in the context of a function's arguments, there are two valid things this
            // could be:
            // (1) a path traversal from the input context;
            // (2) a reference to a resource type.
            // Check if the expression is a reference to a known resource type.
            final ResourceType resourceType;
            try {
                resourceType = ResourceType.fromCode(fhirPath);
            } catch (final FHIRException e) {
                // If the expression is not a resource reference, treat it as a path traversal from the
                // input context.
                final PathTraversalInput pathTraversalInput = new PathTraversalInput(context, context.getThisContext().get(), fhirPath);
                return new PathTraversalOperator().invoke(pathTraversalInput);
            }
            // the current resource reference.
            return ResourcePath.build(context.getFhirContext(), context.getDatabase(), resourceType, fhirPath, true);
        }
    }
}

Example 98 with CURRENT

use of org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus.CURRENT in project pathling by aehrc.

the class ElementPath method build.

/**
 * Builds the appropriate subtype of ElementPath based upon the supplied {@link
 * ElementDefinition}.
 * <p>
 * Use this builder when the path is the child of another path, and will need to be traversable.
 *
 * @param expression the FHIRPath representation of this path
 * @param dataset a {@link Dataset} that can be used to evaluate this path against data
 * @param idColumn a {@link Column} within the dataset containing the identity of the subject
 * resource
 * @param eidColumn a {@link Column} within the dataset containing the element identity
 * @param valueColumn a {@link Column} within the dataset containing the values of the nodes
 * @param singular an indicator of whether this path represents a single-valued collection
 * @param currentResource the current resource within this path
 * @param thisColumn collection values where this path originated from {@code $this}
 * @param definition the HAPI element definition that this path should be based upon
 * @return a new ElementPath
 */
@Nonnull
public static ElementPath build(@Nonnull final String expression, @Nonnull final Dataset<Row> dataset, @Nonnull final Column idColumn, @Nonnull final Optional<Column> eidColumn, @Nonnull final Column valueColumn, final boolean singular, @Nonnull final Optional<ResourcePath> currentResource, @Nonnull final Optional<Column> thisColumn, @Nonnull final ElementDefinition definition) {
    final Optional<FHIRDefinedType> optionalFhirType = definition.getFhirType();
    if (optionalFhirType.isPresent()) {
        final FHIRDefinedType fhirType = optionalFhirType.get();
        final ElementPath path = ElementPath.build(expression, dataset, idColumn, eidColumn, valueColumn, singular, currentResource, thisColumn, fhirType);
        path.definition = Optional.of(definition);
        return path;
    } else {
        throw new IllegalArgumentException("Attempted to build an ElementPath with an ElementDefinition with no fhirType");
    }
}

Example 99 with CURRENT

use of org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus.CURRENT 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 100 with CURRENT

use of org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus.CURRENT in project org.hl7.fhir.core by hapifhir.

the class Display method printCliArgumentsAndInfo.

public static void printCliArgumentsAndInfo(String[] args) throws IOException {
    System.out.println("  Paths:  Current = " + System.getProperty("user.dir") + ", Package Cache = " + new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).getFolder());
    System.out.print("  Params:");
    for (String s : args) {
        System.out.print(s.contains(" ") ? " \"" + s + "\"" : " " + s);
    }
    System.out.println();
}