Examples with BaseResource org.hl7.fhir.r4.model.BaseResource used on opensource projects

Example 6 with BaseResource

use of org.hl7.fhir.r4.model.BaseResource in project redmatch by aehrc.

the class RedmatchGrammarCodeSystemGenerator method createBaseCodeSystem.

private CodeSystem createBaseCodeSystem(VersionedFhirPackage fhirPackage) {
    CodeSystem cs = new CodeSystem();
    cs.setId("redmatch-" + fhirPackage.getName());
    cs.setUrl("http://redmatch." + fhirPackage.getName());
    cs.setVersion(fhirPackage.getVersion());
    cs.setName("Redmatch Validation Code System for " + fhirPackage.getName());
    cs.setStatus(PublicationStatus.ACTIVE);
    cs.setDescription("A code system with all the valid paths used to refer to attributes of resources in " + fhirPackage.getName());
    cs.setValueSet("http://redmatch." + fhirPackage.getName() + "?vs");
    cs.setHierarchyMeaning(CodeSystemHierarchyMeaning.ISA);
    cs.setContent(CodeSystemContentMode.COMPLETE);
    cs.setExperimental(false);
    cs.setCompositional(false);
    cs.setVersionNeeded(false);
    cs.addProperty().setCode("parent").setDescription("Parent codes.").setType(PropertyType.CODE);
    cs.addProperty().setCode("root").setDescription("Indicates if this concept is a root concept.").setType(PropertyType.BOOLEAN);
    cs.addProperty().setCode("deprecated").setDescription("Indicates if this concept is deprecated.").setType(PropertyType.BOOLEAN);
    cs.addProperty().setCode("parentResourceOrProfile").setDescription("If this concept represents an attribute then this property represents the resource or profile" + "that contains the attribute. If this concepts is a profile or resource then the parent resource is Object.").setType(PropertyType.CODE);
    cs.addProperty().setCode("min").setDescription("Minimum cardinality").setType(PropertyType.INTEGER);
    cs.addProperty().setCode("max").setDescription("Maximum cardinality").setType(PropertyType.STRING);
    cs.addProperty().setCode("type").setDescription("Data type for this element.").setType(PropertyType.STRING);
    cs.addProperty().setCode("targetProfile").setDescription("If this code represents a Reference attribute, contains an allowed target profile.").setType(PropertyType.STRING);
    cs.addProperty().setCode("profile").setDescription("Indicates if this code represents a profile.").setType(PropertyType.BOOLEAN);
    cs.addProperty().setCode("baseResource").setDescription("For profiles, indicates the resource the profile constrains.").setType(PropertyType.CODE);
    cs.addProperty().setCode("extensionUrl").setDescription("If this code represents an extension, then this is its url.").setType(PropertyType.STRING);
    cs.addProperty().setCode("profileUrl").setDescription("If this code represents a profile, then this is its url.").setType(PropertyType.STRING);
    cs.addFilter().setCode("root").setValue("True or false.").addOperator(FilterOperator.EQUAL);
    cs.addFilter().setCode("deprecated").setValue("True or false.").addOperator(FilterOperator.EQUAL);
    cs.addFilter().setCode("parentResourceOrProfile").setValue("The parent resource or profile code.").addOperator(FilterOperator.EQUAL);
    cs.addFilter().setCode("profile").setValue("True or false.").addOperator(FilterOperator.EQUAL);
    // Create root concept
    ConceptDefinitionComponent objectRoot = cs.addConcept().setCode("Object").setDisplay("Object");
    objectRoot.addProperty().setCode("root").setValue(new BooleanType(true));
    objectRoot.addProperty().setCode("deprecated").setValue(new BooleanType(false));
    ConceptDefinitionComponent complexTypeRoot = cs.addConcept().setCode("ComplexType").setDisplay("ComplexType");
    complexTypeRoot.addProperty().setCode("root").setValue(new BooleanType(false));
    complexTypeRoot.addProperty().setCode("deprecated").setValue(new BooleanType(false));
    complexTypeRoot.addProperty().setCode("parent").setValue(new CodeType("Object"));
    ConceptDefinitionComponent resourceRoot = cs.addConcept().setCode("Resource").setDisplay("Resource");
    resourceRoot.addProperty().setCode("root").setValue(new BooleanType(false));
    resourceRoot.addProperty().setCode("deprecated").setValue(new BooleanType(false));
    resourceRoot.addProperty().setCode("parent").setValue(new CodeType("Object"));
    ConceptDefinitionComponent profileRoot = cs.addConcept().setCode("Profile").setDisplay("Profile");
    profileRoot.addProperty().setCode("root").setValue(new BooleanType(false));
    profileRoot.addProperty().setCode("deprecated").setValue(new BooleanType(false));
    profileRoot.addProperty().setCode("parent").setValue(new CodeType("Object"));
    return cs;
}

Example 7 with BaseResource

use of org.hl7.fhir.r4.model.BaseResource in project CRD by HL7-DaVinci.

the class CdsConnectFileStore method processFhirFiles.

private void processFhirFiles(List<CdsConnectFile> files, String topic) {
    // process the fhir resource files
    // setup the proper FHIR Context for the version of FHIR we are dealing with
    FhirContext r4ctx = new org.hl7.davinci.r4.FhirComponents().getFhirContext();
    IParser r4parser = r4ctx.newJsonParser();
    // suppress the unknown element warnings
    r4parser.setParserErrorHandler(new SuppressParserErrorHandler());
    // process all of the files found within the topic/artifact
    for (CdsConnectFile file : files) {
        String path = file.getPath();
        String filename = file.getFilename();
        if (filename.endsWith(".json")) {
            logger.info("        process: FHIR Resource: " + filename);
            String[] parts = filename.split("-");
            if (parts.length > 2) {
                // String resourceType = parts[0];
                String fhirVersion = parts[1];
                String name = parts[2];
                IBaseResource baseResource = null;
                byte[] fileContents = file.getCqlBundle();
                if (fhirVersion.equalsIgnoreCase("R4")) {
                    baseResource = r4parser.parseResource(new ByteArrayInputStream(fileContents));
                }
                processFhirResource(baseResource, path, filename, fhirVersion, topic);
            }
        }
    }
}

Example 8 with BaseResource

use of org.hl7.fhir.r4.model.BaseResource in project CRD by HL7-DaVinci.

the class GitHubFileStore method processFhirFolder.

private void processFhirFolder(String topic, String fhirVersion, String fhirPath) {
    fhirVersion = fhirVersion.toUpperCase();
    logger.info("      GitHubFileStore::processFhirFolder(): " + fhirVersion + ": " + fhirPath);
    // setup the proper FHIR Context for the version of FHIR we are dealing with
    FhirContext ctx = null;
    if (fhirVersion.equalsIgnoreCase("R4")) {
        ctx = new org.hl7.davinci.r4.FhirComponents().getFhirContext();
    } else {
        logger.warn("unsupported FHIR version: " + fhirVersion + ", skipping folder");
        return;
    }
    IParser parser = ctx.newJsonParser();
    // suppress the unknown element warnings
    parser.setParserErrorHandler(new SuppressParserErrorHandler());
    for (String folder : connection.getDirectory(fhirPath)) {
        if (folder.equalsIgnoreCase("resources")) {
            String fullFolderPath = fhirPath + "/" + folder;
            for (String resource : connection.getDirectory(fullFolderPath)) {
                String filename = resource;
                String fullFilePath = fullFolderPath + "/" + filename;
                logger.info("        process: FHIR Resource: " + filename);
                String[] parts = filename.split("-");
                if (parts.length > 2) {
                    // = parts[0];
                    String resourceType;
                    if (!parts[1].equalsIgnoreCase(fhirVersion)) {
                        logger.warn("GitHubFileStore::processFhirFolder() warning: FhirVersion doesn't match!");
                        continue;
                    }
                    InputStream inputStream = connection.getFile(fullFilePath);
                    if (inputStream != null) {
                        IBaseResource baseResource = parser.parseResource(inputStream);
                        processFhirResource(baseResource, filename, filename, fhirVersion, topic);
                    } else {
                        logger.warn("could not find file: " + fullFilePath);
                        continue;
                    }
                }
            }
        }
    }
}

Example 9 with BaseResource

use of org.hl7.fhir.r4.model.BaseResource in project dpc-app by CMSgov.

the class RESTUtils method bulkResourceHandler.

/**
 * Helper method for bulk submitting a {@link Bundle} of specific resources
 *
 * @param clazz          - {@link Class} of type of filter {@link Bundle} entries
 * @param params         - {@link Parameters} which has a {@link Parameters#getParameterFirstRep()}
 * @param resourceAction - {@link Function} which performs the actual bulk action for a single {@link BaseResource} of type {@link T}
 * @param <T>            - {@link T} generic type parameter which extends {@link BaseResource}
 * @return - {@link Bundle} containing the processed results from the bulk submission
 */
@SuppressWarnings("unchecked")
public static <T extends BaseResource> List<T> bulkResourceHandler(Class<T> clazz, Parameters params, Function<T, Response> resourceAction) {
    final Bundle resourceBundle = (Bundle) params.getParameterFirstRep().getResource();
    final Bundle bundle = new Bundle();
    bundle.setType(Bundle.BundleType.COLLECTION);
    return resourceBundle.getEntry().stream().filter(Bundle.BundleEntryComponent::hasResource).map(Bundle.BundleEntryComponent::getResource).filter(resource -> resource.getClass().equals(clazz)).map(clazz::cast).map(resource -> {
        final Response response = resourceAction.apply(resource);
        if (HttpStatus.isSuccess(response.getStatus())) {
            return (Resource) response.getEntity();
        }
        // If there's an error, rethrow the original method
        throw new WebApplicationException(response);
    }).map(r -> (T) r).collect(Collectors.toList());
}

Example 10 with BaseResource

use of org.hl7.fhir.r4.model.BaseResource in project kindling by HL7.

the class ProfileGenerator method generate.

public StructureDefinition generate(Profile pack, ConstraintStructure profile, ResourceDefn resource, String id, String html, ImplementationGuideDefn usage, List<ValidationMessage> issues, ResourceDefn baseResource) throws Exception {
    if (profile.getResource() != null)
        return profile.getResource();
    StructureDefinition p = new StructureDefinition();
    p.setId(FormatUtilities.makeId(id));
    p.setUrl("http://hl7.org/fhir/StructureDefinition/" + id);
    if (usage != null && !usage.isCore()) {
        if (!id.startsWith(usage.getCode() + "-"))
            throw new Exception("Error: " + id + " must start with " + usage.getCode() + "-");
    }
    if (!resource.getRoot().getTypes().isEmpty() && (resource.getRoot().getTypes().get(0).getProfile() != null))
        p.setBaseDefinition(resource.getRoot().getTypes().get(0).getProfile());
    else
        p.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/" + resource.getName());
    if (definitions.hasType(resource.getName()))
        p.setKind(StructureDefinitionKind.COMPLEXTYPE);
    else
        p.setKind(StructureDefinitionKind.RESOURCE);
    p.setType(resource.getName());
    p.setDerivation(TypeDerivationRule.CONSTRAINT);
    p.setAbstract(false);
    p.setUserData("filename", id);
    p.setUserData("path", ((usage == null || usage.isCore()) ? "" : usage.getCode() + File.separator) + id + ".html");
    p.setTitle(pack.metadata("display"));
    p.setFhirVersion(version);
    p.setVersion(version.toCode());
    if (pack.hasMetadata("summary-" + profile.getTitle()))
        ToolingExtensions.addMarkdownExtension(p, "http://hl7.org/fhir/StructureDefinition/structuredefinition-summary", pack.metadata("summary-" + profile.getTitle()));
    ToolResourceUtilities.updateUsage(p, usage.getCode());
    p.setName(pack.metadata("name"));
    p.setPublisher(pack.metadata("author.name"));
    if (pack.hasMetadata("author.reference"))
        p.addContact().getTelecom().add(Factory.newContactPoint(ContactPointSystem.URL, pack.metadata("author.reference")));
    // <code> opt Zero+ Coding assist with indexing and finding</code>
    p.setDescription(resource.getRoot().getShortDefn());
    if (!p.hasDescriptionElement() && pack.hasMetadata("description"))
        p.setDescription(preProcessMarkdown(pack.metadata("description"), "pack.description"));
    p.setPurpose(resource.getRoot().getRequirements());
    if (!p.hasPurpose() && pack.hasMetadata("requirements"))
        p.setPurpose(pack.metadata("requirements"));
    p.setExperimental(Utilities.existsInList(pack.metadata("Experimental"), "y", "Y", "true", "TRUE", "1"));
    if (pack.hasMetadata("date"))
        p.setDateElement(Factory.newDateTime(pack.metadata("date").substring(0, 10)));
    else
        p.setDate(genDate.getTime());
    if (pack.hasMetadata("fmm-level"))
        ToolingExtensions.addIntegerExtension(p, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(pack.getFmmLevel()));
    else if (pack.hasMetadata("fmm"))
        ToolingExtensions.addIntegerExtension(p, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(pack.metadata("fmm")));
    else if (!Utilities.noString(resource.getFmmLevel()))
        ToolingExtensions.addIntegerExtension(p, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(resource.getFmmLevel()));
    else if (baseResource != null && !Utilities.noString(baseResource.getFmmLevel()))
        ToolingExtensions.addIntegerExtension(p, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(baseResource.getFmmLevel()));
    if (pack.hasMetadata("workgroup"))
        ToolingExtensions.setCodeExtension(p, ToolingExtensions.EXT_WORKGROUP, pack.getWg());
    else if (resource.getWg() != null)
        ToolingExtensions.setCodeExtension(p, ToolingExtensions.EXT_WORKGROUP, resource.getWg().getCode());
    else if (baseResource != null && baseResource.getWg() != null)
        ToolingExtensions.setCodeExtension(p, ToolingExtensions.EXT_WORKGROUP, baseResource.getWg().getCode());
    if (pack.hasMetadata("Standards-Status"))
        ToolingExtensions.setStandardsStatus(p, StandardsStatus.fromCode(pack.metadata("Standards-Status")), null);
    else
        ToolingExtensions.setStandardsStatus(p, resource.getStatus(), null);
    if (pack.hasMetadata("status"))
        p.setStatus(PublicationStatus.fromCode(pack.metadata("status")));
    if (pack.getMetadata().containsKey("code"))
        for (String s : pack.getMetadata().get("code")) if (!Utilities.noString(s))
            p.getKeyword().add(Factory.makeCoding(s));
    if (pack.hasMetadata("datadictionary"))
        ToolingExtensions.setStringExtension(p, "http://hl7.org/fhir/StructureDefinition/datadictionary", pack.metadata("datadictionary"));
    Set<String> containedSlices = new HashSet<String>();
    p.setDifferential(new StructureDefinitionDifferentialComponent());
    defineElement(pack, p, p.getDifferential().getElement(), resource.getRoot(), resource.getName(), containedSlices, new ArrayList<ProfileGenerator.SliceHandle>(), SnapShotMode.None, true, null, null, false);
    List<String> names = new ArrayList<String>();
    names.addAll(resource.getSearchParams().keySet());
    Collections.sort(names);
    for (String pn : names) {
        pack.getSearchParameters().add(makeSearchParam(p, pack.getId() + "-" + resource.getName() + "-" + pn, resource.getName(), resource.getSearchParams().get(pn), resource));
    }
    StructureDefinition base = definitions.getSnapShotForBase(p.getBaseDefinition());
    List<String> errors = new ArrayList<String>();
    new ProfileUtilities(context, null, pkp).sortDifferential(base, p, p.getName(), errors, false);
    for (String s : errors) issues.add(new ValidationMessage(Source.ProfileValidator, IssueType.STRUCTURE, -1, -1, p.getUrl(), s, IssueSeverity.WARNING));
    reset();
    // ok, c is the differential. now we make the snapshot
    new ProfileUtilities(context, issues, pkp).generateSnapshot(base, p, "http://hl7.org/fhir/StructureDefinition/" + p.getType(), "http://hl7.org/fhir", p.getName());
    reset();
    p.getDifferential().getElement().get(0).getType().clear();
    p.getSnapshot().getElement().get(0).getType().clear();
    addElementConstraintToSnapshot(p);
    XhtmlNode div = new XhtmlNode(NodeType.Element, "div");
    div.addText("to do");
    p.setText(new Narrative());
    p.getText().setStatus(NarrativeStatus.GENERATED);
    p.getText().setDiv(div);
    new ProfileUtilities(context, issues, pkp).setIds(p, false);
    checkHasTypes(p);
    return p;
}