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OclFhirUtil.java
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OclFhirUtil.java
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package org.openconceptlab.fhir.util;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.server.exceptions.*;
import com.google.gson.*;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.openconceptlab.fhir.model.*;
import org.openconceptlab.fhir.repository.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Component;
import javax.annotation.PostConstruct;
import java.nio.file.Paths;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import static org.openconceptlab.fhir.util.OclFhirConstants.*;
@Component
public class OclFhirUtil {
@Value("${server.port}")
private String port;
private static final Log log = LogFactory.getLog(OclFhirUtil.class);
private static final FhirContext context;
private SourceRepository sourceRepository;
private ConceptRepository conceptRepository;
private ConceptsSourceRepository conceptsSourceRepository;
@Autowired
public OclFhirUtil(SourceRepository sourceRepository, ConceptRepository conceptRepository, ConceptsSourceRepository conceptsSourceRepository) {
this.sourceRepository = sourceRepository;
this.conceptRepository = conceptRepository;
this.conceptsSourceRepository = conceptsSourceRepository;
}
public OclFhirUtil(){
super();
}
static {
context = FhirContext.forR4();
}
private String serverBase = "";
public static IParser parser = context.newJsonParser();
public static JsonParser jsonParser = new JsonParser();
public static Gson gson = new Gson();
@PostConstruct
private void init() {
serverBase = String.format("http://localhost:%s/fhir",port);
}
public static FhirContext getFhirContext() {
return context;
}
public static <T extends Resource> Bundle getBundle(List<T> resource, String fhirBase, String requestPath) {
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.SEARCHSET);
bundle.setTotal(resource.size());
resource.forEach(r -> {
Bundle.BundleEntryComponent component = new Bundle.BundleEntryComponent();
component.setResource(r);
//component.setFullUrl(getCompleteUrl(fhirBase, requestPath, r.getId()));
bundle.addEntry(component);
});
return bundle;
}
private static String getCompleteUrl(final String fhirBase, final String requestPath, final String id) {
return fhirBase + "/" + Paths.get(requestPath, id).toString();
}
public Source getSourceVersion(String id, String version, List<String> access, String ownerType, String owner) {
return getSourceVersion(new StringType(id), new StringType(version), access, ownerType, owner);
}
public Source getSourceVersion(StringType id, StringType version, List<String> access, String ownerType, String ownerId) {
final Source source;
if (!isValid(version)) {
// get most recent released version
source = getMostRecentReleasedSourceByOwner(id.getValue(), ownerId, ownerType, access);
} else {
// get a given version
if (ORG.equals(ownerType)) {
source = sourceRepository.findFirstByMnemonicAndVersionAndOrganizationMnemonicAndPublicAccessIn(
id.getValue(), version.getValue(), ownerId, access);
} else {
source = sourceRepository.findFirstByMnemonicAndVersionAndUserIdUsernameAndPublicAccessIn(
id.getValue(), version.getValue(), ownerId, access);
}
}
return source;
}
public Source getMostRecentReleasedSourceByOwner(String id, String owner, String ownerType, List<String> access) {
if (ORG.equals(ownerType)) {
return sourceRepository.findFirstByMnemonicAndReleasedAndPublicAccessInAndOrganizationMnemonicOrderByCreatedAtDesc(
id, true, access, owner);
}
return sourceRepository.findFirstByMnemonicAndReleasedAndPublicAccessInAndUserIdUsernameOrderByCreatedAtDesc(
id, true, access, owner);
}
public Source getSourceByOwnerAndUrl(StringType owner, StringType url, StringType version, List<String> access) {
Source source = null;
String ownerType = getOwnerType(owner.getValue());
String value = getOwner(owner.getValue());
if (!isValid(version)) {
// get most recent released version
source = getMostRecentReleasedSourceByOwnerAndUrl(value, ownerType, url, access);
} else {
// get a given version
source = getSourceVersionByOwnerAndUrl(value, ownerType, url, version, access);
}
if (source == null)
throw new ResourceNotFoundException(notFound(CodeSystem.class, url, version));
return source;
}
public Source getMostRecentReleasedSourceByUrl(StringType url, List<String> access) {
return sourceRepository.findFirstByCanonicalUrlAndReleasedAndPublicAccessInOrderByCreatedAtDesc(
url.getValue(), true, access
);
}
private Source getMostRecentReleasedSourceByOwnerAndUrl(String owner, String ownerType, StringType url, List<String> access) {
if (ORG.equals(ownerType))
return sourceRepository.findFirstByCanonicalUrlAndReleasedAndOrganizationMnemonicAndPublicAccessInOrderByCreatedAtDesc(
url.getValue(), true, owner, access
);
return sourceRepository.findFirstByCanonicalUrlAndReleasedAndUserIdUsernameAndPublicAccessInOrderByCreatedAtDesc(
url.getValue(), true, owner, access
);
}
private Source getSourceVersionByOwnerAndUrl(String owner, String ownerType, StringType url, StringType version, List<String> access) {
if (ORG.equals(ownerType))
return sourceRepository.findFirstByCanonicalUrlAndVersionAndOrganizationMnemonicAndPublicAccessIn(url.getValue(), version.getValue(), owner, access);
return sourceRepository.findFirstByCanonicalUrlAndVersionAndUserIdUsernameAndPublicAccessIn(url.getValue(), version.getValue(), owner, access);
}
public IGenericClient getClient() {
return context.newRestfulGenericClient(serverBase);
}
public String getResourceAsString(Resource resource) {
return parser.encodeResourceToString(resource);
}
public static IBaseResource getResource(String resource) {
return getFhirContext().newJsonParser().parseResource(resource);
}
public OperationOutcome getNotFoundOutcome(IdType id) {
OperationOutcome o = new OperationOutcome();
o.getIssueFirstRep()
.setSeverity(OperationOutcome.IssueSeverity.ERROR)
.setCode(OperationOutcome.IssueType.NOTFOUND)
.setDiagnostics("Resource " + id + " does not exist.");
return o;
}
public static OperationOutcome getError(OperationOutcome.IssueType errorType, final String error) {
OperationOutcome o = new OperationOutcome();
o.getIssueFirstRep()
.setSeverity(OperationOutcome.IssueSeverity.ERROR)
.setCode(errorType)
.setDiagnostics(error);
return o;
}
public static OperationOutcome getError(OperationOutcome.IssueType errorType) {
OperationOutcome o = new OperationOutcome();
o.getIssueFirstRep()
.setSeverity(OperationOutcome.IssueSeverity.ERROR)
.setCode(errorType);
return o;
}
public static boolean isValid(final String value) {
return StringUtils.isNotBlank(value);
}
public static boolean isValid(final StringType value) {
return value != null && StringUtils.isNotBlank(value.getValue());
}
public static boolean isValid(final CodeType code) {
return code != null && StringUtils.isNotBlank(code.getCode());
}
public static boolean isTrue(final BooleanType booleanType) {
return isValid(booleanType) && booleanType.getValue();
}
public static boolean isValid(final PrimitiveType type) {
return type != null && !type.isEmpty();
}
public static String getOwnerType(String owner) {
return owner.split(SEP)[0];
}
public static String getOwner(String owner) {
String[] arr = owner.split(SEP);
return String.join(SEP, ArrayUtils.subarray(arr, 1, arr.length));
}
public static <T extends MetadataResource> String toFhirString(final T resource) {
String fhirString = getFhirContext().newJsonParser().encodeResourceToString(resource);
JsonObject object = new JsonObject();
object.add("__fhir", jsonParser.parse(fhirString));
return gson.toJson(object);
}
public static Optional<Identifier> getIdentifier(String value) {
if (!isValid(value))
return Optional.empty();
Identifier identifier = new Identifier();
identifier.setSystem(OCL_SYSTEM);
identifier.setValue(value.replace("sources", CODESYSTEM).replace("collections", VALUESET));
identifier.getType().setText("Accession ID");
identifier.getType().getCodingFirstRep().setSystem(ACSN_SYSTEM).setCode(ACSN).setDisplay("Accession ID");
return isValid(value) ? Optional.of(identifier) : Optional.empty();
}
public static void addConceptDesignation(Concept concept, CodeSystem.ConceptDefinitionComponent definitionComponent) {
concept.getConceptsNames().parallelStream().forEach(name -> {
CodeSystem.ConceptDefinitionDesignationComponent designation = new CodeSystem.ConceptDefinitionDesignationComponent();
LocalizedText lt = name.getLocalizedText();
if(lt != null) {
designation.setLanguage(lt.getLocale());
if (isValid(lt.getType()))
designation.getUse().setCode(lt.getType());
designation.setValue(lt.getName());
definitionComponent.getDesignation().add(designation);
}
});
}
public static void addStatus(MetadataResource resource, boolean retired, boolean released) {
if (retired) {
resource.setStatus(Enumerations.PublicationStatus.RETIRED);
return;
}
if (released) {
resource.setStatus(Enumerations.PublicationStatus.ACTIVE);
} else {
resource.setStatus(Enumerations.PublicationStatus.DRAFT);
}
}
private Optional<LocalizedText> getPreferred(Stream<LocalizedText> texts) {
return texts.filter(LocalizedText::getLocalePreferred).findFirst();
}
private Optional<LocalizedText> getNonPreferred(Stream<LocalizedText> texts) {
return texts.filter(f -> !f.getLocalePreferred()).findFirst();
}
public Optional<Concept> getSourceConcept(Source source, String conceptId, String conceptVersion) {
List<ConceptsSource> cs = conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(
source.getId(),
conceptRepository.findByMnemonic(conceptId).stream().map(Concept::getId).collect(Collectors.toList())
);
return cs
.stream().map(ConceptsSource::getConcept)
.filter(c -> !isValid(conceptVersion) || conceptVersion.equals(c.getVersion()))
.findFirst();
}
public List<LocalizedText> getNames(Concept concept) {
return concept.getConceptsNames().stream().map(ConceptsName::getLocalizedText).collect(Collectors.toList());
}
public boolean validateDisplay(List<LocalizedText> names, final StringType display, final CodeType displayLanguage) {
return names.parallelStream()
.filter(name -> name.getName().equals(display.getValue()))
.anyMatch(name -> !isValid(displayLanguage) || name.getLocale().equals(displayLanguage.getCode()));
}
public Optional<String> getDisplayForLanguage(List<LocalizedText> names, String displayLanguage) {
return names.stream()
.sorted(Comparator.comparing(LocalizedText::getLocalePreferred, Comparator.reverseOrder()))
.filter(name -> !isValid(displayLanguage) || name.getLocale().equals(displayLanguage))
.map(LocalizedText::getName)
.findFirst();
}
public static String notFound(Class<? extends MetadataResource> cls, StringType url, StringType version) {
return String.format("Resource of type %s with URL %s%s is not known",
cls.getSimpleName(),
url,
isValid(version) ? " and version "+version : "");
}
public static String notFound(Class<? extends MetadataResource> cls, StringType owner, StringType id, StringType version) {
return String.format("Resource of type %s with owner %s and ID %s/%s is not known",
cls.getSimpleName(),
getOwner(owner.getValue()),
id,
isValid(version) ? VERSION + "/" + version : "");
}
public static boolean isVersionAll(StringType version) {
return isValid(version) && version.getValue().equals("*");
}
public static ResponseEntity<String> badRequest() {
return ResponseEntity.badRequest().body("{\"exception\":\"Could not process the request.\"}");
}
public static ResponseEntity<String> badRequest(String msg) {
return ResponseEntity.badRequest().body("{\"exception\":\"" + msg + "\"}");
}
public static StringType newStringType(UriType type) {
StringType stringType = new StringType();
if (type != null) stringType.setValue(type.getValue());
return stringType;
}
public static StringType newStringType(CodeType type) {
StringType stringType = new StringType();
if (type != null) stringType.setValue(type.getCode());
return stringType;
}
public static StringType newStringType(String value) {
return new StringType(value);
}
public static UriType newUri(String url) {
return new UriType(url);
}
public static BooleanType newBoolean(Boolean value) {
return new BooleanType(value);
}
public static IntegerType newInteger(Integer value) {
return new IntegerType(value);
}
public static String newString(CodeType type) {
return newStringType(type).getValue();
}
public static String getCode(CodeType type) {
return isValid(type) ? type.getCode() : EMPTY;
}
public static int getPage(StringType page) {
if (isValid(page) && !StringUtils.isNumeric(page.getValue())) {
throw new InvalidRequestException("Page value must be positive numeric value.");
}
return page == null || page.getValue().matches("0|1") ? 0 : Integer.parseInt(page.getValue()) - 1;
}
public static <T extends MetadataResource> void addJsonFields(T resource, String identifier, String contact, String jurisdiction) {
JsonObject object = new JsonObject();
object.addProperty(RESOURCE_TYPE, resource.getClass().getSimpleName());
addJsonProperty(object, resource.getClass().getSimpleName(), IDENTIFIER, identifier);
addJsonProperty(object, resource.getClass().getSimpleName(), CONTACT, contact);
addJsonProperty(object, resource.getClass().getSimpleName(), JURISDICTION, jurisdiction);
if (resource instanceof CodeSystem) {
CodeSystem cs = (CodeSystem) getFhirContext().newJsonParser().parseResource(gson.toJson(object));
if (!cs.getIdentifier().isEmpty())
((CodeSystem) resource).setIdentifier(cs.getIdentifier());
resource.setContact(cs.getContact());
resource.setJurisdiction(cs.getJurisdiction());
} else if (resource instanceof ValueSet) {
ValueSet vs = (ValueSet) getFhirContext().newJsonParser().parseResource(gson.toJson(object));
if (!vs.getIdentifier().isEmpty())
((ValueSet) resource).setIdentifier(vs.getIdentifier());
resource.setContact(vs.getContact());
resource.setJurisdiction(vs.getJurisdiction());
}
}
private static void addJsonProperty(JsonObject object, String resourceType, String property, String value) {
if (isValid(value)) {
try {
JsonArray array = jsonArray(value);
object.add(property, array);
} catch (Exception e) {
log.warn(String.format("Error parsing %s.%s ", resourceType, property) + e.getMessage(), e);
}
}
}
public static JsonArray jsonArray(String value) {
JsonElement e = jsonParser.parse(value);
JsonArray ar = new JsonArray();
if (! (e instanceof JsonArray)) {
ar.add(e);
} else {
ar = e.getAsJsonArray();
}
return ar;
}
public static String formatExpression(String expression) {
String uri = expression.trim();
if (!uri.startsWith(FW_SLASH)) uri = FW_SLASH + uri;
if (!uri.endsWith(FW_SLASH)) uri = uri + FW_SLASH;
return uri;
}
public static String getAccessionIdentifier(CodeSystem codeSystem) {
if (codeSystem != null) {
Optional<Identifier> hasIdentifier = hasAccessionIdentifier(codeSystem.getIdentifier());
if (hasIdentifier.isPresent())
return hasIdentifier.get().getValue().trim();
}
return EMPTY;
}
public static Optional<Identifier> hasAccessionIdentifier(List<Identifier> identifiers) {
for (Identifier identifier : identifiers) {
Optional<Coding> coding = identifier.getType().getCoding().stream()
.filter(t -> ACSN_SYSTEM.equals(t.getSystem()))
.filter(t -> ACSN.equals(t.getCode()))
.findAny();
if (coding.isPresent()) {
if (isValid(identifier.getSystem())
&& OCL_SYSTEM.equals(identifier.getSystem())
&& isValid(identifier.getValue())) {
return Optional.of(identifier);
}
}
}
return Optional.empty();
}
}