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CodeSystemResourceProvider.java
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CodeSystemResourceProvider.java
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package org.openconceptlab.fhir.provider;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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.converter.CodeSystemConverter;
import org.openconceptlab.fhir.converter.ConceptMapConverter;
import org.openconceptlab.fhir.converter.ValueSetConverter;
import org.openconceptlab.fhir.model.Source;
import org.openconceptlab.fhir.repository.CollectionRepository;
import org.openconceptlab.fhir.repository.SourceRepository;
import org.openconceptlab.fhir.util.OclFhirUtil;
import org.springframework.stereotype.Component;
import javax.transaction.Transactional;
import java.util.List;
import static org.openconceptlab.fhir.util.OclFhirConstants.*;
import static org.openconceptlab.fhir.util.OclFhirUtil.*;
/**
* The CodeSystemResourceProvider.
* @author harpatel1
*/
@Component
public class CodeSystemResourceProvider extends BaseProvider implements IResourceProvider {
private static final Log log = LogFactory.getLog(CodeSystemResourceProvider.class);
public CodeSystemResourceProvider(SourceRepository sourceRepository, CodeSystemConverter codeSystemConverter,
CollectionRepository collectionRepository, ValueSetConverter valueSetConverter,
ConceptMapConverter conceptMapConverter, OclFhirUtil oclFhirUtil) {
super(sourceRepository, codeSystemConverter, collectionRepository, valueSetConverter, conceptMapConverter, oclFhirUtil);
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return CodeSystem.class;
}
@Create
@Transactional
public MethodOutcome createCodeSystem(@ResourceParam CodeSystem codeSystem, RequestDetails requestDetails) {
if (codeSystem == null) {
throw new InvalidRequestException("The CodeSystem can not be empty");
}
String accessionId = getAccessionIdentifier(codeSystem.getIdentifier());
if (!isValid(accessionId)) {
throw new InvalidRequestException("The CodeSystem.identifier is empty or identifier of type ACSN is empty.");
}
if (!isValid(codeSystem.getUrl())) {
throw new InvalidRequestException("The CodeSystem.url can not be empty. Please provide canonical url.");
}
codeSystemConverter.createCodeSystem(codeSystem, accessionId, requestDetails.getHeader(AUTHORIZATION));
return new MethodOutcome();
}
@Update
@Transactional
public MethodOutcome updateCodeSystem(@IdParam IdType idType,
@ResourceParam CodeSystem codeSystem,
RequestDetails requestDetails) {
if (codeSystem == null) {
throw new InvalidRequestException("The CodeSystem can not be empty");
}
if (idType == null || !isValid(idType.getIdPart()) || !isValid(idType.getVersionIdPart()) ||
isVersionAll(newStringType(idType.getVersionIdPart()))) {
throw new InvalidRequestException("Invalid CodeSystem.id or CodeSystem.version provided. Both parameters are required.");
}
StringType owner = newStringType(requestDetails.getHeader(OWNER));
if (!isValid(owner))
throw new InvalidRequestException("Owner can not be empty.");
List<Source> sources = filterSourceHead(
getSourceByOwnerAndIdAndVersion(idType.getIdPart(), owner.getValue(), idType.getVersionIdPart(), publicAccess));
if (sources.isEmpty()) {
throw new InvalidRequestException("CodeSystem is not found.");
}
String accessionId = buildAccessionId(CODESYSTEM, idType, owner);
codeSystemConverter.updateCodeSystem(codeSystem, sources.get(0), accessionId, requestDetails.getHeader(AUTHORIZATION));
return new MethodOutcome();
}
/**
* Returns all public {@link CodeSystem}.
*
* @return {@link Bundle}
*/
@Search()
@Transactional
public Bundle searchCodeSystems(@OptionalParam(name = PAGE) StringType page,
@OptionalParam(name = OWNER_URL) StringType ownerUrl,
RequestDetails details) {
List<Source> sources = filterSourceHead(getSources(publicAccess));
StringBuilder hasNext = new StringBuilder();
List<CodeSystem> codeSystems = codeSystemConverter.convertToCodeSystem(sources, false,
getPage(page), hasNext);
log.info("Found " + codeSystems.size() + " CodeSystems.");
return OclFhirUtil.getBundle(codeSystems, isValid(ownerUrl) ? ownerUrl.getValue() : details.getCompleteUrl(),
getPrevPage(page), getNextPage(page, hasNext));
}
/**
* Returns public {@link CodeSystem} for a given Url.
* @param url
* @param version
* @return {@link Bundle}
*/
@Search
@Transactional
public Bundle searchCodeSystemByUrl(@RequiredParam(name = CodeSystem.SP_URL) StringType url,
@OptionalParam(name = VERSION) StringType version,
@OptionalParam(name = PAGE) StringType page,
@OptionalParam(name = OWNER_URL) StringType ownerUrl,
RequestDetails details) {
List<Source> sources = filterSourceHead(getSourceByUrl(url, version, publicAccess));
boolean includeConcepts = !isValid(version) || !isVersionAll(version);
StringBuilder hasNext = new StringBuilder();
List<CodeSystem> codeSystems = codeSystemConverter.convertToCodeSystem(sources, includeConcepts,
getPage(page), hasNext);
log.info("Found " + codeSystems.size() + " CodeSystems.");
return OclFhirUtil.getBundle(codeSystems, isValid(ownerUrl) ? ownerUrl.getValue() : details.getCompleteUrl(),
getPrevPage(page), getNextPage(page, hasNext));
}
/**
* Returns all public {@link CodeSystem} for a given owner.
* @param owner
* @return {@link Bundle}
*/
@Search
@Transactional
public Bundle searchCodeSystemByOwner(@RequiredParam(name = OWNER) StringType owner,
@OptionalParam(name = PAGE) StringType page,
@OptionalParam(name = OWNER_URL) StringType ownerUrl,
RequestDetails details) {
List<Source> sources = filterSourceHead(getSourceByOwner(owner, publicAccess));
StringBuilder hasNext = new StringBuilder();
List<CodeSystem> codeSystems = codeSystemConverter.convertToCodeSystem(sources, false, getPage(page),
hasNext);
log.info("Found " + codeSystems.size() + " CodeSystems.");
return OclFhirUtil.getBundle(codeSystems, isValid(ownerUrl) ? ownerUrl.getValue() : details.getCompleteUrl(),
getPrevPage(page), getNextPage(page, hasNext));
}
/**
* Returns public {@link CodeSystem} for a given owner and Id. Returns given version if provided, otherwise
* most recent released version is returned.
* @param owner
* @param id
* @param version
* @return {@link Bundle}
*/
@Search
@Transactional
public Bundle searchCodeSystemByOwnerAndId(@RequiredParam(name = OWNER) StringType owner,
@RequiredParam(name = ID) StringType id,
@OptionalParam(name = VERSION) StringType version,
@OptionalParam(name = PAGE) StringType page,
@OptionalParam(name = OWNER_URL) StringType ownerUrl,
RequestDetails details) {
List<Source> sources = filterSourceHead(getSourceByOwnerAndIdAndVersion(id, owner, version, publicAccess));
boolean includeConcepts = !isVersionAll(version);
StringBuilder hasNext = new StringBuilder();
List<CodeSystem> codeSystems = codeSystemConverter.convertToCodeSystem(sources, includeConcepts, getPage(page)
, hasNext);
log.info("Found " + codeSystems.size() + " CodeSystems.");
return OclFhirUtil.getBundle(codeSystems, isValid(ownerUrl) ? ownerUrl.getValue() : details.getCompleteUrl(),
getPrevPage(page), getNextPage(page, hasNext));
}
/**
* CodeSystem $lookup operation.
*
* @param code - (Mandatory) Code that is to be located
* @param system - (Mandatory) System for the code that is to be located
* @param version - (Optional) The version of system
* @param displayLanguage - (Optional) The display language
* @return Parameters
*/
@Operation(name = LOOKUP, idempotent = true)
@Transactional
public Parameters codeSystemLookUp(@OperationParam(name = CODE, type = CodeType.class, min = 1) CodeType code,
@OperationParam(name = SYSTEM, type = UriType.class, min = 1) UriType system,
@OperationParam(name = VERSION, type = StringType.class) StringType version,
@OperationParam(name = DISP_LANG, type = CodeType.class) CodeType displayLanguage,
@OperationParam(name = OWNER, type = StringType.class) StringType owner,
RequestDetails requestDetails) {
// $lookup by id
String id = requestDetails.getHeader(RESOURCE_ID);
if (isValid(id) && isValid(owner)) {
validateOperation(code, id, LOOKUP, version);
List<Source> sources = getSourceByOwnerAndIdAndVersion(newStringType(id), owner, version, publicAccess);
if (sources.isEmpty()) throw new ResourceNotFoundException(notFound(CodeSystem.class, owner, newStringType(id), version));
return codeSystemConverter.getLookupParameters(sources.get(0), code, displayLanguage);
}
// $lookup by url
validateOperation(code, system, LOOKUP, version);
Source source = isValid(owner) ? oclFhirUtil.getSourceByOwnerAndUrl(owner, newStringType(system), version, publicAccess) :
getSourceByUrl(newStringType(system), version, publicAccess).get(0);
return codeSystemConverter.getLookupParameters(source, code, displayLanguage);
}
@Operation(name = VALIDATE_CODE, idempotent = true)
@Transactional
public Parameters codeSystemValidateCode(@OperationParam(name = URL, type = UriType.class, min = 1) UriType url,
@OperationParam(name = CODE, type = CodeType.class, min = 1) CodeType code,
@OperationParam(name = VERSION, type = StringType.class) StringType version,
@OperationParam(name = DISPLAY, type = StringType.class) StringType display,
@OperationParam(name = DISP_LANG, type = CodeType.class) CodeType displayLanguage,
@OperationParam(name = CODING, type = Coding.class) Coding coding,
@OperationParam(name = OWNER, type = StringType.class) StringType owner,
RequestDetails requestDetails) {
// $validate-code by id
String id = requestDetails.getHeader(RESOURCE_ID);
if (isValid(id) && isValid(owner)) {
/*
* Valid for POST call since you can't user Coding in GET call.
* Scenario : coding != null
* code = coding.code (override code parameter)
* display = coding.display (override display parameter)
*
* Version preference order:
* 1. Path version (Ignore coding.version)
* 2. Parameter version (Ignore coding.version)
* 3. Coding.version (use coding.version)
*
*/
if (coding != null) {
code = new CodeType(coding.getCode());
display = new StringType(coding.getDisplay());
if (!isValid(version))
version = new StringType(coding.getVersion());
}
validateOperation(code, id, VALIDATE_CODE, version);
List<Source> sources = getSourceByOwnerAndIdAndVersion(newStringType(id), owner, version, publicAccess);
if (sources.isEmpty()) throw new ResourceNotFoundException(notFound(CodeSystem.class, owner, newStringType(id), version));
return codeSystemConverter.validateCode(sources.get(0), getCode(code), display, displayLanguage);
}
// $validate-code by url
if (coding != null) {
url = new UriType(coding.getSystem());
code = new CodeType(coding.getCode());
version = new StringType(coding.getVersion());
display = new StringType(coding.getDisplay());
}
validateOperation(code, url, VALIDATE_CODE, version);
Source source = isValid(owner) ? oclFhirUtil.getSourceByOwnerAndUrl(owner, newStringType(url), version, publicAccess) :
getSourceByUrl(newStringType(url), version, publicAccess).get(0);
return codeSystemConverter.validateCode(source, getCode(code), display, displayLanguage);
}
private void validateOperation(CodeType code, UriType system, String operation, StringType version) {
if (!isValid(code) || !isValid(system)) {
String msg = "Could not perform CodeSystem %s operation, both code and %s parameters are required.";
throw new InvalidRequestException(String.format(msg, operation, LOOKUP.equals(operation) ? SYSTEM : URL));
}
if (isVersionAll(version)) throw new InvalidRequestException("Invalid version provided.");
}
protected void validateOperation(CodeType code, String id, String operation, StringType version) {
if (!isValid(code) || !isValid(id)) {
String msg = "Could not perform CodeSystem %s operation, both code and %s parameters are required.";
throw new InvalidRequestException(String.format(msg, operation, id));
}
if (isVersionAll(version)) throw new InvalidRequestException("Invalid version provided.");
}
}