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CodeSystemConverter.java
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CodeSystemConverter.java
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package org.openconceptlab.fhir.converter;
import java.util.*;
import java.util.stream.Collectors;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import com.google.gson.*;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeSystem.CodeSystemFilterComponent;
import org.hl7.fhir.r4.model.CodeSystem.ConceptPropertyComponent;
import org.hl7.fhir.r4.model.CodeSystem.FilterOperator;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.openconceptlab.fhir.model.*;
import static org.openconceptlab.fhir.util.OclFhirConstants.*;
import static org.openconceptlab.fhir.util.OclFhirUtil.*;
import org.openconceptlab.fhir.repository.ConceptRepository;
import org.openconceptlab.fhir.repository.ConceptsSourceRepository;
import org.openconceptlab.fhir.repository.SourceRepository;
import org.openconceptlab.fhir.util.OclFhirUtil;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.stereotype.Component;
/**
* The CodeSystemConverter.
* @author harpatel1
*/
@Component
public class CodeSystemConverter {
JsonParser parser = new JsonParser();
SourceRepository sourceRepository;
ConceptRepository conceptRepository;
OclFhirUtil oclFhirUtil;
UserProfile oclUser;
ConceptsSourceRepository conceptsSourceRepository;
@Autowired
public CodeSystemConverter(SourceRepository sourceRepository, ConceptRepository conceptRepository, OclFhirUtil oclFhirUtil
, UserProfile oclUser, ConceptsSourceRepository conceptsSourceRepository) {
this.sourceRepository = sourceRepository;
this.conceptRepository = conceptRepository;
this.oclFhirUtil = oclFhirUtil;
this.oclUser = oclUser;
this.conceptsSourceRepository = conceptsSourceRepository;
}
public List<CodeSystem> convertToCodeSystem(List<Source> sources, boolean includeConcepts, int page) {
List<CodeSystem> codeSystems = new ArrayList<>();
sources.forEach(source -> {
// convert to base
CodeSystem codeSystem = toBaseCodeSystem(source);
if (includeConcepts) {
// add concepts
addConceptsToCodeSystem(codeSystem, source, page);
}
codeSystems.add(codeSystem);
});
return codeSystems;
}
private CodeSystem toBaseCodeSystem(final Source source){
CodeSystem codeSystem = new CodeSystem();
// Url
if(StringUtils.isNotBlank(source.getCanonicalUrl())) {
codeSystem.setUrl(source.getCanonicalUrl());
}
// id
codeSystem.setId(source.getMnemonic());
// identifier
getIdentifier(source.getUri())
.ifPresent(i -> codeSystem.getIdentifier().add(i));
// version
codeSystem.setVersion(source.getVersion());
// name
codeSystem.setName(source.getName());
// title
if(StringUtils.isNotBlank(source.getFullName())) {
codeSystem.setTitle(source.getFullName());
}
// status
addStatus(codeSystem, source.getIsActive(), source.getRetired() != null ? source.getRetired() : false,
source.getReleased() != null ? source.getReleased() : false);
// language
codeSystem.setLanguage(source.getDefaultLocale());
// description
if(StringUtils.isNotBlank(source.getDescription())) {
codeSystem.setDescription(source.getDescription());
}
// count
codeSystem.setCount(conceptRepository.findConceptCountInSource(source.getId()));
// property
addProperty(codeSystem);
return codeSystem;
}
private void addProperty(final CodeSystem codeSystem) {
// concept class
codeSystem.getProperty().add(getPropertyComponent(CONCEPT_CLASS,
SYSTEM_CC,
DESC_CC,
CodeSystem.PropertyType.STRING));
// data type
codeSystem.getProperty().add(getPropertyComponent(DATATYPE,
SYSTEM_DT,
DESC_DT,
CodeSystem.PropertyType.STRING));
// inactive - http://hl7.org/fhir/concept-properties
codeSystem.getProperty().add(getPropertyComponent(INACTIVE, SYSTEM_HL7_CONCEPT_PROP,
DESC_HL7_CONCEPT_PROP, CodeSystem.PropertyType.CODING));
}
private CodeSystem.PropertyComponent getPropertyComponent(String code, String system, String description, CodeSystem.PropertyType type) {
CodeSystem.PropertyComponent component = new CodeSystem.PropertyComponent();
component.setCode(code);
component.setUri(system);
component.setDescription(description);
component.setType(type);
return component;
}
private long getConceptsCount(final Source source) {
return source.getConceptsSources().parallelStream().map(m -> m.getConcept().getMnemonic()).distinct().count();
}
private void addConceptsToCodeSystem(final CodeSystem codeSystem, final Source source, int page) {
List<Concept> concepts = conceptRepository.findConcepts(source.getId(), PageRequest.of(page, 100));
for (Concept concept : concepts) {
CodeSystem.ConceptDefinitionComponent definitionComponent = new CodeSystem.ConceptDefinitionComponent();
// code
definitionComponent.setCode(concept.getMnemonic());
// display
List<LocalizedText> names = concept.getConceptsNames().stream()
.filter(c -> c.getLocalizedText() != null)
.map(ConceptsName::getLocalizedText)
.collect(Collectors.toList());
definitionComponent.setDisplay(oclFhirUtil.getDefinition(names, source.getDefaultLocale()));
// definition
List<LocalizedText> definitions = concept.getConceptsDescriptions().stream()
.filter(c -> c.getLocalizedText() != null)
.filter(c -> isValid(c.getLocalizedText().getType()) && "definition".equalsIgnoreCase(c.getLocalizedText().getType()))
.map(ConceptsDescription::getLocalizedText)
.collect(Collectors.toList());
definitionComponent.setDefinition(oclFhirUtil.getDefinition(definitions, source.getDefaultLocale()));
// designation
addConceptDesignation(concept, definitionComponent);
// property - concept_class, data_type, ,inactive
definitionComponent.getProperty().add(new ConceptPropertyComponent(new CodeType(CONCEPT_CLASS),
new StringType(concept.getConceptClass())));
definitionComponent.getProperty().add(new ConceptPropertyComponent(new CodeType(DATATYPE),
new StringType(concept.getDatatype())));
definitionComponent.getProperty().add(new ConceptPropertyComponent(new CodeType(INACTIVE),
new BooleanType(concept.getRetired())));
// add concept in CodeSystem
codeSystem.getConcept().add(definitionComponent);
}
}
private void addExtras(CodeSystem codeSystem, String extras) {
if(StringUtils.isNotBlank(extras)) {
JsonObject obj = parseExtras(extras);
// filters
JsonArray filters = obj.getAsJsonArray(FILTERS);
if (filters != null && filters.isJsonArray()) {
for(JsonElement je : filters) {
JsonObject filter = je.getAsJsonObject();
if(filter.get(CODE) != null) {
String code = filter.get(CODE).getAsString();
if(CONCEPT_CLASS.equals(code)) {
addFilter(codeSystem, CONCEPT_CLASS, filter.get(DESC), filter.get(OPERATOR),
filter.get(VALUE));
} else if (DATATYPE.equals(code)) {
addFilter(codeSystem, DATATYPE, filter.get(DESC), filter.get(OPERATOR),
filter.get(VALUE));
}
}
}
}
// identifier
JsonArray identifiers = obj.getAsJsonArray(IDENTIFIERS);
codeSystem.setIdentifier(getIdentifiers(identifiers));
// purpose
if(isValidElement(obj.get(PURPOSE)))
codeSystem.setPurpose(obj.get(PURPOSE).getAsString());
// copyright
if(isValidElement(obj.get(COPYRIGHT)))
codeSystem.setCopyright(obj.get(COPYRIGHT).getAsString());
}
}
private void addFilter(CodeSystem codeSystem, String code, JsonElement description, JsonElement operator,
JsonElement value) {
if(StringUtils.isNotBlank(code)) {
CodeSystemFilterComponent c = new CodeSystemFilterComponent();
c.setCode(code);
if (description != null && description.getAsString() != null)
c.setDescription(description.getAsString());
if (operator != null && operator.getAsString() != null) {
if(allowedFilterOperators.contains(operator.getAsString())) {
c.addOperator(FilterOperator.fromCode(operator.getAsString()));
}
}
if (value != null && value.getAsString() != null)
c.setValue(value.getAsString());
codeSystem.getFilter().add(c);
}
}
public Parameters getLookupParameters(final Source source, final CodeType code, final CodeType displayLanguage) {
Optional<Concept> conceptOpt = oclFhirUtil.getSourceConcept(source, code.getCode(), EMPTY);
if (conceptOpt.isPresent()) {
Concept concept = conceptOpt.get();
Parameters parameters = new Parameters();
parameters.addParameter(getParameter(NAME, source.getName()));
parameters.addParameter(getParameter(VERSION, source.getVersion()));
List<LocalizedText> names = oclFhirUtil.getNames(concept);
getDisplayForLookUp(names, isValid(displayLanguage) ? displayLanguage.getCode() : EMPTY, source.getDefaultLocale())
.ifPresent(display -> parameters.addParameter(getParameter(DISPLAY, display)));
addDesignationParameters(parameters, names, getCode(displayLanguage));
return parameters;
} else {
throw new ResourceNotFoundException("The code " + code.getCode() + " is invalid.");
}
}
private Optional<String> anyDisplay(List<LocalizedText> names) {
return names.stream().map(LocalizedText::getName).findFirst();
}
private Optional<String> getDisplayForLookUp(List<LocalizedText> names, String displayLanguage, String defaultLocale) {
if (isValid(displayLanguage)) {
return oclFhirUtil.getDisplayForLanguage(names, displayLanguage);
}
Optional<String> defaultLocaleDisp = oclFhirUtil.getDisplayForLanguage(names, defaultLocale);
if (defaultLocaleDisp.isPresent()) {
return defaultLocaleDisp;
} else {
return anyDisplay(names);
}
}
private void addDesignationParameters(Parameters parameters, List<LocalizedText> names, String displayLanguage) {
names.stream()
.filter(name -> !isValid(displayLanguage) || name.getLocale().equals(displayLanguage))
.forEach(name -> {
parameters.addParameter().setName(DESIGNATION).setPart(getDesignationParameters(name));
});
}
public Parameters validateCode(final Source source, final String code, final StringType display, final CodeType displayLanguage) {
Parameters parameters = new Parameters();
BooleanType result = new BooleanType(false);
parameters.addParameter().setName(RESULT).setValue(result);
Optional<Concept> conceptOpt = oclFhirUtil.getSourceConcept(source, code, EMPTY);
if (conceptOpt.isPresent()) {
if (isValid(display)) {
StringType updated = newStringType(display.getValue().replaceAll("^\"", "")
.replaceAll("\"$", ""));
List<LocalizedText> names = oclFhirUtil.getNames(conceptOpt.get());
boolean match = oclFhirUtil.validateDisplay(names, updated, displayLanguage);
if (!match) {
parameters.addParameter().setName(MESSAGE).setValue(newStringType("Invalid display."));
} else {
result.setValue(true);
}
} else {
result.setValue(true);
}
}
return parameters;
}
private List<Parameters.ParametersParameterComponent> getDesignationParameters(final LocalizedText text) {
List<Parameters.ParametersParameterComponent> componentList = new ArrayList<>();
if (isValid(text.getLocale()))
componentList.add(getParameter(LANGUAGE, new CodeType(text.getLocale())));
if (isValid(text.getType()))
componentList.add(getParameter(USE, new Coding(EMPTY, EMPTY, text.getType())));
if (isValid(text.getName()))
componentList.add(getParameter(VALUE, new StringType(text.getName())));
return componentList;
}
private Parameters.ParametersParameterComponent getParameter(String name, Type value) {
Parameters.ParametersParameterComponent component = new Parameters.ParametersParameterComponent();
component.setName(name).setValue(value);
return component;
}
private Parameters.ParametersParameterComponent getParameter(String name, String value) {
Parameters.ParametersParameterComponent component = new Parameters.ParametersParameterComponent();
component.setName(name).setValue(new StringType(value));
return component;
}
private void addParameter(String name, String value, Parameters parameters) {
addParameter(name, new StringType(value), parameters);
}
private void addParameter(String name, Type value, Parameters parameters) {
parameters.addParameter().setName(name).setValue(value);
}
/**
* TODO: Update when ready to implement POST
* @param codeSystem
*/
public void validateCodeSystem(CodeSystem codeSystem) {
Optional<Identifier> id = codeSystem.getIdentifier().stream().filter(i -> i.getType().hasCoding("http://hl7.org/fhir/v2/0203", "ACSN"))
.filter(i -> "http://fhir.openconceptlab.org".equals(i.getSystem()))
.filter(i -> isValid(i.getValue()))
.findFirst();
String url = codeSystem.getUrl();
if (!id.isPresent() && !isValid(url)) {
throw new UnprocessableEntityException("CodeSystem must have either Identifier or URL value.");
}
// check for unique id
if(id.isPresent()) {
if (!sourceRepository.findByMnemonicAndPublicAccessIn(id.get().getValue(), publicAccess).isEmpty()) {
throw new UnprocessableEntityException(String.format("The CodeSystem of Id '%s' already exists", id.get().getValue()));
}
codeSystem.setId(id.get().getValue());
}
// check for unique URL
if(isValid(url) && !sourceRepository.findByCanonicalUrlAndPublicAccessIn(url, publicAccess).isEmpty())
throw new UnprocessableEntityException(String.format("The CodeSystem of URL '%s' already exists", url));
// check publisher
validatePublisher(codeSystem.getPublisher());
// meta.updatedAt = source.updated_at
toSource(codeSystem);
}
/**
* TODO: Update when ready to implement POST
* @param codeSystem
*/
public void toSource(final CodeSystem codeSystem){
Source source = new Source();
source.setMnemonic(codeSystem.getId());
source.setCanonicalUrl(codeSystem.getUrl());
source.setCreatedBy(new UserProfile(oclUser.getId()));
source.setUpdatedBy(new UserProfile(oclUser.getId()));
source.setIsActive(PublicationStatus.ACTIVE.equals(codeSystem.getStatus()));
source.setRetired(PublicationStatus.RETIRED.equals(codeSystem.getStatus()));
if (isValid(codeSystem.getVersion())) source.setVersion(codeSystem.getVersion());
if (isValid(codeSystem.getName())) source.setName(codeSystem.getName());
if (isValid(codeSystem.getLanguage())) source.setDefaultLocale(codeSystem.getLanguage());
source.setActiveConcepts(codeSystem.getCount() == 0 ? codeSystem.getConcept().size() : codeSystem.getCount());
source.setExtras(getExtras(codeSystem));
if (isValid(source.getMnemonic())) {
sourceRepository.save(source);
} else {
source.setMnemonic("TEMP");
Source temp = sourceRepository.save(source);
sourceRepository.updateMnemonic(temp.getId());
}
}
private String getExtras(final CodeSystem codeSystem) {
CodeSystem system = codeSystem.copy();
nullifyBaseFields(system);
return toFhirString(system);
}
private void nullifyBaseFields(final CodeSystem codeSystem) {
codeSystem.setIdentifier(null);
codeSystem.setUrl(null);
codeSystem.setStatus(null);
codeSystem.setVersion(null);
codeSystem.setName(null);
codeSystem.setLanguage(null);
}
}