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ValueSetConverter.java
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ValueSetConverter.java
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package org.openconceptlab.fhir.converter;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.codesystems.PublicationStatus;
import org.openconceptlab.fhir.model.Collection;
import org.openconceptlab.fhir.model.Organization;
import org.openconceptlab.fhir.model.*;
import org.openconceptlab.fhir.repository.*;
import org.openconceptlab.fhir.util.OclFhirUtil;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.jdbc.core.BatchPreparedStatementSetter;
import org.springframework.jdbc.core.RowMapper;
import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
import org.springframework.jdbc.core.simple.SimpleJdbcInsert;
import org.springframework.stereotype.Component;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.sql.DataSource;
import javax.transaction.Transactional;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.Timestamp;
import java.util.*;
import java.util.stream.Collectors;
import static org.openconceptlab.fhir.util.OclFhirConstants.*;
import static org.openconceptlab.fhir.util.OclFhirUtil.*;
/**
* The ValueSerConverter.
* @author harpatel1
*/
@Component
public class ValueSetConverter extends BaseConverter {
@Value("${ocl.servlet.baseurl}")
private String baseUrl;
private String validateConceptIdSql =
"select c1.id, c1.mnemonic from concepts c1 " +
"inner join (" +
"select c2.mnemonic as mnemonic, max(c2.created_at) as created_at from concepts c2 " +
"inner join concepts_sources cs on c2.id = cs.concept_id " +
"inner join sources s ON s.id = cs.source_id " +
"where cs.source_id = :sourceId and c2.mnemonic in (:conceptIds) group by c2.mnemonic) c3 " +
"on c1.mnemonic = c3.mnemonic and c1.created_at = c3.created_at";
private static final Map<String,Object> collReferenceParamMap = new HashMap<>();
private static final String insertCollectionsReferences = "insert into collections_references (collection_id,collectionreference_id) values (?,?) on conflict do nothing";
private static final String insertCollectionsConcepts = "insert into collections_concepts (collection_id,concept_id) values (?,?) on conflict do nothing";
private static final Log log = LogFactory.getLog(ValueSetConverter.class);
@Autowired
protected EntityManager entityManager;
public ValueSetConverter(SourceRepository sourceRepository, ConceptRepository conceptRepository, OclFhirUtil oclFhirUtil,
UserProfile oclUser, ConceptsSourceRepository conceptsSourceRepository, DataSource dataSource,
AuthtokenRepository authtokenRepository, UserProfilesOrganizationRepository userProfilesOrganizationRepository,
OrganizationRepository organizationRepository, UserRepository userRepository, CollectionRepository collectionRepository,
MappingRepository mappingRepository) {
super(sourceRepository, conceptRepository, oclFhirUtil, oclUser, conceptsSourceRepository, dataSource, authtokenRepository,
userProfilesOrganizationRepository, organizationRepository, userRepository, collectionRepository, mappingRepository);
}
@PostConstruct
public void initValueSetConverter() {
this.insertCollectionReference = new SimpleJdbcInsert(jdbcTemplate).withTableName("collection_references");
}
public List<ValueSet> convertToValueSet(List<Collection> collections, boolean includeCompose, Integer page, StringBuilder hasNext) {
List<ValueSet> valueSets = new ArrayList<>();
if (!includeCompose) {
int offset = page * 10;
int count = 10;
if (page == 0) {
if (collections.size() > count) hasNext.append(True);
} else if (page < collections.size()/count) {
hasNext.append(True);
}
collections = paginate(collections, offset, count);
}
collections.forEach(collection -> {
ValueSet valueSet = toBaseValueSet(collection);
if (includeCompose)
addCompose(valueSet, collection, False, page, hasNext);
valueSets.add(valueSet);
});
return valueSets;
}
private ValueSet toBaseValueSet(final Collection collection) {
ValueSet valueSet = new ValueSet();
// set id
valueSet.setId(collection.getMnemonic());
// set Url
if(isValid(collection.getCanonicalUrl()))
valueSet.setUrl(collection.getCanonicalUrl());
// set version
valueSet.setVersion(collection.getVersion());
// set name
valueSet.setName(collection.getName());
// set title
if(isValid(collection.getFullName()))
valueSet.setTitle(collection.getFullName());
// set description
if(isValid(collection.getDescription()))
valueSet.setDescription(collection.getDescription());
// set status
addStatus(valueSet, collection.getRetired() != null ? collection.getRetired() : False,
collection.getReleased());
// publisher
if (isValid(collection.getPublisher()))
valueSet.setPublisher(collection.getPublisher());
// identifier, contact, jurisdiction
addJsonFields(valueSet, isValid(collection.getIdentifier()) && !EMPTY_JSON.equals(collection.getIdentifier())
? collection.getIdentifier() : EMPTY, collection.getContact(), collection.getJurisdiction(), collection.getText(),
collection.getMeta());
// add lastUpdated date is not populated in valueSet.meta.lastUpdated
if (valueSet.getMeta().getLastUpdated() == null) {
valueSet.getMeta().setLastUpdated(collection.getUpdatedAt());
}
// add accession identifier if not present
Optional<Identifier> identifierOpt = valueSet.getIdentifier().stream()
.filter(i -> i.getType().hasCoding(ACSN_SYSTEM, ACSN)).findAny();
if (valueSet.getIdentifier().isEmpty() || identifierOpt.isEmpty()) {
getIdentifier(collection.getUri())
.ifPresent(i -> valueSet.getIdentifier().add(i));
}
// purpose
if (isValid(collection.getPurpose()))
valueSet.setPurpose(collection.getPurpose());
// copyright
if (isValid(collection.getCopyright()))
valueSet.setCopyright(collection.getCopyright());
// immutable
if (collection.getImmutable() != null)
valueSet.setImmutable(collection.getImmutable());
// revision date
if (collection.getRevisionDate() != null)
valueSet.setDate(collection.getRevisionDate());
// experimental
if (collection.isExperimental() != null)
valueSet.setExperimental(collection.isExperimental());
return valueSet;
}
private Optional<Concept> getConcept(List<ConceptsSource> conceptsSources, String conceptId, String conceptVersion) {
if (isValid(conceptVersion)) {
return conceptsSources.parallelStream().map(ConceptsSource::getConcept)
.filter(c -> c.getMnemonic().equals(conceptId) && conceptVersion.equals(c.getVersion()))
.findAny();
} else {
return conceptsSources.parallelStream().map(ConceptsSource::getConcept)
.filter(c -> c.getMnemonic().equals(conceptId))
.max(Comparator.comparing(Concept::getId));
}
}
private void addCompose(ValueSet valueSet, Collection collection, boolean includeConceptDesignation, Integer page, StringBuilder hasNext) {
// We have to use expressions to determine actual Source version since its not possible through CollectionsConcepts
IntegerType offset = new IntegerType(page * 100);
IntegerType count = new IntegerType(100);
List<String> allExpressions = getAllExpressions(collection);
if (page < allExpressions.size()/count.getValue() + 1) hasNext.append(True);
List<String> expressions = getExpressions(allExpressions, offset, count);
// lets get all the source versions first to reduce the database calls
List<Source> sources = getSourcesFromExpressions(expressions);
// for each source let's evaluate expressions for concept and concept version and populate compose
sources.forEach(source -> {
expressions.stream().map(m -> formatExpression(m).split(FS))
.filter(m -> source.getMnemonic().equals(getSourceId(m)) &&
(!isValid(getSourceVersion(m)) ? source.getIsLatestVersion() : source.getVersion().equals(getSourceVersion(m))) )
.forEachOrdered(m -> {
String expSrcVersion = getSourceVersion(m);
String conceptId = getConceptId(m);
String conceptVersion = getConceptVersion(m);
if (isValid(conceptId)) {
// we can not simply get concepts list from the source considering huge number of concepts, this is alternate
// way to get only concepts that we care about and not retrieve whole list. This has improved performance and consumes less memory
Optional<Concept> conceptOpt = oclFhirUtil.getSourceConcept(source, conceptId, isValid(expSrcVersion) ? conceptVersion : EMPTY);
conceptOpt.ifPresent(c -> {
populateCompose(valueSet, includeConceptDesignation, c, isValid(source.getCanonicalUrl()) ? source.getCanonicalUrl() : source.getUri()
, source.getVersion(), source.getDefaultLocale(), collection.getLockedDate());
});
}
});
});
}
private List<Source> getSourcesFromExpressions(List<String> expressions, List<String> sourceVersions) {
if (sourceVersions.isEmpty()) return getSourcesFromExpressions(expressions);
// get the sources given based on input parameter source-version
List<Source> sourcesProvided = new ArrayList<>();
for (String sv : sourceVersions) {
String[] ar = sv.split("\\|");
if (ar.length == 2) {
Source source = sourceRepository.findFirstByCanonicalUrlAndVersionAndPublicAccessIn(ar[0], ar[1], publicAccess);
if (source == null)
throw new InvalidRequestException("Code system of url=" + ar[0] + ", version=" + ar[1] + " does not exist.");
sourcesProvided.add(source);
}
}
Map<String, String> map = sourcesProvided.parallelStream().collect(Collectors.toMap(Source::getMnemonic, Source::getVersion));
// final list of sources and will only include sources that are referenced in expressions
// this is to cover the edge case where user provides source that is not referenced in expression and we would
// want to use sources that are referenced in expressions
List<Source> filtered = new ArrayList<>();
expressions.parallelStream().map(m -> formatExpression(m).split(FS))
.map(m -> ownerType(m) + "|" + ownerId(m) + "|" + getSourceId(m) + "|" + getSourceVersion(m))
.distinct()
.map(m -> m.split("\\|"))
.filter(m -> m.length == 4)
.map(m -> {
String sourceId = m[2];
String sourceVersion = m[3];
// If sourceId is part of input system-version and expression's source's version is HEAD only then we'll
// want to override the source.
if (map.containsKey(sourceId) && !isValid(sourceVersion)) {
return sourcesProvided.parallelStream().filter(s -> s.getMnemonic().equals(sourceId)).findFirst().get();
} else {
// if source is not part of the system-version then don't override
return oclFhirUtil.getSourceVersion(m[2], m[3], publicAccess, m[0], m[1]);
}
})
.filter(Objects::nonNull)
.forEach(filtered::add);
// List<Source> sources = getSourcesFromExpressions(expressions);
//sources.addAll(filtered);
return filtered.stream().sorted(Comparator.comparing(Source::getCanonicalUrl).thenComparing(Source::getCreatedAt).reversed())
.collect(Collectors.toList());
}
private List<Source> getSourcesFromExpressions(List<String> expressions) {
List<Source> sources =
expressions.parallelStream().map(m -> formatExpression(m).split(FS))
.map(m -> ownerType(m) + "|" + ownerId(m) + "|" + getSourceId(m) + "|" + getSourceVersion(m))
.distinct()
.map(m -> m.split("\\|"))
.filter(m -> m.length == 4)
.map(m -> oclFhirUtil.getSourceVersion(m[2], m[3], publicAccess, m[0], m[1]))
.map(Optional::ofNullable)
.filter(Optional::isPresent)
.map(Optional::get)
.sorted(Comparator.comparing(Source::getCanonicalUrl).thenComparing(Source::getCreatedAt).reversed())
.collect(Collectors.toList());
return sources;
}
private List<String> getAllExpressions(Collection collection) {
Map<String, String> map = new TreeMap<>();
collection.getCollectionsReferences().stream()
.map(CollectionsReference::getCollectionReference)
.map(CollectionReference::getExpression)
.forEach(e -> {
String [] ar = formatExpression(e).split(FS);
String conceptId = getConceptId(ar);
if (isValid(conceptId))
map.put(conceptId + getConceptVersion(ar) + getSourceId(ar) + getSourceVersion(ar),
formatExpression(e));
});
return new ArrayList<>(map.values());
}
private List<String> getExpressions(Collection collection, IntegerType offset, IntegerType count) {
List<String> expressions = getAllExpressions(collection);
return getExpressions(expressions, offset, count);
}
private List<String> getExpressions(List<String> expressions, IntegerType offset, IntegerType count) {
if (count.getValue() == 0)
return expressions;
if (offset.getValue() < expressions.size()) {
int start = offset.getValue();
int end = expressions.size();
if (start + count.getValue() < end)
end = start + count.getValue();
expressions = expressions.subList(start, end);
} else {
expressions.clear();
}
return expressions;
}
private void populateCompose(ValueSet valueSet, boolean includeConceptDesignation, Concept concept, String sourceCanonicalUrl,
String sourceVersion, String sourceDefaultLocale, Date lockedDate) {
// compose.include
if (isValid(sourceCanonicalUrl)) {
ValueSet.ValueSetComposeComponent compose = valueSet.getCompose();
Optional<ValueSet.ConceptSetComponent> includeComponent = compose.getInclude().parallelStream()
.filter(i -> sourceCanonicalUrl.equals(i.getSystem()) &&
sourceVersion.equals(i.getVersion())).findAny();
if (includeComponent.isPresent()) {
ValueSet.ConceptSetComponent include = includeComponent.get();
// compose.include.concept
addConceptReference(include, concept.getMnemonic(), concept.getName(), concept.getConceptsNames(),
sourceDefaultLocale, includeConceptDesignation);
} else {
ValueSet.ConceptSetComponent include = new ValueSet.ConceptSetComponent();
include.setSystem(sourceCanonicalUrl);
include.setVersion(sourceVersion);
// compose.include.concept
addConceptReference(include, concept.getMnemonic(), concept.getName(), concept.getConceptsNames(),
sourceDefaultLocale, includeConceptDesignation);
compose.addInclude(include);
}
// compose.inactive
if (!compose.getInactive() && concept.getRetired()) {
compose.setInactive(True);
}
// compose.locked_date
if (lockedDate != null)
compose.setLockedDate(lockedDate);
}
}
private void addConceptReference(ValueSet.ConceptSetComponent includeComponent, String code, String display,
List<ConceptsName> names, String dictDefaultLocale, boolean includeConceptDesignation) {
ValueSet.ConceptReferenceComponent referenceComponent = new ValueSet.ConceptReferenceComponent();
// code
referenceComponent.setCode(code);
// display
if (isValid(display)) {
referenceComponent.setDisplay(display);
} else {
List<LocalizedText> lts = names.stream().filter(c -> c.getLocalizedText() != null).map(ConceptsName::getLocalizedText)
.collect(Collectors.toList());
referenceComponent.setDisplay(oclFhirUtil.getDisplayForLanguage(lts, dictDefaultLocale).orElse(EMPTY));
}
// designation
List<LocalizedText> lts = names.stream().filter(c -> c.getLocalizedText() != null).map(ConceptsName::getLocalizedText)
.collect(Collectors.toList());
if (includeConceptDesignation)
addConceptReferenceDesignation(lts, referenceComponent);
includeComponent.getConcept().add(referenceComponent);
}
private void addConceptReferenceDesignation(List<LocalizedText> names, ValueSet.ConceptReferenceComponent referenceComponent) {
names.parallelStream().forEach(lt -> {
ValueSet.ConceptReferenceDesignationComponent component = toConceptRefDesignationComp(lt);
if (component != null)
referenceComponent.addDesignation(component);
});
}
private void addConceptReferenceDesignation(List<LocalizedText> names, ValueSet.ValueSetExpansionContainsComponent expansionComponent) {
names.parallelStream().forEach(lt -> {
ValueSet.ConceptReferenceDesignationComponent component = toConceptRefDesignationComp(lt);
if (component != null)
expansionComponent.addDesignation(component);
});
}
private ValueSet.ConceptReferenceDesignationComponent toConceptRefDesignationComp(LocalizedText text) {
if (text != null) {
ValueSet.ConceptReferenceDesignationComponent designationComponent = new ValueSet.ConceptReferenceDesignationComponent();
designationComponent.setLanguage(text.getLocale());
if (isValid(text.getType()))
designationComponent.getUse().setCode(text.getType());
designationComponent.setValue(text.getName());
return designationComponent;
}
return null;
}
public Parameters validateCode(Collection collection, UriType system, StringType systemVersion, String code, StringType display,
CodeType displayLanguage, StringType owner, List<String> access) {
Parameters parameters = new Parameters();
BooleanType result = new BooleanType(False);
parameters.addParameter().setName(RESULT).setValue(result);
// determine owner
owner = !isValid(owner) ? determineOwner(collection) : owner;
String ownerType = getOwnerType(owner.getValue());
String ownerId = getOwner(owner.getValue());
// determine source
Source source = oclFhirUtil.getSourceByOwnerAndUrl(owner, newStringType(system.getValue()), systemVersion, access);
// determine expression
String expression = buildExpression(source.getMnemonic(), source.getVersion(), code, ownerType, ownerId);
Optional<CollectionReference> reference = collection.getCollectionsReferences().parallelStream()
.map(CollectionsReference::getCollectionReference)
.filter(f -> f.getExpression().contains(expression))
.findAny();
if (reference.isPresent()) {
if (isValid(display)) {
StringType updated = newStringType(display.getValue().replaceAll("^\"", "")
.replaceAll("\"$", ""));
Optional<Concept> conceptOpt = oclFhirUtil.getSourceConcept(source, code, EMPTY);
if (conceptOpt.isPresent()) {
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;
}
public ValueSet expand(Collection collection, IntegerType offset, IntegerType count, BooleanType includeDesignations,
BooleanType includeDefinition, BooleanType activeOnly, CodeType displayLanguage,
List<String> excludeSystem, List<String> systemVersion, StringType filter) {
ValueSet valueSet;
if (isTrue(includeDefinition)) {
valueSet = toBaseValueSet(collection);
} else {
valueSet = new ValueSet();
addStatus(valueSet, collection.getRetired() != null ? collection.getRetired() : False,
collection.getReleased());
}
CanonicalType canonicalReference = new CanonicalType(
collection.getCanonicalUrl() + "|" + collection.getVersion());
valueSet.getCompose().getIncludeFirstRep().getValueSet().add(canonicalReference);
ValueSet.ValueSetExpansionComponent expansion = valueSet.getExpansion();
// identifier
expansion.setIdentifier(UUID.randomUUID().toString());
// timestamp
expansion.setTimestamp(new Date());
// add expansion parameters
addParameter(expansion, URL, new UriType(collection.getCanonicalUrl()));
addParameter(expansion, VALUESET_VERSION, newStringType(collection.getVersion()));
addParameter(expansion, OFFSET, offset);
addParameter(expansion, COUNT, count);
addParameter(expansion, INCLUDE_DESIGNATIONS, includeDesignations);
addParameter(expansion, INCLUDE_DEFINITION, includeDefinition);
addParameter(expansion, ACTIVE_ONLY, activeOnly);
if (isValid(displayLanguage))
addParameter(expansion, DISPLAY_LANGUAGE, displayLanguage);
if (isValid(filter))
addParameter(expansion, FILTER, filter);
excludeSystem.forEach(e -> addParameter(expansion, EXCLUDE_SYSTEM, newStringType(e)));
systemVersion.forEach(e -> addParameter(expansion, SYSTEMVERSION, newStringType(e)));
// offset
expansion.setOffset(offset.getValue());
// get expressions and filter by offset and count
// returns all expression if count = 0
List<String> expressions = getExpressions(collection, offset, count);
// if count = 0 then client is asking how large the expansion is.(As per FHIR spec)
if (count.getValue() == 0) {
expansion.setTotal(expressions.size());
return valueSet;
}
// separator = __ and if value itself has _ then enclose value in ""
// filter = EMR__HRP__KP , match on EMR, HRP and KP
// filter = EMR__"HRH_"__KP, match on EMR, HRP_ and KP
List<String> filters = new ArrayList<>();
if (isValid(filter)) {
String[] arr = filter.getValue().split("__");
for (String s : arr) {
filters.add(s.replaceAll("\"", EMPTY));
}
}
Set<Source> sources = getSourcesFromExpressions(expressions, systemVersion)
.stream()
.filter(s -> {
for(String es : excludeSystem) {
String [] ar = es.split("\\|");
if ((ar.length == 2 && !isValid(ar[1])) || ar.length == 1) {
if (s.getCanonicalUrl().equals(es) || s.getCanonicalUrl().equals(ar[0])) {
return False;
}
} else {
return !es.equals(canonical(s.getCanonicalUrl(), s.getVersion()));
}
}
return True;
})
.collect(Collectors.toSet());
Map<String, String> map = systemVersion.parallelStream().map(m -> m.split("\\|"))
.filter(m -> m.length == 2)
.collect(Collectors.toMap(m -> m[0], m->m[1]));
sources.forEach(source -> {
expressions.stream().map(m -> formatExpression(m).split(FS))
.filter(m -> {
if (map.containsKey(source.getCanonicalUrl()) && !isValid(getSourceVersion(m)))
return map.get(source.getCanonicalUrl()).equals(source.getVersion());
return source.getMnemonic().equals(getSourceId(m)) && (!isValid(getSourceVersion(m)) ? source.getIsLatestVersion() : source.getVersion().equals(getSourceVersion(m)));
})
.forEachOrdered(m -> {
String expSrcVersion = getSourceVersion(m);
String conceptId = getConceptId(m);
String conceptVersion = getConceptVersion(m);
if (isValid(conceptId)) {
Optional<Concept> conceptOpt = oclFhirUtil.getSourceConcept(source, conceptId, isValid(expSrcVersion) ? conceptVersion : EMPTY);
conceptOpt.ifPresent(c -> {
// only return non retired concepts when activeOnly is True
if (c.getRetired() && activeOnly.booleanValue()) {
return;
}
// apply concept code filter if provided
if (!filters.isEmpty()) {
if (filters.parallelStream().noneMatch(conceptId::contains))
return;
}
ValueSet.ValueSetExpansionContainsComponent component = new ValueSet.ValueSetExpansionContainsComponent();
component.setSystem(source.getCanonicalUrl());
component.setVersion(source.getVersion());
component.setInactive(c.getRetired());
component.setCode(c.getMnemonic());
List<LocalizedText> names = oclFhirUtil.getNames(c);
if (isValid(displayLanguage)) {
oclFhirUtil.getDisplayForLanguage(names, displayLanguage.getCode())
.ifPresent(component::setDisplay);
} else {
oclFhirUtil.getDisplayForLanguage(names, source.getDefaultLocale())
.ifPresent(component::setDisplay);
}
if (includeDesignations.getValue()) {
addConceptReferenceDesignation(names, component);
}
expansion.getContains().add(component);
});
}
});
});
// sort based on canonical_url,version desc and code asc
List<ValueSet.ValueSetExpansionContainsComponent> sorted = expansion.getContains().stream()
.sorted(Comparator.comparing(ValueSet.ValueSetExpansionContainsComponent::getSystem)
.thenComparing(Comparator.nullsLast(Comparator.comparing(ValueSet.ValueSetExpansionContainsComponent::getVersion)))
.reversed()
.thenComparing(ValueSet.ValueSetExpansionContainsComponent::getCode))
.collect(Collectors.toList());
expansion.setContains(sorted);
// total
expansion.setTotal(expansion.getContains().size());
return valueSet;
}
private String canonical(String url, String version) {
return url + "|" + version;
}
private void addParameter(ValueSet.ValueSetExpansionComponent expansion, String name, Type value) {
ValueSet.ValueSetExpansionParameterComponent component = new ValueSet.ValueSetExpansionParameterComponent();
component.setName(name);
component.setValue(value);
expansion.getParameter().add(component);
}
private StringType determineOwner(Collection collection) {
if (collection.getOrganization() != null) {
return new StringType(ORG_ + collection.getOrganization().getMnemonic());
} else {
return new StringType(USER_ + collection.getUserId().getUsername());
}
}
private String buildExpression(String sourceId, String sourceVersion, String conceptId, String ownerType, String ownerId) {
return FS + (ORG.equals(ownerType) ? ORGS : USERS) +
FS + ownerId +
FS + SOURCES +
FS + sourceId +
FS + (!isValid(sourceVersion) || HEAD.equals(sourceVersion) ? EMPTY : sourceVersion + FS) +
CONCEPTS + FS + conceptId + FS;
}
private String getSourceId(String[] ar) {
return ar.length >= 5 && !ar[4].isEmpty() ? ar[4] : EMPTY;
}
private String getSourceVersion(String[] ar) {
return ar.length >= 6 && !ar[5].isEmpty() && ar[5].equals(CONCEPTS) ? " " : ar[5];
}
private String getConceptId(String[] ar) {
return ar.length >= 6 && !ar[5].isEmpty() && ar[5].equals(CONCEPTS) ?
ar.length >= 7 ? ar[6] : EMPTY :
ar.length >= 8 ? ar[7] : EMPTY;
}
private String getConceptVersion(String[] ar) {
if (ar[6].equals(CONCEPTS)) {
if (ar.length >=9 && !ar[8].isEmpty()) return ar[8];
} else if (ar.length >= 8 && !ar[7].trim().isEmpty()) {
return ar[7];
}
return EMPTY;
}
private String ownerType(String [] ar) {
return ar[1].contains(ORG) ? ORG : USER;
}
private String ownerId(String [] ar) {
return ar[2];
}
@Transactional
public void createValueSet(ValueSet valueSet, String accessionId, String authToken) {
// validate and authenticate
OclEntity oclEntity = new OclEntity(valueSet, accessionId, authToken, true);
UserProfile user = oclEntity.getUserProfile();
// base collection
Collection collection = toBaseCollection(valueSet, user, oclEntity.getAccessionId());
collection.setPublicAccess(VIEW);
// add parent and access
addParent(collection, oclEntity.getOwner());
// add identifier, contact and jurisdiction
addJsonStrings(valueSet, collection);
// add concepts
Map<Source,List<String>> sourceToConceptMap = toConcepts(valueSet.getCompose(), valueSet.getLanguage());
Map<Long,String> validatedConceptIds = new HashMap<>();
Set<String> expressions = new HashSet<>();
sourceToConceptMap.forEach((source,conceptIds) -> {
// validate source-concept relationship and build reference expressions
String ownerType = source.getOrganization() != null ? ORGS : USERS;
String owner = source.getOrganization() != null ? source.getOrganization().getMnemonic() :
source.getUserId().getUsername();
Map<Long,String> validated = getValidatedConceptIds(source.getId(), conceptIds);
validatedConceptIds.putAll(validated);
expressions.addAll(toExpression(ownerType, owner, source.getMnemonic(), source.getVersion(), validated));
});
// save
saveCollection(collection, validatedConceptIds, expressions);
// clear data
sourceToConceptMap.clear();
validatedConceptIds.clear();
expressions.clear();
// populate index
oclFhirUtil.populateIndex(getToken(), COLLECTIONS);
}
private Map<Source,List<String>> toConcepts(ValueSet.ValueSetComposeComponent component, String defaultLocale) {
Map<Source,List<String>> map = new HashMap<>();
component.getInclude().forEach(c -> {
// validate CodeSystem
Source source;
String system = c.getSystem();
String version = c.getVersion();
if (!isValid(system))
throw new InvalidRequestException("Field 'system' of compose.include.* is required.");
if (isValid(version)) {
source = sourceRepository.findFirstByCanonicalUrlAndVersionAndPublicAccessIn(system, version, publicAccess);
} else {
source = sourceRepository.findFirstByCanonicalUrlAndPublicAccessInAndIsLatestVersionOrderByCreatedAtDesc(
system, publicAccess, true
);
// we need to update source version for later use. If version if not provided then we don't want to store
// source version info in expressions. This won't be persisted in db, it is for internal user only.
entityManager.detach(source);
source.setVersion(EMPTY);
}
if (source == null)
throw new InvalidRequestException(String.format("The CodeSystem %s|%s does not exist.", system, version));
// extract concept codes
List<String> conceptIds = c.getConcept().parallelStream()
.filter(f -> isValid(f.getCode()))
.map(ValueSet.ConceptReferenceComponent::getCode)
.collect(Collectors.toList());
// clear extra source data
//source.getConcepts().clear();
//source.getMappings().clear();
//source.getConceptsSources().clear();
//source.getMappingsSources().clear();
map.put(source, conceptIds);
});
return map;
}
protected Map<Long,String> getValidatedConceptIds(Long sourceId, List<String> conceptIds) {
MapSqlParameterSource parameters = new MapSqlParameterSource();
parameters.addValue("sourceId", sourceId);
parameters.addValue("conceptIds", conceptIds);
Map<Long,String> map = new HashMap<>();
namedParameterJdbcTemplate.query(validateConceptIdSql, parameters, (RowMapper<Void>) (rs, rowNum) -> {
map.put(rs.getLong(1), rs.getString(2));
return null;
});
return map;
}
private List<String> toExpression(String ownerType, String owner, String sourceId, String sourceVersion,
Map<Long, String> conceptIdMap) {
return conceptIdMap.entrySet().parallelStream()
.map(m -> toExpression(ownerType, owner, sourceId, sourceVersion, m.getValue(), m.getKey()))
.collect(Collectors.toList());
}
private String toExpression(String ownerType, String owner, String sourceId, String sourceVersion, String conceptId,
Long conceptVersionId) {
String pre = FS + ownerType + FS + owner + FS + SOURCES + FS + sourceId + FS;
if (isValid(sourceVersion) && !HEAD.equals(sourceVersion))
pre = pre + sourceVersion + FS;
return pre + CONCEPTS + FS + conceptId + FS + conceptVersionId + FS;
}
private Collection toBaseCollection(final ValueSet valueSet, final UserProfile user, final String uri) {
Collection collection = new Collection();
// mnemonic
collection.setMnemonic(valueSet.getId());
// canonical url
collection.setCanonicalUrl(valueSet.getUrl());
// created by
collection.setCreatedBy(user);
// updated by
collection.setUpdatedBy(user);
// draft or unknown or empty
collection.setIsActive(True);
collection.setIsLatestVersion(True);
collection.setRetired(False);
collection.setReleased(False);
if (valueSet.getStatus() != null) {
// active
if (PublicationStatus.ACTIVE.toCode().equals(valueSet.getStatus().toCode())) {
collection.setReleased(True);
// retired
} else if (PublicationStatus.RETIRED.toCode().equals(valueSet.getStatus().toCode())) {
collection.setRetired(True);
collection.setReleased(False);
collection.setIsActive(False);
collection.setIsLatestVersion(False);
}
}
// version
collection.setVersion(valueSet.getVersion());
// uri
collection.setUri(toOclUri(uri));
// name
String name = isValid(valueSet.getName()) ? valueSet.getName() : valueSet.getId();
collection.setName(name);
// default locale
collection.setDefaultLocale(isValid(valueSet.getLanguage()) ? valueSet.getLanguage() : EN_LOCALE);
// common fields
addCommonFields(valueSet, collection);
// extras
collection.setExtras(EMPTY_JSON);
// experimental
if (valueSet.getExperimentalElement().getValue() != null)
collection.setExperimental(valueSet.getExperimentalElement().booleanValue());
// locked_date
if (valueSet.getCompose().getLockedDate() != null)
collection.setLockedDate(new Timestamp(valueSet.getCompose().getLockedDate().getTime()));
return collection;
}
private void addParent(final Collection collection, final BaseOclEntity owner) {
if (owner instanceof Organization) {
Organization organization = (Organization) owner;
collection.setOrganization(organization);
collection.setPublicAccess(organization.getPublicAccess());
} else if (owner instanceof UserProfile){
collection.setUserId((UserProfile) owner);
}
}
private static Map<String,Object> toMap(String expression) {
Timestamp timestamp = new Timestamp(System.currentTimeMillis());
collReferenceParamMap.put(EXPRESSION, expression);
collReferenceParamMap.put(CREATED_AT, timestamp);
collReferenceParamMap.put(UPDATED_AT, timestamp);
collReferenceParamMap.put(LAST_RESOLVED_AT, timestamp);
return collReferenceParamMap;
}
private void batchInsert(String sql, Integer collectionId, List<Integer> integerList) {
this.jdbcTemplate.batchUpdate(sql, new BatchPreparedStatementSetter() {
public void setValues(PreparedStatement ps, int i)
throws SQLException {
ps.setInt(1, collectionId);
ps.setInt(2, integerList.get(i));
}
public int getBatchSize() {
return integerList.size();
}
});
}
private void addCommonFields(final ValueSet valueSet, final Collection collection) {
// title
if (isValid(valueSet.getTitle()))
collection.setFullName(valueSet.getTitle());
// description
if (isValid(valueSet.getDescription()))
collection.setDescription(valueSet.getDescription());
// copyright
if (isValid(valueSet.getCopyright()))
collection.setCopyright(valueSet.getCopyright());
// publisher
if (isValid(valueSet.getPublisher()))
collection.setPublisher(valueSet.getPublisher());
// purpose
if (isValid(valueSet.getPurpose()))
collection.setPurpose(valueSet.getPurpose());
// revision date
if (valueSet.getDate() != null)
collection.setRevisionDate(valueSet.getDate());
// immutable
collection.setImmutable(valueSet.getImmutable());
}
public void updateValueSet(final ValueSet valueSet, final Collection collection, final String accessionId, final String authToken) {
// update and save in database
update(valueSet, collection, accessionId, authToken);
// update index
oclFhirUtil.updateIndex(getToken(), COLLECTIONS, collection.getMnemonic());
}
@Transactional
void update(final ValueSet valueSet, final Collection collection, final String accessionId, final String authToken) {
final OclEntity oclEntity = new OclEntity(valueSet, accessionId, authToken, false);
// update status
if (valueSet.getStatus() != null) {
if (PublicationStatus.DRAFT.toCode().equals(valueSet.getStatus().toCode()) || PublicationStatus.UNKNOWN.toCode().equals(valueSet.getStatus().toCode())) {
collection.setReleased(False);
collection.setRetired(False);
} else if (PublicationStatus.ACTIVE.toCode().equals(valueSet.getStatus().toCode())) {
collection.setReleased(True);
collection.setRetired(False);
} else if (PublicationStatus.RETIRED.toCode().equals(valueSet.getStatus().toCode())) {
collection.setRetired(True);
collection.setReleased(False);
}
}
// update canonical url
if (isValid(valueSet.getUrl()))
collection.setCanonicalUrl(valueSet.getUrl());
// update name
if (isValid(valueSet.getName()))
collection.setName(valueSet.getName());
// update language
if (isValid(valueSet.getLanguage()))
collection.setDefaultLocale(valueSet.getLanguage());
// update common fields
addCommonFields(valueSet, collection);
// updated by
collection.setUpdatedBy(oclEntity.getUserProfile());
// updated at
collection.setUpdatedAt(new Timestamp(System.currentTimeMillis()));
// we won't allow to update accession identifier, so let's remove it if its present
removeAccessionIdentifier(valueSet.getIdentifier());
// update identifier, contact and jurisdiction
addJsonStrings(valueSet, collection);
// experimental
if (valueSet.getExperimentalElement().getValue() != null)
collection.setExperimental(valueSet.getExperimentalElement().booleanValue());
// locked_date
if (valueSet.getCompose().getLockedDate() != null)
collection.setLockedDate(new Timestamp(valueSet.getCompose().getLockedDate().getTime()));
// existing references
List<String> existing = getAllExpressions(collection);
// source to all concepts
Map<Source, List<String>> sourceToConceptMap = toConcepts(valueSet.getCompose(), valueSet.getLanguage());
// conceptId to mnemonic
Map<Long, String> validatedConceptIds = new HashMap<>();
// new expressions
Set<String> newExpressions = new HashSet<>();
sourceToConceptMap.forEach((source, conceptIds) -> {
// all valid concepts for given source
Map<Long, String> conceptIdMap = getValidatedConceptIds(source.getId(), conceptIds);
String ownerType = source.getOrganization() != null ? ORGS : USERS;
String owner = source.getOrganization() != null ? source.getOrganization().getMnemonic() :
source.getUserId().getUsername();
for (String conceptId : conceptIds) {
// check if concept code is valid
Optional<Long> conceptVersionId = conceptIdMap.entrySet().stream()
.filter(e -> e.getValue().equals(conceptId)).map(Map.Entry::getKey).findFirst();
if (conceptVersionId.isPresent()) {
String expression = toExpression(ownerType, owner, source.getMnemonic(), source.getVersion(), conceptId, conceptVersionId.get());
// check if the expression already exists
if (existing.contains(expression)) {
// remove existing concept from the validated list of concepts
conceptIdMap.remove(conceptVersionId.get());
}
}
}
// only save new concepts and references
if (!conceptIdMap.isEmpty()) {
// conceptId to mnemonic
validatedConceptIds.putAll(conceptIdMap);
newExpressions.addAll(toExpression(ownerType, owner, source.getMnemonic(), source.getVersion(), conceptIdMap));
}
});
// save collection
saveCollection(collection, validatedConceptIds, newExpressions);
log.info("updated valueset - " + collection.getMnemonic());
// clear data
sourceToConceptMap.clear();
validatedConceptIds.clear();
newExpressions.clear();
}
@Transactional
protected void saveCollection(Collection collection, Map<Long, String> validatedConceptIds, Set<String> expressions) {
// save base collection
collectionRepository.saveAndFlush(collection);
// save collection reference
List<Integer> referenceIds = expressions.stream().map(m -> insert(insertCollectionReference, toMap(m)))
.map(Long::intValue)
.collect(Collectors.toList());
// save collections references
batchInsert(insertCollectionsReferences, collection.getId().intValue(), referenceIds);
// save collections concepts
batchInsert(insertCollectionsConcepts, collection.getId().intValue(),
validatedConceptIds.keySet().stream().map(Long::intValue).collect(Collectors.toList()));
}
}