code stringlengths 73 34.1k | label stringclasses 1
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@PostMapping("/removeMappingProject")
public String deleteMappingProject(@RequestParam() String mappingProjectId) {
MappingProject project = mappingService.getMappingProject(mappingProjectId);
LOG.info("Deleting mappingProject {}", project.getName());
mappingService.deleteMappingProject(mappingProjectId);... | java |
@PostMapping("/removeAttributeMapping")
public String removeAttributeMapping(
@RequestParam() String mappingProjectId,
@RequestParam() String target,
@RequestParam() String source,
@RequestParam() String attribute) {
MappingProject project = mappingService.getMappingProject(mappingProjectI... | java |
@GetMapping("/mappingproject/{id}")
public String viewMappingProject(@PathVariable("id") String identifier, Model model) {
MappingProject project = mappingService.getMappingProject(identifier);
MappingTarget mappingTarget = project.getMappingTargets().get(0);
String target = mappingTarget.getName();
m... | java |
void autoGenerateAlgorithms(
EntityMapping mapping,
EntityType sourceEntityType,
EntityType targetEntityType,
MappingProject project) {
algorithmService.autoGenerateAlgorithm(sourceEntityType, targetEntityType, mapping);
mappingService.updateMappingProject(project);
} | java |
private List<EntityType> getNewSources(MappingTarget target) {
return dataService
.getEntityTypeIds()
.filter(name -> isValidSource(target, name))
.map(dataService::getEntityType)
.collect(toList());
} | java |
@GetMapping
public String init(Model model) {
final UriComponents uriComponents =
ServletUriComponentsBuilder.fromCurrentContextPath().build();
model.addAttribute("molgenisUrl", uriComponents.toUriString() + URI + "/swagger.yml");
model.addAttribute("baseUrl", uriComponents.toUriString());
f... | java |
@GetMapping(value = "/swagger.yml", produces = "text/yaml")
public String swagger(Model model, HttpServletResponse response) {
response.setContentType("text/yaml");
response.setCharacterEncoding("UTF-8");
final UriComponents uriComponents =
ServletUriComponentsBuilder.fromCurrentContextPath().buil... | java |
public static String getLanguageCode(String name) {
if (!isI18n(name)) return null;
return name.substring(name.indexOf('-') + 1, name.length());
} | java |
public void executeScript(String pythonScript, PythonOutputHandler outputHandler) {
// Check if Python is installed
File file = new File(pythonScriptExecutable);
if (!file.exists()) {
throw new MolgenisPythonException("File [" + pythonScriptExecutable + "] does not exist");
}
// Check if Pyth... | java |
public Entity toEntity(final EntityType meta, final Map<String, Object> request) {
final Entity entity = entityManager.create(meta, POPULATE);
for (Attribute attr : meta.getAtomicAttributes()) {
if (attr.getExpression() == null) {
String paramName = attr.getName();
if (request.containsKey... | java |
public Object toEntityValue(Attribute attr, Object paramValue, Object id) {
// Treat empty strings as null
if ((paramValue instanceof String) && ((String) paramValue).isEmpty()) {
paramValue = null;
}
Object value;
AttributeType attrType = attr.getDataType();
switch (attrType) {
cas... | java |
public Schema loadSchema(String schema) {
try {
JSONObject rawSchema = new JSONObject(new JSONTokener(schema));
return SchemaLoader.load(rawSchema);
} catch (JSONException | SchemaException e) {
throw new InvalidJsonSchemaException(e);
}
} | java |
public void validate(String json, String schemaJson) {
Schema schema = loadSchema(schemaJson);
validate(json, schema);
} | java |
private QueryBuilder nestedQueryBuilder(
List<Attribute> attributePath, QueryBuilder queryBuilder) {
if (attributePath.size() == 1) {
return queryBuilder;
} else if (attributePath.size() == 2) {
return QueryBuilders.nestedQuery(
getQueryFieldName(attributePath.get(0)), queryBuilder, ... | java |
public static String concatAttributeHref(
String baseUri, String qualifiedEntityName, Object entityIdValue, String attributeName) {
return String.format(
"%s/%s/%s/%s",
baseUri,
encodePathSegment(qualifiedEntityName),
encodePathSegment(DataConverter.toString(entityIdValue)),
... | java |
public static String concatMetaAttributeHref(
String baseUri, String entityParentName, String attributeName) {
return String.format(
"%s/%s/meta/%s",
baseUri, encodePathSegment(entityParentName), encodePathSegment(attributeName));
} | java |
public static String concatEntityHref(
String baseUri, String qualifiedEntityName, Object entityIdValue) {
if (null == qualifiedEntityName) {
qualifiedEntityName = "";
}
return String.format(
"%s/%s/%s",
baseUri,
encodePathSegment(qualifiedEntityName),
encodePath... | java |
public static String concatMetaEntityHref(String baseUri, String qualifiedEntityName) {
return String.format("%s/%s/meta", baseUri, encodePathSegment(qualifiedEntityName));
} | java |
public static String concatEntityCollectionHref(
String baseUri,
String qualifiedEntityName,
String qualifiedIdAttributeName,
List<String> entitiesIds) {
String ids;
ids = entitiesIds.stream().map(Href::encodeIdToRSQL).collect(Collectors.joining(","));
return String.format(
"... | java |
@Override
@Transactional(readOnly = true, isolation = Isolation.SERIALIZABLE)
public void export(
List<EntityType> entityTypes,
List<Package> packages,
Path downloadFilePath,
Progress progress) {
requireNonNull(progress);
if (!(entityTypes.isEmpty() && packages.isEmpty())) {
tr... | java |
void writeEntityTypes(Collection<EntityType> entityTypes, XlsxWriter writer) {
LinkedList<EntityType> sortedEntityTypes = sortEntityTypesAbstractFirst(entityTypes);
if (!writer.hasSheet(EMX_ENTITIES)) {
writer.createSheet(EMX_ENTITIES, newArrayList(ENTITIES_ATTRS.keySet()));
}
writer.writeRows(sor... | java |
public static Attribute getQueryRuleAttribute(QueryRule queryRule, EntityType entityType) {
String queryRuleField = queryRule.getField();
if (queryRuleField == null) {
return null;
}
Attribute attr = null;
String[] queryRuleFieldTokens = StringUtils.split(queryRuleField, NESTED_ATTRIBUTE_SEPA... | java |
private static Function<EntityTypeNode, Set<EntityTypeNode>> getDependencies() {
return entityTypeNode -> {
// get referenced entities excluding entities of mappedBy attributes
EntityType entityType = entityTypeNode.getEntityType();
Set<EntityTypeNode> refEntityMetaSet =
stream(entityTyp... | java |
private static Set<EntityTypeNode> expandEntityTypeDependencies(EntityTypeNode entityTypeNode) {
if (LOG.isTraceEnabled()) {
LOG.trace(
"expandEntityTypeDependencies(EntityTypeNode entityTypeNode) --- entity: [{}], skip: [{}]",
entityTypeNode.getEntityType().getId(),
entityTypeNo... | java |
private boolean hasAuthenticatedMolgenisToken() {
boolean hasAuthenticatedMolgenisToken = false;
Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
if (authentication instanceof RestAuthenticationToken) {
hasAuthenticatedMolgenisToken = authentication.isAuthenticat... | java |
public static Map<String, Attribute> deepCopyAttributes(
EntityType entityType, EntityType entityTypeCopy, AttributeFactory attrFactory) {
Map<String, Attribute> copiedAttributes = new LinkedHashMap<>();
// step #1: deep copy attributes
Map<String, Attribute> ownAttrMap =
stream(entityType.ge... | java |
public String getLabel(String languageCode) {
String i18nLabel = getString(getI18nAttributeName(LABEL, languageCode));
return i18nLabel != null ? i18nLabel : getLabel();
} | java |
@Nullable
@CheckForNull
public String getDescription(String languageCode) {
String i18nDescription = getString(getI18nAttributeName(DESCRIPTION, languageCode));
return i18nDescription != null ? i18nDescription : getDescription();
} | java |
public Attribute getIdAttribute() {
Attribute idAttr = getOwnIdAttribute();
if (idAttr == null) {
EntityType extend = getExtends();
if (extend != null) {
idAttr = extend.getIdAttribute();
}
}
return idAttr;
} | java |
public Attribute getLabelAttribute() {
Attribute labelAttr = getOwnLabelAttribute();
if (labelAttr == null) {
EntityType extend = getExtends();
if (extend != null) {
labelAttr = extend.getLabelAttribute();
}
}
return labelAttr;
} | java |
public Attribute getLabelAttribute(String langCode) {
Attribute labelAttr = getLabelAttribute();
Attribute i18nLabelAttr =
labelAttr != null ? getAttribute(labelAttr.getName() + '-' + langCode) : null;
return i18nLabelAttr != null ? i18nLabelAttr : labelAttr;
} | java |
public Attribute getAttribute(String attrName) {
Attribute attr = getCachedOwnAttrs().get(attrName);
if (attr == null) {
// look up attribute in parent entity
EntityType extendsEntityType = getExtends();
if (extendsEntityType != null) {
attr = extendsEntityType.getAttribute(attrName);
... | java |
static void addSequenceNumber(Attribute attr, Iterable<Attribute> attrs) {
Integer sequenceNumber = attr.getSequenceNumber();
if (null == sequenceNumber) {
int i =
stream(attrs)
.filter(a -> null != a.getSequenceNumber())
.mapToInt(Attribute::getSequenceNumber)
... | java |
public void initialize(ContextRefreshedEvent event) {
ApplicationContext ctx = event.getApplicationContext();
Stream<String> languageCodes = LanguageService.getLanguageCodes();
EntityTypeMetadata entityTypeMeta = ctx.getBean(EntityTypeMetadata.class);
AttributeMetadata attrMetaMeta = ctx.getBean(Attrib... | java |
public void populate(Entity entity) {
// auto date
generateAutoDateOrDateTime(singletonList(entity), entity.getEntityType().getAttributes());
// auto id
Attribute idAttr = entity.getEntityType().getIdAttribute();
if (idAttr != null
&& idAttr.isAuto()
&& entity.getIdValue() == null
... | java |
public void populateL10nStrings() {
AllPropertiesMessageSource allPropertiesMessageSource = new AllPropertiesMessageSource();
String[] namespaces =
localizationMessageSources
.stream()
.map(PropertiesMessageSource::getNamespace)
.toArray(String[]::new);
allPropert... | java |
public void populateLanguages() {
dataService.add(
LANGUAGE,
languageFactory.create(
LanguageService.DEFAULT_LANGUAGE_CODE, LanguageService.DEFAULT_LANGUAGE_NAME, true));
dataService.add(
LANGUAGE,
languageFactory.create("nl", new Locale("nl").getDisplayName(new Local... | java |
List<Boolean> resolveBooleanExpressions(List<String> expressions, Entity entity) {
if (expressions.isEmpty()) {
return Collections.emptyList();
}
return jsMagmaScriptEvaluator
.eval(expressions, entity)
.stream()
.map(this::convertToBoolean)
.collect(toList());
} | java |
@PreAuthorize("hasAnyRole('ROLE_SU')")
@PostMapping(value = "/add-bootstrap-theme")
public @ResponseBody Style addBootstrapTheme(
@RequestParam(value = "bootstrap3-style") MultipartFile bootstrap3Style,
@RequestParam(value = "bootstrap4-style", required = false) MultipartFile bootstrap4Style)
thro... | java |
private static List<File> unzip(File file, NameMapper nameMapper) {
try {
File parentFile = file.getParentFile();
TrackingNameMapper trackingNameMapper = new TrackingNameMapper(parentFile, nameMapper);
ZipUtil.unpack(file, parentFile, trackingNameMapper);
return trackingNameMapper.getFiles()... | java |
public static Map<String, Integer> createNGrams(String inputQuery, boolean removeStopWords) {
List<String> wordsInString =
Lists.newArrayList(Stemmer.replaceIllegalCharacter(inputQuery).split(" "));
if (removeStopWords) wordsInString.removeAll(STOPWORDSLIST);
List<String> stemmedWordsInString =
... | java |
private static double calculateScore(
Map<String, Integer> inputStringTokens, Map<String, Integer> ontologyTermTokens) {
if (inputStringTokens.size() == 0 || ontologyTermTokens.size() == 0) return (double) 0;
int totalToken = getTotalNumTokens(inputStringTokens) + getTotalNumTokens(ontologyTermTokens);
... | java |
public void addListener(SettingsEntityListener settingsEntityListener) {
RunAsSystemAspect.runAsSystem(
() ->
entityListenersService.addEntityListener(
entityTypeId,
new EntityListener() {
@Override
public void postUpdate(Entity... | java |
public void removeListener(SettingsEntityListener settingsEntityListener) {
RunAsSystemAspect.runAsSystem(
() ->
entityListenersService.removeEntityListener(
entityTypeId,
new EntityListener() {
@Override
public void postUpdate... | java |
@Override
public void add(Entity entity) {
if (entity == null) throw new IllegalArgumentException("Entity cannot be null");
if (cachedAttributes == null)
throw new MolgenisDataException(
"The attribute names are not defined, call writeAttributeNames first");
int i = 0;
Row poiRow = sh... | java |
public void writeAttributeHeaders(
Iterable<Attribute> attributes, AttributeWriteMode attributeWriteMode) {
if (attributes == null) throw new IllegalArgumentException("Attributes cannot be null");
if (attributeWriteMode == null)
throw new IllegalArgumentException("AttributeWriteMode cannot be null")... | java |
public Tag getTagEntity(String objectIRI, String label, Relation relation, String codeSystemIRI) {
Tag tag =
dataService
.query(TAG, Tag.class)
.eq(OBJECT_IRI, objectIRI)
.and()
.eq(RELATION_IRI, relation.getIRI())
.and()
.eq(CODE_SYSTE... | java |
public boolean populate(ContextRefreshedEvent event) {
boolean databasePopulated = isDatabasePopulated();
if (!databasePopulated) {
LOG.trace("Populating database with I18N strings ...");
i18nPopulator.populateLanguages();
LOG.trace("Populated database with I18N strings");
}
LOG.trace... | java |
public void validate(Query<? extends Entity> query, EntityType entityType) {
query.getRules().forEach(queryRule -> validateQueryRule(queryRule, entityType));
} | java |
public void setValue(Object value) {
if (value instanceof Iterable<?>) {
this.value = stream((Iterable<?>) value).map(this::toValue).collect(toList());
} else {
this.value = toValue(value);
}
} | java |
Set<String> findMatchedWords(Explanation explanation) {
Set<String> words = new HashSet<>();
String description = explanation.getDescription();
if (description.startsWith(Options.SUM_OF.toString())
|| description.startsWith(Options.PRODUCT_OF.toString())) {
if (newArrayList(explanation.getDeta... | java |
Map<String, Double> findMatchQueries(
String matchedWordsString, Map<String, String> collectExpandedQueryMap) {
Map<String, Double> qualifiedQueries = new HashMap<>();
Set<String> matchedWords = splitIntoTerms(matchedWordsString);
for (Entry<String, String> entry : collectExpandedQueryMap.entrySet()) ... | java |
@Override
@GetMapping
public String init(final Model model) {
super.init(model);
model.addAttribute("adminEmails", userService.getSuEmailAddresses());
if (SecurityUtils.currentUserIsAuthenticated()) {
User currentUser = userService.getUser(SecurityUtils.getCurrentUsername());
if (currentUser... | java |
@SuppressWarnings("squid:S3457") // do not use platform specific line ending
private SimpleMailMessage createFeedbackMessage(FeedbackForm form) {
SimpleMailMessage message = new SimpleMailMessage();
message.setTo(userService.getSuEmailAddresses().toArray(new String[] {}));
if (form.hasEmail()) {
mes... | java |
private static String getFormattedName(User user) {
List<String> parts = new ArrayList<>();
if (user.getTitle() != null) {
parts.add(user.getTitle());
}
if (user.getFirstName() != null) {
parts.add(user.getFirstName());
}
if (user.getMiddleNames() != null) {
parts.add(user.getM... | java |
private byte[] generateRandomBytes(int nBytes, Random random) {
byte[] randomBytes = new byte[nBytes];
random.nextBytes(randomBytes);
return randomBytes;
} | java |
synchronized void unschedule(String scheduledJobId) {
try {
quartzScheduler.deleteJob(new JobKey(scheduledJobId, SCHEDULED_JOB_GROUP));
} catch (SchedulerException e) {
String message = format("Error deleting ScheduledJob ''{0}''", scheduledJobId);
LOG.error(message, e);
throw new Schedu... | java |
private static void validateMappedBy(Attribute attr, Attribute mappedByAttr) {
if (mappedByAttr != null) {
if (!isSingleReferenceType(mappedByAttr)) {
throw new MolgenisDataException(
format(
"Invalid mappedBy attribute [%s] data type [%s].",
mappedByAttr.ge... | java |
private static void validateOrderBy(Attribute attr, Sort orderBy) {
if (orderBy != null) {
EntityType refEntity = attr.getRefEntity();
if (refEntity != null) {
for (Sort.Order orderClause : orderBy) {
String refAttrName = orderClause.getAttr();
if (refEntity.getAttribute(refA... | java |
public ImportService getImportService(File file, RepositoryCollection source) {
final Map<String, ImportService> importServicesMappedToExtensions = Maps.newHashMap();
importServices
.stream()
.filter(importService -> importService.canImport(file, source))
.forEach(
importServ... | java |
public static String cleanStemPhrase(String phrase) {
StringBuilder stringBuilder = new StringBuilder();
for (String word : replaceIllegalCharacter(phrase).split(" ")) {
String stemmedWord = stem(word);
if (StringUtils.isNotEmpty(stemmedWord)) {
if (stringBuilder.length() > 0) {
st... | java |
private String constructNodePath(String parentNodePath, int currentPosition) {
StringBuilder nodePathStringBuilder = new StringBuilder();
if (!StringUtils.isEmpty(parentNodePath))
nodePathStringBuilder.append(parentNodePath).append('.');
nodePathStringBuilder
.append(currentPosition)
.... | java |
public static Object getTypedValue(String valueStr, Attribute attr) {
// Reference types cannot be processed because we lack an entityManager in this route.
if (EntityTypeUtils.isReferenceType(attr)) {
throw new MolgenisDataException(
"getTypedValue(String, AttributeMetadata) can't be used for a... | java |
public static Object getTypedValue(String valueStr, Attribute attr, EntityManager entityManager) {
if (valueStr == null) return null;
switch (attr.getDataType()) {
case BOOL:
return Boolean.valueOf(valueStr);
case CATEGORICAL:
case FILE:
case XREF:
EntityType xrefEntity =... | java |
public static boolean equalsEntities(
Iterable<Entity> entityIterable, Iterable<Entity> otherEntityIterable) {
List<Entity> attrs = newArrayList(entityIterable);
List<Entity> otherAttrs = newArrayList(otherEntityIterable);
if (attrs.size() != otherAttrs.size()) return false;
for (int i = 0; i < a... | java |
public List<String> getEnumOptions() {
String enumOptionsStr = getString(ENUM_OPTIONS);
return enumOptionsStr != null ? asList(enumOptionsStr.split(",")) : emptyList();
} | java |
public Attribute getInversedBy() {
// FIXME besides checking mappedBy attr name also check
// attr.getRefEntity().getFullyQualifiedName
if (hasRefEntity()) {
return Streams.stream(getRefEntity().getAtomicAttributes())
.filter(Attribute::isMappedBy)
.filter(attr -> getName().equals(... | java |
public void grantDefaultPermissions(GroupValue groupValue) {
PackageIdentity packageIdentity = new PackageIdentity(groupValue.getRootPackage().getName());
GroupIdentity groupIdentity = new GroupIdentity(groupValue.getName());
aclService.createAcl(groupIdentity);
groupValue
.getRoles()
.f... | java |
public Fetch field(String field, Fetch fetch) {
attrFetchMap.put(field, fetch);
return this;
} | java |
public List<String> getTracksString(Map<String, GenomeBrowserTrack> entityTracks) {
List<String> results = new ArrayList<>();
if (hasPermission()) {
Map<String, GenomeBrowserTrack> allTracks = new HashMap<>(entityTracks);
for (GenomeBrowserTrack track : entityTracks.values()) {
allTracks.put... | java |
public Entity get(Repository<Entity> repository, Object id) {
LoadingCache<Object, Optional<Map<String, Object>>> cache = getEntityCache(repository);
EntityType entityType = repository.getEntityType();
return cache.getUnchecked(id).map(e -> entityHydration.hydrate(e, entityType)).orElse(null);
} | java |
public List<Entity> getBatch(Repository<Entity> repository, Iterable<Object> ids) {
try {
return getEntityCache(repository)
.getAll(ids)
.values()
.stream()
.filter(Optional::isPresent)
.map(Optional::get)
.map(e -> entityHydration.hydrate(e, reposit... | java |
private LoadingCache<Object, Optional<Map<String, Object>>> createEntityCache(
Repository<Entity> repository) {
Caffeine<Object, Object> cacheBuilder =
Caffeine.newBuilder().recordStats().expireAfterAccess(10, MINUTES);
if (!MetaDataService.isMetaEntityType(repository.getEntityType())) {
cac... | java |
private void removeMappedByAttributes(Map<String, EntityType> resolvedEntityTypes) {
resolvedEntityTypes
.values()
.stream()
.flatMap(EntityType::getMappedByAttributes)
.filter(attribute -> resolvedEntityTypes.containsKey(attribute.getEntity().getId()))
.forEach(attribute -> ... | java |
<T> T call(Job<T> job, Progress progress, JobExecutionContext jobExecutionContext) {
return runWithContext(jobExecutionContext, () -> tryCall(job, progress));
} | java |
private Entity findSynonymWithHighestNgramScore(
String ontologyIri, String queryString, Entity ontologyTermEntity) {
Iterable<Entity> entities =
ontologyTermEntity.getEntities(OntologyTermMetadata.ONTOLOGY_TERM_SYNONYM);
if (Iterables.size(entities) > 0) {
String cleanedQueryString = remove... | java |
private static String generateBase64Authentication(String username, String password) {
requireNonNull(username, password);
String userPass = username + ":" + password;
String userPassBase64 = Base64.getEncoder().encodeToString(userPass.getBytes(UTF_8));
return "Basic " + userPassBase64;
} | java |
private String executeScriptExecuteRequest(String rScript) throws IOException {
URI uri = getScriptExecutionUri();
HttpPost httpPost = new HttpPost(uri);
NameValuePair nameValuePair = new BasicNameValuePair("x", rScript);
httpPost.setEntity(new UrlEncodedFormEntity(singletonList(nameValuePair)));
S... | java |
private String executeScriptGetResponseRequest(
String openCpuSessionKey, String scriptOutputFilename, String outputPathname)
throws IOException {
String responseValue;
if (scriptOutputFilename != null) {
executeScriptGetFileRequest(openCpuSessionKey, scriptOutputFilename, outputPathname);
... | java |
private void executeScriptGetFileRequest(
String openCpuSessionKey, String scriptOutputFilename, String outputPathname)
throws IOException {
URI scriptGetValueResponseUri =
getScriptGetFileResponseUri(openCpuSessionKey, scriptOutputFilename);
HttpGet httpGet = new HttpGet(scriptGetValueRespo... | java |
private String executeScriptGetValueRequest(String openCpuSessionKey) throws IOException {
URI scriptGetValueResponseUri = getScriptGetValueResponseUri(openCpuSessionKey);
HttpGet httpGet = new HttpGet(scriptGetValueResponseUri);
String responseValue;
try (CloseableHttpResponse response = httpClient.exe... | java |
@Bean
public ViewResolver viewResolver() {
FreeMarkerViewResolver resolver = new FreeMarkerViewResolver();
resolver.setCache(true);
resolver.setSuffix(".ftl");
resolver.setContentType("text/html;charset=UTF-8");
return resolver;
} | java |
@Bean
public FreeMarkerConfigurer freeMarkerConfigurer() {
FreeMarkerConfigurer result =
new FreeMarkerConfigurer() {
@Override
protected void postProcessConfiguration(Configuration config) {
config.setObjectWrapper(new MolgenisFreemarkerObjectWrapper(VERSION_2_3_23));
... | java |
private String toAttributeName(String vcfInfoFieldKey) {
String attrName = infoFieldKeyToAttrNameMap.get(vcfInfoFieldKey);
if (attrName == null) {
throw new RuntimeException(
format("Missing attribute for VCF info field [%s]", vcfInfoFieldKey));
}
return attrName;
} | java |
private static Set<String> determineVcfInfoFlagFields(VcfMeta vcfMeta) {
return stream(vcfMeta.getInfoMeta())
.filter(vcfInfoMeta -> vcfInfoMeta.getType().equals(VcfMetaInfo.Type.FLAG))
.map(VcfMetaInfo::getId)
.collect(toSet());
} | java |
private static Map<String, String> createInfoFieldKeyToAttrNameMap(
VcfMeta vcfMeta, String entityTypeId) {
Map<String, String> infoFieldIdToAttrNameMap =
newHashMapWithExpectedSize(size(vcfMeta.getInfoMeta()));
for (VcfMetaInfo info : vcfMeta.getInfoMeta()) {
// according to the VCF standar... | java |
public Optional<CacheHit<Entity>> get(String entityTypeId, Object id, EntityType entityType) {
CombinedEntityCache cache = caches.get();
if (cache == null) {
return Optional.empty();
}
Optional<CacheHit<Entity>> result = cache.getIfPresent(entityType, id);
if (result.isPresent()) {
LOG.d... | java |
public void put(String entityTypeId, Entity entity) {
CombinedEntityCache entityCache = caches.get();
if (entityCache != null) {
entityCache.put(entity);
LOG.trace(
"Added dehydrated row [{}] from entity {} to the L1 cache",
entity.getIdValue(),
entityTypeId);
}
} | java |
private List<Entity> findAllBatch(List<Object> batch) {
String entityId = getEntityType().getId();
EntityType entityType = getEntityType();
List<Object> missingIds =
batch
.stream()
.filter(id -> !l1Cache.get(entityId, id, entityType).isPresent())
.collect(toList(... | java |
private void evictBiDiReferencedEntityTypes() {
getEntityType().getMappedByAttributes().map(Attribute::getRefEntity).forEach(l1Cache::evictAll);
getEntityType()
.getInversedByAttributes()
.map(Attribute::getRefEntity)
.forEach(l1Cache::evictAll);
} | java |
private void evictBiDiReferencedEntities(Entity entity) {
Stream<EntityKey> backreffingEntities =
getEntityType()
.getMappedByAttributes()
.flatMap(mappedByAttr -> Streams.stream(entity.getEntities(mappedByAttr.getName())))
.map(EntityKey::create);
Stream<EntityKey> m... | java |
public Hits<ExplainedAttribute> findAttributes(
EntityType sourceEntityType, Set<String> queryTerms, Collection<OntologyTerm> ontologyTerms) {
Iterable<String> attributeIdentifiers =
semanticSearchServiceHelper.getAttributeIdentifiers(sourceEntityType);
QueryRule disMaxQueryRule =
semanti... | java |
public Set<String> createLexicalSearchQueryTerms(
Attribute targetAttribute, Set<String> searchTerms) {
Set<String> queryTerms = new HashSet<>();
if (searchTerms != null && !searchTerms.isEmpty()) {
queryTerms.addAll(searchTerms);
}
if (queryTerms.isEmpty()) {
if (StringUtils.isNotBl... | java |
public Set<ExplainedQueryString> convertAttributeToExplainedAttribute(
Attribute attribute, Map<String, String> collectExpandedQueryMap, Query<Entity> query) {
EntityType attributeMetaData = dataService.getEntityType(ATTRIBUTE_META_DATA);
String attributeID = attribute.getIdentifier();
Explanation exp... | java |
public static List<Entity> resolvePackages(Iterable<Entity> packageRepo) {
List<Entity> resolved = new LinkedList<>();
if ((packageRepo == null) || Iterables.isEmpty(packageRepo)) return resolved;
List<Entity> unresolved = new ArrayList<>();
Map<String, Entity> resolvedByName = new HashMap<>();
fo... | java |
public int getOntologyTermDistance(OntologyTerm ontologyTerm1, OntologyTerm ontologyTerm2) {
String nodePath1 = getOntologyTermNodePath(ontologyTerm1);
String nodePath2 = getOntologyTermNodePath(ontologyTerm2);
if (StringUtils.isEmpty(nodePath1)) {
throw new MolgenisDataAccessException(
"Th... | java |
public List<OntologyTerm> getChildren(OntologyTerm ontologyTerm) {
Iterable<org.molgenis.ontology.core.meta.OntologyTerm> ontologyTermEntities =
() ->
dataService
.query(ONTOLOGY_TERM, org.molgenis.ontology.core.meta.OntologyTerm.class)
.eq(ONTOLOGY_TERM_IRI, onto... | java |
static String toValue(Cell cell, List<CellProcessor> cellProcessors) {
String value;
switch (cell.getCellTypeEnum()) {
case BLANK:
value = null;
break;
case STRING:
value = cell.getStringCellValue();
break;
case NUMERIC:
if (DateUtil.isCellDateFormatted(... | java |
private static String formatUTCDateAsLocalDateTime(Date javaDate) {
// Now back from start of day in UTC to LocalDateTime to express that we don't know the
// timezone.
LocalDateTime localDateTime = javaDate.toInstant().atZone(UTC).toLocalDateTime();
// And format to string
return localDateTime.toSt... | java |
public static String getCurrentUri() {
HttpServletRequest request =
((ServletRequestAttributes) RequestContextHolder.currentRequestAttributes()).getRequest();
StringBuilder uri = new StringBuilder();
uri.append(request.getAttribute("javax.servlet.forward.request_uri"));
if (StringUtils.isNotBl... | java |
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