idx int64 0 41.2k | question stringlengths 74 4.04k | target stringlengths 7 750 |
|---|---|---|
41,100 | @ PostMapping ( "/removeMappingProject" ) public String deleteMappingProject ( @ RequestParam ( ) String mappingProjectId ) { MappingProject project = mappingService . getMappingProject ( mappingProjectId ) ; LOG . info ( "Deleting mappingProject {}" , project . getName ( ) ) ; mappingService . deleteMappingProject ( m... | Removes a mapping project |
41,101 | @ PostMapping ( "/removeAttributeMapping" ) public String removeAttributeMapping ( @ RequestParam ( ) String mappingProjectId , @ RequestParam ( ) String target , @ RequestParam ( ) String source , @ RequestParam ( ) String attribute ) { MappingProject project = mappingService . getMappingProject ( mappingProjectId ) ;... | Removes a attribute mapping |
41,102 | @ 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 . ... | Displays a mapping project . |
41,103 | void autoGenerateAlgorithms ( EntityMapping mapping , EntityType sourceEntityType , EntityType targetEntityType , MappingProject project ) { algorithmService . autoGenerateAlgorithm ( sourceEntityType , targetEntityType , mapping ) ; mappingService . updateMappingProject ( project ) ; } | Generate algorithms based on semantic matches between attribute tags and descriptions |
41,104 | private List < EntityType > getNewSources ( MappingTarget target ) { return dataService . getEntityTypeIds ( ) . filter ( name -> isValidSource ( target , name ) ) . map ( dataService :: getEntityType ) . collect ( toList ( ) ) ; } | Lists the entities that may be added as new sources to this mapping project s selected target |
41,105 | public String init ( Model model ) { final UriComponents uriComponents = ServletUriComponentsBuilder . fromCurrentContextPath ( ) . build ( ) ; model . addAttribute ( "molgenisUrl" , uriComponents . toUriString ( ) + URI + "/swagger.yml" ) ; model . addAttribute ( "baseUrl" , uriComponents . toUriString ( ) ) ; final S... | Serves the Swagger UI which allows you to try out the documented endpoints . Sets the url parameter to the swagger yaml that describes the REST API . Creates an apiKey token for the current user . |
41,106 | @ 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 ( ) .... | Serves the Swagger description of the REST API . As host fills in the host where the controller lives . As options for the entity names contains only those entity names that the user can actually see . |
41,107 | public static String getLanguageCode ( String name ) { if ( ! isI18n ( name ) ) return null ; return name . substring ( name . indexOf ( '-' ) + 1 , name . length ( ) ) ; } | Get the language code of a new with language suffix . |
41,108 | public void executeScript ( String pythonScript , PythonOutputHandler outputHandler ) { File file = new File ( pythonScriptExecutable ) ; if ( ! file . exists ( ) ) { throw new MolgenisPythonException ( "File [" + pythonScriptExecutable + "] does not exist" ) ; } if ( ! file . canExecute ( ) ) { throw new MolgenisPytho... | Execute a python script and wait for it to finish |
41,109 | 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 . contain... | Creates a new entity based from a HttpServletRequest . For file attributes persists the file in the file store and persist a file meta data entity . |
41,110 | public Object toEntityValue ( Attribute attr , Object paramValue , Object id ) { if ( ( paramValue instanceof String ) && ( ( String ) paramValue ) . isEmpty ( ) ) { paramValue = null ; } Object value ; AttributeType attrType = attr . getDataType ( ) ; switch ( attrType ) { case BOOL : value = convertBool ( attr , para... | Converts a HTTP request parameter to a entity value of which the type is defined by the attribute . For file attributes persists the file in the file store and persist a file meta data entity . |
41,111 | 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 ) ; } } | Loads JSON schema . The schema may contain remote references . |
41,112 | public void validate ( String json , String schemaJson ) { Schema schema = loadSchema ( schemaJson ) ; validate ( json , schema ) ; } | Validates that a JSON string conforms to a JSON schema . |
41,113 | 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 , Scor... | Wraps the query in a nested query when a query is done on a reference entity . Returns the original query when it is applied to the current entity . |
41,114 | 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 ) ) , encodePathSegment ( a... | Create an encoded href for an attribute |
41,115 | public static String concatMetaAttributeHref ( String baseUri , String entityParentName , String attributeName ) { return String . format ( "%s/%s/meta/%s" , baseUri , encodePathSegment ( entityParentName ) , encodePathSegment ( attributeName ) ) ; } | Create an encoded href for an attribute meta |
41,116 | public static String concatEntityHref ( String baseUri , String qualifiedEntityName , Object entityIdValue ) { if ( null == qualifiedEntityName ) { qualifiedEntityName = "" ; } return String . format ( "%s/%s/%s" , baseUri , encodePathSegment ( qualifiedEntityName ) , encodePathSegment ( DataConverter . toString ( enti... | Create an encoded href for an entity |
41,117 | public static String concatMetaEntityHref ( String baseUri , String qualifiedEntityName ) { return String . format ( "%s/%s/meta" , baseUri , encodePathSegment ( qualifiedEntityName ) ) ; } | Create an encoded href for an entity meta |
41,118 | 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 ( "%s/%s?q=%s... | Create an encoded href for an entity collection |
41,119 | @ 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 ( ) ) ) { try ( XlsxWriter wr... | Isolation level needs to be SERIALIZABLE in case IndexActions are being downloaded . The entities have their own transaction and can change during the download when executed with a default isolation level . |
41,120 | 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... | package private for test |
41,121 | 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_SEPARATOR )... | Returns the attribute for a query rule field . |
41,122 | private static Function < EntityTypeNode , Set < EntityTypeNode > > getDependencies ( ) { return entityTypeNode -> { EntityType entityType = entityTypeNode . getEntityType ( ) ; Set < EntityTypeNode > refEntityMetaSet = stream ( entityType . getOwnAllAttributes ( ) ) . filter ( attribute -> isProcessableAttribute ( att... | Returns dependencies of the given entity meta data . |
41,123 | private static Set < EntityTypeNode > expandEntityTypeDependencies ( EntityTypeNode entityTypeNode ) { if ( LOG . isTraceEnabled ( ) ) { LOG . trace ( "expandEntityTypeDependencies(EntityTypeNode entityTypeNode) --- entity: [{}], skip: [{}]" , entityTypeNode . getEntityType ( ) . getId ( ) , entityTypeNode . isSkip ( )... | Returns whole tree dependencies of the given entity meta data . |
41,124 | private boolean hasAuthenticatedMolgenisToken ( ) { boolean hasAuthenticatedMolgenisToken = false ; Authentication authentication = SecurityContextHolder . getContext ( ) . getAuthentication ( ) ; if ( authentication instanceof RestAuthenticationToken ) { hasAuthenticatedMolgenisToken = authentication . isAuthenticated... | Check on authenticated RestAuthenticationToken |
41,125 | public static Map < String , Attribute > deepCopyAttributes ( EntityType entityType , EntityType entityTypeCopy , AttributeFactory attrFactory ) { Map < String , Attribute > copiedAttributes = new LinkedHashMap < > ( ) ; Map < String , Attribute > ownAttrMap = stream ( entityType . getOwnAllAttributes ( ) ) . map ( att... | Deep copy all attributes of an EntityType to its copy . Returns a LinkedMap of the old attribute IDs to the newly copied Attributes . |
41,126 | public String getLabel ( String languageCode ) { String i18nLabel = getString ( getI18nAttributeName ( LABEL , languageCode ) ) ; return i18nLabel != null ? i18nLabel : getLabel ( ) ; } | Label of the entity in the requested language |
41,127 | public String getDescription ( String languageCode ) { String i18nDescription = getString ( getI18nAttributeName ( DESCRIPTION , languageCode ) ) ; return i18nDescription != null ? i18nDescription : getDescription ( ) ; } | Description of the entity in the requested language |
41,128 | public Attribute getIdAttribute ( ) { Attribute idAttr = getOwnIdAttribute ( ) ; if ( idAttr == null ) { EntityType extend = getExtends ( ) ; if ( extend != null ) { idAttr = extend . getIdAttribute ( ) ; } } return idAttr ; } | Attribute that is used as unique Id . Id attribute should always be provided . |
41,129 | public Attribute getLabelAttribute ( ) { Attribute labelAttr = getOwnLabelAttribute ( ) ; if ( labelAttr == null ) { EntityType extend = getExtends ( ) ; if ( extend != null ) { labelAttr = extend . getLabelAttribute ( ) ; } } return labelAttr ; } | Attribute that is used as unique label . If no label exist returns null . |
41,130 | public Attribute getLabelAttribute ( String langCode ) { Attribute labelAttr = getLabelAttribute ( ) ; Attribute i18nLabelAttr = labelAttr != null ? getAttribute ( labelAttr . getName ( ) + '-' + langCode ) : null ; return i18nLabelAttr != null ? i18nLabelAttr : labelAttr ; } | Gets the correct label attribute for the given language or the default if not found |
41,131 | public Attribute getAttribute ( String attrName ) { Attribute attr = getCachedOwnAttrs ( ) . get ( attrName ) ; if ( attr == null ) { EntityType extendsEntityType = getExtends ( ) ; if ( extendsEntityType != null ) { attr = extendsEntityType . getAttribute ( attrName ) ; } } return attr ; } | Get attribute by name |
41,132 | 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 ) . max ( ) . orElse ( - 1 ) ... | Add a sequence number to the attribute . If the sequence number exists add it ot the attribute . If the sequence number does not exists then find the highest sequence number . If Entity has not attributes with sequence numbers put 0 . |
41,133 | public void initialize ( ContextRefreshedEvent event ) { ApplicationContext ctx = event . getApplicationContext ( ) ; Stream < String > languageCodes = LanguageService . getLanguageCodes ( ) ; EntityTypeMetadata entityTypeMeta = ctx . getBean ( EntityTypeMetadata . class ) ; AttributeMetadata attrMetaMeta = ctx . getBe... | Initialize internationalization attributes |
41,134 | public void populate ( Entity entity ) { generateAutoDateOrDateTime ( singletonList ( entity ) , entity . getEntityType ( ) . getAttributes ( ) ) ; Attribute idAttr = entity . getEntityType ( ) . getIdAttribute ( ) ; if ( idAttr != null && idAttr . isAuto ( ) && entity . getIdValue ( ) == null && ( idAttr . getDataType... | Populates an entity with auto values |
41,135 | public void populateL10nStrings ( ) { AllPropertiesMessageSource allPropertiesMessageSource = new AllPropertiesMessageSource ( ) ; String [ ] namespaces = localizationMessageSources . stream ( ) . map ( PropertiesMessageSource :: getNamespace ) . toArray ( String [ ] :: new ) ; allPropertiesMessageSource . addMolgenisN... | Populates dataService with localization strings from property files on the classpath . |
41,136 | 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 Locale ( "nl" ) ) , fal... | Populate data store with default languages |
41,137 | 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 ( ) ) ; } | Resolved boolean expressions |
41,138 | @ PreAuthorize ( "hasAnyRole('ROLE_SU')" ) @ PostMapping ( value = "/add-bootstrap-theme" ) public Style addBootstrapTheme ( @ RequestParam ( value = "bootstrap3-style" ) MultipartFile bootstrap3Style , @ RequestParam ( value = "bootstrap4-style" , required = false ) MultipartFile bootstrap4Style ) throws MolgenisStyle... | Add a new bootstrap theme theme is passed as a bootstrap css file . It is mandatory to pass a bootstrap3 style file but optional to pass a bootstrap 4 style file |
41,139 | 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 ( ... | Unzips a zipfile into the directory it resides in . |
41,140 | 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 > stemmedWo... | create n - grams tokens of the string . |
41,141 | 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 ( ontology... | Calculate the ngram distance |
41,142 | public void addListener ( SettingsEntityListener settingsEntityListener ) { RunAsSystemAspect . runAsSystem ( ( ) -> entityListenersService . addEntityListener ( entityTypeId , new EntityListener ( ) { public void postUpdate ( Entity entity ) { settingsEntityListener . postUpdate ( entity ) ; } public Object getEntityI... | Adds a listener for this settings entity that fires on entity updates |
41,143 | public void removeListener ( SettingsEntityListener settingsEntityListener ) { RunAsSystemAspect . runAsSystem ( ( ) -> entityListenersService . removeEntityListener ( entityTypeId , new EntityListener ( ) { public void postUpdate ( Entity entity ) { settingsEntityListener . postUpdate ( entity ) ; } public Object getE... | Removes a listener for this settings entity that fires on entity updates |
41,144 | 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 = sheet . createRow ( row ++ ) ; f... | Add a new row to the sheet |
41,145 | 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" ) ; ... | Write sheet column headers |
41,146 | 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_SYSTEM , codeSystemIRI ) . findOne ( ) ; if ( tag == ... | Fetches a tag from the repository . Creates a new one if it does not yet exist . |
41,147 | 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 ( "Pop... | Returns whether the database was populated previously . |
41,148 | public void validate ( Query < ? extends Entity > query , EntityType entityType ) { query . getRules ( ) . forEach ( queryRule -> validateQueryRule ( queryRule , entityType ) ) ; } | Validates query based on the given entity type converts query values to the expected type if necessary . |
41,149 | public void setValue ( Object value ) { if ( value instanceof Iterable < ? > ) { this . value = stream ( ( Iterable < ? > ) value ) . map ( this :: toValue ) . collect ( toList ( ) ) ; } else { this . value = toValue ( value ) ; } } | Sets a new value for this rule . |
41,150 | 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 (... | This method is able to recursively collect all the matched words from Elasticsearch Explanation document |
41,151 | 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 : collectExpandedQueryMa... | This method is able to find the queries that are used in the matching . Only queries that contain all matched words are potential queries . |
41,152 | 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 != null ) { ... | Serves feedback form . |
41,153 | @ SuppressWarnings ( "squid:S3457" ) private SimpleMailMessage createFeedbackMessage ( FeedbackForm form ) { SimpleMailMessage message = new SimpleMailMessage ( ) ; message . setTo ( userService . getSuEmailAddresses ( ) . toArray ( new String [ ] { } ) ) ; if ( form . hasEmail ( ) ) { message . setCc ( form . getEmail... | Creates a MimeMessage based on a FeedbackForm . |
41,154 | 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 ... | Formats a MolgenisUser s name . |
41,155 | private byte [ ] generateRandomBytes ( int nBytes , Random random ) { byte [ ] randomBytes = new byte [ nBytes ] ; random . nextBytes ( randomBytes ) ; return randomBytes ; } | Generates a number of random bytes . |
41,156 | 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 ScheduledJo... | Remove a job from the quartzScheduler |
41,157 | 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 . getName ( ) , mappedByAttr . getDataType ( ) ) ... | Validate whether the mappedBy attribute is part of the referenced entity . |
41,158 | 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 ( refAttrName ) == null... | Validate whether the attribute names defined by the orderBy attribute point to existing attributes in the referenced entity . |
41,159 | public ImportService getImportService ( File file , RepositoryCollection source ) { final Map < String , ImportService > importServicesMappedToExtensions = Maps . newHashMap ( ) ; importServices . stream ( ) . filter ( importService -> importService . canImport ( file , source ) ) . forEach ( importService -> { for ( S... | Finds a suitable ImportService for a FileRepositoryCollection . |
41,160 | 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 ) { stringB... | Remove illegal characters from the string and stem each single word |
41,161 | private String constructNodePath ( String parentNodePath , int currentPosition ) { StringBuilder nodePathStringBuilder = new StringBuilder ( ) ; if ( ! StringUtils . isEmpty ( parentNodePath ) ) nodePathStringBuilder . append ( parentNodePath ) . append ( '.' ) ; nodePathStringBuilder . append ( currentPosition ) . app... | Constructs the node path string for a child node |
41,162 | public static Object getTypedValue ( String valueStr , Attribute attr ) { if ( EntityTypeUtils . isReferenceType ( attr ) ) { throw new MolgenisDataException ( "getTypedValue(String, AttributeMetadata) can't be used for attributes referencing entities" ) ; } return getTypedValue ( valueStr , attr , null ) ; } | Convert a string value to a typed value based on a non - entity - referencing attribute data type . |
41,163 | 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 = attr . getRefEntity ( )... | Convert a string value to a typed value based on the attribute data type . |
41,164 | 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 ... | Returns true if an Iterable equals another Iterable . |
41,165 | public List < String > getEnumOptions ( ) { String enumOptionsStr = getString ( ENUM_OPTIONS ) ; return enumOptionsStr != null ? asList ( enumOptionsStr . split ( "," ) ) : emptyList ( ) ; } | For enum fields returns the possible enum values |
41,166 | public Attribute getInversedBy ( ) { if ( hasRefEntity ( ) ) { return Streams . stream ( getRefEntity ( ) . getAtomicAttributes ( ) ) . filter ( Attribute :: isMappedBy ) . filter ( attr -> getName ( ) . equals ( attr . getMappedBy ( ) . getName ( ) ) ) . findFirst ( ) . orElse ( null ) ; } else { return null ; } } | For a reference type attribute searches the referenced entity for its inversed attribute . This is the one - to - many attribute that has mappedBy set to this attribute . Returns null if this is not a reference type attribute or no inverse attribute exists . |
41,167 | public void grantDefaultPermissions ( GroupValue groupValue ) { PackageIdentity packageIdentity = new PackageIdentity ( groupValue . getRootPackage ( ) . getName ( ) ) ; GroupIdentity groupIdentity = new GroupIdentity ( groupValue . getName ( ) ) ; aclService . createAcl ( groupIdentity ) ; groupValue . getRoles ( ) . ... | Grants default permissions on the root package and group to the roles of the group |
41,168 | public Fetch field ( String field , Fetch fetch ) { attrFetchMap . put ( field , fetch ) ; return this ; } | Updates this fetch adding a single field . If the field is a reference the reference will be fetched with the Fetch that is provided . |
41,169 | 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 ( ) ) { all... | Get readable genome entities |
41,170 | 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 ... | Retrieves an entity from the cache or the underlying repository . |
41,171 | 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 , repository . getEntityType ( ) ... | Retrieves a list of entities from the cache . If the cache doesn t yet exist will create the cache . |
41,172 | 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 . getEntit... | Creates a new Entity cache |
41,173 | private void removeMappedByAttributes ( Map < String , EntityType > resolvedEntityTypes ) { resolvedEntityTypes . values ( ) . stream ( ) . flatMap ( EntityType :: getMappedByAttributes ) . filter ( attribute -> resolvedEntityTypes . containsKey ( attribute . getEntity ( ) . getId ( ) ) ) . forEach ( attribute -> dataS... | Removes the mappedBy attributes of each OneToMany pair in the supplied map of EntityTypes |
41,174 | < T > T call ( Job < T > job , Progress progress , JobExecutionContext jobExecutionContext ) { return runWithContext ( jobExecutionContext , ( ) -> tryCall ( job , progress ) ) ; } | Executes a job in the calling thread . |
41,175 | 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 = removeIllega... | A helper function to calculate the best NGram score from a list ontologyTerm synonyms |
41,176 | 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 ; } | Generate base64 authentication based on username and password . |
41,177 | 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 ) )... | Execute R script using OpenCPU |
41,178 | private String executeScriptGetResponseRequest ( String openCpuSessionKey , String scriptOutputFilename , String outputPathname ) throws IOException { String responseValue ; if ( scriptOutputFilename != null ) { executeScriptGetFileRequest ( openCpuSessionKey , scriptOutputFilename , outputPathname ) ; responseValue = ... | Retrieve R script response using OpenCPU |
41,179 | private void executeScriptGetFileRequest ( String openCpuSessionKey , String scriptOutputFilename , String outputPathname ) throws IOException { URI scriptGetValueResponseUri = getScriptGetFileResponseUri ( openCpuSessionKey , scriptOutputFilename ) ; HttpGet httpGet = new HttpGet ( scriptGetValueResponseUri ) ; try ( ... | Retrieve R script file response using OpenCPU and write to file |
41,180 | private String executeScriptGetValueRequest ( String openCpuSessionKey ) throws IOException { URI scriptGetValueResponseUri = getScriptGetValueResponseUri ( openCpuSessionKey ) ; HttpGet httpGet = new HttpGet ( scriptGetValueResponseUri ) ; String responseValue ; try ( CloseableHttpResponse response = httpClient . exec... | Retrieve and return R script STDOUT response using OpenCPU |
41,181 | public ViewResolver viewResolver ( ) { FreeMarkerViewResolver resolver = new FreeMarkerViewResolver ( ) ; resolver . setCache ( true ) ; resolver . setSuffix ( ".ftl" ) ; resolver . setContentType ( "text/html;charset=UTF-8" ) ; return resolver ; } | Enable spring freemarker viewresolver . All freemarker template names should end with . ftl |
41,182 | public FreeMarkerConfigurer freeMarkerConfigurer ( ) { FreeMarkerConfigurer result = new FreeMarkerConfigurer ( ) { protected void postProcessConfiguration ( Configuration config ) { config . setObjectWrapper ( new MolgenisFreemarkerObjectWrapper ( VERSION_2_3_23 ) ) ; } protected void postProcessTemplateLoaders ( List... | Configure freemarker . All freemarker templates should be on the classpath in a package called freemarker |
41,183 | 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 ; } | Returns the corresponding attribute name for a VCF info field key |
41,184 | private static Set < String > determineVcfInfoFlagFields ( VcfMeta vcfMeta ) { return stream ( vcfMeta . getInfoMeta ( ) ) . filter ( vcfInfoMeta -> vcfInfoMeta . getType ( ) . equals ( VcfMetaInfo . Type . FLAG ) ) . map ( VcfMetaInfo :: getId ) . collect ( toSet ( ) ) ; } | Returns a set of all possible VCF info fields of type Flag |
41,185 | private static Map < String , String > createInfoFieldKeyToAttrNameMap ( VcfMeta vcfMeta , String entityTypeId ) { Map < String , String > infoFieldIdToAttrNameMap = newHashMapWithExpectedSize ( size ( vcfMeta . getInfoMeta ( ) ) ) ; for ( VcfMetaInfo info : vcfMeta . getInfoMeta ( ) ) { String postFix = "" ; switch ( ... | Returns a mapping of VCF info field keys to MOLGENIS attribute names |
41,186 | 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 ( )... | Retrieves an entity from the L1 cache based on a combination of entity name and entity id . |
41,187 | 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 ) ; } } | Puts an entity into the L1 cache if the cache exists for the current thread . |
41,188 | 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 ( ) ) ; Map ... | Looks up the Entities for a List of entity IDs . Those present in the cache are returned from cache . The missing ones are retrieved from the decoratedRepository . |
41,189 | private void evictBiDiReferencedEntityTypes ( ) { getEntityType ( ) . getMappedByAttributes ( ) . map ( Attribute :: getRefEntity ) . forEach ( l1Cache :: evictAll ) ; getEntityType ( ) . getInversedByAttributes ( ) . map ( Attribute :: getRefEntity ) . forEach ( l1Cache :: evictAll ) ; } | Evict all entries for entity types referred to by this entity type through a bidirectional relation . |
41,190 | private void evictBiDiReferencedEntities ( Entity entity ) { Stream < EntityKey > backreffingEntities = getEntityType ( ) . getMappedByAttributes ( ) . flatMap ( mappedByAttr -> Streams . stream ( entity . getEntities ( mappedByAttr . getName ( ) ) ) ) . map ( EntityKey :: create ) ; Stream < EntityKey > manyToOneEntit... | Evict all entity instances referenced by this entity instance through a bidirectional relation . |
41,191 | public Hits < ExplainedAttribute > findAttributes ( EntityType sourceEntityType , Set < String > queryTerms , Collection < OntologyTerm > ontologyTerms ) { Iterable < String > attributeIdentifiers = semanticSearchServiceHelper . getAttributeIdentifiers ( sourceEntityType ) ; QueryRule disMaxQueryRule = semanticSearchSe... | public for testability |
41,192 | 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 . isNo... | A helper function to create a list of queryTerms based on the information from the targetAttribute as well as user defined searchTerms . If the user defined searchTerms exist the targetAttribute information will not be used . |
41,193 | public Set < ExplainedQueryString > convertAttributeToExplainedAttribute ( Attribute attribute , Map < String , String > collectExpandedQueryMap , Query < Entity > query ) { EntityType attributeMetaData = dataService . getEntityType ( ATTRIBUTE_META_DATA ) ; String attributeID = attribute . getIdentifier ( ) ; Explanat... | A helper function to explain each of the matched attributes returned by the explain - API |
41,194 | 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 = ne... | Resolves package fullNames by looping through all the packages and their parents |
41,195 | public int getOntologyTermDistance ( OntologyTerm ontologyTerm1 , OntologyTerm ontologyTerm2 ) { String nodePath1 = getOntologyTermNodePath ( ontologyTerm1 ) ; String nodePath2 = getOntologyTermNodePath ( ontologyTerm2 ) ; if ( StringUtils . isEmpty ( nodePath1 ) ) { throw new MolgenisDataAccessException ( "The nodePat... | Calculate the distance between any two ontology terms in the ontology tree structure by calculating the difference in nodePaths . |
41,196 | 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 , ontologyTerm . getI... | Retrieve all descendant ontology terms |
41,197 | 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 ( cell ) ) { try { LocaleUtil . setUse... | Gets a cell value as String and process the value with the given cellProcessors |
41,198 | private static String formatUTCDateAsLocalDateTime ( Date javaDate ) { LocalDateTime localDateTime = javaDate . toInstant ( ) . atZone ( UTC ) . toLocalDateTime ( ) ; return localDateTime . toString ( ) ; } | Formats parsed Date as LocalDateTime string at zone UTC to express that we don t know the timezone . |
41,199 | 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 . i... | Gets the uri which is currently visible in the browser . |
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