A B C D E F G H I J K L M N O P R S T U V W

A

addEntry(String, GafListValidationError) - Method in class org.molgenis.gaf.GafListValidationReport

addFreemarkerVariables(Map<String, Object>) - Method in class org.molgenis.app.WebAppConfig

addGlobalErrorMessage(String) - Method in class org.molgenis.gaf.GafListValidationReport

addReposToReindex(DataServiceImpl, MySqlEntityFactory) - Method in class org.molgenis.app.WebAppConfig

addUpgrades() - Method in class org.molgenis.app.WebAppConfig

ALT - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

annotationDrivenTransactionManager() - Method in class org.molgenis.DatabaseConfig

B

BackgroundController - Class in org.molgenis.app.controller

Controller that handles contact page requests

BackgroundController() - Constructor for class org.molgenis.app.controller.BackgroundController

C

CategoryParser - Class in org.molgenis.tools.compare

CategoryParser() - Constructor for class org.molgenis.tools.compare.CategoryParser

check(String, String) - Method in class org.molgenis.tools.compare.CategoryParser

check(String, String, BufferedWriter) - Method in class org.molgenis.tools.compare.Validator

checkForMultipleConsults(String, String, PrintWriter) - Method in class org.molgenis.tools.compare.IBDParser

checkIfDouble(String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

CHROM - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

cleanUp() - Method in class org.molgenis.gaf.GafListValidationReport

COLUMNS - Static variable in class org.molgenis.gaf.GafListValidator

compareDate(String, String, String, String, PrintWriter) - Method in class org.molgenis.tools.compare.IBDParser

compareRows(String, String, Entity, Entity, List<String>, BufferedWriter) - Static method in class org.molgenis.tools.compare.Validator

compareTo(GafListValidationError) - Method in class org.molgenis.gaf.GafListValidationError

configureUrlAuthorization(ExpressionUrlAuthorizationConfigurer<HttpSecurity>.ExpressionInterceptUrlRegistry) - Method in class org.molgenis.app.WebAppSecurityConfig

ContactController - Class in org.molgenis.app.controller

Controller that handles contact page requests

ContactController() - Constructor for class org.molgenis.app.controller.ContactController

convert(InputStream, OutputStream, String, String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

ConvertGidsMain - Class in org.molgenis.tools.gids.convertor

ConvertGidsMain() - Constructor for class org.molgenis.tools.gids.convertor.ConvertGidsMain

createAnonymousUserAuthorities() - Method in class org.molgenis.app.WebAppSecurityConfig

D

DatabaseConfig - Class in org.molgenis

Database configuration

DatabaseConfig() - Constructor for class org.molgenis.DatabaseConfig

dataSource() - Method in class org.molgenis.DatabaseConfig

E

emptySample() - Method in class org.molgenis.tools.gids.convertor.SampleConverter

EntitiesImporterImpl - Class in org.molgenis

EntitiesImporterImpl(FileRepositoryCollectionFactory, EntityImportService) - Constructor for class org.molgenis.EntitiesImporterImpl

EntitiesValidatorImpl - Class in org.molgenis

EntitiesValidatorImpl(FileRepositoryCollectionFactory) - Constructor for class org.molgenis.EntitiesValidatorImpl

F

freeMarkerConfigurer() - Method in class org.molgenis.app.WebAppConfig

G

GAFCol - Enum in org.molgenis.gaf

GafListDbSettings - Class in org.molgenis.gaf

GafListDbSettings(DataService) - Constructor for class org.molgenis.gaf.GafListDbSettings

GafListDbSettings.Meta - Class in org.molgenis.gaf

GafListFileImporterService - Class in org.molgenis.gaf

GafListFileImporterService() - Constructor for class org.molgenis.gaf.GafListFileImporterService

GafListFileRepository - Class in org.molgenis.gaf

Google spreadsheet repository that only exposes valid GAF list runs

GafListFileRepository(File, List<CellProcessor>, Character, GafListValidationReport) - Constructor for class org.molgenis.gaf.GafListFileRepository

GafListImporterController - Class in org.molgenis.gaf

GafListImporterController(GafListFileImporterService) - Constructor for class org.molgenis.gaf.GafListImporterController

GafListSettings - Interface in org.molgenis.gaf

GafListValidationError - Class in org.molgenis.gaf

GafListValidationError(int, String, String, String) - Constructor for class org.molgenis.gaf.GafListValidationError

GafListValidationReport - Class in org.molgenis.gaf

GafListValidationReport() - Constructor for class org.molgenis.gaf.GafListValidationReport

GafListValidator - Class in org.molgenis.gaf

GafListValidator() - Constructor for class org.molgenis.gaf.GafListValidator

GeneticRepositoryMergerController - Class in org.molgenis.merge

GeneticRepositoryMergerController(RepositoryMerger, DataService) - Constructor for class org.molgenis.merge.GeneticRepositoryMergerController

getAllColumnsNames() - Static method in enum org.molgenis.gaf.GAFCol

getAllRunIds() - Method in class org.molgenis.gaf.GafListValidationReport

getBackend() - Method in class org.molgenis.app.WebAppConfig

getColName() - Method in class org.molgenis.gaf.GafListValidationError

getDataSetIdentifier() - Method in class org.molgenis.gaf.GafListValidationReport

getDataSetName() - Method in class org.molgenis.gaf.GafListValidationReport

getDateType() - Method in class org.molgenis.tools.gids.convertor.MakeObservableFeature

getDescription() - Method in class org.molgenis.tools.gids.convertor.MakeObservableFeature

getEntitiesImportable() - Method in class org.molgenis.EntitiesImporterImpl

getEntityName() - Method in class org.molgenis.gaf.GafListDbSettings

getEntityName() - Method in interface org.molgenis.gaf.GafListSettings

getEntries() - Method in class org.molgenis.gaf.GafListValidationReport

getExample(String) - Method in class org.molgenis.gaf.GafListDbSettings

getExample(String) - Method in interface org.molgenis.gaf.GafListSettings

getFeatures_Identifier() - Method in class org.molgenis.tools.gids.convertor.MakeEntityNameAndIdentifier

getHash() - Method in class org.molgenis.tools.compare.ValidationFile

getIdentifier() - Method in class org.molgenis.tools.gids.convertor.MakeEntityNameAndIdentifier

getIdentifier() - Method in class org.molgenis.tools.gids.convertor.MakeObservableFeature

getIdentifier() - Method in class org.molgenis.tools.gids.convertor.MakeObservationTarget

getInvalidRunIds() - Method in class org.molgenis.gaf.GafListValidationReport

getListOfHeaders() - Method in class org.molgenis.tools.compare.ValidationFile

getMsg() - Method in class org.molgenis.gaf.GafListValidationError

getName() - Method in class org.molgenis.tools.gids.convertor.MakeEntityNameAndIdentifier

getName() - Method in class org.molgenis.tools.gids.convertor.MakeObservableFeature

getName() - Method in class org.molgenis.tools.gids.convertor.MakeObservationTarget

getRegExpPattern(String) - Method in class org.molgenis.gaf.GafListDbSettings

getRegExpPattern(String) - Method in interface org.molgenis.gaf.GafListSettings

getRow() - Method in class org.molgenis.gaf.GafListValidationError

getTempFile() - Method in class org.molgenis.gaf.GafListValidationReport

getTempFileName() - Method in class org.molgenis.gaf.GafListValidationReport

getTempFileOriginalName() - Method in class org.molgenis.gaf.GafListValidationReport

getValidationGlobalErrorMessages() - Method in class org.molgenis.gaf.GafListValidationReport

getValidRunIds() - Method in class org.molgenis.gaf.GafListValidationReport

getValue() - Method in class org.molgenis.gaf.GafListValidationError

H

handleRuntimeException(RuntimeException) - Method in class org.molgenis.merge.GeneticRepositoryMergerController

handleThrowable(Throwable) - Method in class org.molgenis.gaf.GafListImporterController

hasErrors(String) - Method in class org.molgenis.gaf.GafListValidationReport

hasGlobalErrors() - Method in class org.molgenis.gaf.GafListValidationReport

hasRunIdsErrors() - Method in class org.molgenis.gaf.GafListValidationReport

HomeController - Class in org.molgenis.app.controller

Controller that handles home page requests

HomeController() - Constructor for class org.molgenis.app.controller.HomeController

I

IBDParser - Class in org.molgenis.tools.compare

IBDParser() - Constructor for class org.molgenis.tools.compare.IBDParser

ID - Static variable in class org.molgenis.app.controller.BackgroundController

ID - Static variable in class org.molgenis.app.controller.ContactController

ID - Static variable in class org.molgenis.app.controller.HomeController

ID - Static variable in class org.molgenis.app.controller.NewsController

ID - Static variable in class org.molgenis.app.controller.ReferencesController

ID - Static variable in class org.molgenis.gaf.GafListImporterController

ID - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

importGAFList(GafListValidationReport, String) - Method in class org.molgenis.gaf.GafListFileImporterService

importGAFList(Model) - Method in class org.molgenis.gaf.GafListImporterController

importGAFList(HttpServletRequest, Model) - Method in class org.molgenis.gaf.GafListImporterController

init() - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

init(Model) - Method in class org.molgenis.gaf.GafListImporterController

init(Model) - Method in class org.molgenis.merge.GeneticRepositoryMergerController

isDatabasePopulated() - Method in class org.molgenis.app.WebAppDatabasePopulatorServiceImpl

iterator() - Method in class org.molgenis.gaf.GafListFileRepository

J

JDBCMetaDatabase - Class in org.molgenis

This class is an in memory representation of the contents of your *_db.xml file Utility of this class is to allow for dynamic querying and/or user interfacing for example within a query tool or a security module.

JDBCMetaDatabase() - Constructor for class org.molgenis.JDBCMetaDatabase

jpaDialect() - Method in class org.molgenis.DatabaseConfig

JpaRepositoryCollection - Class in org.molgenis.data.jpa

JpaRepositoryCollection(SearchService) - Constructor for class org.molgenis.data.jpa.JpaRepositoryCollection

jpaVendorAdapter() - Method in class org.molgenis.DatabaseConfig

K

KEY_GAF_LIST_DATASET_IDENTIFIER - Static variable in class org.molgenis.gaf.GafListImporterController

KEY_GAF_LIST_PROTOCOL_NAME - Static variable in class org.molgenis.gaf.GafListImporterController

L

localEntityManagerFactoryBean() - Method in class org.molgenis.DatabaseConfig

M

main(String[]) - Static method in class org.molgenis.tools.compare.CategoryParser

main(String[]) - Static method in class org.molgenis.tools.compare.IBDParser

main(String[]) - Static method in class org.molgenis.tools.compare.Validator

main(String[]) - Static method in class org.molgenis.tools.gids.convertor.ConvertGidsMain

MakeEntityNameAndIdentifier - Class in org.molgenis.tools.gids.convertor

MakeEntityNameAndIdentifier(String, String) - Constructor for class org.molgenis.tools.gids.convertor.MakeEntityNameAndIdentifier

MakeEntityNameAndIdentifier(String, String, String) - Constructor for class org.molgenis.tools.gids.convertor.MakeEntityNameAndIdentifier

MakeObservableFeature - Class in org.molgenis.tools.gids.convertor

MakeObservableFeature(String, String, String, String) - Constructor for class org.molgenis.tools.gids.convertor.MakeObservableFeature

MakeObservationTarget - Class in org.molgenis.tools.gids.convertor

MakeObservationTarget(String, String) - Constructor for class org.molgenis.tools.gids.convertor.MakeObservationTarget

merge(String, String[]) - Method in class org.molgenis.merge.GeneticRepositoryMergerController

Meta() - Constructor for class org.molgenis.gaf.GafListDbSettings.Meta

mkmetadataExcelFile(ArrayList<String>) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

mkMetadataFileDataSet(WritableFactory, String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

mkMetadataFileObservableFeature(WritableFactory, String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

mkMetadataFileProtocol(WritableFactory, String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

molgenisAccessDecisionVoter() - Method in class org.molgenis.app.WebAppSecurityConfig

N

NAME - Static variable in class org.molgenis.data.jpa.JpaRepositoryCollection

NewsController - Class in org.molgenis.app.controller

Controller that handles news page requests

NewsController() - Constructor for class org.molgenis.app.controller.NewsController

O

onStartup(ServletContext) - Method in class org.molgenis.app.WebAppInitializer

org.molgenis - package org.molgenis

org.molgenis.app - package org.molgenis.app

org.molgenis.app.controller - package org.molgenis.app.controller

org.molgenis.data.jpa - package org.molgenis.data.jpa

org.molgenis.gaf - package org.molgenis.gaf

org.molgenis.merge - package org.molgenis.merge

org.molgenis.tools.compare - package org.molgenis.tools.compare

org.molgenis.tools.gids.convertor - package org.molgenis.tools.gids.convertor

P

populateDatabase() - Method in class org.molgenis.app.WebAppDatabasePopulatorServiceImpl

populateStatusImportedRuns() - Method in class org.molgenis.gaf.GafListValidationReport

POS - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

printAsList(Map<String, List<String>>) - Method in class org.molgenis.tools.compare.CategoryParser

printForCategoryTab(Map<String, List<String>>) - Method in class org.molgenis.tools.compare.CategoryParser

R

readFile(Repository, String, String) - Method in class org.molgenis.tools.compare.ValidationFile

REF - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

ReferencesController - Class in org.molgenis.app.controller

Controller that handles references page requests

ReferencesController() - Constructor for class org.molgenis.app.controller.ReferencesController

roleHierarchy() - Method in class org.molgenis.app.WebAppSecurityConfig

S

SampleConverter - Class in org.molgenis.tools.gids.convertor

SampleConverter() - Constructor for class org.molgenis.tools.gids.convertor.SampleConverter

setDataSetIdentifier(String) - Method in class org.molgenis.gaf.GafListValidationReport

setDataSetName(String) - Method in class org.molgenis.gaf.GafListValidationReport

setFreemarkerTemplateRepository(Repository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setGroupAuthorityRepository(Repository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setImportRunRepository(Repository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setMolgenisGroupMemberRepository(Repository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setMolgenisGroupRepository(Repository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setMolgenisTokenRepository(Repository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setMolgenisUserRepository(Repository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setRuntimePropertyRepository(Repository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setTempFile(File) - Method in class org.molgenis.gaf.GafListValidationReport

setTempFileName(String) - Method in class org.molgenis.gaf.GafListValidationReport

setTempFileOriginalName(String) - Method in class org.molgenis.gaf.GafListValidationReport

setUserAuthorityRepository(Repository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

T

toString() - Method in enum org.molgenis.gaf.GAFCol

toString() - Method in class org.molgenis.gaf.GafListValidationError

toString() - Method in class org.molgenis.gaf.GafListValidationReport

toStringHtml() - Method in class org.molgenis.gaf.GafListValidationError

toStringHtml() - Method in class org.molgenis.gaf.GafListValidationReport

transactionManager() - Method in class org.molgenis.DatabaseConfig

U

uploadCsvFile(MultipartFile) - Method in class org.molgenis.gaf.GafListValidationReport

URI - Static variable in class org.molgenis.app.controller.BackgroundController

URI - Static variable in class org.molgenis.app.controller.ContactController

URI - Static variable in class org.molgenis.app.controller.HomeController

URI - Static variable in class org.molgenis.app.controller.NewsController

URI - Static variable in class org.molgenis.app.controller.ReferencesController

URI - Static variable in class org.molgenis.gaf.GafListImporterController

URI - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

V

validate(File) - Method in class org.molgenis.EntitiesValidatorImpl

validate(GafListValidationReport, Repository, List<String>) - Method in class org.molgenis.gaf.GafListValidator

validateGAFList(GafListValidationReport, MultipartFile) - Method in class org.molgenis.gaf.GafListFileImporterService

validateGAFList(Model) - Method in class org.molgenis.gaf.GafListImporterController

validateGAFList(HttpServletRequest, MultipartFile, Model) - Method in class org.molgenis.gaf.GafListImporterController

ValidationFile - Class in org.molgenis.tools.compare

put in a hashmap

ValidationFile() - Constructor for class org.molgenis.tools.compare.ValidationFile

Validator - Class in org.molgenis.tools.compare

This script is created to compare 2 excelfiles.

Validator() - Constructor for class org.molgenis.tools.compare.Validator

valueOf(String) - Static method in enum org.molgenis.gaf.GAFCol

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.molgenis.gaf.GAFCol

Returns an array containing the constants of this enum type, in the order they are declared.

W

WebAppConfig - Class in org.molgenis.app

WebAppConfig() - Constructor for class org.molgenis.app.WebAppConfig

WebAppDatabasePopulatorServiceImpl - Class in org.molgenis.app

WebAppDatabasePopulatorServiceImpl(DataService, MolgenisSecurityWebAppDatabasePopulatorService) - Constructor for class org.molgenis.app.WebAppDatabasePopulatorServiceImpl

WebAppInitializer - Class in org.molgenis.app

WebAppInitializer() - Constructor for class org.molgenis.app.WebAppInitializer

WebAppSecurityConfig - Class in org.molgenis.app

WebAppSecurityConfig() - Constructor for class org.molgenis.app.WebAppSecurityConfig

A B C D E F G H I J K L M N O P R S T U V W