• Example Search by API
  • Example Search by Word
  • Project Search
  • Top Packages
  • Top Classes
  • Top Methods
  • Top Projects
  • Java
  • C++
  • Python
  • Scala
  • Blog
Project: molgenis (GitHub Link)
  • molgenis-master
    • molgenis-security-core
      • src
        • main
          • resources
            • security-core_en.properties
          • java
            • org
              • molgenis
                • security
                  • acl
                    • ObjectIdentityService.java
                    • AclClassService.java
                    • MutableAclClassService.java
                  • core
                    • UserPermissionEvaluator.java
                    • PrincipalSecurityContextRegistry.java
                    • SecurityContextRegistry.java
                    • runas
                      • SystemSecurityToken.java
                      • RunAsSystemAspect.java
                      • RunnableAsSystem.java
                      • RunAsSystem.java
                    • utils
                      • SecurityUtils.java
                    • GroupValueFactory.java
                    • SecurityContextUpdateAction.java
                    • AuthenticationAuthoritiesUpdater.java
                    • PermissionSet.java
                    • PermissionRegistry.java
                    • Permission.java
                    • MolgenisPasswordEncoder.java
                    • SidUtils.java
                    • token
                      • TokenService.java
                      • UnknownTokenException.java
                    • model
                      • RoleValue.java
                      • GroupValue.java
                      • PackageValue.java
                    • MappedAuthenticatedPrincipal.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • security
                  • core
                    • runas
                      • SystemSecurityTokenTest.java
                      • RunAsSystemAspectTest.java
                    • utils
                      • SecurityUtilsTest.java
                    • PermissionRegistryTest.java
                    • GroupValueFactoryTest.java
                    • SidUtilsTest.java
                    • MolgenisPasswordEncoderTest.java
      • pom.xml
      • .gitignore
    • molgenis-data-migrate
      • src
        • main
          • resources
            • step39-createRootPackageGroups.sql
            • step34-roleMetrics.sql
            • step35-aclSystemSid.sql
            • step36-enableDataRowEdit.sql
            • step33-deferredForeignKeys.sql
            • step38-addAnonymousRole.sql
            • step40-roleSystem.sql
          • java
            • org
              • molgenis
                • data
                  • migrate
                    • bootstrap
                      • MolgenisUpgradeBootstrapper.java
                    • version
                      • Step37AddSettingsPluginToMenu.java
                      • Step38AddAnonymouseRoleToDb.java
                      • Step39CreateRootPackageGroups.java
                      • Step33UpdateForeignKeyDeferred.java
                      • Step36EnableDataRowEdit.java
                      • Step40AddRoleSystem.java
                      • Step34AddRoleMetrics.java
                      • Step35UpdateAclSystemSid.java
                      • MolgenisUpgradeServiceImpl.java
                      • MolgenisVersionService.java
                      • Step41Reindex.java
                    • framework
                      • MolgenisUpgradeService.java
                      • MolgenisUpgrade.java
        • test
          • resources
            • logback-test.xml
            • org
              • molgenis
                • data
                  • version
                    • v1_5
                      • menu-transformed.json
                      • menu.json
          • java
            • org
              • molgenis
                • data
                  • migrate
                    • version
                      • Step41ReindexTest.java
                      • MolgenisUpgradeServiceImplTest.java
                      • MolgenisVersionServiceTest.java
                      • Step40AddRoleSystemTest.java
      • pom.xml
    • molgenis-navigator
      • src
        • main
          • resources
            • templates
              • view-navigator.ftl
            • l10n
              • navigator_en.properties
              • navigator_nl.properties
          • java
            • org
              • molgenis
                • navigator
                  • SearchResourcesResponse.java
                  • NavigatorController.java
                  • NavigatorServiceImpl.java
                  • DownloadResourcesRequest.java
                  • delete
                    • job
                      • ResourceDeleteJobExecutionJobFactory.java
                      • ResourceDeleteJobExecutionMetadata.java
                      • ResourceDeleteJobExecutionFactory.java
                      • ResourceDeleteJobExecution.java
                    • ResourceDeleteService.java
                    • ResourceDeleteServiceImpl.java
                  • CopyResourcesRequest.java
                  • NavigatorService.java
                  • UpdateResourceRequest.java
                  • GetResourcesResponse.java
                  • util
                    • ResourceIdentifierUtil.java
                    • ResourceCollector.java
                    • ResourceCollection.java
                  • download
                    • DownloadResourcesRequest.java
                    • job
                      • ResourceDownloadService.java
                      • ResourceDownloadJobExecutionMetadata.java
                      • ResourceDownloadJobExecutionFactory.java
                      • ResourceDownloadJobExecution.java
                      • ResourceDownloadConfig.java
                    • exception
                      • DownloadFailedException.java
                  • Folder.java
                  • DeleteResourcesRequest.java
                  • copy
                    • job
                      • ResourceCopyJobExecutionMetadata.java
                      • ResourceCopyJobExecutionFactory.java
                      • ResourceCopyJobExecution.java
                      • ResourceCopyJobConfig.java
                    • service
                      • PackageCopier.java
                      • CopyServiceImpl.java
                      • CopyService.java
                      • LabelGenerator.java
                      • CopyState.java
                      • RelationTransformer.java
                      • EntityTypeMetadataCopier.java
                      • PretendingEntity.java
                      • EntityTypeCopier.java
                    • exception
                      • RecursiveCopyException.java
                      • CopyFailedException.java
                      • UnknownCopyFailedException.java
                    • CopyResourceRequest.java
                  • MoveResourcesRequest.java
                  • model
                    • Resource.java
                    • ResourceType.java
                    • ResourceIdentifier.java
                  • NavigatorI18nConfig.java
        • test
          • java
            • org
              • molgenis
                • navigator
                  • delete
                    • ResourceDeleteServiceImplTest.java
                    • job
                      • ResourceDeleteJobExecutionTest.java
                      • ResourceDeleteJobExecutionFactoryTest.java
                  • NavigatorServiceImplTest.java
                  • util
                    • ResourceIdentifierUtilTest.java
                    • ResourceCollectorTest.java
                  • download
                    • job
                      • DownloadServiceTest.java
                      • ResourceDownloadJobExecutionFactoryTest.java
                      • ResourceDownloadJobExecutionTest.java
                    • exception
                      • DownloadFailedExceptionTest.java
                  • copy
                    • job
                      • ResourceCopyJobExecutionTest.java
                      • ResourceCopyJobExecutionFactoryTest.java
                    • service
                      • CopyTestUtils.java
                      • EntityTypeMetadataCopierTest.java
                      • LabelGeneratorTest.java
                      • PretendingEntityTest.java
                      • PackageCopierTest.java
                      • RelationTransformerTest.java
                      • EntityTypeCopierTest.java
                      • CopyServiceImplTest.java
                    • exception
                      • RecursiveCopyExceptionTest.java
                      • UnknownCopyExceptionTest.java
                  • NavigatorControllerTest.java
      • pom.xml
    • .github
      • PULL_REQUEST_TEMPLATE.md
      • ISSUE_TEMPLATE.md
    • molgenis-data-security
      • src
        • main
          • resources
            • l10n
              • data-security_en.properties
              • data-security_nl.properties
          • java
            • org
              • molgenis
                • data
                  • security
                    • SessionSecurityContextUpdater.java
                    • SessionSecurityContextUpdaterImpl.java
                    • PackageIdentity.java
                    • NoWritablePackageException.java
                    • user
                      • UserService.java
                      • UnknownUserException.java
                      • InvalidEmailAddressException.java
                      • UserServiceImpl.java
                    • EntityTypeIdentity.java
                    • GroupIdentity.java
                    • PackagePermission.java
                    • SystemEntityTypeRegistryImpl.java
                    • EntityIdentity.java
                    • config
                      • DataSecurityConfig.java
                    • DataserviceRoleHierarchy.java
                    • exception
                      • SuperUserPermissionsException.java
                      • PackagePermissionDeniedException.java
                      • SystemMetadataModificationException.java
                      • PermissionNotSuitableException.java
                      • CircularRoleHierarchyException.java
                      • GroupNameNotAvailableException.java
                      • EntityTypePermissionDeniedException.java
                      • InsufficientPermissionsException.java
                      • AclAlreadyExistsException.java
                      • PermissionDeniedException.java
                      • UnknownTypeException.java
                      • IsAlreadyMemberException.java
                      • UnknownAceException.java
                      • NullPackageNotSuException.java
                      • ReadPermissionDeniedException.java
                      • InvalidTypeIdException.java
                      • AclClassAlreadyExistsException.java
                      • InsufficientInheritancePermissionsException.java
                      • NotAValidGroupRoleException.java
                      • ParentPackagePermissionDeniedException.java
                      • UnknownRoleException.java
                      • SidPermissionException.java
                      • DuplicatePermissionException.java
                      • EntityPermissionDeniedException.java
                      • GroupPackageDowngradeException.java
                      • SystemRlsModificationException.java
                      • AclNotFoundException.java
                      • NullParentPackageNotSuException.java
                      • GroupPermissionDeniedException.java
                    • aggregation
                      • AggregateAnonymizerImpl.java
                      • AggregateAnonymizer.java
                      • AnonymizedAggregateResult.java
                      • AggregateAnonymizerRepositoryDecorator.java
                    • EntityTypePermission.java
                    • EntityIdentityUtils.java
                    • PackagePermissionUtils.java
                    • RepositorySecurityDecorator.java
                    • permission
                      • inheritance
                        • PermissionInheritanceResolver.java
                        • model
                          • InheritedUserPermissionsResult.java
                          • InheritedPermissionsResult.java
                          • InheritedAclPermissionsResult.java
                      • PermissionsConfig.java
                      • RoleMembershipServiceImpl.java
                      • UserRoleTools.java
                      • DataPermissionConfig.java
                      • PermissionSystemService.java
                      • EntityHelper.java
                      • PermissionServiceDecorator.java
                      • PermissionServiceImpl.java
                      • RoleMembershipService.java
                      • model
                        • LabelledObject.java
                        • LabelledObjectIdentity.java
                        • LabelledPermission.java
                        • Permission.java
                        • LabelledType.java
                      • PermissionService.java
                      • PermissionSetUtils.java
                    • auth
                      • Token.java
                      • UserFactory.java
                      • RoleMetadata.java
                      • UserRepositoryDecoratorFactory.java
                      • MembershipInvitationMetadata.java
                      • RoleMembershipDecorator.java
                      • GroupPermissionService.java
                      • PasswordResetTokenMetadata.java
                      • RoleMembershipValidationException.java
                      • PasswordResetToken.java
                      • UserValidator.java
                      • GroupFactory.java
                      • UserRepositoryDecorator.java
                      • RoleMembershipRepositoryDecoratorFactory.java
                      • TokenFactory.java
                      • SecurityPackage.java
                      • RoleMembershipFactory.java
                      • RoleMembership.java
                      • RoleRepositoryDecoratorFactory.java
                      • GroupPackageService.java
                      • Role.java
                      • UserSuModificationException.java
                      • RoleService.java
                      • UserMetadata.java
                      • CachedRoleHierarchyImpl.java
                      • GroupMetadata.java
                      • GroupPermission.java
                      • MembershipInvitation.java
                      • TokenMetadata.java
                      • RoleRepositoryDecorator.java
                      • GroupService.java
                      • CachedRoleHierarchy.java
                      • User.java
                      • MembershipInvitationFactory.java
                      • PasswordResetTokenFactory.java
                      • RoleFactory.java
                      • GroupPackageRepositoryDecorator.java
                      • UserRepositoryValidationDecorator.java
                      • RoleMembershipValidatorImpl.java
                      • RoleMembershipValidator.java
                      • Group.java
                      • RoleMembershipMetadata.java
                    • owned
                      • AbstractRowLevelSecurityRepositoryDecorator.java
                      • OwnershipDecorator.java
                      • OwnershipDecoratorFactory.java
                      • RowLevelSecurityRepositoryDecoratorFactory.java
                      • RowLevelSecurityRepositoryDecorator.java
                    • EntityPermission.java
                    • GroupPackageServiceImpl.java
                    • meta
                      • EntityTypeRepositorySecurityDecorator.java
                      • PackageRepositorySecurityDecorator.java
                      • AttributeRepositorySecurityDecorator.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • data
                  • security
                    • user
                      • UnknownUserExceptionTest.java
                      • InvalidEmailAddressExceptionTest.java
                      • UserServiceImplTest.java
                    • PackagePermissionTest.java
                    • SystemEntityTypeRegistryImplTest.java
                    • RepositorySecurityDecoratorTest.java
                    • EntityIdentityUtilsTest.java
                    • SessionSecurityContextUpdaterImplTest.java
                    • config
                      • UserTestConfig.java
                      • SecurityTestConfig.java
                    • exception
                      • CircularRoleHierarchyExceptionTest.java
                      • GroupPackageDowngradeExceptionTest.java
                      • PermissionNotSuitableExceptionTest.java
                      • UpdatePermissionDeniedExceptionTest.java
                      • SidPermissionExceptionTest.java
                      • UnknownTypeExceptionTest.java
                      • AclNotFoundExceptionTest.java
                      • InvalidTypeIdExceptionTest.java
                      • AclAlreadyExistsExceptionTest.java
                      • InsufficientInheritancePermissionsExceptionTest.java
                      • SystemRlsModificationExceptionTest.java
                      • SuperUserPermissionsExceptionTest.java
                      • AclClassAlreadyExistsExceptionTest.java
                      • DuplicatePermissionExceptionTest.java
                      • UnknownAceExceptionTest.java
                      • ReadPermissionDeniedExceptionTest.java
                    • aggregation
                      • AggregateAnonymizerRepositoryDecoratorTest.java
                      • AggregateAnonymizerImplTest.java
                    • PackagePermissionUtilsTest.java
                    • DataserviceRoleHierarchyTest.java
                    • permission
                      • inheritance
                        • PermissionInheritanceResolverTest.java
                        • InheritanceTestUtils.java
                      • EntityHelperTest.java
                      • UserRoleToolsTest.java
                      • PermissionSetUtilsTest.java
                      • RoleMembershipServiceImplTest.java
                      • PermissionTestUtils.java
                      • PermissionServiceDecoratorTest.java
                      • PermissionServiceImplTest.java
                    • auth
                      • MembershipInvitationTest.java
                      • UserRepositoryValidationDecoratorTest.java
                      • UserRepositoryDecoratorTest.java
                      • GroupFactoryTest.java
                      • MembershipInvitationFactoryTest.java
                      • UserTest.java
                      • RoleRepositoryDecoratorTest.java
                      • RoleMembershipFactoryTest.java
                      • CachedRoleHierarchyImplTest.java
                      • TokenFactoryTest.java
                      • RoleMembershipValidatorImplTest.java
                      • UserValidatorTest.java
                      • RoleTest.java
                      • RoleRepositoryDecoratorFactoryTest.java
                      • GroupServiceTest.java
                      • RoleFactoryTest.java
                      • UserSuModificationExceptionTest.java
                      • RoleMembershipDecoratorTest.java
                      • GroupPermissionServiceTest.java
                      • UserFactoryTest.java
                      • PasswordResetTokenFactoryTest.java
                      • RoleMembershipTest.java
                      • PasswordResetTokenTest.java
                      • TokenTest.java
                      • RoleMembershipValidationExceptionTest.java
                      • GroupTest.java
                      • GroupPackageRepositoryDecoratorTest.java
                    • owned
                      • OwnershipDecoratorTest.java
                      • RowLevelSecurityRepositoryDecoratorFactoryTest.java
                      • RowLevelSecurityRepositoryDecoratorTest.java
                    • GroupPackageServiceImplTest.java
                    • meta
                      • PackageRepositorySecurityDecoratorTest.java
                      • EntityTypeRepositorySecurityDecoratorTest.java
                      • AttributeRepositorySecurityDecoratorTest.java
      • pom.xml
    • molgenis-metadata-manager
      • src
        • main
          • resources
            • templates
              • view-metadata-manager.ftl
            • l10n
              • metadata-manager_en.properties
              • metadata-manager_nl.properties
          • java
            • org
              • molgenis
                • metadata
                  • manager
                    • config
                      • MetadataManagerConfig.java
                    • service
                      • MetadataManagerServiceImpl.java
                      • MetadataManagerService.java
                    • model
                      • EditorEntityTypeResponse.java
                      • EditorSort.java
                      • EditorTagIdentifier.java
                      • EditorAttributeIdentifier.java
                      • EditorEntityTypeIdentifier.java
                      • EditorAttribute.java
                      • EditorOrder.java
                      • EditorEntityType.java
                      • EditorEntityTypeParent.java
                      • EditorPackageIdentifier.java
                      • EditorAttributeResponse.java
                    • mapper
                      • AttributeReferenceMapper.java
                      • EntityTypeMapper.java
                      • AttributeMapper.java
                      • SortMapper.java
                      • EntityTypeReferenceMapper.java
                      • TagMapper.java
                      • EntityTypeParentMapper.java
                      • PackageMapper.java
                    • controller
                      • MetadataManagerController.java
        • test
          • java
            • org
              • molgenis
                • metadata
                  • manager
                    • service
                      • MetadataManagerServiceTest.java
                    • mapper
                      • EntityTypeParentMapperTest.java
                      • EntityTypeReferenceMapperTest.java
                      • PackageMapperTest.java
                      • EntityTypeMapperTest.java
                      • AttributeReferenceMapperTest.java
                      • TagMapperTest.java
                      • AttributeMapperTest.java
                      • SortMapperTest.java
                    • controller
                      • MetadataManagerControllerTest.java
      • pom.xml
    • .gitbook.yaml
    • molgenis-api-tests
      • src
        • test
          • resources
            • logback-test.xml
            • home
              • molgenis-server.properties
            • RestControllerV2_CopyEMX.xlsx
            • OneClickImport_complex-valid.csv
            • testGetL10nProperties_response.properties
            • beacon_set.vcf
            • tomcat
              • mail.xml
            • RestControllerV1_API_DeleteEMX.xlsx
            • RestControllerV2_API_TestEMX.xlsx
            • RestControllerV1_API_FileEMX.xlsx
            • OneClickImport_complex-valid.xlsx
            • createEntitiesv2.json
            • RestControllerV2_DeleteEMX.xlsx
            • RestControllerV1_TestEMX.xlsx
            • updateEntitiesv2.json
            • testRetrieveEntityCollection_response.csv
            • RestControllerV2_TestEMX.xlsx
            • org
              • molgenis
                • api
                  • tests
                    • search
                      • search_servers.tsv
                      • search_mutations-cases.tsv
                      • search_servers-cases.tsv
                      • attributes.tsv
                      • search_mutations.tsv
                      • tags.tsv
                      • packages.tsv
                      • entities.tsv
                      • search_disease_types-cases.tsv
                    • metadata
                      • v3
                        • partialUpdateMetadataEntityTypeMyStrings.json
                        • createMetadataEntityTypeMyDataset.json
                        • createRetrieveMetadataEntityTypeAttribute.json
                        • createMetadataEntityTypeAttribute.json
                        • partialUpdateRetrieveMetadataEntityTypeAttribute.json
                        • updateRetrieveMetadataEntityTypeAttribute.json
                        • retrieveMetadataPartialUpdateEntityType.json
                        • updateMetadataEntityTypeAttribute.json
                        • createMetadataEntityTypeMyStrings.json
                        • metadata_api_v3_emx.xlsx
                        • createMetadataEntityTypeMyNumbers.json
                        • createMetadataEntityTypeMyOneToMany.json
                        • updateRetrieveMetadataEntityTypeMyNumbers.json
                        • createMetadataEntityTypeIdentifiable.json
                        • createMetadataEntityTypeDescribable.json
                        • updateMetadataEntityTypeMyNumbers.json
                        • retrieveMetadataEntityTypeAttributes.json
                        • retrieveMetadata.json
                        • retrieveMetadataEntityType.json
                        • partialUpdateMetadataEntityTypeAttribute.json
                        • retrieveMetadataEntityTypeAttribute.json
                    • identities
                      • roleResponse.json
                      • V3Role2Response.json
                      • V3Role3Response.json
                      • V3RoleResponse.json
                      • members3Response.json
                      • members1Response.json
                      • members2Response.json
                    • data
                      • v3
                        • retrieveResource.json
                        • retrieveResourceCollectionInvalidInput.json
                        • deleteResourceCollection.json
                        • retrieveResourceCollectionSortQuery.json
                        • retrieveResourceCollectionFilterExpand.json
                        • retrieveSubResourceCollection.json
                        • data_api_v3_emx.xlsx
                        • retrieveResourceCollection.json
                        • updateResource.json
                        • deleteResourceCollectionQuery.json
                    • oneclickimporter
                      • users.json
                    • upload
                      • 123-test-groep_ID-TestMeta.json
                      • 123-test-group.xlsx
                      • 123-test-groep_ID-Test-RefData.json
            • Permissions_TestEMX.xlsx
            • RestControllerV1_API_TestEMX.xlsx
          • java
            • org
              • molgenis
                • api
                  • tests
                    • utils
                      • RestTestUtils.java
                      • JobUtils.java
                    • search
                      • SearchAPIIT.java
                    • metadata
                      • v3
                        • MetadataApiControllerIT.java
                    • identities
                      • IdentitiesApiControllerIT.java
                    • ForwardedHeaderAPIIT.java
                    • twofactor
                      • TwoFactorAuthenticationAPIIT.java
                    • importpublicdata
                      • ImportPublicDataIT.java
                    • AbstractApiTest.java
                    • data
                      • v3
                        • EntityControllerIT.java
                    • oneclickimporter
                      • OneClickImporterControllerAPIIT.java
                    • permissions
                      • PermissionAPIIT.java
                    • beacon
                      • BeaconAPIIT.java
                    • rest
                      • v2
                        • RestControllerV2APIIT.java
                        • RestControllerV2IT.java
                      • v1
                        • RestControllerIT.java
                        • RestControllerV1APIIT.java
                    • AbstractApiTests.java
                    • upload
                      • ImportIT.java
      • env_import_public_data_tests.bash
      • images
      • pom.xml
      • env_import_public_data_tests.bat
      • README.md
    • .ci
      • services
        • install-minio-6.sh
      • jobs
        • api-tests.sh
        • integration-tests.sh
    • molgenis-genomebrowser
      • src
        • main
          • resources
            • js
            • css
              • dalliance.css
          • java
            • org
              • molgenis
                • genomebrowser
                  • GenomeBrowserTrack.java
                  • service
                    • GenomeBrowserService.java
                  • meta
                    • GenomeBrowserAttributes.java
                    • GenomeBrowserSettingsFactory.java
                    • GenomeBrowserAttributesMetadata.java
                    • GenomeBrowserPackage.java
                    • GenomeBrowserAttributesFactory.java
                    • GenomeBrowserSettingsMetadata.java
                    • GenomeBrowserSettings.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • genomebrowser
                  • GenomeBrowserTrackTest.java
                  • service
                    • GenomeBrowserServiceTest.java
                  • meta
                    • GenomeBrowserSettingsFactoryTest.java
                    • GenomeBrowserAttributesFactoryTest.java
                    • GenomeBrowserAttributesTest.java
                    • GenomeBrowserSettingsTest.java
      • pom.xml
      • .gitignore
    • molgenis-api-metadata
      • src
        • main
          • resources
            • l10n
              • api-metadata_en.properties
          • java
            • org
              • molgenis
                • api
                  • metadata
                    • v3
                      • EntityTypeRequestMapper.java
                      • I18nValueMapper.java
                      • Attributes.java
                      • AttributeResponseMapper.java
                      • EntityTypeResponseMapper.java
                      • MetadataApiJobServiceImpl.java
                      • EntityTypeResponseMapperImpl.java
                      • job
                        • EntityTypeSerializer.java
                        • EntityTypeSerializerImpl.java
                        • MetadataDeleteConfig.java
                        • MetadataDeleteJobExecutionFactory.java
                        • MetadataUpsertConfig.java
                        • MetadataUpsertJobExecutionFactory.java
                        • MetadataUpsertJobExecutionMetadata.java
                        • SerializableAttribute.java
                        • MetadataUpsertJobExecution.java
                        • MetadataDeleteJobExecution.java
                        • SerializableEntityType.java
                        • MetadataDeleteJobExecutionMetadata.java
                      • MetadataApiController.java
                      • MetadataApiConfig.java
                      • exception
                        • InvalidKeyException.java
                        • IdModificationException.java
                        • EmptyAttributesException.java
                        • UnsupportedFieldException.java
                        • UnknownLookupAttributesException.java
                        • ReadOnlyFieldException.java
                      • EntityTypes.java
                      • AttributeResponseMapperImpl.java
                      • AttributeRequestMapperImpl.java
                      • MetadataUtils.java
                      • EntityTypeRequestMapperImpl.java
                      • EntityTypeCollection.java
                      • MetadataApiJobService.java
                      • ApiMetadataL10nConfig.java
                      • model
                        • EntityTypeResponseData.java
                        • ReadMetadataRequest.java
                        • DeleteAttributesRequest.java
                        • CreateEntityTypeRequest.java
                        • PackageResponse.java
                        • ReadEntityTypeRequest.java
                        • AttributeResponse.java
                        • AttributesResponse.java
                        • ReadAttributesRequest.java
                        • EntityTypeResponse.java
                        • MetadataResponseData.java
                        • Category.java
                        • AttributeResponseData.java
                        • CreateAttributeRequest.java
                        • Range.java
                        • ReadEntityTypesRequest.java
                        • I18nValue.java
                        • DeleteEntityTypesRequest.java
                        • EntityTypesResponse.java
                      • MetadataApiServiceImpl.java
                      • MetadataApiService.java
                      • AttributeRequestMapper.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • api
                  • metadata
                    • v3
                      • EntityTypeResponseMapperTest.java
                      • EntityTypeRequestMapperImplTest.java
                      • AttributeResponseMapperTest.java
                      • MetadataUtilsTest.java
                      • job
                        • MetadataUpsertJobExecutionTest.java
                        • MetadataDeleteJobExecutionTest.java
                        • EntityTypeSerializerImplTest.java
                        • MetadataUpsertJobExecutionFactoryTest.java
                        • MetadataDeleteJobExecutionFactoryTest.java
                      • MetadataApiControllerTest.java
                      • exception
                        • UnsupportedFieldExceptionTest.java
                        • EmptyAttributesExceptionTest.java
                        • IdModificationExceptionTest.java
                        • ReadOnlyFieldExceptionTest.java
                        • InvalidKeyExceptionTest.java
                        • UnknownLookupAttributesExceptionTest.java
                      • MetadataApiJobServiceImplTest.java
                      • MetadataApiServiceImplTest.java
                      • AttributeRequestMapperTest.java
      • pom.xml
    • .release
      • pull_requests_report.py
    • molgenis-metrics
      • src
        • main
          • java
            • org
              • molgenis
                • metrics
                  • MolgenisTimedAspect.java
                  • MetricsConfig.java
                  • HikariMetrics.java
                  • MeterBindersConfiguration.java
        • test
          • java
            • org
              • molgenis
                • metrics
                  • MolgenisTimedAspectTest.java
      • pom.xml
    • molgenis-searchall
      • src
        • main
          • resources
            • templates
              • view-search-all.ftl
            • l10n
              • searchall_nl.properties
              • searchall_en.properties
          • java
            • org
              • molgenis
                • searchall
                  • service
                    • SearchAllService.java
                  • model
                    • AttributeResult.java
                    • PackageResult.java
                    • Result.java
                    • Described.java
                    • EntityTypeResult.java
                  • SearchAllI18nConfig.java
                  • controller
                    • SearchAllPluginController.java
        • test
          • java
            • org
              • molgenis
                • searchall
                  • controller
                    • SearchAllServiceTest.java
      • pom.xml
    • molgenis-file-ingester
      • src
        • main
          • java
            • org
              • molgenis
                • file
                  • ingest
                    • execution
                      • FileIngestException.java
                      • FileIngestConfig.java
                      • FileStoreDownloadImpl.java
                      • FileIngester.java
                      • FileStoreDownload.java
                    • meta
                      • FileIngestJobExecutionFactory.java
                      • FileIngestJobExecutionMetadata.java
                      • FileIngestJobExecution.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • file
                  • ingest
                    • config
                      • FileIngestTestConfig.java
                    • FileIngesterTest.java
                    • meta
                      • FileIngestJobExecutionTest.java
      • pom.xml
    • molgenis-ontology
      • src
        • main
          • resources
            • templates
              • sorta-match-view-result.ftl
              • sorta-match-list-tasks.ftl
              • sorta-match-view.ftl
              • sorta-match-new-task.ftl
            • js
              • simple_statistics.js
              • biobank-connect.js
              • jasny-bootstrap.min.js
              • ontology-service-result.js
              • common-component.js
            • css
              • ontology-service.css
              • biobank-connect.css
              • jasny-bootstrap.min.css
          • java
            • org
              • molgenis
                • ontology
                  • utils
                    • SortaServiceUtil.java
                  • sorta
                    • job
                      • SortaJobFactory.java
                      • SortaJobExecution.java
                      • SortaJobProcessor.java
                      • SortaJobExecutionFactory.java
                    • request
                      • SortaServiceRequest.java
                      • SortaServiceResponse.java
                    • service
                      • impl
                        • SortaServiceImpl.java
                      • SortaService.java
                    • bean
                      • OntologyTermHitEntity.java
                    • meta
                      • OntologyTermHitMetaData.java
                      • SortaJobExecutionMetadata.java
                      • MatchingTaskContentMetaData.java
                    • repo
                      • SortaCsvRepository.java
                    • controller
                      • AttributeResponse.java
                      • EntityTypeResponse.java
                      • Href.java
                      • SortaController.java
                      • EntityCollectionResponse.java
                      • EntityPager.java
                  • roc
                    • OntologyWord.java
                    • InformationContentService.java
                  • SortaConfig.java
                  • initializer
                    • OntologyScriptInitializer.java
                    • OntologyScriptInitializerImpl.java
        • test
          • resources
            • logback-test.xml
            • sorta-landing-page-sourcecode.ftl
          • java
            • org
              • molgenis
                • ontology
                  • utils
                    • SortaServiceUtilTest.java
                  • sorta
                    • services
                      • SortaServiceImplTest.java
                    • job
                      • SortaJobExecutionFactoryTest.java
                      • SortaJobExecutionTest.java
                    • repo
                      • SortaCsvRepositoryTest.java
                    • controller
                      • SortaControllerTest.java
                  • roc
                    • InformationContentServiceTest.java
                  • importer
                    • OntologyImportServiceTest.java
                    • repository
                      • OntologyRepositoryCollectionTest.java
      • pom.xml
    • molgenis-data-validation
      • src
        • main
          • java
            • org
              • molgenis
                • data
                  • validation
                    • DefaultValueReferenceValidatorImpl.java
                    • QueryValidator.java
                    • DefaultValueReferenceValidator.java
                    • QueryValidationRepositoryDecorator.java
                    • FetchValidatorImpl.java
                    • EntityValidator.java
                    • EntityAttributesValidator.java
                    • EntityErrors.java
                    • FetchValidator.java
                    • RepositoryConstraintViolationException.java
                    • RepositoryValidationDecorator.java
                    • ExpressionValidator.java
                    • meta
                      • PackageRepositoryValidationDecorator.java
                      • TagValidator.java
                      • TagRepositoryValidationDecorator.java
                      • AttributeRepositoryValidationDecorator.java
                      • NameValidator.java
                      • model
                        • AttributeRepositoryDecoratorFactory.java
                        • TagRepositoryDecoratorFactory.java
                        • PackageRepositoryDecoratorFactory.java
                        • EntityTypeRepositoryDecoratorFactory.java
                      • AttributeValidator.java
                      • PackageValidator.java
                      • EntityTypeValidator.java
                      • EntityTypeRepositoryValidationDecorator.java
                    • MolgenisValidationException.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • data
                  • validation
                    • ExpressionValidatorTest.java
                    • EntityValidatorTest.java
                    • QueryValidationRepositoryDecoratorTest.java
                    • RepositoryConstraintViolationExceptionTest.java
                    • FetchValidatorImplTest.java
                    • DefaultValueReferenceValidatorImplTest.java
                    • RepositoryValidationDecoratorTest.java
                    • EntityAttributesValidatorTest.java
                    • meta
                      • EntityTypeValidatorTest.java
                      • TagRepositoryValidationDecoratorTest.java
                      • NameValidatorTest.java
                      • EntityTypeRepositoryValidationDecoratorTest.java
                      • TagValidatorTest.java
                      • AttributeValidatorTest.java
                      • PackageValidatorTest.java
                      • AttributeRepositoryValidationDecoratorTest.java
                      • model
                        • PackageRepositoryDecoratorFactoryTest.java
                      • PackageRepositoryValidationDecoratorTest.java
                    • QueryValidatorTest.java
      • pom.xml
    • molgenis-data-file
      • src
        • main
          • resources
            • l10n
              • file_en.properties
          • java
            • org
              • molgenis
                • data
                  • file
                    • TransactionalBlobStoreDecorator.java
                    • FileMetaRepositoryDecoratorFactory.java
                    • minio
                      • MinioClientFacade.java
                      • MinioBlobStore.java
                      • MinioClientFactoryImpl.java
                      • MinioStoreConfig.java
                      • MinioClientFactory.java
                    • FileRepositoryCollectionFactory.java
                    • processor
                      • TrimProcessor.java
                      • LowerCaseProcessor.java
                      • AbstractCellProcessor.java
                      • CellProcessor.java
                      • MissingValueProcessor.java
                    • BlobMetadata.java
                    • BlobStoreDecorator.java
                    • support
                      • FileRepositoryCollection.java
                    • util
                      • FileDownloadControllerUtils.java
                      • FileExtensionUtils.java
                    • FileConfig.java
                    • FileStore.java
                    • BlobStore.java
                    • FileMetaRepositoryDecorator.java
                    • model
                      • FileMeta.java
                      • FileMetaMetadata.java
                      • FileMetaFactory.java
                    • CodedUnzipException.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • data
                  • file
                    • minio
                      • MinioBlobStoreTest.java
                      • MinioClientFactoryImplTest.java
                      • MinioClientFacadeTest.java
                    • processor
                      • LowerCaseProcessorTest.java
                      • AbstractCellProcessorTest.java
                      • TrimProcessorTest.java
                      • MissingValueProcessorTest.java
                    • FileStoreTest.java
                    • CodedUnzipExceptionTest.java
                    • config
                      • FileTestConfig.java
                    • model
                      • FileMetaTest.java
                      • FileMetaFactoryTest.java
                    • FileMetaRepositoryDecoratorTest.java
                    • TransactionalBlobStoreDecoratorTest.java
      • pom.xml
    • molgenis-data-icd10
      • src
        • main
          • java
            • org
              • molgenis
                • data
                  • icd10
                    • CollectionsQueryTransformerImpl.java
                    • Icd10ExpanderDecoratorFactory.java
                    • Icd10ExpanderDecorator.java
                    • Icd10ClassExpanderImpl.java
                    • Icd10ClassExpander.java
                    • CollectionsQueryTransformer.java
        • test
          • java
            • org
              • molgenis
                • data
                  • icd10
                    • CollectionsQueryTransformerImplTest.java
                    • Icd10ExpanderDecoratorTest.java
                    • Icd10ClassExpanderImplTest.java
      • pom.xml
    • pom.xml
    • molgenis-r
      • src
        • main
          • resources
            • templates
              • molgenis.R.ftl
          • java
            • org
              • molgenis
                • r
                  • OpenCpuSettings.java
                  • MolgenisRController.java
                  • RScriptRunner.java
                  • RScriptExecutor.java
                  • OpenCpuSettingsImpl.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • r
                  • RScriptRunnerTest.java
                  • MolgenisRControllerTest.java
                  • RScriptExecutorTest.java
      • pom.xml
    • molgenis-settings
      • src
        • main
          • java
            • org
              • molgenis
                • settings
                  • mail
                    • MailSettingsImpl.java
                    • JavaMailProperty.java
                    • JavaMailPropertyFactory.java
                    • MailPackage.java
                    • JavaMailPropertyType.java
                  • SettingsPackage.java
                  • PropertyType.java
                  • SettingsEntityType.java
                  • DefaultSettingsEntity.java
                  • SettingsPopulator.java
                  • DefaultSettingsEntityType.java
                  • AppSettings.java
        • test
          • java
            • org
              • molgenis
                • settings
                  • mail
                    • JavaMailPropertyTest.java
                    • MailTestConfig.java
                    • JavaMailPropertyFactoryTest.java
      • pom.xml
    • molgenis-semantic-mapper
      • src
        • main
          • resources
            • templates
              • view-single-mapping-project.ftl
              • view-attribute-mapping-feedback.ftl
              • view-advanced-mapping-editor.ftl
              • view-mapping-projects.ftl
              • view-tag-wizard.ftl
              • view-attribute-mapping.ftl
            • js
              • jquery.ace.js
              • jstat.min.js
              • jquery.highlight.js
              • d3.min.js
              • jquery
                • scrollTableBody
                  • jquery.scrollTableBody-1.0.0.js
                  • LICENSE
              • attribute-mapping.js
              • tag-wizard.js
              • biobankconnect-graph.js
              • mapping-projects.js
              • vega.min.js
              • single-mapping-project.js
            • css
              • validation-spinner.gif
              • mapping-service.css
          • java
            • org
              • molgenis
                • semanticmapper
                  • utils
                    • AlgorithmGeneratorHelper.java
                    • UnitHelper.java
                    • MagmaUnitConverter.java
                  • mapping
                    • model
                      • AttributeMapping.java
                      • CategoryMapping.java
                      • MappingProject.java
                      • EntityMapping.java
                      • AlgorithmResult.java
                      • MappingTarget.java
                  • job
                    • MappingJobExecutionMetadata.java
                    • MappingJobExecution.java
                    • MappingJobExecutionFactory.java
                    • MappingJobConfig.java
                  • config
                    • MappingConfig.java
                  • service
                    • impl
                      • AlgorithmTemplate.java
                      • UnitResolverImpl.java
                      • AlgorithmServiceImpl.java
                      • AlgorithmException.java
                      • AlgorithmTemplateServiceImpl.java
                      • AlgorithmTemplateService.java
                      • MappingServiceImpl.java
                      • AlgorithmEvaluation.java
                    • MappingService.java
                    • UnitResolver.java
                    • AlgorithmService.java
                  • data
                    • request
                      • AutoTagRequest.java
                      • AddTagRequest.java
                      • GetOntologyTermRequest.java
                      • MappingServiceRequest.java
                      • RemoveTagRequest.java
                      • GenerateAlgorithmRequest.java
                  • algorithmgenerator
                    • categorymapper
                      • FrequencyCategoryMapper.java
                      • convertor
                        • SeveralTimesConvertor.java
                        • DailyAmountConvertor.java
                        • AmountConvertor.java
                        • NumberAmountConvertor.java
                      • CategoryMapper.java
                      • CategoryMapperUtil.java
                      • LexicalCategoryMapper.java
                    • service
                      • impl
                        • AlgorithmGeneratorServiceImpl.java
                      • AlgorithmGeneratorService.java
                    • rules
                      • impl
                        • MissingCategoryRule.java
                        • PositiveCategoryRule.java
                        • InternalAbstractCategoryRule.java
                        • NegativeCategoryRule.java
                      • quality
                        • impl
                          • NumericQuality.java
                        • Quality.java
                      • CategoryRule.java
                      • CategoryMatchQuality.java
                    • generator
                      • OneToManyCategoryAlgorithmGenerator.java
                      • OneToOneCategoryAlgorithmGenerator.java
                      • NumericAlgorithmGenerator.java
                      • AlgorithmGenerator.java
                      • AbstractCategoryAlgorithmGenerator.java
                    • bean
                      • GeneratedAlgorithm.java
                      • AmountWrapper.java
                      • Category.java
                  • repository
                    • impl
                      • EntityMappingRepositoryImpl.java
                      • MappingTargetRepositoryImpl.java
                      • AttributeMappingRepositoryImpl.java
                      • MappingProjectRepositoryImpl.java
                    • MappingTargetRepository.java
                    • MappingProjectRepository.java
                    • AttributeMappingRepository.java
                    • EntityMappingRepository.java
                  • meta
                    • MappingProjectMetadata.java
                    • EntityMappingMetadata.java
                    • MapperPackage.java
                    • package-info.java
                    • MappingTargetMetadata.java
                    • AttributeMappingMetadata.java
                  • controller
                    • MappingServiceController.java
                    • TagWizardController.java
                    • FirstAttributeMappingInfo.java
        • test
          • resources
            • logback-test.xml
            • example_data_bbc.xlsx
          • java
            • org
              • molgenis
                • semanticmapper
                  • utils
                    • UnitHelperTest.java
                    • MagmaUnitConverterTest.java
                  • mapping
                    • model
                      • CategoryMappingTest.java
                      • AttributeMappingTest.java
                      • EntityMappingTest.java
                  • job
                    • MappingJobExecutionTest.java
                    • MappingJobExecutionFactoryTest.java
                  • config
                    • MapperTestConfig.java
                  • service
                    • impl
                      • MappingServiceImplTest.java
                      • AlgorithmServiceImplIT.java
                      • UnitResolverImplTest.java
                      • AlgorithmServiceImplTest.java
                      • AlgorithmTemplateServiceImplTest.java
                  • algorithmgenerator
                    • categorymapper
                      • CategoryMapperTest.java
                      • LexicalCategoryMapperTest.java
                    • service
                      • impl
                        • AlgorithmGeneratorServiceImplTest.java
                    • rules
                      • impl
                        • PositiveCategoryRuleTest.java
                        • NegativeCategoryRuleTest.java
                        • InternalAbstractCategoryRuleTest.java
                        • MissingCategoryRuleTest.java
                    • generator
                      • OneToManyCategoryAlgorithmGeneratorTest.java
                      • NumericAlgorithmGeneratorTest.java
                      • OneToOneCategoryAlgorithmGeneratorTest.java
                  • repository
                    • impl
                      • MappingTargetRepositoryImplTest.java
                      • AttributeMappingRepositoryImplTest.java
                      • EntityMappingRepositoryImplTest.java
                      • MappingProjectRepositoryImplTest.java
                  • controller
                    • MappingServiceControllerTest.java
                    • TagWizardControllerTest.java
      • pom.xml
      • doc
        • model.ucls
    • molgenis-data-postgresql
      • src
        • main
          • java
            • org
              • molgenis
                • data
                  • postgresql
                    • PostgreSqlEntityFactory.java
                    • PostgreSqlQueryUtils.java
                    • PostgreSqlExceptionTranslator.java
                    • DatabaseConfig.java
                    • transaction
                      • PostgreSqlTransactionManager.java
                    • PostgreSqlConfiguration.java
                    • PostgreSqlUtils.java
                    • PostgreSqlRepositoryCollection.java
                    • PostgreSqlRepositoryCollectionDecorator.java
                    • PostgreSqlRepository.java
                    • PostgreSqlIdGenerator.java
                    • PostgreSqlNameGenerator.java
                    • PostgreSqlQueryGenerator.java
                    • identifier
                      • EntityTypeRegistry.java
                      • EntityTypeRegistryImpl.java
                      • EntityTypeRegistryPopulator.java
                      • EntityTypeDescription.java
                      • AttributeDescription.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • data
                  • postgresql
                    • transaction
                      • PostgreSqlTransactionManagerTest.java
                    • PostgreSqlExceptionTranslatorTest.java
                    • PostgreSqlRepositoryCollectionDecoratorTest.java
                    • PostgreSqlIdGeneratorTest.java
                    • PostgreSqlEntityFactoryTest.java
                    • PostgreSqlQueryUtilsTest.java
                    • PostgreSqlQueryGeneratorTest.java
                    • PostgreSqlRepositoryTest.java
                    • PostgreSqlRepositoryCollectionTest.java
                    • PostgreSqlNameGeneratorTest.java
                    • identifier
                      • EntityTypeRegistryImplTest.java
                    • PostgreSqlUtilsTest.java
      • pom.xml
    • molgenis-data-platform
      • src
        • main
          • java
            • org
              • molgenis
                • data
                  • platform
                    • bootstrap
                      • SystemEntityTypeBootstrapper.java
                    • decorators
                      • MolgenisRepositoryDecoratorFactory.java
                      • SystemRepositoryDecoratorRegistryImpl.java
                    • config
                      • PlatformConfig.java
                    • RepositoryCollectionDecoratorFactoryImpl.java
                  • meta
                    • system
                      • SystemEntityTypePersister.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • data
                  • platform
                    • decorators
                      • SystemRepositoryDecoratorRegistryImplTest.java
                  • meta
                    • system
                      • SystemEntityTypePersisterTest.java
      • pom.xml
    • molgenis-security-ui
      • src
        • main
          • resources
            • templates
              • view-security-ui.ftl
            • l10n
              • security-ui_en.properties
              • security-ui_nl.properties
          • java
            • org
              • molgenis
                • securityui
                  • controller
                    • SecurityUiController.java
                    • SecurityUiI18nConfig.java
        • test
          • java
            • org
              • molgenis
                • securityui
                  • controller
                    • SecurityUiControllerTest.java
      • pom.xml
    • molgenis-app-manager
      • src
        • main
          • resources
            • templates
              • view-app-manager.ftl
              • view-app.ftl
            • l10n
              • app-manager_en.properties
          • java
            • org
              • molgenis
                • app
                  • manager
                    • decorator
                      • AppRepositoryDecorator.java
                      • AppsRepositoryDecoratorFactory.java
                    • config
                      • AppManagerConfig.java
                    • service
                      • impl
                        • AppManagerServiceImpl.java
                      • AppManagerService.java
                    • exception
                      • AppForIDDoesNotExistException.java
                      • AppConfigMissingParametersException.java
                      • InvalidAppConfigException.java
                      • AppForURIDoesNotExistException.java
                      • InvalidAppArchiveException.java
                      • AppIsInactiveException.java
                      • CouldNotUploadAppException.java
                      • AppArchiveMissingFilesException.java
                      • IllegalAppNameException.java
                      • AppAlreadyExistsException.java
                      • CouldNotDeleteAppException.java
                    • model
                      • AppResponse.java
                      • AppConfig.java
                    • meta
                      • AppFactory.java
                      • AppMetadata.java
                      • App.java
                    • controller
                      • AppManagerController.java
                      • AppController.java
        • test
          • resources
            • config.json
            • config-missing-keys.json
            • fake-app
              • img
              • js
                • test.js
              • css
                • test.css
            • index.html
            • invalid-app.txt
          • java
            • org
              • molgenis
                • app
                  • manager
                    • decorator
                      • AppRepositoryDecoratorTest.java
                    • service
                      • impl
                        • AppManagerServiceImplTest.java
                    • exception
                      • CouldNotDeleteAppExceptionTest.java
                      • CouldNotUploadAppExceptionTest.java
                    • meta
                      • AppTest.java
                    • controller
                      • AppControllerTest.java
                      • AppManagerControllerTest.java
      • pom.xml
    • molgenis-semantic-search
      • src
        • main
          • resources
            • explain_api_example.json
          • java
            • org
              • molgenis
                • semanticsearch
                  • explain
                    • service
                      • ExplainServiceHelper.java
                      • ElasticSearchExplainService.java
                      • ElasticSearchExplainServiceImpl.java
                    • bean
                      • ExplainedAttribute.java
                      • ExplainedAttributeDto.java
                      • AttributeSearchResults.java
                      • ExplainedQueryString.java
                      • EntityTypeSearchResults.java
                  • config
                    • SemanticSearchConfig.java
                  • service
                    • impl
                      • SemanticSearchServiceHelper.java
                      • SemanticSearchServiceImpl.java
                      • OntologyTagServiceImpl.java
                      • UntypedTagService.java
                    • OntologyTagService.java
                    • SemanticSearchService.java
                    • TagService.java
                  • semantic
                    • OntologyTag.java
                    • Hits.java
                    • Hit.java
                  • repository
                    • TagRepository.java
                  • string
                    • NGramDistanceAlgorithm.java
                    • Stemmer.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • semanticsearch
                  • explain
                    • service
                      • ExplainServiceHelperTest.java
                      • ElasticSearchExplainServiceImplTest.java
                  • service
                    • impl
                      • SemanticSearchServiceImplTest.java
                      • SemanticSearchServiceHelperTest.java
                      • OntologyTagServiceTest.java
                  • repository
                    • TagRepositoryTest.java
                  • string
                    • StemmerTest.java
                    • NgramDistanceAlgorithmTest.java
      • pom.xml
    • LICENSE
    • molgenis-data-csv
      • src
        • main
          • java
            • org
              • molgenis
                • data
                  • csv
                    • CsvRepository.java
                    • CsvIterator.java
                    • CsvWriter.java
                    • CsvDataConfig.java
                    • CsvRepositoryCollection.java
                    • CsvFileExtensions.java
        • test
          • resources
            • logback-test.xml
            • testdatamissingvalue2.csv
            • testdatamissingvalue3.csv
            • emptyvalues.csv
            • case-sensitivity.csv
            • test.tsv
            • emptylines.csv
            • testdatamissingvalue.csv
            • novalues.csv
            • duplicate-sheet-header.csv
            • emptylinessinglecol.csv
            • testdata.csv
            • testDataWithBom.csv
            • test.csv
          • java
            • org
              • molgenis
                • data
                  • csv
                    • CsvWriterTest.java
                    • CsvIteratorTest.java
                    • CsvRepositoryTest.java
                    • CsvRepositoryCollectionTest.java
      • pom.xml
      • doc
        • molgenis-data-csv.md
        • molgenis-data-csv.dia
    • molgenis-validation
      • src
        • main
          • resources
            • l10n
              • validation_en.properties
              • validation_nl.properties
          • java
            • org
              • molgenis
                • validation
                  • ConstraintViolation.java
                  • JsonValidator.java
                  • exception
                    • LocalhostNotAllowedException.java
                    • RelativePathNotAllowedException.java
                  • UriValidator.java
                  • InvalidJsonSchemaException.java
                  • JsonValidationException.java
                  • ValidationI18nConfig.java
        • test
          • java
            • org
              • molgenis
                • validation
                  • UriValidatorTest.java
                  • ConstraintViolationTest.java
                  • exception
                    • LocalhostNotAllowedExceptionTest.java
                    • RelativePathNotAllowedExceptionTest.java
                  • JsonValidatorTest.java
      • pom.xml
    • molgenis-data-plugin
      • src
        • main
          • resources
            • l10n
              • data-plugin_en.properties
          • java
            • org
              • molgenis
                • data
                  • plugin
                    • model
                      • PluginFactory.java
                      • PluginRepositoryDecorator.java
                      • PluginPermission.java
                      • Plugin.java
                      • PluginPermissionConfig.java
                      • PluginSecurityRepositoryDecorator.java
                      • PluginIdentity.java
                      • PluginPermissionDeniedException.java
                      • PluginMetadata.java
                      • PluginRepositoryDecoratorFactory.java
        • test
          • java
            • org
              • molgenis
                • data
                  • plugin
                    • model
                      • PluginPermissionDeniedExceptionTest.java
                      • PluginSecurityRepositoryDecoratorTest.java
                      • PluginRepositoryDecoratorTest.java
                      • PluginTest.java
                      • PluginFactoryTest.java
      • pom.xml
    • molgenis-beacon
      • src
        • main
          • java
            • org
              • molgenis
                • beacon
                  • config
                    • BeaconDataset.java
                    • BeaconDatasetMetadata.java
                    • BeaconOrganization.java
                    • Beacon.java
                    • BeaconMetadata.java
                    • BeaconPackage.java
                    • BeaconDatasetFactory.java
                    • BeaconOrganizationMetadata.java
                    • BeaconFactory.java
                    • BeaconOrganizationFactory.java
                  • service
                    • impl
                      • BeaconQueryServiceImpl.java
                      • BeaconInfoServiceImpl.java
                    • BeaconQueryService.java
                    • BeaconInfoService.java
                  • controller
                    • BeaconController.java
                    • model
                      • BeaconResponse.java
                      • BeaconAlleleResponse.java
                      • BeaconOrganizationResponse.java
                      • BeaconDatasetResponse.java
                      • BeaconAlleleRequest.java
                      • BeaconError.java
                      • exceptions
                        • BeaconExceptionHandler.java
                        • NestedBeaconException.java
                        • UnknownBeaconException.java
                        • BeaconException.java
        • test
          • java
            • org
              • molgenis
                • beacon
                  • config
                    • BeaconTestConfig.java
                    • BeaconDatasetTest.java
                    • BeaconOrganizationFactoryTest.java
                    • BeaconOrganizationTest.java
                    • BeaconDatasetFactoryTest.java
                  • service
                    • BeaconQueryServiceTest.java
                    • BeaconInfoServiceImplTest.java
                  • controller
                    • BeaconControllerTest.java
      • pom.xml
    • molgenis-jobs
      • src
        • main
          • resources
            • l10n
              • jobs_en.properties
              • jobs_nl.properties
          • java
            • org
              • molgenis
                • jobs
                  • schedule
                    • MolgenisQuartzJob.java
                    • ScheduledJobRepositoryDecorator.java
                    • ScheduledJobException.java
                    • JobScheduler.java
                    • ScheduledJobRepositoryDecoratorFactory.java
                  • JobExecutionUpdaterImpl.java
                  • JobExecutionUriUtils.java
                  • ActiveJobExecutionDeleteForbiddenException.java
                  • JobFactory.java
                  • JobExecutionTemplate.java
                  • JobBootstrapper.java
                  • JobExecutionException.java
                  • JobsServiceImpl.java
                  • JobExecutor.java
                  • ProgressImpl.java
                  • JobExecutionContextFactoryImpl.java
                  • JobExecutionRegistryImpl.java
                  • JobFactoryRegistry.java
                  • ProgressCancellationDecorator.java
                  • JobExecutorTokenService.java
                  • scheduler
                    • SchedulerConfig.java
                    • AutowiringSpringBeanJobFactory.java
                  • JobUtils.java
                  • InactiveJobExecutionException.java
                  • JobExecutionRegistry.java
                  • JobsL10nConfig.java
                  • JobExecutorLocaleServiceImpl.java
                  • ProgressFactory.java
                  • JobExecutionHolder.java
                  • JobConfig.java
                  • JobFactoryRegistrar.java
                  • ProgressFactoryImpl.java
                  • JobExecutionContext.java
                  • InvalidJobExecutionTypeException.java
                  • model
                    • ScheduledJobTypeMetadata.java
                    • JobExecutionMetaData.java
                    • JobExecution.java
                    • JobPackage.java
                    • ScheduledJobType.java
                    • ScheduledJob.java
                    • JobExecutionLogAppender.java
                    • ScheduledJobMetadata.java
                    • JobExecutionRepositoryDecorator.java
                    • ScheduledJobTypeFactory.java
                    • ScheduledJobFactory.java
                    • JobExecutionRepositoryDecoratorFactory.java
                  • Progress.java
                  • JobExecutionUpdater.java
                  • JobExecutorLocaleService.java
                  • JobsService.java
                  • JobExecutionContextFactory.java
                  • JobExecutionConfig.java
                  • JobExecutorTokenServiceImpl.java
                  • Job.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • jobs
                  • schedule
                    • JobSchedulerTest.java
                    • ScheduledJobRepositoryDecoratorTest.java
                  • JobsServiceImplTest.java
                  • ActiveJobExecutionDeleteForbiddenExceptionTest.java
                  • JobExecutionUriUtilsTest.java
                  • JobExecutionTemplateTest.java
                  • ProgressImplTest.java
                  • JobExecutorTokenServiceImplTest.java
                  • JobExecutorLocaleServiceImplTest.java
                  • JobBootstrapperTest.java
                  • JobExecutorTest.java
                  • config
                    • JobTestConfig.java
                  • JobUtilsTest.java
                  • InvalidJobExecutionTypeExceptionTest.java
                  • model
                    • ScheduledJobTest.java
                    • ScheduledJobTypeTest.java
                    • ScheduledJobFactoryTest.java
                    • JobExecutionRepositoryDecoratorTest.java
                    • ScheduledJobTypeFactoryTest.java
                  • ProgressCancellationDecoratorTest.java
      • pom.xml
    • local-maven-repo
      • com
        • baggonius
          • gson
            • guava-gson-serializers
              • 1.0.1
                • guava-gson-serializers-1.0.1-sources.jar
                • guava-gson-serializers-1.0.1-sources.jar.md5
                • guava-gson-serializers-1.0.1.jar.sha1
                • guava-gson-serializers-1.0.1.jar.md5
                • guava-gson-serializers-1.0.1.pom.md5
                • guava-gson-serializers-1.0.1.jar
                • guava-gson-serializers-1.0.1.pom
                • guava-gson-serializers-1.0.1-sources.jar.sha1
                • guava-gson-serializers-1.0.1.pom.sha1
              • maven-metadata.xml
              • maven-metadata.xml.md5
              • maven-metadata.xml.sha1
    • molgenis-api-metrics
      • src
        • main
          • java
            • org
              • molgenis
                • api
                  • metrics
                    • MetricsController.java
        • test
          • java
            • org
              • molgenis
                • api
                  • metrics
                    • MetricsControllerTest.java
      • pom.xml
    • molgenis-scripts-core
      • src
        • main
          • java
            • org
              • molgenis
                • script
                  • core
                    • ScriptTypePopulator.java
                    • ScriptFactory.java
                    • ScriptParameterFactory.java
                    • ScriptUtils.java
                    • ScriptParameter.java
                    • Script.java
                    • ScriptRunner.java
                    • ScriptMetadata.java
                    • ScriptException.java
                    • ScriptPackage.java
                    • ScriptTypeFactory.java
                    • ScriptType.java
                    • ScriptParameterMetadata.java
                    • GenerateScriptException.java
                    • ScriptRunnerFactory.java
                    • ScriptRunnerRegistrar.java
                    • ScriptTypeMetadata.java
                    • UnknownScriptException.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • script
                  • core
                    • ScriptFactoryTest.java
                    • ScriptUtilsTest.java
                    • ScriptTypeFactoryTest.java
                    • ScriptParameterFactoryTest.java
                    • config
                      • ScriptTestConfig.java
                    • ScriptTypeTest.java
                    • ScriptParameterTest.java
                    • ScriptTypePopulatorTest.java
                    • ScriptTest.java
      • pom.xml
      • .gitignore
    • intellij-molgenis-style.xml
    • molgenis-data-vcf
      • src
        • main
          • java
            • org
              • molgenis
                • data
                  • vcf
                    • utils
                      • VcfUtils.java
                    • VcfFileExtensions.java
                    • VcfDataConfig.java
                    • format
                      • VcfToEntity.java
                    • VcfRepository.java
                    • importer
                      • VcfImporterService.java
                    • VcfRepositoryCollection.java
                    • model
                      • VcfAttributes.java
        • test
          • resources
            • logback-test.xml
            • testdata.vcf
            • testlargeinsertdelete.vcf
            • testnodata.vcf
          • java
            • org
              • molgenis
                • data
                  • vcf
                    • utils
                      • test
                        • VcfUtilsTest.java
                    • format
                      • VcfToEntityTest.java
                    • config
                      • VcfTestConfig.java
                    • importer
                      • VcfImporterServiceTest.java
                    • VcfRepositoryTest.java
      • pom.xml
    • molgenis-swagger
      • src
        • main
          • resources
            • templates
              • view-swagger-ui.ftl
              • view-swagger.ftl
          • java
            • org
              • molgenis
                • swagger
                  • controller
                    • SwaggerController.java
        • test
          • java
            • org
              • molgenis
                • swagger
                  • controller
                    • SwaggerControllerTest.java
      • pom.xml
    • molgenis-data-index
      • src
        • main
          • java
            • org
              • molgenis
                • data
                  • index
                    • bootstrap
                      • IndexBootstrapper.java
                    • IndexActionRepositoryCollectionDecorator.java
                    • transaction
                      • IndexTransactionListener.java
                    • IndexedRepositoryDecoratorFactory.java
                    • Impact.java
                    • job
                      • IndexJobExecutionFactory.java
                      • IndexStatus.java
                      • IndexJobSchedulerImpl.java
                      • IndexJobService.java
                      • IndexJobExecution.java
                      • IndexJobScheduler.java
                      • IndexJobExecutionMetadata.java
                    • IndexService.java
                    • exception
                      • IndexAlreadyExistsException.java
                      • UnknownIndexException.java
                      • IndexException.java
                    • IndexDependencyModel.java
                    • IndexedRepositoryDecorator.java
                    • IndexConfig.java
                    • IndexActionRepositoryDecorator.java
                    • SearchService.java
                    • IndexingStrategy.java
                    • IndexActionRegisterServiceImpl.java
                    • meta
                      • IndexActionFactory.java
                      • IndexActionGroupMetadata.java
                      • IndexActionGroupFactory.java
                      • IndexActionGroup.java
                      • IndexPackage.java
                      • IndexActionMetadata.java
                      • IndexAction.java
                    • IndexActionRegisterService.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • data
                  • index
                    • bootstrap
                      • IndexBootstrapperTest.java
                    • IndexingStrategyTest.java
                    • IndexedRepositoryDecoratorTest.java
                    • IndexActionRepositoryCollectionDecoratorTest.java
                    • job
                      • IndexJobSchedulerTest.java
                      • IndexJobExecutionFactoryTest.java
                      • IndexJobServiceTest.java
                      • IndexJobExecutionTest.java
                    • IndexActionRegisterServiceTest.java
                    • config
                      • IndexTestConfig.java
                    • IndexDependencyModelTest.java
                    • IndexActionRepositoryDecoratorTest.java
                    • meta
                      • IndexActionGroupTest.java
                      • IndexActionFactoryTest.java
                      • IndexActionGroupFactoryTest.java
                      • IndexActionTest.java
      • pom.xml
    • molgenis-security
      • src
        • main
          • resources
            • sql
              • create_table_acl_object_identity.sql
              • create_table_acl_class.sql
              • create_table_acl_sid.sql
              • create_table_acl_entry.sql
            • templates
              • view-permissionmanager-entity-class.ftl
              • view-2fa-imports.ftl
              • view-2fa-activation-modal.ftl
              • view-2fa-configured-modal.ftl
              • view-login.ftl
              • login-modal.ftl
              • view-permissionmanager.ftl
              • view-activate-success.ftl
              • view-activate.ftl
              • view-permissionmanager-package.ftl
              • view-logmanager.ftl
              • resetpassword-modal.ftl
              • view-change-password.ftl
              • view-usermanager.ftl
              • view-permissionmanager-plugin.ftl
              • view-useraccount.ftl
              • register-modal.ftl
              • view-permissionmanager-entity.ftl
            • l10n
              • security_en.properties
              • security_nl.properties
            • js
              • permissionmanager.js
          • java
            • org
              • molgenis
                • security
                  • captcha
                    • ReCaptchaHttpPostFactory.java
                    • ReCaptchaService.java
                    • ReCaptchaValidationRequest.java
                    • ReCaptchaController.java
                    • CaptchaException.java
                    • ReCaptchaValidationResponse.java
                  • UriConstants.java
                  • acl
                    • AclCacheTransactionListener.java
                    • AclConfig.java
                    • MutableAclClassServiceImpl.java
                    • DataSourceAclTablesPopulator.java
                    • ObjectIdentityServiceImpl.java
                    • TransactionalJdbcMutableAclService.java
                    • BitMaskPermissionGrantingStrategy.java
                  • NoOpAuditLogger.java
                  • AjaxAwareLoginUrlAuthenticationEntryPoint.java
                  • user
                    • UserAccountConstants.java
                    • UserDetailsServiceImpl.java
                    • MolgenisUserException.java
                    • UserAccountService.java
                    • MolgenisUserDetailsChecker.java
                    • UserAccountServiceImpl.java
                  • twofactor
                    • service
                      • TwoFactorAuthenticationServiceImpl.java
                      • RecoveryService.java
                      • OtpServiceImpl.java
                      • TwoFactorAuthenticationService.java
                      • OtpService.java
                      • RecoveryServiceImpl.java
                    • exceptions
                      • InvalidVerificationCodeException.java
                      • TooManyLoginAttemptsException.java
                    • auth
                      • TwoFactorAuthenticationFilter.java
                      • RecoveryAuthenticationToken.java
                      • TwoFactorAuthenticationToken.java
                      • TwoFactorAuthenticationProviderImpl.java
                      • RecoveryAuthenticationProvider.java
                      • TwoFactorAuthenticationProvider.java
                      • TwoFactorAuthenticationSetting.java
                      • RecoveryAuthenticationProviderImpl.java
                    • model
                      • RecoveryCodeFactory.java
                      • UserSecretMetadata.java
                      • UserSecretFactory.java
                      • RecoveryCode.java
                      • UserSecret.java
                      • RecoveryCodeMetadata.java
                    • TwoFactorAuthenticationController.java
                  • MolgenisWebAppSecurityConfig.java
                  • exception
                    • WebAppSecurityConfigException.java
                  • oidc
                    • OidcUserMissingEmailException.java
                    • MappedOidcUser.java
                    • DataServiceClientRegistrationRepository.java
                    • OidcUserMapper.java
                    • OidcUserMapperImpl.java
                    • MappedOidcUserService.java
                    • model
                      • OidcClient.java
                      • OidcUserMapping.java
                      • OidcPackage.java
                      • OidcClientMetadata.java
                      • OidcClientRepositoryDecoratorFactory.java
                      • OidcUserMappingFactory.java
                      • OidcClientRepositoryDecorator.java
                      • OidcClientFactory.java
                      • OidcUserMappingMetadata.java
                    • OidcUserEmailVerificationException.java
                    • ResettableOAuth2AuthorizedClientService.java
                  • SecurityL10nConfig.java
                  • token
                    • RunAsUserTokenFactory.java
                    • RestAuthenticationToken.java
                    • TokenExtractor.java
                    • DataServiceTokenService.java
                    • TokenParam.java
                    • TokenAuthenticationFilter.java
                    • TokenGenerator.java
                    • TokenAuthenticationProvider.java
                  • WebAppSecurityInitializer.java
                  • permission
                    • PermissionSystemServiceImpl.java
                    • AuthenticationAuthoritiesUpdaterImpl.java
                    • Permissions.java
                    • MolgenisPermissionController.java
                    • PrincipalSecurityContextRegistryImpl.java
                    • UserPermissionEvaluatorImpl.java
                    • SecurityContextRegistryImpl.java
                    • Permission.java
                  • freemarker
                    • NotHasPermissionDirective.java
                    • HasPermissionDirective.java
                    • PermissionDirective.java
                  • account
                    • PasswordResetTokenRepository.java
                    • RegisterRequest.java
                    • ChangePasswordForm.java
                    • UnknownPasswordResetTokenException.java
                    • ExpiredPasswordResetTokenException.java
                    • AccountController.java
                    • PasswordResetTokenRepositoryImpl.java
                    • PasswordResetterImpl.java
                    • UsernameAlreadyExistsException.java
                    • InvalidPasswordResetTokenException.java
                    • AccountService.java
                    • EmailAlreadyExistsException.java
                    • PasswordResetRequest.java
                    • PasswordResetTokenCreationException.java
                    • PasswordResetter.java
                    • AccountServiceImpl.java
                  • metrics
                    • SessionMetrics.java
                  • settings
                    • AuthenticationSettingsImpl.java
                    • AuthenticationSettings.java
                  • TokenAwareSecurityContextRepository.java
                  • MolgenisChangePasswordFilter.java
                  • login
                    • MolgenisLoginController.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • security
                  • captcha
                    • ReCaptchaHttpPostFactoryTest.java
                    • ReCaptchaServiceTest.java
                  • acl
                    • BitMaskPermissionGrantingStrategyTest.java
                    • MutableAclClassServiceImplTest.java
                    • AclCacheTransactionListenerTest.java
                    • ObjectIdentityServiceImplTest.java
                  • AjaxAwareLoginUrlAuthenticationEntryPointTest.java
                  • MolgenisChangePasswordFilterTest.java
                  • user
                    • UserAccountServiceImplTest.java
                    • UserDetailsCheckerTest.java
                    • UserDetailsServiceImplTest.java
                  • twofactor
                    • service
                      • OtpServiceImplTest.java
                      • RecoveryServiceImplTest.java
                      • TwoFactorAuthenticationServiceImplTest.java
                    • auth
                      • TwoFactorAuthenticationFilterTest.java
                      • RecoveryAuthenticationProviderTest.java
                      • TwoFactorAuthenticationProviderTest.java
                    • model
                      • UserSecretTest.java
                      • UserSecretFactoryTest.java
                      • RecoveryCodeFactoryTest.java
                      • RecoveryCodeTest.java
                    • TwoFactorAuthenticationControllerTest.java
                  • oidc
                    • MappedOidcUserServiceTest.java
                    • DataServiceClientRegistrationRepositoryTest.java
                    • OidcUserMapperImplTest.java
                    • OidcUserMissingEmailExceptionTest.java
                    • model
                      • OidcUserMappingTest.java
                      • OidcClientTest.java
                      • OidcUserMappingFactoryTest.java
                      • OidcClientRepositoryDecoratorTest.java
                      • OidcClientFactoryTest.java
                      • OidcTestConfig.java
                    • OidcUserEmailVerificationExceptionTest.java
                    • ResettableOAuth2AuthorizedClientServiceTest.java
                  • token
                    • TokenAuthenticationFilterTest.java
                    • RunAsUserTokenFactoryTest.java
                    • TokenAuthenticationProviderTest.java
                    • TokenGeneratorTest.java
                    • DataServiceTokenServiceTest.java
                    • TokenExtractorTest.java
                  • permission
                    • AuthenticationAuthoritiesUpdaterImplTest.java
                    • PrincipalSecurityContextRegistryImplTest.java
                    • UserPermissionEvaluatorImplTest.java
                    • PermissionSystemServiceImplTest.java
                    • SecurityContextRegistryImplTest.java
                    • MolgenisPermissionControllerTest.java
                  • freemarker
                    • HasPermissionDirectiveTest.java
                  • account
                    • ExpiredPasswordResetTokenExceptionTest.java
                    • PasswordResetTokenRepositoryImplTest.java
                    • PasswordResetterImplTest.java
                    • InvalidPasswordResetTokenExceptionTest.java
                    • PasswordResetTokenCreationExceptionTest.java
                    • AccountServiceImplTest.java
                    • UnknownPasswordResetTokenExceptionTest.java
                    • AccountControllerTest.java
                  • settings
                    • AuthenticationSettingsImplTest.java
                  • login
                    • MolgenisLoginControllerTest.java
                  • TokenAwareSecurityContextRepositoryTest.java
            • .gitignore
      • pom.xml
      • .gitignore
    • molgenis-api-fair
      • src
        • main
          • resources
            • templates
              • view-entityreport-specific-fdp_Metadata.ftl
              • view-entityreport-specific-fdp_Dataset.ftl
              • view-entityreport-specific-fdp_Catalog.ftl
              • view-entityreport-specific-fdp_Distribution.ftl
            • FDP.xlsx
          • java
            • org
              • molgenis
                • api
                  • fair
                    • controller
                      • FairController.java
                      • config
                        • FairConfig.java
                      • EntityModelWriter.java
        • test
          • resources
            • FDP_test_data.xlsx
          • java
            • org
              • molgenis
                • api
                  • fair
                    • controller
                      • EntityModelWriterTest.java
                      • FairControllerTest.java
      • pom.xml
    • molgenis-data-cache
      • src
        • main
          • java
            • org
              • molgenis
                • data
                  • cache
                    • l1
                      • L1CacheJanitorImpl.java
                      • L1CacheJanitor.java
                      • L1CacheRepositoryDecorator.java
                      • L1Cache.java
                    • utils
                      • CacheHit.java
                      • EntityHydration.java
                      • CombinedEntityCache.java
                    • l3
                      • L3Cache.java
                      • L3CacheRepositoryDecorator.java
                    • l2
                      • L2CacheRepositoryDecorator.java
                      • L2Cache.java
        • test
          • resources
            • logback-test.xml
          • java
            • org
              • molgenis
                • data
                  • cache
                    • l1
                      • L1CacheJanitorImplTest.java
                      • L1CacheRepositoryDecoratorTest.java
                      • L1CacheTest.java
                    • utils
                      • EntityHydrationTest.java
                      • CombinedEntityCacheTest.java
                    • l3
                      • L3CacheRepositoryDecoratorTest.java
                      • L3CacheTest.java
                    • l2
                      • L2CacheTest.java
                      • L2CacheRepositoryDecoratorTest.java
      • pom.xml
    • molgenis-api-data
      • src
        • main
          • resources
            • l10n
              • api-data_en.properties
          • java
            • org
              • molgenis
                • api
                  • data
                    • SortConverter.java
                    • v3
                      • NullMrefValueException.java
                      • EntityMapperImpl.java
                      • DataApiV3Config.java
                      • DataServiceV3Impl.java
                      • EntityController.java
                      • FetchMapper.java
                      • DataServiceV3.java
                      • EntityManagerV3.java
                      • UnsupportedAttributeTypeException.java
                      • Entities.java
                      • EntityMapper.java
                      • EntityCollection.java
                      • EntityManagerV3Impl.java
                      • model
                        • ReadSubresourceRequest.java
                        • DeleteEntitiesRequest.java
                        • DeleteEntityRequest.java
                        • AbstractReadRequest.java
                        • EntitiesResponse.java
                        • AbstractEntityTypeRequest.java
                        • ReadEntitiesRequest.java
                        • ReadEntityRequest.java
                        • EntityResponse.java
                    • RestService.java
                    • SortMapper.java
                    • QueryMapper.java
                    • v2
                      • AttributeFilter.java
                      • AttributeResponseV2.java
                      • CopyEntityRequestV2.java
                      • UriUtils.java
                      • RestConfig.java
                      • CategoricalOptionV2.java
                      • EntityCollectionResponseV2.java
                      • EntityCollectionBatchCreateResponseBodyV2.java
                      • EntityTypeResponseV2.java
                      • EntityCollectionDeleteRequestV2.java
                      • ResourcesResponseV2.java
                      • AttributeFilterToFetchConverter.java
                      • AttributeFilterConverter.java
                      • RestControllerV2.java
                      • EntityCollectionBatchRequestV2.java
                      • EntityAggregatesResponse.java
                      • CategoricalUtils.java
                      • EntityCollectionRequestV2.java
                    • v1
                      • Link.java
                      • UriUtils.java
                      • AttributeResponse.java
                      • SortV1.java
                      • RestController.java
                      • EntityTypeResponse.java
                      • QueryStringParser.java
                      • EntityTypeRequest.java
                      • LoginResponse.java
                      • LoginRequest.java
                      • EntityCollectionRequest.java
                      • EntityCollectionResponse.java
                      • EntityPager.java
                    • ServletUriComponentsBuilderFactory.java
                    • ApiDataL10nConfig.java
                    • DataApiConfig.java
        • test
          • resources
            • logback-test.xml
            • org
              • molgenis
                • api
                  • data
                    • v2
                      • resourceResponseIncludingCategories.json
                      • resourcePartialAttributeResponse.json
                      • resourcePartialSubSubAttributesResponse.json
                      • resourcePartialAttributeInCompoundInCompoundResponse.json
                      • resourceCollectionResponse.json
                      • resourcePartialSubAttributesResponse.json
                      • resourcePartialSubAttributeResponse.json
                      • resourceCollectionResponseUnknownEntityType.json
                      • resourceResponse.json
                      • resourcePartialAttributeInCompoundResponse.json
                      • resourceCollectionResponseIncludingCategories.json
                      • resourcePartialAttributesResponse.json
          • java
            • org
              • molgenis
                • api
                  • data
                    • v3
                      • DataServiceV3ImplTest.java
                      • FetchMapperTest.java
                      • NullMrefValueExceptionTest.java
                      • UnsupportedAttributeTypeExceptionTest.java
                      • EntityMapperImplTest.java
                      • EntityControllerTest.java
                      • EntityManagerV3ImplTest.java
                    • v2
                      • UriUtilsTest.java
                      • RestControllerV2Test.java
                      • AttributeFilterToFetchConverterTest.java
                      • AttributeFilterConverterTest.java
                      • EntityAggregatesResponseTest.java
                    • v1
                      • UriUtilsTest.java
                      • EntityPagerTest.java
                      • EntityCollectionResponseTest.java
                      • RestControllerTest.java
                    • SortConverterTest.java
                    • QueryMapperTest.java
                    • RestServiceTest.java
                    • SortMapperTest.java
      • pom.xml
    • molgenis-data-import
      • src
        • main
          • resources
            • templates
              • PackageWizardPage.ftl
              • ValidationResultWizardPage.ftl
              • ImportResultsWizardPage.ftl
              • OptionsWizardPage.ftl
              • UploadWizardPage.ftl
            • l10n
              • data-import_nl.properties
              • data-import_en.properties
            • js
              • .gitignore
            • css
              • .gitignore
          • java
            • org
              • molgenis
                • data
                  • export
                    • EmxExportService.java
                    • TimeZoneProviderImpl.java
                    • TimeZoneProvider.java
                    • exception
                      • EmptyExportRequestException.java
                      • InvalidEmxIdentifierException.java
                      • EmxExportException.java
                    • mapper
                      • EntityTypeMapper.java
                      • AttributeMapper.java
                      • DataRowMapper.java
                      • PackageMapper.java
                    • EmxExportServiceImpl.java
                  • importer
                    • EntityImportReport.java
                    • ImportI18nConfig.java
                    • MetadataAction.java
                    • ImportBootstrapper.java
                    • ImportRunMetadata.java
                    • ImportServiceFactory.java
                    • ImportRunFactory.java
                    • DataPersister.java
                    • ImportService.java
                    • EntitiesValidationReportImpl.java
                    • MyEntitiesValidationReport.java
                    • emx
                      • ImporterConfiguration.java
                      • EmxAttribute.java
                      • ImportWriter.java
                      • IntermediateParseResults.java
                      • exception
                        • UnknownDataTypeException.java
                        • NillableReferenceAggregatableException.java
                        • SelfReferencingCompoundException.java
                        • InvalidDataTypeException.java
                        • DuplicateAttributeNameException.java
                        • InvalidCompoundException.java
                        • MissingEmxAttributeAttributeValueException.java
                        • EmxImportException.java
                        • PackageResolveException.java
                        • MissingRootPackageException.java
                        • InconsistentPackageStructureException.java
                        • InvalidReferenceDataTypeException.java
                        • InvalidRangeException.java
                        • MissingEmxAttributeValueException.java
                        • UnknownEmxAttributeException.java
                        • InvalidValueException.java
                        • AttributeNameCaseMismatchException.java
                        • MissingCompoundException.java
                        • UnknownEntityValueException.java
                        • InvalidEmxAttributeException.java
                      • EmxDataProvider.java
                      • EmxFileExtensions.java
                      • EmxImportService.java
                      • EmxImportJob.java
                      • EmxMetadataParser.java
                    • ImportJob.java
                    • PersistResult.java
                    • MetadataParser.java
                    • ParsedMetaData.java
                    • ImportRun.java
                    • ImportServiceRegistrar.java
                    • DataProvider.java
                    • ImportRunService.java
                    • DataPersisterImpl.java
                    • PackageResolver.java
                    • ImportStatus.java
                    • EntitiesValidationReport.java
        • test
          • resources
            • example_no_meta.xlsx
            • logback-test.xml
            • it_emx_autodate.xlsx
            • example_invalid.xlsx
            • example_extra_column.xlsx
            • example.xlsx
            • platform-map.properties
          • java
            • org
              • molgenis
                • data
                  • export
                    • DataRowMapperTest.java
                    • exception
                      • InvalidEmxIdentifierExceptionTest.java
                      • EmptyExportRequestExceptionTest.java
                      • EmxExportExceptionTest.java
                    • PackageMapperTest.java
                    • EntityTypeMapperTest.java
                    • EmxExportServiceImplTest.java
                    • AttributeMapperTest.java
                  • importer
                    • ImportBootstrapperTest.java
                    • ImportRunFactoryTest.java
                    • ImportRunTest.java
                    • PackageResolverTest.java
                    • config
                      • ImportTestConfig.java
                    • emx
                      • EmxImportServiceTest.java
                      • IntermediateParseResultsTest.java
                      • exception
                        • EmxImportExceptionTest.java
                        • MissingCompoundExceptionTest.java
                        • InvalidEmxAttributeExceptionTest.java
                        • MissingRootPackageExceptionTest.java
                        • InvalidValueExceptionTest.java
                        • UnknownEntityValueExceptionTest.java
                        • MissingEmxAttributeValueExceptionTest.java
                        • InvalidReferenceDataTypeExceptionTest.java
                        • InvalidRangeExceptionTest.java
                        • UnknownEmxAttributeExceptionTest.java
                        • PackageResolveExceptionTest.java
                        • InvalidCompoundExceptionTest.java
                        • UnknownDataTypeExceptionTest.java
                        • InvalidDataTypeExceptionTest.java
                        • InconsistentPackageStructureExceptionTest.java
                        • MissingEmxAttributeAttributeValueExceptionTest.java
                        • AttributeNameCaseMismatchExceptionTest.java
                        • SelfReferencingCompoundExceptionTest.java
                        • NillableReferenceAggregatableExceptionTest.java
                        • DuplicateAttributeNameExceptionTest.java
                      • EmxDataProviderTest.java
                      • ImportWriterTest.java
                      • EmxMetadataParserTest.java
                    • ImportRunServiceTest.java
                    • DataPersisterImplTest.java
      • pom.xml
    • molgenis-app
      • src
        • main
          • resources
            • img
              • logo_triumph_big.jpg
              • logo_trait.jpg
            • logback.xml
            • html
              • biomedbridges-d43.html
            • molgenis.properties
            • templates
              • view-monogenicDisorder-entitiesreport.ftl
              • view-GenomeReport-entitiesreport.ftl
            • molgenis_ui.json
            • sentry.properties
            • css
              • .gitignore
          • java
            • org
              • molgenis
                • app
                  • WebAppSystemEntityRegistry.java
                  • WebAppContextCleanupListener.java
                  • WebAppInitializer.java
                  • WebAppConfig.java
                  • WebAppPermissionRegistry.java
                  • WebAppSecurityConfig.java
                  • controller
                    • NewsController.java
                    • BackgroundController.java
                    • ReferencesController.java
                    • ContactController.java
                    • HomeController.java
        • test
          • resources
            • logback-test.xml
            • csv
              • TypeTestRef.csv
              • org_molgenis_test_TypeTest.csv
              • attributes.csv
              • entities.csv
              • packages.csv
            • file_datatype-test.xlsx
            • vcf
              • [email protected]$&.vcf
            • genome_browser_test_emx.xls
            • mutations
              • test_no_samples_1.vcf
              • test_no_samples_2.vcf
              • test_samples.vcf
              • mutations_emx.xls
            • tsv
              • TypeTestRef.tsv
            • zip
            • test_annotate_computed.xlsx
            • xls
              • emx_all_datatypes_metadata_only.xlsx
              • emx_violation_unique.xlsx
              • emx_violation_foreignkey.xlsx
              • emx_violation_notnull.xlsx
          • java
            • org
              • molgenis
                • app
                  • WebAppPermissionRegistryTest.java
                  • controller
                    • ContentControllersTest.java
            • .gitignore
      • dev-env
        • .env.example
        • init_db.sql
        • backend.conf.template
        • intellij-tomcat-env
        • docker-compose.yml
      • pom.xml
      • owasp-check-suppressions.xml
      • rpm
        • templates
          • molgenis-server.properties
        • preinstall.bash
        • postinstall.bash
      • README.md
      • Dockerfile
      • .gitignore
    • molgenis-questionnaires
      • src
        • main
          • resources
            • templates
              • view-questionnaire.ftl
            • l10n
              • questionnaire_en.properties
          • java
            • org
              • molgenis
                • questionnaires
                  • response
                    • QuestionnaireResponse.java
                  • config
                    • QuestionnaireConfig.java
                  • service
                    • impl
                      • QuestionnaireServiceImpl.java
                    • QuestionnaireService.java
                  • exception
                    • QuestionnaireNotRowLevelSecuredException.java
                  • meta
                    • QuestionnaireStatus.java
                    • QuestionnaireMetaData.java
                    • QuestionnaireFactory.java
                    • Questionnaire.java
                  • controller
                    • QuestionnaireController.java
        • test
          • resources
            • logback-test.xml
            • emx-questionnaire.xls
          • java
            • org
              • molgenis
                • questionnaires
                  • service
                    • QuestionnaireServiceTest.java
                  • controller
                    • QuestionnaireControllerTest.java
      • pom.xml
    • molgenis-settings-ui
      • src
        • main
          • resources
            • templates
              • view-settings.ftl
          • java
            • org
              • molgenis
                • settings
                  • controller
                    • SettingsController.java
        • test
          • java
            • org
              • molgenis
                • settings
                  • controller
                    • SettingsControllerTest.java
      • pom.xml
    • molgenis-test
      • src
        • main
          • java
            • org
              • molgenis
                • test
                  • AbstractMockitoSpringContextTests.java
                  • IsEqualJson.java
                  • TestResourceUtils.java
                  • AbstractMockitoTest.java
      • pom.xml
    • molgenis-api-permissions
      • src
        • main
          • resources
            • l10n
              • api-permissions_en.properties
          • java
            • org
              • molgenis
                • api
                  • permissions
                    • rsql
                      • PermissionsQuery.java
                      • PermissionRsqlVisitor.java
                    • PermissionsApiI18nConfig.java
                    • exceptions
                      • rsql
                        • PermissionQueryParseException.java
                        • UnsupportedPermissionQueryOperatorException.java
                        • UnknownPermissionQueryParamException.java
                      • UserAndRoleException.java
                      • MissingUserOrRoleException.java
                      • PageWithoutPageSizeException.java
                      • UnsupportedPermissionQueryException.java
                    • PermissionResponseUtils.java
                    • model
                      • response
                        • TypePermissionsResponse.java
                        • ObjectResponse.java
                        • PermissionResponse.java
                        • AllPermissionsResponse.java
                        • LabelledPermissionResponse.java
                        • ObjectPermissionResponse.java
                        • TypeResponse.java
                      • request
                        • SetTypePermissionsRequest.java
                        • SetObjectPermissionRequest.java
                        • DeletePermissionRequest.java
                        • TypePermissionsRequest.java
                        • ObjectPermissionsRequest.java
                        • PermissionRequest.java
                    • PermissionsController.java
        • test
          • java
            • org
              • molgenis
                • api
                  • permissions
                    • rsql
                      • PermissionRsqlVisitorTest.java
                    • PermissionsControllerTest.java
                    • exceptions
                      • PageWithoutPageSizeExceptionTest.java
                      • MissingUserOrRoleExceptionTest.java
                      • UnsupportedPermissionQueryExceptionTest.java
                      • rsql
                        • PermissionQueryParseExceptionTest.java
                        • UnknownPermissionQueryParamExceptionTest.java
                        • UnsupportedPermissionQueryOperatorExceptionTest.java
                      • UserAndRoleExceptionTest.java
      • pom.xml
    • .commit_template.txt
    • .travis.yml
    • README.md
    • molgenis-core
      • src
        • main
          • java
            • org
              • molgenis
                • core
                  • util
                    • FileUploadUtils.java
                    • package-info.java
                    • SchemaLoader.java
                    • CountryCodes.java
                    • ResourceFingerprintRegistry.java
                  • framework
                    • db
                      • WebAppDatabasePopulatorService.java
                    • ui
                      • ResourcePathPatterns.java
        • test
          • resources
            • logback-test.xml
            • test.xls
            • resource.txt
            • example.xsd
          • java
            • org
              • molgenis
                • core
                  • util
                    • ResourceFingerprintRegistryTest.java
                    • SchemaLoaderTest.java
                    • CountryCodesTest.java
                    • FileUploadUtilsTest.java
      • pom.xml
      • .gitignore
    • molgenis-core-ui
      • src
        • main
          • resources
            • img
              • sort_asc.gif
              • _logo_molgenis_old.gif
              • Logo_Green_Small.svg
              • grid-manage-icon.gif
              • editview.gif
              • sort_desc.gif
              • exit.bmp
              • update.gif
              • Logo_Black_Small.svg
              • favicon.ico
              • bg-body.jpg
              • pulldown.gif
              • bg-footer.jpg
              • Logo_White_Small.svg
              • _logo_molgenis.gif
              • waiting-spinner.gif
              • Logo_Blue_Small.svg
              • logo_molgenis.gif
              • bg-mainNav.jpg
            • html
              • unsupported-browser-message.html
            • templates
              • view-feedback.ftl
              • view-job.ftl
              • view-wizard.ftl
              • theme-macros.ftl
              • view-void.ftl
              • view-staticcontent-edit.ftl
              • view-menumanager.ftl
              • resource-macros.ftl
              • molgenis-header.ftl
              • molgenis-footer.ftl
              • molgenis-header-tracking.ftl
              • view-jobs.ftl
              • view-staticcontent.ftl
              • view-scheduled-jobs.ftl
              • view-thememanager.ftl
              • polyfill-macros.ftl
            • l10n
              • feedback_en.properties
              • core-ui_nl.properties
              • core-ui_en.properties
              • ui-form_en.properties
              • ui-form_nl.properties
              • feedback_nl.properties
              • form_en.properties
              • form_nl.properties
              • dataexplorer_en.properties
            • fonts
              • fontawesome-webfont.674f50d.eot
              • glyphicons-halflings-regular.woff
              • glyphicons-halflings-regular.eot
              • glyphicons-halflings-regular.woff2
              • IBM_Plex_Mono
                • IBMPlexMono-Regular.woff
                • IBMPlexMono-Regular.ttf
                • IBMPlexMono-Regular.woff2
              • glyphicons-halflings-regular.ttf
              • fontawesome-webfont.af7ae50.woff2
              • IBM_Plex_Sans
                • IBMPlexSans-Regular.woff
                • IBMPlexSans-Regular.ttf
                • IBMPlexSans-Regular.woff2
              • BebasNeue
                • BebasNeue-Regular.woff2
                • BebasNeue-Regular.ttf
                • BebasNeue-Regular.woff
              • fontawesome-webfont.fee66e7.woff
              • glyphicons-halflings-regular.svg
              • fontawesome-webfont.b06871f.ttf
            • js
              • ace
                • src-min-noconflict
                  • mode-rust.js
                  • mode-curly.js
                  • worker-json.js
                  • ext-statusbar.js
                  • mode-jade.js
                  • theme-tomorrow_night_bright.js
                  • mode-autohotkey.js
                  • ext-language_tools.js
                  • mode-groovy.js
                  • mode-eiffel.js
                  • theme-dawn.js
                  • theme-clouds_midnight.js
                  • theme-solarized_light.js
                  • theme-xcode.js
                  • mode-twig.js
                  • theme-textmate.js
                  • mode-stylus.js
                  • ext-searchbox.js
                  • worker-javascript.js
                  • mode-json.js
                  • mode-ftl.js
                  • worker-php.js
                  • mode-jack.js
                  • theme-solarized_dark.js
                  • mode-c_cpp.js
                  • mode-lua.js
                  • mode-yaml.js
                  • theme-tomorrow_night.js
                  • theme-merbivore_soft.js
                  • worker-xml.js
                  • mode-svg.js
                  • mode-typescript.js
                  • mode-xml.js
                  • mode-matlab.js
                  • mode-javascript.js
                  • mode-perl.js
                  • mode-live_script.js
                  • mode-space.js
                  • mode-gitignore.js
                  • theme-tomorrow_night_blue.js
                  • mode-django.js
                  • mode-scala.js
                  • mode-r.js
                  • snippets
                    • yaml.js
                    • haml.js
                    • rust.js
                    • scheme.js
                    • pgsql.js
                    • praat.js
                    • cirru.js
                    • html.js
                    • pascal.js
                    • jsoniq.js
                    • coldfusion.js
                    • csharp.js
                    • java.js
                    • powershell.js
                    • logiql.js
                    • toml.js
                    • snippets.js
                    • asciidoc.js
                    • glsl.js
                    • php.js
                    • haxe.js
                    • live_script.js
                    • textile.js
                    • lucene.js
                    • space.js
                    • sjs.js
                    • scad.js
                    • vala.js
                    • xquery.js
                    • jack.js
                    • rdoc.js
                    • less.js
                    • mysql.js
                    • makefile.js
                    • forth.js
                    • vbscript.js
                    • tcl.js
                    • gcode.js
                    • dot.js
                    • mushcode.js
                    • matlab.js
                    • javascript.js
                    • jade.js
                    • properties.js
                    • css.js
                    • curly.js
                    • sass.js
                    • lisp.js
                    • tex.js
                    • autohotkey.js
                    • diff.js
                    • gitignore.js
                    • scala.js
                    • typescript.js
                    • prolog.js
                    • coffee.js
                    • verilog.js
                    • mipsassembler.js
                    • actionscript.js
                    • soy_template.js
                    • lua.js
                    • elixir.js
                    • elm.js
                    • ada.js
                    • text.js
                    • julia.js
                    • ocaml.js
                    • jsp.js
                    • django.js
                    • lean.js
                    • dart.js
                    • mel.js
                    • objectivec.js
                    • c9search.js
                    • livescript.js
                    • twig.js
                    • erlang.js
                    • ini.js
                    • rhtml.js
                    • perl.js
                    • golang.js
                    • cobol.js
                    • plain_text.js
                    • velocity.js
                    • clojure.js
                    • groovy.js
                    • sh.js
                    • nix.js
                    • assembly_x86.js
                    • abc.js
                    • markdown.js
                    • mips_assembler.js
                    • ruby.js
                    • gherkin.js
                    • c_cpp.js
                    • applescript.js
                    • python.js
                    • jsx.js
                    • ejs.js
                    • protobuf.js
                    • sql.js
                    • html_ruby.js
                    • abap.js
                    • batchfile.js
                    • vhdl.js
                    • haskell.js
                    • dockerfile.js
                    • handlebars.js
                    • lsl.js
                    • liquid.js
                    • luapage.js
                    • svg.js
                    • io.js
                    • mask.js
                    • d.js
                    • xml.js
                    • apache_conf.js
                    • r.js
                    • smarty.js
                    • stylus.js
                    • json.js
                    • scss.js
                    • latex.js
                    • eiffel.js
                    • ftl.js
                  • mode-applescript.js
                  • mode-csharp.js
                  • mode-html_ruby.js
                  • theme-twilight.js
                  • mode-io.js
                  • mode-glsl.js
                  • mode-haml.js
                  • ext-linking.js
                  • theme-kr_theme.js
                  • mode-abap.js
                  • mode-sass.js
                  • mode-mysql.js
                  • theme-tomorrow.js
                  • mode-cobol.js
                  • mode-liquid.js
                  • mode-mel.js
                  • mode-coffee.js
                  • mode-powershell.js
                  • mode-scss.js
                  • mode-protobuf.js
                  • mode-livescript.js
                  • mode-ini.js
                  • mode-python.js
                  • mode-tcl.js
                  • ext-error_marker.js
                  • mode-erlang.js
                  • mode-luapage.js
                  • mode-gherkin.js
                  • theme-idle_fingers.js
                  • mode-rdoc.js
                  • ext-emmet.js
                  • mode-batchfile.js
                  • mode-tex.js
                  • mode-lean.js
                  • mode-forth.js
                  • mode-cirru.js
                  • mode-markdown.js
                  • mode-diff.js
                  • mode-logiql.js
                  • mode-ruby.js
                  • mode-vala.js
                  • mode-lisp.js
                  • mode-coldfusion.js
                  • mode-prolog.js
                  • ext-static_highlight.js
                  • mode-sql.js
                  • mode-smarty.js
                  • mode-php.js
                  • mode-jsx.js
                  • mode-haskell.js
                  • mode-vbscript.js
                  • ext-elastic_tabstops_lite.js
                  • mode-assembly_x86.js
                  • theme-kuroir.js
                  • mode-less.js
                  • ext-settings_menu.js
                  • mode-mipsassembler.js
                  • mode-toml.js
                  • theme-katzenmilch.js
                  • ext-keybinding_menu.js
                  • mode-asciidoc.js
                  • mode-scad.js
                  • ext-whitespace.js
                  • mode-nix.js
                  • mode-mips_assembler.js
                  • ext-spellcheck.js
                  • theme-monokai.js
                  • theme-eclipse.js
                  • ext-old_ie.js
                  • mode-java.js
                  • mode-html.js
                  • theme-mono_industrial.js
                  • mode-properties.js
                  • ext-split.js
                  • ext-beautify.js
                  • mode-actionscript.js
                  • mode-dart.js
                  • mode-dot.js
                  • mode-apache_conf.js
                  • mode-latex.js
                  • mode-julia.js
                  • ext-chromevox.js
                  • mode-sjs.js
                  • theme-github.js
                  • mode-objectivec.js
                  • theme-terminal.js
                  • mode-ada.js
                  • worker-css.js
                  • ext-textarea.js
                  • mode-dockerfile.js
                  • theme-dreamweaver.js
                  • theme-crimson_editor.js
                  • mode-snippets.js
                  • mode-sh.js
                  • theme-merbivore.js
                  • mode-verilog.js
                  • mode-textile.js
                  • mode-golang.js
                  • theme-ambiance.js
                  • mode-vhdl.js
                  • mode-scheme.js
                  • mode-plain_text.js
                  • theme-cobalt.js
                  • mode-ejs.js
                  • mode-mask.js
                  • ext-themelist.js
                  • theme-vibrant_ink.js
                  • mode-elm.js
                  • theme-tomorrow_night_eighties.js
                  • mode-jsp.js
                  • mode-praat.js
                  • mode-pgsql.js
                  • keybinding-emacs.js
                  • mode-handlebars.js
                  • mode-text.js
                  • worker-lua.js
                  • mode-lucene.js
                  • mode-soy_template.js
                  • ext-modelist.js
                  • mode-ocaml.js
                  • theme-clouds.js
                  • mode-gcode.js
                  • mode-css.js
                  • theme-chrome.js
                  • mode-elixir.js
                  • mode-mushcode.js
                  • mode-d.js
                  • mode-c9search.js
                  • mode-rhtml.js
                  • theme-pastel_on_dark.js
                  • theme-chaos.js
                  • mode-haxe.js
                  • keybinding-vim.js
                  • mode-pascal.js
                  • mode-lsl.js
                  • mode-clojure.js
                  • mode-velocity.js
                  • mode-abc.js
                  • mode-makefile.js
              • molgenis.js
              • bootstrap.min.js
              • bootstrap-datetimepicker.min.js
              • jquery.form.min.js
              • URI.js
              • jquery.cookie-1.4.1.min.js
              • additional-methods.min.js
              • thememanager.js
              • svg-pan-zoom.min.js
              • handlebars.min.js
              • bootstrap-fileupload.min.js
              • select2-patched.js
              • jquery-ui-1.9.2.custom.min.js
              • bootbox.min.js
              • menumanager.js
              • direct-repository-query.js
              • qrcode.min.js
              • logmanager.js
              • ckeditor
                • samples
                  • toolbarconfigurator
                    • lib
                      • codemirror
                        • codemirror.js
                        • show-hint.js
                        • javascript.js
                        • LICENSE
                        • neo.css
                        • show-hint.css
                        • codemirror.css
                    • js
                      • abstracttoolbarmodifier.js
                      • toolbartextmodifier.js
                      • toolbarmodifier.js
                      • fulltoolbareditor.js
                    • index.html
                    • font
                      • config.json
                      • fontello.svg
                      • fontello.eot
                      • fontello.woff
                      • fontello.ttf
                      • LICENSE.txt
                    • css
                      • fontello.css
                  • img
                  • old
                    • divreplace.html
                    • dialog
                      • dialog.html
                      • assets
                        • my_dialog.js
                    • sample.js
                    • sample.css
                    • readonly.html
                    • toolbar
                      • toolbar.html
                    • inlinebycode.html
                    • magicline
                      • magicline.html
                    • replacebyclass.html
                    • htmlwriter
                      • outputhtml.html
                      • outputforflash.html
                      • assets
                        • outputforflash
                          • outputforflash.fla
                          • swfobject.js
                          • outputforflash.swf
                    • datafiltering.html
                    • jquery.html
                    • xhtmlstyle.html
                    • tabindex.html
                    • inlinetextarea.html
                    • ajax.html
                    • wysiwygarea
                      • fullpage.html
                    • uicolor.html
                    • appendto.html
                    • inlineall.html
                    • sample_posteddata.php
                    • enterkey
                      • enterkey.html
                    • index.html
                    • api.html
                    • replacebycode.html
                    • uilanguages.html
                    • assets
                      • outputxhtml
                        • outputxhtml.css
                      • sample.jpg
                      • posteddata.php
                      • uilanguages
                        • languages.js
                      • inlineall
                  • js
                    • sf.js
                    • sample.js
                  • index.html
                  • css
                    • samples.css
                • skins
                  • moono
                    • editor_gecko.css
                    • dialog_ie7.css
                    • editor_ie8.css
                    • images
                      • hidpi
                      • spinner.gif
                    • dialog_ie.css
                    • editor_iequirks.css
                    • editor.css
                    • readme.md
                    • editor_ie7.css
                    • dialog.css
                    • dialog_ie8.css
                    • editor_ie.css
                    • dialog_iequirks.css
                • CHANGES.md
                • styles.js
                • plugins
                  • dialog
                    • dialogDefinition.js
                  • about
                    • dialogs
                      • hidpi
                      • about.js
                  • scayt
                    • dialogs
                      • options.js
                      • toolbar.css
                    • CHANGELOG.md
                    • LICENSE.md
                    • README.md
                  • magicline
                    • images
                      • hidpi
                  • clipboard
                    • dialogs
                      • paste.js
                  • link
                    • dialogs
                      • link.js
                      • anchor.js
                    • images
                      • hidpi
                  • specialchar
                    • dialogs
                      • lang
                        • nl.js
                        • si.js
                        • tr.js
                        • ca.js
                        • sl.js
                        • el.js
                        • ja.js
                        • ug.js
                        • eu.js
                        • cy.js
                        • de-ch.js
                        • th.js
                        • eo.js
                        • zh.js
                        • cs.js
                        • tt.js
                        • de.js
                        • fr-ca.js
                        • en.js
                        • fi.js
                        • en-gb.js
                        • es.js
                        • fr.js
                        • et.js
                        • no.js
                        • hu.js
                        • gl.js
                        • nb.js
                        • bg.js
                        • sk.js
                        • pt-br.js
                        • uk.js
                        • af.js
                        • ko.js
                        • lt.js
                        • lv.js
                        • he.js
                        • zh-cn.js
                        • vi.js
                        • pl.js
                        • ku.js
                        • ar.js
                        • ru.js
                        • sv.js
                        • _translationstatus.txt
                        • da.js
                        • fa.js
                        • hr.js
                        • sq.js
                        • id.js
                        • km.js
                        • pt.js
                        • it.js
                      • specialchar.js
                  • table
                    • dialogs
                      • table.js
                  • pastefromword
                    • filter
                      • default.js
                  • a11yhelp
                    • dialogs
                      • lang
                        • nl.js
                        • hi.js
                        • si.js
                        • tr.js
                        • ca.js
                        • sl.js
                        • el.js
                        • ja.js
                        • ug.js
                        • mk.js
                        • eu.js
                        • cy.js
                        • de-ch.js
                        • mn.js
                        • th.js
                        • eo.js
                        • zh.js
                        • cs.js
                        • fo.js
                        • tt.js
                        • de.js
                        • fr-ca.js
                        • en.js
                        • fi.js
                        • ro.js
                        • en-gb.js
                        • es.js
                        • fr.js
                        • et.js
                        • no.js
                        • hu.js
                        • gl.js
                        • nb.js
                        • bg.js
                        • sr.js
                        • gu.js
                        • sk.js
                        • pt-br.js
                        • uk.js
                        • af.js
                        • ko.js
                        • lt.js
                        • lv.js
                        • he.js
                        • zh-cn.js
                        • vi.js
                        • pl.js
                        • ku.js
                        • ar.js
                        • ru.js
                        • sr-latn.js
                        • sv.js
                        • _translationstatus.txt
                        • da.js
                        • fa.js