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

A

activateCatalog(String) - Method in interface org.molgenis.catalogmanager.CatalogManagerService

Activate a catalog

activateCatalog(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

add(Entity) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

add(Iterable<? extends Entity>) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

addChild(CatalogModelFolder) - Method in class org.molgenis.catalog.CatalogModelFolder

addItem(CatalogModelItem) - Method in class org.molgenis.catalog.CatalogModelFolder

addToCart(ProtocolViewerController.CartUpdateRequest, Integer) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

addToStudyDefinitionDraftForCurrentUser(String, String) - Method in interface org.molgenis.omx.protocolviewer.ProtocolViewerService

Add a catalog item or catalog group (implies all items in a group) to the study definition draft

addToStudyDefinitionDraftForCurrentUser(String, String) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

addUserRule(Query) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

C

canLoadStudyData() - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

canLoadStudyData() - Method in interface org.molgenis.studymanager.StudyManagerService

Returns whether study data loading is enabled

Catalog - Interface in org.molgenis.catalog

CatalogFolder - Interface in org.molgenis.catalog

CatalogItem - Interface in org.molgenis.catalog

CatalogManagerController - Class in org.molgenis.catalogmanager

CatalogManagerController(CatalogManagerService) - Constructor for class org.molgenis.catalogmanager.CatalogManagerController

CatalogManagerService - Interface in org.molgenis.catalogmanager

Manage catalog releases

CatalogMeta - Class in org.molgenis.catalog

Catalog meta data

CatalogMeta(String, String) - Constructor for class org.molgenis.catalog.CatalogMeta

CatalogMetaModel - Class in org.molgenis.catalogmanager

CatalogMetaModel(String, String, boolean, boolean) - Constructor for class org.molgenis.catalogmanager.CatalogMetaModel

CatalogModel - Class in org.molgenis.catalog

CatalogModel() - Constructor for class org.molgenis.catalog.CatalogModel

CatalogModelBuilder - Class in org.molgenis.catalog

CatalogModelFolder - Class in org.molgenis.catalog

CatalogModelFolder() - Constructor for class org.molgenis.catalog.CatalogModelFolder

CatalogModelItem - Class in org.molgenis.catalog

CatalogModelItem(String, String, boolean) - Constructor for class org.molgenis.catalog.CatalogModelItem

CatalogService - Interface in org.molgenis.catalog

containsItem(CatalogItem) - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

containsItem(CatalogItem) - Method in interface org.molgenis.study.StudyDefinition

containsItem(CatalogItem) - Method in class org.molgenis.study.StudyDefinitionImpl

count() - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

count(Query) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

create(Catalog) - Static method in class org.molgenis.catalog.CatalogModelBuilder

create(Catalog, StudyDefinition) - Static method in class org.molgenis.catalog.CatalogModelBuilder

create(Catalog, StudyDefinition, boolean) - Static method in class org.molgenis.catalog.CatalogModelBuilder

createStudyDefinition(String, String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

createStudyDefinition(String, String, String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

createStudyDefinition(String, String) - Method in interface org.molgenis.studymanager.StudyManagerService

Creates a new study definition for the given user based on a catalog

createStudyDefinitionDraftForCurrentUser(String) - Method in interface org.molgenis.omx.protocolviewer.ProtocolViewerService

Creates a study definition draft for the current logged in user

createStudyDefinitionDraftForCurrentUser(String) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

createStudyDefinitionDraftXlsForCurrentUser(OutputStream, String) - Method in interface org.molgenis.omx.protocolviewer.ProtocolViewerService

Write the study definition draft for the current user to the given stream

createStudyDefinitionDraftXlsForCurrentUser(OutputStream, String) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

D

deactivateCatalog(String, Model) - Method in class org.molgenis.catalogmanager.CatalogManagerController

deactivateCatalog(String) - Method in interface org.molgenis.catalogmanager.CatalogManagerService

Deactivate a catalog

deactivateCatalog(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

delete(Entity) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

delete(Iterable<? extends Entity>) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

deleteAll() - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

deleteById(Object) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

deleteById(Iterable<Object>) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

downloadSelection(HttpServletResponse, Integer) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

downloadStudyDefinition(String, HttpServletResponse) - Method in class org.molgenis.studymanager.StudyManagerController

E

ENTITY_NAME - Static variable in class org.molgenis.omx.study.StudyDataRequest

equals(Object) - Method in class org.molgenis.catalogmanager.CatalogMetaModel

equals(Object) - Method in class org.molgenis.omx.study.StudyDataRequest

equals(Object) - Method in class org.molgenis.studymanager.StudyDefinitionMetaModel

EXPORT_BTN_TITLE - Static variable in class org.molgenis.studymanager.StudyManagerController

EXPORT_ENABLED - Static variable in class org.molgenis.studymanager.StudyManagerController

exportStudyDefinition(String, String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

exportStudyDefinition(String) - Method in class org.molgenis.studymanager.StudyManagerController

exportStudyDefinition(String, String) - Method in interface org.molgenis.studymanager.StudyManagerService

Submit the draft study definition for the given catalog

F

FEATURES - Static variable in class org.molgenis.omx.study.StudyDataRequest

findAll(Query) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

findAll(Iterable<Object>) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

findAll(Query, Class<E>) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

findAll(Iterable<Object>, Class<E>) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

findItem(String) - Method in interface org.molgenis.catalog.Catalog

findItem(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalog

findOne(Query) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

findOne(Object) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

findStudyDefinitions(StudyDefinition.Status, String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

findStudyDefinitions(StudyDefinition.Status, String) - Method in interface org.molgenis.studymanager.StudyManagerService

Search study definitions

G

get(String) - Method in class org.molgenis.omx.study.StudyDataRequest

Generic getter.

getAttributeNames() - Method in class org.molgenis.omx.study.StudyDataRequest

getAuthorEmail() - Method in interface org.molgenis.catalog.Catalog

getAuthorEmail() - Method in class org.molgenis.omx.catalogmanager.OmxCatalog

getAuthorEmail() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getAuthorEmail() - Method in interface org.molgenis.study.StudyDefinition

getAuthorEmail() - Method in class org.molgenis.study.StudyDefinitionImpl

getAuthors() - Method in interface org.molgenis.catalog.Catalog

getAuthors() - Method in class org.molgenis.catalog.CatalogMeta

getAuthors() - Method in class org.molgenis.catalog.CatalogModel

getAuthors() - Method in class org.molgenis.omx.catalogmanager.OmxCatalog

getAuthors() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getAuthors() - Method in interface org.molgenis.study.StudyDefinition

getAuthors() - Method in class org.molgenis.study.StudyDefinitionImpl

getCatalog(String) - Method in interface org.molgenis.catalog.CatalogService

Get the catalog with the given id

getCatalog(String) - Method in class org.molgenis.catalogmanager.CatalogManagerController

getCatalog(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

getCatalogItemIds() - Method in class org.molgenis.studymanager.StudyManagerController.StudyDefinitionUpdateRequest

getCatalogOfStudyDefinition(String) - Method in interface org.molgenis.catalog.CatalogService

Get the catalog of the study definition with the given id

getCatalogOfStudyDefinition(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

getCatalogs() - Method in interface org.molgenis.catalog.CatalogService

Gets all available catalogs

getCatalogs() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

getCatalogs() - Method in interface org.molgenis.omx.protocolviewer.ProtocolViewerService

Gets all active catalog meta data

getCatalogs() - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

getCatalogWithStudyDefinition(String) - Method in class org.molgenis.studymanager.StudyManagerController

getChildren() - Method in interface org.molgenis.catalog.CatalogFolder

getChildren() - Method in class org.molgenis.catalog.CatalogModelFolder

getChildren() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogFolder

getCode() - Method in interface org.molgenis.catalog.CatalogItem

getCode() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogItem

getCode() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinitionItem

getCodeSystem() - Method in interface org.molgenis.catalog.CatalogItem

getCodeSystem() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogItem

getCodeSystem() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinitionItem

getDate() - Method in class org.molgenis.study.StudyDefinitionMeta

getDate() - Method in class org.molgenis.studymanager.StudyDefinitionMetaModel

getDateCreated() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getDateCreated() - Method in interface org.molgenis.study.StudyDefinition

getDateCreated() - Method in class org.molgenis.study.StudyDefinitionImpl

getDescription() - Method in interface org.molgenis.catalog.CatalogFolder

getDescription() - Method in interface org.molgenis.catalog.CatalogItem

getDescription() - Method in class org.molgenis.catalog.CatalogMeta

getDescription() - Method in class org.molgenis.catalog.CatalogModel

getDescription() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogFolder

getDescription() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogItem

getDescription() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getDescription() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinitionItem

getDescription() - Method in interface org.molgenis.study.StudyDefinition

getDescription() - Method in class org.molgenis.study.StudyDefinitionImpl

getEmail() - Method in class org.molgenis.study.StudyDefinitionMeta

getEntityMetaData() - Method in class org.molgenis.omx.study.StudyDataRequest

getEntityName() - Method in class org.molgenis.omx.study.StudyDataRequest

getFeatures() - Method in class org.molgenis.omx.study.StudyDataRequest

Get the .

getId() - Method in interface org.molgenis.catalog.CatalogFolder

getId() - Method in interface org.molgenis.catalog.CatalogItem

getId() - Method in class org.molgenis.catalog.CatalogMeta

getId() - Method in class org.molgenis.catalog.CatalogModelFolder

getId() - Method in class org.molgenis.catalog.CatalogModelItem

getId() - Method in class org.molgenis.catalogmanager.CatalogMetaModel

getId() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogFolder

getId() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogItem

getId() - Method in class org.molgenis.omx.study.StudyDataRequest

Get the automatically generated internal id, only for internal use..

getId() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getId() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinitionItem

getId() - Method in interface org.molgenis.study.StudyDefinition

getId() - Method in class org.molgenis.study.StudyDefinitionImpl

getIdentifier() - Method in class org.molgenis.omx.study.StudyDataRequest

Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

getIdValue() - Method in class org.molgenis.omx.study.StudyDataRequest

getItems() - Method in interface org.molgenis.catalog.CatalogFolder

getItems() - Method in class org.molgenis.catalog.CatalogModelFolder

getItems() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogFolder

getItems() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getItems() - Method in interface org.molgenis.study.StudyDefinition

getItems() - Method in class org.molgenis.study.StudyDefinitionImpl

getItemsFromIndex(Map<String, Object>) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

getLabelAttributeNames() - Method in class org.molgenis.omx.study.StudyDataRequest

getMolgenisUser() - Method in class org.molgenis.omx.study.StudyDataRequest

Get the .

getName() - Method in interface org.molgenis.catalog.CatalogFolder

getName() - Method in interface org.molgenis.catalog.CatalogItem

getName() - Method in class org.molgenis.catalog.CatalogMeta

getName() - Method in class org.molgenis.catalog.CatalogModelFolder

getName() - Method in class org.molgenis.catalog.CatalogModelItem

getName() - Method in class org.molgenis.catalogmanager.CatalogMetaModel

getName() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogFolder

getName() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogItem

getName() - Method in class org.molgenis.omx.study.StudyDataRequest

Get the human readible name, not necessary unique..

getName() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getName() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinitionItem

getName() - Method in interface org.molgenis.study.StudyDefinition

getName() - Method in class org.molgenis.study.StudyDefinitionImpl

getOrderDataForm() - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

getOrderDetailsForm(Integer) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

getOrders() - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

getOrdersForm() - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

getPath() - Method in interface org.molgenis.catalog.CatalogItem

getPath() - Method in class org.molgenis.omx.catalogmanager.OmxCatalogItem

getPath() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinitionItem

getProtocol() - Method in class org.molgenis.omx.study.StudyDataRequest

Get the protocol used to create request.

getRequestDate() - Method in class org.molgenis.omx.study.StudyDataRequest

Get the request date.

getRequestForm() - Method in class org.molgenis.omx.study.StudyDataRequest

Get the request form filename.

getRequestProposalForm() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getRequestProposalForm() - Method in interface org.molgenis.study.StudyDefinition

Get the request proposal form filename

getRequestProposalForm() - Method in class org.molgenis.study.StudyDefinitionImpl

getRequestStatus() - Method in class org.molgenis.omx.study.StudyDataRequest

Get the .

getRequestStatusLabel() - Method in class org.molgenis.omx.study.StudyDataRequest

Get tha label for enum RequestStatus.

getRequestStatusOptions() - Method in class org.molgenis.omx.study.StudyDataRequest

RequestStatus is enum.

getSelection(Integer, Integer, Integer, String[]) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

getStatus() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getStatus() - Method in interface org.molgenis.study.StudyDefinition

getStatus() - Method in class org.molgenis.study.StudyDefinitionImpl

getStatus() - Method in class org.molgenis.studymanager.StudyManagerController.StudyDefinitionUpdateRequest

getStudyDataRequest() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getStudyDefinition(String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

getStudyDefinition(String) - Method in interface org.molgenis.studymanager.StudyManagerService

Find the study definition with the given id

getStudyDefinitionAsCatalog(String) - Method in class org.molgenis.studymanager.StudyManagerController

getStudyDefinitionDraftForCurrentUser(String) - Method in interface org.molgenis.omx.protocolviewer.ProtocolViewerService

Gets the current study definition draft for the current logged in user

getStudyDefinitionDraftForCurrentUser(String) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

getStudyDefinitionForCurrentUser(Integer) - Method in interface org.molgenis.omx.protocolviewer.ProtocolViewerService

Returns the given order for the current user

getStudyDefinitionForCurrentUser(Integer) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

getStudyDefinitions() - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

getStudyDefinitions(StudyDefinition.Status) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

getStudyDefinitions(String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

getStudyDefinitions(Model) - Method in class org.molgenis.studymanager.StudyManagerController

Show the available studydefinitions.

getStudyDefinitions() - Method in class org.molgenis.studymanager.StudyManagerController.StudyDefinitionsMetaResponse

getStudyDefinitions() - Method in interface org.molgenis.studymanager.StudyManagerService

Find all study definitions

getStudyDefinitions(StudyDefinition.Status) - Method in interface org.molgenis.studymanager.StudyManagerService

Find all study definition with the given status

getStudyDefinitions(String) - Method in interface org.molgenis.studymanager.StudyManagerService

Find all studydefinitions of a user

getStudyDefinitionsForCurrentUser() - Method in interface org.molgenis.omx.protocolviewer.ProtocolViewerService

Returns order for the current user

getStudyDefinitionsForCurrentUser() - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

getStudyDefinitionsMeta(StudyDefinition.Status, String) - Method in class org.molgenis.studymanager.StudyManagerController

Returns a list of meta data for each study definition

getTitle() - Method in class org.molgenis.catalog.CatalogModel

getUser() - Method in class org.molgenis.studymanager.StudyDefinitionMetaModel

getVersion() - Method in interface org.molgenis.catalog.Catalog

getVersion() - Method in class org.molgenis.catalog.CatalogMeta

getVersion() - Method in class org.molgenis.catalog.CatalogModel

getVersion() - Method in class org.molgenis.omx.catalogmanager.OmxCatalog

getVersion() - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

getVersion() - Method in interface org.molgenis.study.StudyDefinition

getVersion() - Method in class org.molgenis.study.StudyDefinitionImpl

H

handleException(Exception, HttpServletRequest) - Method in class org.molgenis.catalogmanager.CatalogManagerController

handleException(Exception) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

handleException(Exception) - Method in class org.molgenis.studymanager.StudyManagerController

handleRuntimeException(RuntimeException) - Method in class org.molgenis.studymanager.StudyManagerController

handleUnknownCatalogException(UnknownCatalogException) - Method in class org.molgenis.catalogmanager.CatalogManagerController

hashCode() - Method in class org.molgenis.catalogmanager.CatalogMetaModel

hashCode() - Method in class org.molgenis.omx.study.StudyDataRequest

hashCode() - Method in class org.molgenis.studymanager.StudyDefinitionMetaModel

I

ID - Static variable in class org.molgenis.catalogmanager.CatalogManagerController

ID - Static variable in class org.molgenis.omx.protocolviewer.ProtocolViewerController

ID - Static variable in class org.molgenis.omx.study.StudyDataRequest

ID - Static variable in class org.molgenis.studymanager.StudyManagerController

IDENTIFIER - Static variable in class org.molgenis.omx.study.StudyDataRequest

init(Model) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

isActivated() - Method in class org.molgenis.catalogmanager.CatalogMetaModel

isCatalogActivated(String) - Method in interface org.molgenis.catalog.CatalogService

Returns whether the catalog with the given id is activated

isCatalogActivated(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

isCatalogLoaded(String) - Method in interface org.molgenis.catalog.CatalogService

Returns whether the catalog with the given id is loaded

isCatalogLoaded(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

isCatalogOfStudyDefinitionLoaded(String) - Method in interface org.molgenis.catalog.CatalogService

Returns whether the catalog for the study definition with the given id is loaded

isCatalogOfStudyDefinitionLoaded(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

isLoaded() - Method in class org.molgenis.catalogmanager.CatalogMetaModel

isSelected() - Method in class org.molgenis.catalog.CatalogModelFolder

isSelected() - Method in class org.molgenis.catalog.CatalogModelItem

isStudyDataActivated(String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

isStudyDataActivated(String) - Method in interface org.molgenis.studymanager.StudyManagerService

Returns whether study definition data is loaded

isStudyDataLoaded(String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

isStudyDataLoaded(String) - Method in interface org.molgenis.studymanager.StudyManagerService

Returns whether study definition data is loaded

iterator() - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

iterator(Class<E>) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

J

JDBCMetaDatabase - Class in org.molgenis

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

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

K

KEY_ACTION_DOWNLOAD - Static variable in class org.molgenis.omx.protocolviewer.ProtocolViewerController

KEY_ACTION_ORDER - Static variable in class org.molgenis.omx.protocolviewer.ProtocolViewerController

L

listCatalogs(Model) - Method in class org.molgenis.catalogmanager.CatalogManagerController

Show the available catalogs.

LOAD_LIST_URI - Static variable in class org.molgenis.catalogmanager.CatalogManagerController

loadCatalog(String, Model) - Method in class org.molgenis.catalogmanager.CatalogManagerController

Loads a catalog by it's id.

loadCatalog(String) - Method in interface org.molgenis.catalogmanager.CatalogManagerService

Retrieves a catalog and store it in the database

loadCatalog(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

loadCatalogOfStudyDefinition(String) - Method in interface org.molgenis.catalogmanager.CatalogManagerService

Retrieves a catalog of a study definition and store it in the database

loadCatalogOfStudyDefinition(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

loadStudyData(String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

loadStudyData(String) - Method in interface org.molgenis.studymanager.StudyManagerService

Retrieve a study definition and save it in the database

loadStudyDefinition(String, Model) - Method in class org.molgenis.studymanager.StudyManagerController

Loads a studydefinition by it's id.

M

MOLGENISUSER - Static variable in class org.molgenis.omx.study.StudyDataRequest

N

NAME - Static variable in class org.molgenis.omx.study.StudyDataRequest

O

OmxCatalog - Class in org.molgenis.omx.catalogmanager

OmxCatalog(Protocol, DataService) - Constructor for class org.molgenis.omx.catalogmanager.OmxCatalog

OmxCatalogFolder - Class in org.molgenis.omx.catalogmanager

OmxCatalogFolder(Protocol) - Constructor for class org.molgenis.omx.catalogmanager.OmxCatalogFolder

OmxCatalogItem - Class in org.molgenis.omx.catalogmanager

OmxCatalogItem(ObservableFeature) - Constructor for class org.molgenis.omx.catalogmanager.OmxCatalogItem

OmxCatalogManagerService - Class in org.molgenis.omx.catalogmanager

OmxCatalogManagerService(DataService) - Constructor for class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

OmxStudyDefinition - Class in org.molgenis.omx.studymanager

OmxStudyDefinition(StudyDataRequest, DataService) - Constructor for class org.molgenis.omx.studymanager.OmxStudyDefinition

OmxStudyDefinitionItem - Class in org.molgenis.omx.studymanager

OmxStudyDefinitionItem(ObservableFeature, Integer) - Constructor for class org.molgenis.omx.studymanager.OmxStudyDefinitionItem

OmxStudyManagerService - Class in org.molgenis.omx.studymanager

OmxStudyManagerService(DataService, MolgenisUserService) - Constructor for class org.molgenis.omx.studymanager.OmxStudyManagerService

orderData(Integer, String, Part) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

org.molgenis - package org.molgenis

org.molgenis.catalog - package org.molgenis.catalog

org.molgenis.catalogmanager - package org.molgenis.catalogmanager

org.molgenis.omx.catalogmanager - package org.molgenis.omx.catalogmanager

org.molgenis.omx.protocolviewer - package org.molgenis.omx.protocolviewer

org.molgenis.omx.study - package org.molgenis.omx.study

org.molgenis.omx.studymanager - package org.molgenis.omx.studymanager

org.molgenis.study - package org.molgenis.study

org.molgenis.studymanager - package org.molgenis.studymanager

P

PROTOCOL - Static variable in class org.molgenis.omx.study.StudyDataRequest

ProtocolViewerController - Class in org.molgenis.omx.protocolviewer

ProtocolViewerController(ProtocolViewerService, MolgenisSettings, SearchService) - Constructor for class org.molgenis.omx.protocolviewer.ProtocolViewerController

ProtocolViewerService - Interface in org.molgenis.omx.protocolviewer

ProtocolViewerServiceImpl - Class in org.molgenis.omx.protocolviewer

ProtocolViewerServiceImpl() - Constructor for class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

R

removeFromCart(ProtocolViewerController.CartUpdateRequest, Integer) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

removeFromStudyDefinitionDraftForCurrentUser(String, String) - Method in interface org.molgenis.omx.protocolviewer.ProtocolViewerService

Remove a catalog item or catalog group (implies all items in a group) from the study definition draft

removeFromStudyDefinitionDraftForCurrentUser(String, String) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

REQUESTDATE - Static variable in class org.molgenis.omx.study.StudyDataRequest

REQUESTFORM - Static variable in class org.molgenis.omx.study.StudyDataRequest

REQUESTSTATUS - Static variable in class org.molgenis.omx.study.StudyDataRequest

S

searchItems(Map<String, Object>) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerController

set(Entity, boolean) - Method in class org.molgenis.omx.study.StudyDataRequest

set(String, Object) - Method in class org.molgenis.omx.study.StudyDataRequest

setAuthorEmail(String) - Method in class org.molgenis.study.StudyDefinitionImpl

setAuthors(List<String>) - Method in class org.molgenis.catalog.CatalogMeta

setAuthors(List<String>) - Method in class org.molgenis.catalog.CatalogModel

setAuthors(List<String>) - Method in class org.molgenis.study.StudyDefinitionImpl

setCatalogItemIds(List<String>) - Method in class org.molgenis.studymanager.StudyManagerController.StudyDefinitionUpdateRequest

setDateCreated(Date) - Method in class org.molgenis.study.StudyDefinitionImpl

setDescription(String) - Method in class org.molgenis.catalog.CatalogMeta

setDescription(String) - Method in class org.molgenis.catalog.CatalogModel

setDescription(String) - Method in class org.molgenis.study.StudyDefinitionImpl

setFeatures(List<ObservableFeature>) - Method in class org.molgenis.omx.study.StudyDataRequest

Set the .

setId(String) - Method in class org.molgenis.catalog.CatalogModelFolder

setId(Integer) - Method in class org.molgenis.omx.study.StudyDataRequest

Set the automatically generated internal id, only for internal use..

setId(String) - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

setId(String) - Method in interface org.molgenis.study.StudyDefinition

setId(String) - Method in class org.molgenis.study.StudyDefinitionImpl

setIdentifier(String) - Method in class org.molgenis.omx.study.StudyDataRequest

Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

setItems(Iterable<CatalogItem>) - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

setItems(Iterable<CatalogItem>) - Method in interface org.molgenis.study.StudyDefinition

setItems(Iterable<CatalogItem>) - Method in class org.molgenis.study.StudyDefinitionImpl

setMolgenisUser(MolgenisUser) - Method in class org.molgenis.omx.study.StudyDataRequest

Set the .

setName(String) - Method in class org.molgenis.catalog.CatalogModelFolder

setName(String) - Method in class org.molgenis.omx.study.StudyDataRequest

Set the human readible name, not necessary unique..

setName(String) - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

setName(String) - Method in interface org.molgenis.study.StudyDefinition

setName(String) - Method in class org.molgenis.study.StudyDefinitionImpl

setProtocol(Protocol) - Method in class org.molgenis.omx.study.StudyDataRequest

Set the protocol used to create request.

setRequestDate(Date) - Method in class org.molgenis.omx.study.StudyDataRequest

Set the request date.

setRequestForm(String) - Method in class org.molgenis.omx.study.StudyDataRequest

Set the request form filename.

setRequestForm(String) - Method in class org.molgenis.study.StudyDefinitionImpl

setRequestProposalForm(String) - Method in class org.molgenis.omx.studymanager.OmxStudyDefinition

setRequestProposalForm(String) - Method in interface org.molgenis.study.StudyDefinition

setRequestProposalForm(String) - Method in class org.molgenis.study.StudyDefinitionImpl

setRequestStatus(String) - Method in class org.molgenis.omx.study.StudyDataRequest

Set the .

setSelected(boolean) - Method in class org.molgenis.catalog.CatalogModelFolder

setStatus(StudyDefinition.Status) - Method in class org.molgenis.study.StudyDefinitionImpl

setStatus(StudyDefinition.Status) - Method in class org.molgenis.studymanager.StudyManagerController.StudyDefinitionUpdateRequest

setStudyDefinitions(List<StudyDefinitionMetaModel>) - Method in class org.molgenis.studymanager.StudyManagerController.StudyDefinitionsMetaResponse

setTitle(String) - Method in class org.molgenis.catalog.CatalogModel

setVersion(String) - Method in class org.molgenis.catalog.CatalogMeta

setVersion(String) - Method in class org.molgenis.catalog.CatalogModel

setVersion(String) - Method in class org.molgenis.study.StudyDefinitionImpl

StudyDataRequest - Class in org.molgenis.omx.study

StudyDataRequest: .

StudyDataRequest() - Constructor for class org.molgenis.omx.study.StudyDataRequest

StudyDataRequestDecorator - Class in org.molgenis.omx.study

decorator for StudyDataRequest, Checks for every read, update and delete operation if the user requesting the operation matches the user owning the StudyDataRequest on which the operation is requested

StudyDataRequestDecorator(CrudRepository) - Constructor for class org.molgenis.omx.study.StudyDataRequestDecorator

StudyDataRequestMetaData - Class in org.molgenis.omx.study

StudyDataRequestMetaData() - Constructor for class org.molgenis.omx.study.StudyDataRequestMetaData

StudyDataRequestRepository - Class in org.molgenis.omx.study

StudyDataRequestRepository(QueryResolver) - Constructor for class org.molgenis.omx.study.StudyDataRequestRepository

StudyDataRequestRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.study.StudyDataRequestRepository

For testing purposes

StudyDefinition - Interface in org.molgenis.study

StudyDefinition.Status - Enum in org.molgenis.study

StudyDefinitionImpl - Class in org.molgenis.study

StudyDefinitionImpl() - Constructor for class org.molgenis.study.StudyDefinitionImpl

StudyDefinitionImpl(StudyDefinition) - Constructor for class org.molgenis.study.StudyDefinitionImpl

StudyDefinitionMeta - Class in org.molgenis.study

Study definition meta data

StudyDefinitionMeta(String, String, String, Date) - Constructor for class org.molgenis.study.StudyDefinitionMeta

StudyDefinitionMetaModel - Class in org.molgenis.studymanager

StudyDefinitionMetaModel(String, String, String, Date, boolean, boolean) - Constructor for class org.molgenis.studymanager.StudyDefinitionMetaModel

StudyManagerController - Class in org.molgenis.studymanager

StudyManagerController(StudyManagerService, CatalogManagerService, MolgenisPermissionService) - Constructor for class org.molgenis.studymanager.StudyManagerController

StudyManagerController.StudyDefinitionsMetaResponse - Class in org.molgenis.studymanager

StudyManagerController.StudyDefinitionsMetaResponse() - Constructor for class org.molgenis.studymanager.StudyManagerController.StudyDefinitionsMetaResponse

StudyManagerController.StudyDefinitionUpdateRequest - Class in org.molgenis.studymanager

StudyManagerController.StudyDefinitionUpdateRequest() - Constructor for class org.molgenis.studymanager.StudyManagerController.StudyDefinitionUpdateRequest

StudyManagerService - Interface in org.molgenis.studymanager

Find, retrieve and persist study definitions

submitStudyDefinition(String, String) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

submitStudyDefinition(String, String) - Method in interface org.molgenis.studymanager.StudyManagerService

Submit the draft study definition for the given catalog

submitStudyDefinitionDraftForCurrentUser(String, Part, String) - Method in interface org.molgenis.omx.protocolviewer.ProtocolViewerService

Place an order for the current user

submitStudyDefinitionDraftForCurrentUser(String, Part, String) - Method in class org.molgenis.omx.protocolviewer.ProtocolViewerServiceImpl

T

toString() - Method in class org.molgenis.omx.study.StudyDataRequest

toString(boolean) - Method in class org.molgenis.omx.study.StudyDataRequest

U

UnknownCatalogException - Exception in org.molgenis.catalog

UnknownCatalogException() - Constructor for exception org.molgenis.catalog.UnknownCatalogException

UnknownCatalogException(String, Throwable) - Constructor for exception org.molgenis.catalog.UnknownCatalogException

UnknownCatalogException(String) - Constructor for exception org.molgenis.catalog.UnknownCatalogException

UnknownCatalogException(Throwable) - Constructor for exception org.molgenis.catalog.UnknownCatalogException

UnknownStudyDefinitionException - Exception in org.molgenis.study

UnknownStudyDefinitionException() - Constructor for exception org.molgenis.study.UnknownStudyDefinitionException

UnknownStudyDefinitionException(String) - Constructor for exception org.molgenis.study.UnknownStudyDefinitionException

UnknownStudyDefinitionException(Throwable) - Constructor for exception org.molgenis.study.UnknownStudyDefinitionException

UnknownStudyDefinitionException(String, Throwable) - Constructor for exception org.molgenis.study.UnknownStudyDefinitionException

unloadCatalog(String) - Method in interface org.molgenis.catalogmanager.CatalogManagerService

Removes a catalog from the database

unloadCatalog(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

unloadCatalogOfStudyDefinition(String) - Method in interface org.molgenis.catalogmanager.CatalogManagerService

Retrieves a catalog of a study definition from the database

unloadCatalogOfStudyDefinition(String) - Method in class org.molgenis.omx.catalogmanager.OmxCatalogManagerService

update(Entity) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

update(Iterable<? extends Entity>) - Method in class org.molgenis.omx.study.StudyDataRequestDecorator

updateStudyDefinition(StudyDefinition) - Method in class org.molgenis.omx.studymanager.OmxStudyManagerService

updateStudyDefinition(String, StudyManagerController.StudyDefinitionUpdateRequest) - Method in class org.molgenis.studymanager.StudyManagerController

updateStudyDefinition(StudyDefinition) - Method in interface org.molgenis.studymanager.StudyManagerService

Updates an existing study definition

URI - Static variable in class org.molgenis.catalogmanager.CatalogManagerController

URI - Static variable in class org.molgenis.omx.protocolviewer.ProtocolViewerController

URI - Static variable in class org.molgenis.studymanager.StudyManagerController

V

valueOf(String) - Static method in enum org.molgenis.study.StudyDefinition.Status

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

values() - Static method in enum org.molgenis.study.StudyDefinition.Status

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

VIEW_NAME - Static variable in class org.molgenis.catalogmanager.CatalogManagerController

VIEW_NAME - Static variable in class org.molgenis.studymanager.StudyManagerController

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