Package ch.systemsx.cisd.openbis.generic.server.api.v1

Class GeneralInformationChangingService

java.lang.Object

ch.systemsx.cisd.openbis.common.spring.AbstractServiceWithLogger<T>

ch.systemsx.cisd.openbis.generic.server.AbstractServer<IGeneralInformationChangingService>

ch.systemsx.cisd.openbis.generic.server.api.v1.GeneralInformationChangingService

All Implemented Interfaces:

IRpcService, ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerFactory<IGeneralInformationChangingService>, IGeneralInformationChangingService, ch.systemsx.cisd.openbis.generic.shared.IServer, ch.systemsx.cisd.openbis.generic.shared.ISessionProvider

@Component("general-information-changing-api-server-v1")
public class GeneralInformationChangingService
extends ch.systemsx.cisd.openbis.generic.server.AbstractServer<IGeneralInformationChangingService>
implements IGeneralInformationChangingService

Nested Class Summary

Nested classes/interfaces inherited from class ch.systemsx.cisd.openbis.generic.server.AbstractServer

ch.systemsx.cisd.openbis.generic.server.AbstractServer.AuthenticatedPersonBasedPrincipalProvider

Field Summary

Fields

Modifier and Type	Field	Description
static int	MINOR_VERSION
ch.systemsx.cisd.common.servlet.IRequestContextProvider	requestContextProvider

Fields inherited from class ch.systemsx.cisd.openbis.generic.server.AbstractServer

CISDHelpdeskEmail, configurer, displaySettingsProvider, executor, mailClientParameters, sessionManager

Fields inherited from class ch.systemsx.cisd.openbis.common.spring.AbstractServiceWithLogger

authenticationLog, notificationLog, operationLog

Fields inherited from interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService

JSON_SERVICE_URL, SERVICE_NAME, SERVICE_URL

Fields inherited from interface ch.systemsx.cisd.openbis.generic.shared.IServer

VERSION

Constructor Summary

Constructors

Constructor	Description
GeneralInformationChangingService()

Method Summary

Modifier and Type	Method	Description
void	addToMetaproject(java.lang.String sessionToken, IMetaprojectId metaprojectId, MetaprojectAssignmentsIds assignmentsToAdd)	Adds given entities to an existing metaproject.
void	addUnofficialVocabularyTerm(java.lang.String sessionToken, ch.systemsx.cisd.openbis.generic.shared.basic.TechId vocabularyId, java.lang.String code, java.lang.String label, java.lang.String description, java.lang.Long previousTermOrdinal)	Adds new unofficial terms to a vocabulary starting from specified ordinal + 1.
void	addUnofficialVocabularyTerm(java.lang.String sessionToken, java.lang.Long vocabularyId, NewVocabularyTerm term)	Adds new unofficial terms to a vocabulary starting from specified ordinal + 1.
IGeneralInformationChangingService	createLogger(ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext context)
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject	createMetaproject(java.lang.String sessionToken, java.lang.String name, java.lang.String descriptionOrNull)	Creates a new metaproject.
void	deleteDataSets(java.lang.String sessionToken, java.util.List<java.lang.String> dataSetCodes, java.lang.String reason, DeletionType deletionType)	Deletes or trashes the specified data sets depending on the chosen deletion type.
void	deleteDataSetsForced(java.lang.String sessionToken, java.util.List<java.lang.String> dataSetCodes, java.lang.String reason, DeletionType deletionType)	Deletes or trashes the specified data sets depending on the chosen deletion type.
void	deleteExperiments(java.lang.String sessionToken, java.util.List<java.lang.Long> experimentIds, java.lang.String reason, DeletionType deletionType)	Deletes or trashes the specified experiments depending on the chosen deletion type.
void	deleteMetaproject(java.lang.String sessionToken, IMetaprojectId metaprojectId)	Deletes an existing metaproject.
void	deletePermanently(java.lang.String sessionToken, java.util.List<java.lang.Long> deletionIds)	Permanently deletes entities moved to trash in specified deletions.
void	deletePermanentlyForced(java.lang.String sessionToken, java.util.List<java.lang.Long> deletionIds)	Permanently deletes entities moved to trash in specified deletions.
void	deleteProjects(java.lang.String sessionToken, java.util.List<java.lang.Long> projectIds, java.lang.String reason)	Deletes the specified projects.
void	deleteSamples(java.lang.String sessionToken, java.util.List<java.lang.Long> sampleIds, java.lang.String reason, DeletionType deletionType)	Deletes or trashes the specified samples depending on the chosen deletion type.
int	getMajorVersion()	Returns the major version of the server side interface.
int	getMinorVersion()	Returns the minor version of this server side interface.
WebAppSettings	getWebAppSettings(java.lang.String sessionToken, java.lang.String webAppId)	Returns the persistent settings for a given custom web app.
void	registerPerson(java.lang.String sessionToken, java.lang.String userID)	Registers Person, this person should be available in one of the configured login systems to be usable.
void	registerPersonSpaceRole(java.lang.String sessionToken, java.lang.String spaceCode, java.lang.String userID, java.lang.String roleCode)	Registers a space role for a given person.
java.lang.String	registerSamples(java.lang.String sessionToken, java.lang.String sampleTypeCode, java.lang.String sessionKey, java.lang.String defaultGroupIdentifier)	Registers samples parsing a file stored on the HTTP Session.
java.lang.String	registerSamplesWithSilentOverrides(java.lang.String sessionToken, java.lang.String sampleTypeCode, java.lang.String spaceIdentifierSilentOverrideOrNull, java.lang.String experimentIdentifierSilentOverrideOrNull, java.lang.String sessionKey, java.lang.String defaultGroupIdentifier)	Registers samples parsing a file stored on the HTTP Session.
void	registerSpace(java.lang.String sessionToken, java.lang.String spaceCode, java.lang.String spaceDescription)	Registers a space.
void	removeFromMetaproject(java.lang.String sessionToken, IMetaprojectId metaprojectId, MetaprojectAssignmentsIds assignmentsToRemove)	Removes given entities from an existing metaproject.
void	revertDeletions(java.lang.String sessionToken, java.util.List<java.lang.Long> deletionIds)	Reverts specified deletions (puts back all entities moved to trash in the deletions).
void	setWebAppSettings(java.lang.String sessionToken, WebAppSettings webAppSettings)	Sets the persistent settings for a given custom web app.
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject	updateMetaproject(java.lang.String sessionToken, IMetaprojectId metaprojectId, java.lang.String name, java.lang.String descriptionOrNull)	Updates an existing metaproject.
void	updateSampleProperties(java.lang.String sessionToken, long sampleID, java.util.Map<java.lang.String,java.lang.String> properties)
java.lang.String	updateSamples(java.lang.String sessionToken, java.lang.String sampleTypeCode, java.lang.String sessionKey, java.lang.String defaultGroupIdentifier)	Updates samples parsing a file stored on the HTTP Session.
java.lang.String	updateSamplesWithSilentOverrides(java.lang.String sessionToken, java.lang.String sampleTypeCode, java.lang.String spaceIdentifierSilentOverrideOrNull, java.lang.String experimentIdentifierSilentOverrideOrNull, java.lang.String sessionKey, java.lang.String defaultGroupIdentifier)	Updates samples parsing a file stored on the HTTP Session.
java.util.Map<java.lang.String,java.lang.Object>	uploadedSamplesInfo(java.lang.String sessionToken, java.lang.String sampleTypeCode, java.lang.String sessionKey)	Returns information regarding the uploaded file without discarding it.

Methods inherited from class ch.systemsx.cisd.openbis.generic.server.AbstractServer

changeUserHomeSpace, checkSession, countActivePersons, createPerson, deactivatePersons, executeASync, expireSession, fillHomeSpace, getAuthSession, getBaseIndexURL, getDAOFactory, getDataSetTypeSlaveServerPlugin, getDefaultDisplaySettings, getPropertiesBatchManager, getSampleTypeSlaveServerPlugin, getServerInformation, getSession, getSessionManager, getSystemUser, getVersion, injectPerson, isArchivingConfigured, isProjectLevelAuthorizationEnabled, isProjectLevelAuthorizationUser, isProjectSamplesEnabled, listGridCustomColumns, logout, registerAtSessionManager, registerSamples, saveDisplaySettings, sendEmail, setBaseIndexURL, setCISDHelpdeskEmail, setDataSetTypeSlaveServerPlugin, setDisplaySettingsProvider, setDssFactory, setSampleTypeSlaveServerPlugin, setSessionUser, setSessionWorkspaceProvider, tryAuthenticate, tryAuthenticateAnonymously, tryAuthenticateAs, tryGetDisabledText, tryGetSession, tryToAuthenticate, tryToAuthenticateAsSystem, updateDisplaySettings

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MINOR_VERSION

public static final int MINOR_VERSION

See Also:

Constant Field Values

requestContextProvider

public ch.systemsx.cisd.common.servlet.IRequestContextProvider requestContextProvider

Constructor Detail

GeneralInformationChangingService

public GeneralInformationChangingService()

Method Detail

createLogger

public IGeneralInformationChangingService createLogger(ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext context)

Specified by:

createLogger in interface ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerFactory<IGeneralInformationChangingService>

updateSampleProperties

@Transactional
public void updateSampleProperties(java.lang.String sessionToken,
                                   long sampleID,
                                   java.util.Map<java.lang.String,java.lang.String> properties)

Specified by:

updateSampleProperties in interface IGeneralInformationChangingService

addUnofficialVocabularyTerm

@Transactional
public void addUnofficialVocabularyTerm(java.lang.String sessionToken,
                                        ch.systemsx.cisd.openbis.generic.shared.basic.TechId vocabularyId,
                                        java.lang.String code,
                                        java.lang.String label,
                                        java.lang.String description,
                                        java.lang.Long previousTermOrdinal)

Description copied from interface: IGeneralInformationChangingService

Adds new unofficial terms to a vocabulary starting from specified ordinal + 1.

Specified by:

addUnofficialVocabularyTerm in interface IGeneralInformationChangingService

addUnofficialVocabularyTerm

@Transactional
public void addUnofficialVocabularyTerm(java.lang.String sessionToken,
                                        java.lang.Long vocabularyId,
                                        NewVocabularyTerm term)

Description copied from interface: IGeneralInformationChangingService

Adds new unofficial terms to a vocabulary starting from specified ordinal + 1.

Specified by:

addUnofficialVocabularyTerm in interface IGeneralInformationChangingService

getWebAppSettings

@Transactional(readOnly=true)
public WebAppSettings getWebAppSettings(java.lang.String sessionToken,
                                        java.lang.String webAppId)

Description copied from interface: IGeneralInformationChangingService

Returns the persistent settings for a given custom web app.

Specified by:

getWebAppSettings in interface IGeneralInformationChangingService

webAppId - The id of the custom web app to get the display settings for.

setWebAppSettings

@Transactional(readOnly=false)
public void setWebAppSettings(java.lang.String sessionToken,
                              WebAppSettings webAppSettings)

Description copied from interface: IGeneralInformationChangingService

Sets the persistent settings for a given custom web app.

Specified by:

setWebAppSettings in interface IGeneralInformationChangingService

webAppSettings - The new display settings

createMetaproject

@Transactional(readOnly=false)
public ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject createMetaproject(java.lang.String sessionToken,
                                                                                       java.lang.String name,
                                                                                       java.lang.String descriptionOrNull)

Description copied from interface: IGeneralInformationChangingService

Creates a new metaproject.

Specified by:

createMetaproject in interface IGeneralInformationChangingService

name - Name of the metaproject

descriptionOrNull - Description of the metaproject

Returns:

Newly created metaproject

updateMetaproject

@Transactional(readOnly=false)
public ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject updateMetaproject(java.lang.String sessionToken,
                                                                                       IMetaprojectId metaprojectId,
                                                                                       java.lang.String name,
                                                                                       java.lang.String descriptionOrNull)

Description copied from interface: IGeneralInformationChangingService

Updates an existing metaproject.

Specified by:

updateMetaproject in interface IGeneralInformationChangingService

metaprojectId - Id of the metaproject to update

name - New name of the metaproject

descriptionOrNull - New description of the metaproject

Returns:

Updated metaproject

deleteMetaproject

@Transactional(readOnly=false)
public void deleteMetaproject(java.lang.String sessionToken,
                              IMetaprojectId metaprojectId)

Description copied from interface: IGeneralInformationChangingService

Deletes an existing metaproject.

Specified by:

deleteMetaproject in interface IGeneralInformationChangingService

metaprojectId - Id of the metaproject to delete

addToMetaproject

@Transactional(readOnly=false)
public void addToMetaproject(java.lang.String sessionToken,
                             IMetaprojectId metaprojectId,
                             MetaprojectAssignmentsIds assignmentsToAdd)

Description copied from interface: IGeneralInformationChangingService

Adds given entities to an existing metaproject.

Specified by:

addToMetaproject in interface IGeneralInformationChangingService

metaprojectId - Id of the metaproject

assignmentsToAdd - Assignments that should be added to the metaproject

removeFromMetaproject

@Transactional(readOnly=false)
public void removeFromMetaproject(java.lang.String sessionToken,
                                  IMetaprojectId metaprojectId,
                                  MetaprojectAssignmentsIds assignmentsToRemove)

Description copied from interface: IGeneralInformationChangingService

Removes given entities from an existing metaproject.

Specified by:

removeFromMetaproject in interface IGeneralInformationChangingService

metaprojectId - Id of the metaproject

assignmentsToRemove - Assignments that should be removed from the metaproject

getMajorVersion

public int getMajorVersion()

Description copied from interface: IRpcService

Returns the major version of the server side interface. Different major versions are incompatible with one another.

Specified by:

getMajorVersion in interface IRpcService

getMinorVersion

public int getMinorVersion()

Description copied from interface: IRpcService

Returns the minor version of this server side interface. Different minor versions, within the same major version, are compatible with one another.

Specified by:

getMinorVersion in interface IRpcService

registerSamplesWithSilentOverrides

public final java.lang.String registerSamplesWithSilentOverrides(java.lang.String sessionToken,
                                                                 java.lang.String sampleTypeCode,
                                                                 java.lang.String spaceIdentifierSilentOverrideOrNull,
                                                                 java.lang.String experimentIdentifierSilentOverrideOrNull,
                                                                 java.lang.String sessionKey,
                                                                 java.lang.String defaultGroupIdentifier)

Description copied from interface: IGeneralInformationChangingService

Registers samples parsing a file stored on the HTTP Session.

Specified by:

registerSamplesWithSilentOverrides in interface IGeneralInformationChangingService

sampleTypeCode - Sample type to parse

spaceIdentifierSilentOverrideOrNull - Silently overrides Space identifier if given

experimentIdentifierSilentOverrideOrNull - Silently overrides Experiment identifier if given

sessionKey - key of the file stored on the HTTP Session

registerSamples

public final java.lang.String registerSamples(java.lang.String sessionToken,
                                              java.lang.String sampleTypeCode,
                                              java.lang.String sessionKey,
                                              java.lang.String defaultGroupIdentifier)

Description copied from interface: IGeneralInformationChangingService

Registers samples parsing a file stored on the HTTP Session.

Specified by:

registerSamples in interface IGeneralInformationChangingService

sampleTypeCode - Sample type to parse

sessionKey - key of the file stored on the HTTP Session

updateSamplesWithSilentOverrides

public final java.lang.String updateSamplesWithSilentOverrides(java.lang.String sessionToken,
                                                               java.lang.String sampleTypeCode,
                                                               java.lang.String spaceIdentifierSilentOverrideOrNull,
                                                               java.lang.String experimentIdentifierSilentOverrideOrNull,
                                                               java.lang.String sessionKey,
                                                               java.lang.String defaultGroupIdentifier)

Description copied from interface: IGeneralInformationChangingService

Updates samples parsing a file stored on the HTTP Session.

Specified by:

updateSamplesWithSilentOverrides in interface IGeneralInformationChangingService

sampleTypeCode - Sample type to parse

sessionKey - key of the file stored on the HTTP Session

updateSamples

public final java.lang.String updateSamples(java.lang.String sessionToken,
                                            java.lang.String sampleTypeCode,
                                            java.lang.String sessionKey,
                                            java.lang.String defaultGroupIdentifier)

Description copied from interface: IGeneralInformationChangingService

Updates samples parsing a file stored on the HTTP Session.

Specified by:

updateSamples in interface IGeneralInformationChangingService

sampleTypeCode - Sample type to parse

sessionKey - key of the file stored on the HTTP Session

uploadedSamplesInfo

public final java.util.Map<java.lang.String,java.lang.Object> uploadedSamplesInfo(java.lang.String sessionToken,
                                                                                        java.lang.String sampleTypeCode,
                                                                                        java.lang.String sessionKey)

Description copied from interface: IGeneralInformationChangingService

Returns information regarding the uploaded file without discarding it.

Specified by:

uploadedSamplesInfo in interface IGeneralInformationChangingService

sampleTypeCode - Sample type to parse

sessionKey - key of the file stored on the HTTP Session

deleteProjects

public void deleteProjects(java.lang.String sessionToken,
                           java.util.List<java.lang.Long> projectIds,
                           java.lang.String reason)

Description copied from interface: IGeneralInformationChangingService

Deletes the specified projects.

Specified by:

deleteProjects in interface IGeneralInformationChangingService

projectIds - Ids of projects to delete

reason - Reason of the deletion

deleteExperiments

public void deleteExperiments(java.lang.String sessionToken,
                              java.util.List<java.lang.Long> experimentIds,
                              java.lang.String reason,
                              DeletionType deletionType)

Description copied from interface: IGeneralInformationChangingService

Deletes or trashes the specified experiments depending on the chosen deletion type.

Specified by:

deleteExperiments in interface IGeneralInformationChangingService

experimentIds - Ids of experiments to delete

reason - Reason of the deletion

deletionType - Type of the deletion

deleteSamples

public void deleteSamples(java.lang.String sessionToken,
                          java.util.List<java.lang.Long> sampleIds,
                          java.lang.String reason,
                          DeletionType deletionType)

Description copied from interface: IGeneralInformationChangingService

Deletes or trashes the specified samples depending on the chosen deletion type.

Specified by:

deleteSamples in interface IGeneralInformationChangingService

sampleIds - Ids of samples to delete

reason - Reason of the deletion

deletionType - Type of the deletion

deleteDataSets

public void deleteDataSets(java.lang.String sessionToken,
                           java.util.List<java.lang.String> dataSetCodes,
                           java.lang.String reason,
                           DeletionType deletionType)

Description copied from interface: IGeneralInformationChangingService

Deletes or trashes the specified data sets depending on the chosen deletion type. This method CANNOT delete data sets with deletion_disallow flag set to true in their type (compare with IGeneralInformationChangingService.deleteDataSetsForced(String, List, String, DeletionType).

Specified by:

deleteDataSets in interface IGeneralInformationChangingService

dataSetCodes - Codes of data sets to delete

reason - Reason of the deletion

deletionType - Type of the deletion

deleteDataSetsForced

public void deleteDataSetsForced(java.lang.String sessionToken,
                                 java.util.List<java.lang.String> dataSetCodes,
                                 java.lang.String reason,
                                 DeletionType deletionType)

Description copied from interface: IGeneralInformationChangingService

Deletes or trashes the specified data sets depending on the chosen deletion type. This method CAN delete data sets with deletion_disallow flag set to true in their type but requires special user privileges (compare with IGeneralInformationChangingService.deleteDataSets(String, List, String, DeletionType).

Specified by:

deleteDataSetsForced in interface IGeneralInformationChangingService

dataSetCodes - Codes of data sets to delete

reason - Reason of the deletion

deletionType - Type of the deletion

revertDeletions

public void revertDeletions(java.lang.String sessionToken,
                            java.util.List<java.lang.Long> deletionIds)

Description copied from interface: IGeneralInformationChangingService

Reverts specified deletions (puts back all entities moved to trash in the deletions).

Specified by:

revertDeletions in interface IGeneralInformationChangingService

deletionIds - Ids of deletions to be reverted

deletePermanently

public void deletePermanently(java.lang.String sessionToken,
                              java.util.List<java.lang.Long> deletionIds)

Description copied from interface: IGeneralInformationChangingService

Permanently deletes entities moved to trash in specified deletions. This method CANNOT delete data sets with deletion_disallow flag set to true in their type (compare with IGeneralInformationChangingService.deletePermanentlyForced(String, List))

Specified by:

deletePermanently in interface IGeneralInformationChangingService

deletionIds - Ids of deletions to be deleted permanently

deletePermanentlyForced

public void deletePermanentlyForced(java.lang.String sessionToken,
                                    java.util.List<java.lang.Long> deletionIds)

Description copied from interface: IGeneralInformationChangingService

Permanently deletes entities moved to trash in specified deletions. It CAN delete data sets with deletion_disallow flag set to true in their type (compare with IGeneralInformationChangingService.deletePermanently(String, List)).

Specified by:

deletePermanentlyForced in interface IGeneralInformationChangingService

deletionIds - Ids of deletions to be deleted permanently

registerPerson

public void registerPerson(java.lang.String sessionToken,
                           java.lang.String userID)

Description copied from interface: IGeneralInformationChangingService

Registers Person, this person should be available in one of the configured login systems to be usable.

Specified by:

registerPerson in interface IGeneralInformationChangingService

userID - user to be added to the system

registerSpace

public void registerSpace(java.lang.String sessionToken,
                          java.lang.String spaceCode,
                          java.lang.String spaceDescription)

Description copied from interface: IGeneralInformationChangingService

Registers a space.

Specified by:

registerSpace in interface IGeneralInformationChangingService

spaceCode - space code

spaceDescription - space description

registerPersonSpaceRole

public void registerPersonSpaceRole(java.lang.String sessionToken,
                                    java.lang.String spaceCode,
                                    java.lang.String userID,
                                    java.lang.String roleCode)

Description copied from interface: IGeneralInformationChangingService

Registers a space role for a given person.

Specified by:

registerPersonSpaceRole in interface IGeneralInformationChangingService

spaceCode - space code

userID - user id

roleCode - openBIS role