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

Class GeneralInformationService

java.lang.Object

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

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

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

All Implemented Interfaces:

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

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

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

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.IGeneralInformationService

JSON_SERVICE_URL, SERVICE_NAME, SERVICE_URL

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

VERSION

Constructor Summary

Constructors

Constructor	Description
GeneralInformationService()

Method Summary

Modifier and Type	Method	Description
java.lang.Long	countNumberOfSamplesForType(java.lang.String sessionToken, java.lang.String sampleTypeCode)	Returns number of samples for a sample type code.
IGeneralInformationService	createLogger(ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext context)
protected ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.samplelister.ISampleLister	createSampleLister(ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE person)
java.util.List<DataSet>	filterDataSetsVisibleToUser(java.lang.String sessionToken, java.util.List<DataSet> allDataSets, java.lang.String userId)	Returns a filtered list of allDataSets containing those data sets which are visible to userId.
java.util.List<Experiment>	filterExperimentsVisibleToUser(java.lang.String sessionToken, java.util.List<Experiment> allExperiments, java.lang.String userId)	Returns a filtered list of allExperiments containing those experiments which are visible to userId.
java.util.List<Sample>	filterSamplesVisibleToUser(java.lang.String sessionToken, java.util.List<Sample> allSamples, java.lang.String userId)	Returns a filtered list of allSamples containing those samples which are visible to userId.
java.lang.String	generateCode(java.lang.String sessionToken, java.lang.String prefix, java.lang.String entityKind)	Generate Code.
java.util.List<DataSet>	getDataSetMetaData(java.lang.String sessionToken, java.util.List<java.lang.String> dataSetCodes)	Returns meta data for all specified data sets.
java.util.List<DataSet>	getDataSetMetaData(java.lang.String sessionToken, java.util.List<java.lang.String> dataSetCodes, java.util.EnumSet<DataSetFetchOption> fetchOptions)	Returns meta data for all specified data sets.
java.util.List<DataStoreURLForDataSets>	getDataStoreBaseURLs(java.lang.String sessionToken, java.util.List<java.lang.String> dataSetCodes)	Returns the download URL for the data store of specified data sets.
java.lang.String	getDefaultPutDataStoreBaseURL(java.lang.String sessionToken)	Returns the URL for the default data store server for this openBIS AS.
int	getMajorVersion()	Returns the major version of the server side interface.
java.util.List<Material>	getMaterialByCodes(java.lang.String sessionToken, java.util.List<MaterialIdentifier> materialIdentifier)	Returns the materials with specified identifiers (i.e.
MetaprojectAssignments	getMetaproject(java.lang.String sessionToken, IMetaprojectId metaprojectId)	Returns all entities tagged with given metaproject.
MetaprojectAssignments	getMetaprojectOnBehalfOfUser(java.lang.String sessionToken, IMetaprojectId metaprojectId, java.lang.String userId)	Returns all entities tagged with given metaproject for specified user.
int	getMinorVersion()	Returns the minor version of this server side interface.
java.util.Map<java.lang.String,java.lang.String>	getUserDisplaySettings(java.lang.String sessionToken)
java.util.HashMap<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary,java.util.List<ControlledVocabularyPropertyType.VocabularyTerm>>	getVocabularyTermsMap(java.lang.String sessionToken)	Returns map of avaialable vocabulary terms.
boolean	isSessionActive(java.lang.String sessionToken)	Returns true if session with the specified token is still active, false otherwise.
java.util.List<Attachment>	listAttachmentsForExperiment(java.lang.String sessionToken, IExperimentId experimentId, boolean allVersions)	Lists attachments of specified experiment.
java.util.List<Attachment>	listAttachmentsForProject(java.lang.String sessionToken, IProjectId projectId, boolean allVersions)	Lists attachments of specified project.
java.util.List<Attachment>	listAttachmentsForSample(java.lang.String sessionToken, ISampleId sampleId, boolean allVersions)	Lists attachments of specified sample.
java.util.List<SearchDomain>	listAvailableSearchDomains(java.lang.String sessionToken)	Lists available search domains.
java.util.List<DataSet>	listDataSets(java.lang.String sessionToken, java.util.List<Sample> samples)	Return all data sets attached to the given samples.
java.util.List<DataSet>	listDataSets(java.lang.String sessionToken, java.util.List<Sample> samples, java.util.EnumSet<DataSet.Connections> connections)	Return all data sets attached to the given samples with connections.
java.util.List<DataSet>	listDataSetsForExperiments(java.lang.String sessionToken, java.util.List<Experiment> experiments, java.util.EnumSet<DataSet.Connections> connections)	Return all data sets attached to the given experiments with connections.
java.util.List<DataSet>	listDataSetsForExperimentsOnBehalfOfUser(java.lang.String sessionToken, java.util.List<Experiment> experiments, java.util.EnumSet<DataSet.Connections> connections, java.lang.String userId)	Return all data sets attached to the given experiments with connections that the user userId is allowed to see.
java.util.List<DataSet>	listDataSetsForSample(java.lang.String sessionToken, Sample sample, boolean areOnlyDirectlyConnectedIncluded)	Return the data sets attached to the specified sample, optionally including child samples.
java.util.List<DataSet>	listDataSetsOnBehalfOfUser(java.lang.String sessionToken, java.util.List<Sample> samples, java.util.EnumSet<DataSet.Connections> connections, java.lang.String userId)	Return all data sets attached to the given samples with connections that the user userId is allowed to see.
java.util.List<DataSetType>	listDataSetTypes(java.lang.String sessionToken)	Returns all data set types.
java.util.List<DataStore>	listDataStores(java.lang.String sessionToken)	Lists all DSS server registered this openBIS server instance.
java.util.List<Deletion>	listDeletions(java.lang.String sessionToken, java.util.EnumSet<DeletionFetchOption> fetchOptions)	Returns all deletions.
java.util.List<Experiment>	listExperiments(java.lang.String sessionToken, java.util.List<Project> projects, java.lang.String experimentTypeString)	Return all experiments of the given type that belong to the supplied projects.
java.util.List<Experiment>	listExperiments(java.lang.String sessionToken, java.util.List<java.lang.String> experimentIdentifiers)	Return all experiments matching a specified set of identifiers.
java.util.List<Experiment>	listExperimentsHavingDataSets(java.lang.String sessionToken, java.util.List<Project> projects, java.lang.String experimentTypeString)	Return all experiments of the given type that belong to the supplied projects and have registered data sets.
java.util.List<Experiment>	listExperimentsHavingSamples(java.lang.String sessionToken, java.util.List<Project> projects, java.lang.String experimentTypeString)	Return all experiments of the given type that belong to the supplied projects and have registered samles.
java.util.List<ExperimentType>	listExperimentTypes(java.lang.String sessionToken)	Returns all experiment types.
java.util.List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject>	listMetaprojects(java.lang.String sessionToken)	Lists all metaprojects belonging to current user.
java.util.List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject>	listMetaprojectsOnBehalfOfUser(java.lang.String sessionToken, java.lang.String userId)	Lists all metaprojects belonging to specified user.
java.util.Map<java.lang.String,java.util.Set<Role>>	listNamedRoleSets(java.lang.String sessionToken)	Returns all named role sets.
java.util.List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person>	listPersons(java.lang.String sessionToken)	Returns all persons.
java.util.List<Project>	listProjects(java.lang.String sessionToken)	Returns all available projects.
java.util.List<Project>	listProjectsOnBehalfOfUser(java.lang.String sessionToken, java.lang.String userId)	Returns all available projects that a particular user is allowed to see.
java.util.List<PropertyType>	listPropertyTypes(java.lang.String sessionToken, boolean withRelations)	Lists property types.
java.util.List<Sample>	listSamplesForExperiment(java.lang.String sessionToken, java.lang.String experimentIdentifierString)	Return all samples that belong to the supplied experiment.
java.util.List<Sample>	listSamplesForExperimentOnBehalfOfUser(java.lang.String sessionToken, java.lang.String experimentIdentifierString, java.lang.String userId)	Return all samples that belong to the supplied experiment that are visible to user userId.
java.util.List<SampleType>	listSampleTypes(java.lang.String sessionToken)	Returns all sample types.
java.util.List<SpaceWithProjectsAndRoleAssignments>	listSpacesWithProjectsAndRoleAssignments(java.lang.String sessionToken, java.lang.String databaseInstanceCodeOrNull)	Returns all spaces of specified database instance enriched with their projects and role assignments.
java.util.List<Vocabulary>	listVocabularies(java.lang.String sessionToken)	Returns all available vocabularies together with the contained terms.
java.util.List<DataSet>	searchForDataSets(java.lang.String sessionToken, SearchCriteria searchCriteria)	Return all data sets matching specified search criteria.
java.util.List<DataSet>	searchForDataSetsOnBehalfOfUser(java.lang.String sessionToken, SearchCriteria searchCriteria, java.lang.String userId)	Return all data sets matching specified search criteria and visible to user userId.
java.util.List<Experiment>	searchForExperiments(java.lang.String sessionToken, SearchCriteria searchCriteria)	Returns all experiments matching specified search criteria.
java.util.List<Material>	searchForMaterials(java.lang.String sessionToken, SearchCriteria searchCriteria)	Returns all material fulfilling specified search criteria.
java.util.List<Sample>	searchForSamples(java.lang.String sessionToken, SearchCriteria searchCriteria)	Return all samples that match the search criteria.
java.util.List<Sample>	searchForSamples(java.lang.String sessionToken, SearchCriteria searchCriteria, java.util.EnumSet<SampleFetchOption> fetchOptions)	Return all samples that match the search criteria.
java.util.List<Sample>	searchForSamplesOnBehalfOfUser(java.lang.String sessionToken, SearchCriteria searchCriteria, java.util.EnumSet<SampleFetchOption> fetchOptions, java.lang.String userId)	Return all samples that match the search criteria and that a particular user is allowed to see.
java.util.List<SearchDomainSearchResult>	searchOnSearchDomain(java.lang.String sessionToken, java.lang.String preferredSearchDomainOrNull, java.lang.String searchString, java.util.Map<java.lang.String,java.lang.String> optionalParametersOrNull)	Searches on a search domain.
java.lang.String	tryGetDataStoreBaseURL(java.lang.String sessionToken, java.lang.String dataSetCode)	Returns the download URL for the data store of specified data set or null if such data set does not exist.
java.lang.String	tryToAuthenticateForAllServices(java.lang.String userID, java.lang.String userPassword)	Tries to authenticate specified user with specified password.

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

Methods inherited from interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService

logout

Field Detail

MINOR_VERSION

public static final int MINOR_VERSION

See Also:

Constant Field Values

Constructor Detail

GeneralInformationService

public GeneralInformationService()

Method Detail

createLogger

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

Specified by:

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

tryToAuthenticateForAllServices

@Transactional
public java.lang.String tryToAuthenticateForAllServices(java.lang.String userID,
                                                        java.lang.String userPassword)

Description copied from interface: IGeneralInformationService

Tries to authenticate specified user with specified password. Returns session token if succeeded otherwise null is returned. The returned session token can be used for all methods and interfaces of the same openBIS server.

Specified by:

tryToAuthenticateForAllServices in interface IGeneralInformationService

isSessionActive

@Transactional(readOnly=true)
public boolean isSessionActive(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns true if session with the specified token is still active, false otherwise.

Specified by:

isSessionActive in interface IGeneralInformationService

listNamedRoleSets

@Transactional(readOnly=true)
public java.util.Map<java.lang.String,java.util.Set<Role>> listNamedRoleSets(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns all named role sets. The name is the key of the returned map.

Specified by:

listNamedRoleSets in interface IGeneralInformationService

listSpacesWithProjectsAndRoleAssignments

@Transactional(readOnly=true)
public java.util.List<SpaceWithProjectsAndRoleAssignments> listSpacesWithProjectsAndRoleAssignments(java.lang.String sessionToken,
                                                                                                    java.lang.String databaseInstanceCodeOrNull)

Description copied from interface: IGeneralInformationService

Returns all spaces of specified database instance enriched with their projects and role assignments.

Specified by:

listSpacesWithProjectsAndRoleAssignments in interface IGeneralInformationService

databaseInstanceCodeOrNull - Code of an imported database instance or null for the home database instance is meant.

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

searchForSamples

@Transactional(readOnly=true)
public java.util.List<Sample> searchForSamples(java.lang.String sessionToken,
                                               SearchCriteria searchCriteria)

Description copied from interface: IGeneralInformationService

Return all samples that match the search criteria. This is a short cut for

 searchForSamples(sessionToken, searchCritera, EnumSet.of(SampleFetchOption.PROPERTIES))
 

Specified by:

searchForSamples in interface IGeneralInformationService

searchCriteria - The sample metadata values to be matched against.

searchForSamples

@Transactional(readOnly=true)
public java.util.List<Sample> searchForSamples(java.lang.String sessionToken,
                                               SearchCriteria searchCriteria,
                                               java.util.EnumSet<SampleFetchOption> fetchOptions)

Description copied from interface: IGeneralInformationService

Return all samples that match the search criteria.

The fetch options set is interpreted by the following rules.

• If it does not contain SampleFetchOption.PROPERTIES only the basic attributes are returned for all samples including possible ancestors and descendants.
• SampleFetchOption.CHILDREN will be ignored if SampleFetchOption.DESCENDANTS is in the set.
• SampleFetchOption.PARENTS will be ignored if SampleFetchOption.ANCESTORS is in the set.
• It is possible to combine SampleFetchOption.CHILDREN/ SampleFetchOption.DESCENDANTS with SampleFetchOption.PARENTS/ SampleFetchOption.ANCESTORS.

The samples of the returned list also contain appropriated fetch options sets which tells whether one can expect properties, children, or parents. Note, that only the top-level samples can have both children or samples. For descendants and ancestors navigation is possible only in one direction.

Specified by:

searchForSamples in interface IGeneralInformationService

searchCriteria - The sample metadata values to be matched against.

fetchOptions - Options that control which parts of the samples are fetched.

searchForSamplesOnBehalfOfUser

@Transactional(readOnly=true)
public java.util.List<Sample> searchForSamplesOnBehalfOfUser(java.lang.String sessionToken,
                                                             SearchCriteria searchCriteria,
                                                             java.util.EnumSet<SampleFetchOption> fetchOptions,
                                                             java.lang.String userId)

Description copied from interface: IGeneralInformationService

Return all samples that match the search criteria and that a particular user is allowed to see.

The fetch options set is interpreted by the following rules.

• If it does not contain SampleFetchOption.PROPERTIES only the basic attributes are returned for all samples including possible ancestors and descendants.
• SampleFetchOption.CHILDREN will be ignored if SampleFetchOption.DESCENDANTS is in the set.
• SampleFetchOption.PARENTS will be ignored if SampleFetchOption.ANCESTORS is in the set.
• It is possible to combine SampleFetchOption.CHILDREN/ SampleFetchOption.DESCENDANTS with SampleFetchOption.PARENTS/ SampleFetchOption.ANCESTORS.

The samples of the returned list also contain appropriated fetch options sets which tells whether one can expect properties, children, or parents. Note, that only the top-level samples can have both children or samples. For descendants and ancestors navigation is possible only in one direction.

May only be called by users who are INSTANCE_OBSERVER.

Specified by:

searchForSamplesOnBehalfOfUser in interface IGeneralInformationService

searchCriteria - The sample metadata values to be matched against.

fetchOptions - Options that control which parts of the samples are fetched.

filterSamplesVisibleToUser

@Transactional(readOnly=true)
public java.util.List<Sample> filterSamplesVisibleToUser(java.lang.String sessionToken,
                                                         java.util.List<Sample> allSamples,
                                                         java.lang.String userId)

Description copied from interface: IGeneralInformationService

Returns a filtered list of allSamples containing those samples which are visible to userId.

Specified by:

filterSamplesVisibleToUser in interface IGeneralInformationService

allSamples - The list of samples that should be filtered.

userId - The user that the samples should be visible to that survive the filtering.

Returns:

The filtered list of allSamples containing those samples which are visible to userId.

createSampleLister

protected ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.samplelister.ISampleLister createSampleLister(ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE person)

listSamplesForExperiment

@Transactional(readOnly=true)
public java.util.List<Sample> listSamplesForExperiment(java.lang.String sessionToken,
                                                       java.lang.String experimentIdentifierString)

Description copied from interface: IGeneralInformationService

Return all samples that belong to the supplied experiment.

Specified by:

listSamplesForExperiment in interface IGeneralInformationService

experimentIdentifierString - The identifier of the experiment samples will be listed for.

listSamplesForExperimentOnBehalfOfUser

@Transactional(readOnly=true)
public java.util.List<Sample> listSamplesForExperimentOnBehalfOfUser(java.lang.String sessionToken,
                                                                     java.lang.String experimentIdentifierString,
                                                                     java.lang.String userId)

Description copied from interface: IGeneralInformationService

Return all samples that belong to the supplied experiment that are visible to user userId.

May only be called by users with capability LIST_PROJECTS_ON_BEHALF_OF_USER.

Specified by:

listSamplesForExperimentOnBehalfOfUser in interface IGeneralInformationService

experimentIdentifierString - The identifier of the experiment samples will be listed for.

userId - The user to run this query on behalf of.

listDataSets

@Transactional(readOnly=true)
public java.util.List<DataSet> listDataSets(java.lang.String sessionToken,
                                            java.util.List<Sample> samples)

Description copied from interface: IGeneralInformationService

Return all data sets attached to the given samples.

Specified by:

listDataSets in interface IGeneralInformationService

samples - The samples for which we return attached data sets.

listExperiments

@Transactional(readOnly=true)
public java.util.List<Experiment> listExperiments(java.lang.String sessionToken,
                                                  java.util.List<Project> projects,
                                                  java.lang.String experimentTypeString)

Description copied from interface: IGeneralInformationService

Return all experiments of the given type that belong to the supplied projects.

Specified by:

listExperiments in interface IGeneralInformationService

projects - The projects for which we return attached experiments.

experimentTypeString - The experiment type of the experiments we want to list. Since version 1.9 NULL are accepted. Specifying a NULL experiment type will result in all experiments for the specified projects being returned.

listExperimentsHavingDataSets

@Transactional(readOnly=true)
public java.util.List<Experiment> listExperimentsHavingDataSets(java.lang.String sessionToken,
                                                                java.util.List<Project> projects,
                                                                java.lang.String experimentTypeString)

Description copied from interface: IGeneralInformationService

Return all experiments of the given type that belong to the supplied projects and have registered data sets.

Specified by:

listExperimentsHavingDataSets in interface IGeneralInformationService

projects - The projects for which we return attached experiments.

experimentTypeString - The experiment type of the experiments we want to list. Specifying a NULL experiment type will result in all experiments for the specified projects being returned.

listExperimentsHavingSamples

@Transactional(readOnly=true)
public java.util.List<Experiment> listExperimentsHavingSamples(java.lang.String sessionToken,
                                                               java.util.List<Project> projects,
                                                               java.lang.String experimentTypeString)

Description copied from interface: IGeneralInformationService

Return all experiments of the given type that belong to the supplied projects and have registered samles.

Specified by:

listExperimentsHavingSamples in interface IGeneralInformationService

projects - The projects for which we return attached experiments.

experimentTypeString - The experiment type of the experiments we want to list. Specifying a NULL experiment type will result in all experiments for the specified projects being returned.

filterExperimentsVisibleToUser

@Transactional(readOnly=true)
public java.util.List<Experiment> filterExperimentsVisibleToUser(java.lang.String sessionToken,
                                                                 java.util.List<Experiment> allExperiments,
                                                                 java.lang.String userId)

Description copied from interface: IGeneralInformationService

Returns a filtered list of allExperiments containing those experiments which are visible to userId.

Specified by:

filterExperimentsVisibleToUser in interface IGeneralInformationService

allExperiments - The list of experiments that should be filtered.

userId - The user that the experiments should be visible to that survive the filtering.

Returns:

The filtered list of allExperiments containing all experiments which are visible to userId.

listDataSetsForSample

@Transactional(readOnly=true)
public java.util.List<DataSet> listDataSetsForSample(java.lang.String sessionToken,
                                                     Sample sample,
                                                     boolean areOnlyDirectlyConnectedIncluded)

Description copied from interface: IGeneralInformationService

Return the data sets attached to the specified sample, optionally including child samples. Note, that for returned container data sets the contained data sets have only code, type and registration date set.

Specified by:

listDataSetsForSample in interface IGeneralInformationService

sample - The sample for which we return attached data sets.

areOnlyDirectlyConnectedIncluded - If true, only data sets that are directly connected to the sample are included, otherwise data sets of child samples are included as well.

listDataStores

@Transactional(readOnly=true)
public java.util.List<DataStore> listDataStores(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Lists all DSS server registered this openBIS server instance. Any of the returned instances could be offline at the time of the listing.

Specified by:

listDataStores in interface IGeneralInformationService

getDefaultPutDataStoreBaseURL

@Transactional(readOnly=true)
public java.lang.String getDefaultPutDataStoreBaseURL(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns the URL for the default data store server for this openBIS AS.

Specified by:

getDefaultPutDataStoreBaseURL in interface IGeneralInformationService

tryGetDataStoreBaseURL

@Transactional(readOnly=true)
public java.lang.String tryGetDataStoreBaseURL(java.lang.String sessionToken,
                                               java.lang.String dataSetCode)

Description copied from interface: IGeneralInformationService

Returns the download URL for the data store of specified data set or null if such data set does not exist.

Specified by:

tryGetDataStoreBaseURL in interface IGeneralInformationService

getDataStoreBaseURLs

@Transactional(readOnly=true)
public java.util.List<DataStoreURLForDataSets> getDataStoreBaseURLs(java.lang.String sessionToken,
                                                                    java.util.List<java.lang.String> dataSetCodes)

Description copied from interface: IGeneralInformationService

Returns the download URL for the data store of specified data sets.

Specified by:

getDataStoreBaseURLs in interface IGeneralInformationService

Returns:

One entry for each data store that has data sets from dataSetCodes, together with the data set codes that are in this data store.

listDataSetTypes

@Transactional(readOnly=true)
public java.util.List<DataSetType> listDataSetTypes(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns all data set types.

Specified by:

listDataSetTypes in interface IGeneralInformationService

listSampleTypes

@Transactional(readOnly=true)
public java.util.List<SampleType> listSampleTypes(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns all sample types.

Specified by:

listSampleTypes in interface IGeneralInformationService

listExperimentTypes

@Transactional(readOnly=true)
public java.util.List<ExperimentType> listExperimentTypes(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns all experiment types.

Specified by:

listExperimentTypes in interface IGeneralInformationService

getVocabularyTermsMap

@Transactional(readOnly=true)
public java.util.HashMap<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary,java.util.List<ControlledVocabularyPropertyType.VocabularyTerm>> getVocabularyTermsMap(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns map of avaialable vocabulary terms.

The method cannot be fully utilized over JSON-RPC, because there is no sensible way to (de)serialize a Vocabulary object to/from String. Any working implementation will make the life of non-java clients (e.g. Javascript) unnecessarily complicated.

Specified by:

getVocabularyTermsMap in interface IGeneralInformationService

listVocabularies

@Transactional(readOnly=true)
public java.util.List<Vocabulary> listVocabularies(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns all available vocabularies together with the contained terms.

Specified by:

listVocabularies in interface IGeneralInformationService

listDataSets

@Transactional(readOnly=true)
public java.util.List<DataSet> listDataSets(java.lang.String sessionToken,
                                            java.util.List<Sample> samples,
                                            java.util.EnumSet<DataSet.Connections> connections)

Description copied from interface: IGeneralInformationService

Return all data sets attached to the given samples with connections.

Specified by:

listDataSets in interface IGeneralInformationService

samples - The samples for which we return attached data sets.

listDataSetsOnBehalfOfUser

@Transactional(readOnly=true)
public java.util.List<DataSet> listDataSetsOnBehalfOfUser(java.lang.String sessionToken,
                                                          java.util.List<Sample> samples,
                                                          java.util.EnumSet<DataSet.Connections> connections,
                                                          java.lang.String userId)

Description copied from interface: IGeneralInformationService

Return all data sets attached to the given samples with connections that the user userId is allowed to see.

May only be called by users with capability LIST_PROJECTS_ON_BEHALF_OF_USER.

Specified by:

listDataSetsOnBehalfOfUser in interface IGeneralInformationService

samples - The samples for which we return attached data sets.

userId - The user to run this query on behalf of.

listDataSetsForExperiments

@Transactional(readOnly=true)
public java.util.List<DataSet> listDataSetsForExperiments(java.lang.String sessionToken,
                                                          java.util.List<Experiment> experiments,
                                                          java.util.EnumSet<DataSet.Connections> connections)

Description copied from interface: IGeneralInformationService

Return all data sets attached to the given experiments with connections.

Specified by:

listDataSetsForExperiments in interface IGeneralInformationService

experiments - The experiments for which we return attached data sets.

listDataSetsForExperimentsOnBehalfOfUser

@Transactional(readOnly=true)
public java.util.List<DataSet> listDataSetsForExperimentsOnBehalfOfUser(java.lang.String sessionToken,
                                                                        java.util.List<Experiment> experiments,
                                                                        java.util.EnumSet<DataSet.Connections> connections,
                                                                        java.lang.String userId)

Description copied from interface: IGeneralInformationService

Return all data sets attached to the given experiments with connections that the user userId is allowed to see.

May only be called by users with capability LIST_PROJECTS_ON_BEHALF_OF_USER.

Specified by:

listDataSetsForExperimentsOnBehalfOfUser in interface IGeneralInformationService

experiments - The experiments for which we return attached data sets.

userId - The user to run this query on behalf of.

getDataSetMetaData

@Transactional(readOnly=true)
public java.util.List<DataSet> getDataSetMetaData(java.lang.String sessionToken,
                                                  java.util.List<java.lang.String> dataSetCodes)

Description copied from interface: IGeneralInformationService

Returns meta data for all specified data sets. This contains data set type, properties, and codes of linked parent and children data sets. For container data sets the contained data sets are not returned. Thus, DataSet.getContainedDataSets() is always empty.

Specified by:

getDataSetMetaData in interface IGeneralInformationService

dataSetCodes - Codes of requested data sets.

Returns:

result in the same order as the list of data set codes.

getDataSetMetaData

@Transactional(readOnly=true)
public java.util.List<DataSet> getDataSetMetaData(java.lang.String sessionToken,
                                                  java.util.List<java.lang.String> dataSetCodes,
                                                  java.util.EnumSet<DataSetFetchOption> fetchOptions)

Description copied from interface: IGeneralInformationService

Returns meta data for all specified data sets. Which parts of the data sets objects are fetched is controlled with the fetchOptions parameter.

Specified by:

getDataSetMetaData in interface IGeneralInformationService

dataSetCodes - Codes of requested data sets.

fetchOptions - Options that control which parts of the data sets are fetched.

Returns:

result in the same order as the list of data set codes.

searchOnSearchDomain

@Transactional(readOnly=true)
public java.util.List<SearchDomainSearchResult> searchOnSearchDomain(java.lang.String sessionToken,
                                                                     java.lang.String preferredSearchDomainOrNull,
                                                                     java.lang.String searchString,
                                                                     java.util.Map<java.lang.String,java.lang.String> optionalParametersOrNull)

Description copied from interface: IGeneralInformationService

Searches on a search domain. If no preferred search domain is specified the first available one will be used. If the preferred sequence search domain doesn't exist or isn't available also the first available one will be used.

Specified by:

searchOnSearchDomain in interface IGeneralInformationService

preferredSearchDomainOrNull - The key of the preferred search domain or null.

searchString - The search string.

optionalParametersOrNull - Optional parameters. Can be null. The semantics depends on the type of search domain.

listAvailableSearchDomains

@Transactional(readOnly=true)
public java.util.List<SearchDomain> listAvailableSearchDomains(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Lists available search domains. Their name attribute can be used when invoking IGeneralInformationService.searchOnSearchDomain(String, String, String, Map).

Specified by:

listAvailableSearchDomains in interface IGeneralInformationService

Returns:

empty list if no search domain is available.

searchForDataSets

@Transactional(readOnly=true)
public java.util.List<DataSet> searchForDataSets(java.lang.String sessionToken,
                                                 SearchCriteria searchCriteria)

Description copied from interface: IGeneralInformationService

Return all data sets matching specified search criteria. Note, that for returned container data sets the contained data sets have only code, type and registration date set.

Specified by:

searchForDataSets in interface IGeneralInformationService

searchCriteria - the criteria used for searching.

searchForDataSetsOnBehalfOfUser

@Transactional(readOnly=true)
public java.util.List<DataSet> searchForDataSetsOnBehalfOfUser(java.lang.String sessionToken,
                                                               SearchCriteria searchCriteria,
                                                               java.lang.String userId)

Description copied from interface: IGeneralInformationService

Return all data sets matching specified search criteria and visible to user userId. Note, that for returned container data sets the contained data sets have only code, type and registration date set.

May only be called by users who are INSTANCE_OBSERVER.

Specified by:

searchForDataSetsOnBehalfOfUser in interface IGeneralInformationService

searchCriteria - the criteria used for searching.

filterDataSetsVisibleToUser

@Transactional(readOnly=true)
public java.util.List<DataSet> filterDataSetsVisibleToUser(java.lang.String sessionToken,
                                                           java.util.List<DataSet> allDataSets,
                                                           java.lang.String userId)

Description copied from interface: IGeneralInformationService

Returns a filtered list of allDataSets containing those data sets which are visible to userId.

Specified by:

filterDataSetsVisibleToUser in interface IGeneralInformationService

allDataSets - The list of data sets that should be filtered.

userId - The user that the data sets should be visible to that survive the filtering.

Returns:

The filtered list of allDataSets containing those data sets which are visible to userId.

listExperiments

@Transactional(readOnly=true)
public java.util.List<Experiment> listExperiments(java.lang.String sessionToken,
                                                  java.util.List<java.lang.String> experimentIdentifiers)

Description copied from interface: IGeneralInformationService

Return all experiments matching a specified set of identifiers.

Specified by:

listExperiments in interface IGeneralInformationService

experimentIdentifiers - the identifiers of the experiments to be returned.

searchForExperiments

@Transactional(readOnly=true)
public java.util.List<Experiment> searchForExperiments(java.lang.String sessionToken,
                                                       SearchCriteria searchCriteria)

Description copied from interface: IGeneralInformationService

Returns all experiments matching specified search criteria. Note, that sub criterias are not supported.

Specified by:

searchForExperiments in interface IGeneralInformationService

listProjects

@Transactional(readOnly=true)
public java.util.List<Project> listProjects(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns all available projects.

Specified by:

listProjects in interface IGeneralInformationService

listProjectsOnBehalfOfUser

@Transactional(readOnly=true)
public java.util.List<Project> listProjectsOnBehalfOfUser(java.lang.String sessionToken,
                                                          java.lang.String userId)

Description copied from interface: IGeneralInformationService

Returns all available projects that a particular user is allowed to see.

May only be called by users with capability LIST_PROJECTS_ON_BEHALF_OF_USER.

Specified by:

listProjectsOnBehalfOfUser in interface IGeneralInformationService

userId - The user identifier of the user to get the projects for.

getMaterialByCodes

@Transactional(readOnly=true)
public java.util.List<Material> getMaterialByCodes(java.lang.String sessionToken,
                                                   java.util.List<MaterialIdentifier> materialIdentifier)

Description copied from interface: IGeneralInformationService

Returns the materials with specified identifiers (i.e. code and type).

Specified by:

getMaterialByCodes in interface IGeneralInformationService

searchForMaterials

@Transactional(readOnly=true)
public java.util.List<Material> searchForMaterials(java.lang.String sessionToken,
                                                   SearchCriteria searchCriteria)

Description copied from interface: IGeneralInformationService

Returns all material fulfilling specified search criteria.

Specified by:

searchForMaterials in interface IGeneralInformationService

listMetaprojects

@Transactional(readOnly=true)
public java.util.List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject> listMetaprojects(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Lists all metaprojects belonging to current user.

Specified by:

listMetaprojects in interface IGeneralInformationService

listMetaprojectsOnBehalfOfUser

@Transactional(readOnly=true)
public java.util.List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject> listMetaprojectsOnBehalfOfUser(java.lang.String sessionToken,
                                                                                                                    java.lang.String userId)

Description copied from interface: IGeneralInformationService

Lists all metaprojects belonging to specified user.

Specified by:

listMetaprojectsOnBehalfOfUser in interface IGeneralInformationService

getMetaproject

@Transactional(readOnly=true)
public MetaprojectAssignments getMetaproject(java.lang.String sessionToken,
                                             IMetaprojectId metaprojectId)

Description copied from interface: IGeneralInformationService

Returns all entities tagged with given metaproject.

Specified by:

getMetaproject in interface IGeneralInformationService

getMetaprojectOnBehalfOfUser

@Transactional(readOnly=true)
public MetaprojectAssignments getMetaprojectOnBehalfOfUser(java.lang.String sessionToken,
                                                           IMetaprojectId metaprojectId,
                                                           java.lang.String userId)

Description copied from interface: IGeneralInformationService

Returns all entities tagged with given metaproject for specified user.

Specified by:

getMetaprojectOnBehalfOfUser in interface IGeneralInformationService

listAttachmentsForProject

@Transactional(readOnly=true)
public java.util.List<Attachment> listAttachmentsForProject(java.lang.String sessionToken,
                                                            IProjectId projectId,
                                                            boolean allVersions)

Description copied from interface: IGeneralInformationService

Lists attachments of specified project.

Specified by:

listAttachmentsForProject in interface IGeneralInformationService

allVersions - If true, return all versions of the attachments, otherwise return only the latest version.

listAttachmentsForExperiment

@Transactional(readOnly=true)
public java.util.List<Attachment> listAttachmentsForExperiment(java.lang.String sessionToken,
                                                               IExperimentId experimentId,
                                                               boolean allVersions)

Description copied from interface: IGeneralInformationService

Lists attachments of specified experiment.

Specified by:

listAttachmentsForExperiment in interface IGeneralInformationService

allVersions - If true, return all versions of the attachments, otherwise return only the latest version.

listAttachmentsForSample

@Transactional(readOnly=true)
public java.util.List<Attachment> listAttachmentsForSample(java.lang.String sessionToken,
                                                           ISampleId sampleId,
                                                           boolean allVersions)

Description copied from interface: IGeneralInformationService

Lists attachments of specified sample.

Specified by:

listAttachmentsForSample in interface IGeneralInformationService

allVersions - If true, return all versions of the attachments, otherwise return only the latest version.

getUserDisplaySettings

@Transactional(readOnly=true)
public final java.util.Map<java.lang.String,java.lang.String> getUserDisplaySettings(java.lang.String sessionToken)

Specified by:

getUserDisplaySettings in interface IGeneralInformationService

listPropertyTypes

@Transactional(readOnly=true)
public java.util.List<PropertyType> listPropertyTypes(java.lang.String sessionToken,
                                                      boolean withRelations)

Description copied from interface: IGeneralInformationService

Lists property types.

Specified by:

listPropertyTypes in interface IGeneralInformationService

withRelations - If true, return relations.

generateCode

@Transactional
public java.lang.String generateCode(java.lang.String sessionToken,
                                     java.lang.String prefix,
                                     java.lang.String entityKind)

Description copied from interface: IGeneralInformationService

Generate Code.

Specified by:

generateCode in interface IGeneralInformationService

listDeletions

@Transactional(readOnly=true)
public java.util.List<Deletion> listDeletions(java.lang.String sessionToken,
                                              java.util.EnumSet<DeletionFetchOption> fetchOptions)

Description copied from interface: IGeneralInformationService

Returns all deletions.

Specified by:

listDeletions in interface IGeneralInformationService

fetchOptions - Options that control which parts of the deletions are fetched.

Returns:

a sorted list of Deletion.

listPersons

public java.util.List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person> listPersons(java.lang.String sessionToken)

Description copied from interface: IGeneralInformationService

Returns all persons.

Specified by:

listPersons in interface IGeneralInformationService

Returns:

a list of maps with the user information.

countNumberOfSamplesForType

@Transactional(readOnly=true)
public java.lang.Long countNumberOfSamplesForType(java.lang.String sessionToken,
                                                  java.lang.String sampleTypeCode)

Description copied from interface: IGeneralInformationService

Returns number of samples for a sample type code.

Specified by:

countNumberOfSamplesForType in interface IGeneralInformationService

Returns:

the number of samples for certain type.