Interface IDataSetRegistrationTransactionV2
- All Known Implementing Classes:
DataSetRegistrationTransaction,DataSetRegistrationTransactionV2Delegate
public interface IDataSetRegistrationTransactionV2
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Method Summary
Modifier and TypeMethodDescriptionvoidassignRoleToSpace(ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode role, ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable space, List<String> userIds, List<String> groupCodes) Give users and/or groups access privileges to a space.Create a new data set for registration in openBIS.createNewDataSet(String dataSetType) Create a new data set with the specified code.createNewDataSet(String dataSetType, ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind datasetKindOrNull) createNewDataSet(String dataSetType, String dataSetCode) Create a new data set with the specified type and code.createNewDataSet(String dataSetType, String dataSetCode, ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind datasetKindOrNull) createNewDirectory(IDataSet dst, String dirName) Create a new directory and return the path.createNewExperiment(String experimentIdentifierString, String experimentTypeCode) Create a new experiment to register with the openBIS AS.createNewFile(IDataSet dst, String fileName) Create a new empty file and return the path.createNewFile(IDataSet dst, String dstInDataset, String fileName) Create a new empty file and return the path.createNewLink(IDataSet dst, String dstInDataset, String linkName, String linkTarget) Create a new symbolic link and return the path.createNewMaterial(String materialCode, String materialType) Create a new material to register with the openBIS AS.createNewMetaproject(String name, String description) Creates the new metaproject for the current user.createNewMetaproject(String name, String description, String ownerId) Creates the new metaproject for the specified user.createNewProject(String projectIdentifier) Create a new project to register with the openBIS AS.createNewProjectSampleWithGeneratedCode(String projectIdentifier, String sampleTypeCode) Create a new project sample to register with the openBIS AS.createNewSample(String sampleIdentifierString, String sampleTypeCode) Create a new sample to register with the openBIS AS.createNewSampleWithGeneratedCode(String spaceCode, String sampleTypeCode) Create a new sample to register with the openBIS AS.createNewSpace(String spaceCode, String spaceAdminUserIdOrNull) Create a new space to register with the openBIS AS.Creates a new vocabulary term, which has to be assigned to aIVocabulary.getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment, String fileName, Integer versionOrNull) Returns an experiment attachment content.getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project, String fileName, Integer versionOrNull) Returns a project attachment content.getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample, String fileName, Integer versionOrNull) Returns a sample attachment content.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.authorization.IAuthorizationServicenet.lemnik.eodsql.DynamicTransactionQuerygetDatabaseQuery(String dataSourceName) Gets a database query object for the data source with the specified name.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutablegetDataSet(String dataSetCode) Deprecated.getDataSetForUpdate(String dataSetCode) Get a data set from the openBIS AS for the purpose of modifying it.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutablegetExperiment(String experimentIdentifierString) Deprecated.getExperimentForUpdate(String experimentIdentifierString) Get an experiment from the openBIS AS for the purpose of modifying it.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExternalDataManagementSystemImmutablegetExternalDataManagementSystem(String externalDataManagementSystemCode) Get an external data management system from the openBIS AS.ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalStateReturns the file representing the logical incoming file.Returns the logger object that logs messages to openbis operation log and data store server registration logs.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutablegetMaterial(String identifier) Deprecated.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutablegetMaterial(String materialCode, String materialType) Get a material from the openBIS AS.getMaterialForUpdate(String identifier) Get a material from the openBIS AS for the purpose of modifying it.getMaterialForUpdate(String materialCode, String materialType) Get a material from the openBIS AS for the purpose of modifying it.getMetaproject(String name) Only allowed when the user is available.getMetaproject(String name, String ownerId) Only allowed when the user is not available.Returns the currently used session token by the openBIS servicech.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutablegetProject(String projectIdentifier) Deprecated.getProjectForUpdate(String projectIdentifierString) Get an project from the openBIS AS for the purpose of modifying it.ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationContextReturn a registration context object which can be used to store information that needs to be accessed through the registration process.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutableDeprecated.getSampleForUpdate(String sampleIdentifierString) Get a sample from the openBIS AS for the purpose of modifying it.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchServiceRetrieve the search service for this transaction.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchServiceRetrieve the search service for this transaction.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchServiceRetrieve the search service for this transaction.Returns information about the openBIS server.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutableDeprecated.Get the id of the user on whose behalf this registration transaction is performed.ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IVocabularyImmutablegetVocabulary(String code) Deprecated.getVocabularyForUpdate(String code) Get the vocabulary with given codeList<ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IAttachmentImmutable>listAttachments(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment) Returns a list of experiment attachments with all versions.List<ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IAttachmentImmutable>listAttachments(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project) Returns a list of project attachments with all versions.List<ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IAttachmentImmutable>listAttachments(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample) Returns a list of sample attachments with all versions.makeDataSetMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable dataSet) Given an immutable data set, make it mutable.makeExperimentMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment) Given an immutable experiment, make it mutable.makeMaterialMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable material) Given an immutable material, make it mutable.makeProjectMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project) Given an immutable project, make it mutable.makeSampleMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample) Given an immutable sample, make it mutable.Move a file from into the root of a data set.Move a file to a specified location in a data set.voidrevokeRoleFromSpace(ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode role, ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable space, List<String> userIds, List<String> groupCodes) Take away users and/or groups access privileges to a space.voidSet the id of the user on whose behalf this registration transaction is performed.
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Method Details
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createNewDataSet
IDataSet createNewDataSet()Create a new data set for registration in openBIS. -
createNewDataSet
Create a new data set with the specified code. -
createNewDataSet
Create a new data set with the specified type and code. -
getDataSet
@Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable getDataSet(String dataSetCode) Deprecated.Get a data set from the openBIS AS. Returns null if the data set does not exist.- Returns:
- A data set or null
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getDataSetForUpdate
Get a data set from the openBIS AS for the purpose of modifying it. Returns null if the data set does not exist.- Returns:
- A data set or null
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getSample
@Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable getSample(String sampleIdentifierString) Deprecated.Get a sample from the openBIS AS. Returns null if the sample does not exist.- Returns:
- A sample or null
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getSampleForUpdate
Get a sample from the openBIS AS for the purpose of modifying it. Returns null if the sample does not exist.- Returns:
- A sample or null
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createNewSample
Create a new sample to register with the openBIS AS. The sample will have a permId.- Parameters:
sampleIdentifierString- The identifier for the new samplesampleTypeCode- The code of the type for the new sample
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createNewSampleWithGeneratedCode
Create a new sample to register with the openBIS AS. The sample will have a permId and automatically created identifier.- Parameters:
spaceCode- The space in which to create the sample identifier for the new samplesampleTypeCode- The code of the type for the new sample
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createNewProjectSampleWithGeneratedCode
Create a new project sample to register with the openBIS AS. The sample will have a permId and automatically created identifier.- Parameters:
projectIdentifier- The project in which to create the sample identifier for the new samplesampleTypeCode- The code of the type for the new sample
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getExperiment
@Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable getExperiment(String experimentIdentifierString) Deprecated.Get an experiment from the openBIS AS. -
getExperimentForUpdate
Get an experiment from the openBIS AS for the purpose of modifying it. -
createNewExperiment
Create a new experiment to register with the openBIS AS. The experiment will have a permId.- Parameters:
experimentIdentifierString- The identifier for the new experimentexperimentTypeCode- The code of the type for the new experiment
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createNewProject
Create a new project to register with the openBIS AS.- Parameters:
projectIdentifier- .
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getProject
@Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable getProject(String projectIdentifier) Deprecated.Get a project from the openBIS AS. Returns null if the project does not exist.- Returns:
- A project or null
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getProjectForUpdate
Get an project from the openBIS AS for the purpose of modifying it. -
createNewSpace
Create a new space to register with the openBIS AS.- Parameters:
spaceCode- the code of the spacespaceAdminUserIdOrNull- the user id of the person, who will receive space admin priviliges.
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getSpace
@Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable getSpace(String spaceCode) Deprecated.Get a space from the openBIS AS. Returns null if the space does not exist.- Returns:
- A space or null
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getMaterial
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable getMaterial(String materialCode, String materialType) Get a material from the openBIS AS. Returns null if the material does not exist.- Returns:
- A material or null
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getMaterial
@Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable getMaterial(String identifier) Deprecated.Get a material from the openBIS AS. Returns null if the material does not exist.- Returns:
- A material or null
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getMaterialForUpdate
Get a material from the openBIS AS for the purpose of modifying it. Returns null if the material does not exist.- Returns:
- A material or null
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getMaterialForUpdate
Get a material from the openBIS AS for the purpose of modifying it. Returns null if the material does not exist.- Returns:
- A material or null
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createNewMaterial
Create a new material to register with the openBIS AS.- Parameters:
materialCode- the code of the materialmaterialType- the type of the material
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createNewMetaproject
Creates the new metaproject for the current user. Only allowed when there is a user available. -
createNewMetaproject
Creates the new metaproject for the specified user. Only allowed when there is no user available. -
getMetaproject
Only allowed when the user is available.- Returns:
- metaproject with given name for current user.
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getMetaproject
Only allowed when the user is not available.- Returns:
- metaproject with given name for specified user.
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getVocabulary
@Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IVocabularyImmutable getVocabulary(String code) Deprecated.Get the read-only vocabulary with given code -
getVocabularyForUpdate
Get the vocabulary with given code -
createNewVocabularyTerm
IVocabularyTerm createNewVocabularyTerm()Creates a new vocabulary term, which has to be assigned to aIVocabulary. -
moveFile
Move a file from into the root of a data set.- Parameters:
src- The path of the file to move.dst- The data set to add the file to.- Returns:
- The absolute path after the move.
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moveFile
Move a file to a specified location in a data set. Any necessary intermediate folders are automatically created.- Parameters:
src- The path of the file to move.dst- The data set to add the file to.dstInDataset- The path of the file in the data set- Returns:
- The absolute path after the move.
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createNewDirectory
Create a new directory and return the path.- Parameters:
dst- The data set to add the file to.dirName- The name of the new file to create. (Can be a simple file or directory.)- Returns:
- The absolute path of the new file.
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createNewFile
Create a new empty file and return the path.- Parameters:
dst- The data set to add the file to.fileName- The name of the new file to create. (Can be a simple file or directory.)- Returns:
- The absolute path of the new file.
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createNewFile
Create a new empty file and return the path.- Parameters:
dst- The data set to add the file to.dstInDataset- The path of the file in the data setfileName- The name of the new file to create. (Can be a simple file or directory.)- Returns:
- The absolute path of the new file.
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createNewLink
Create a new symbolic link and return the path.- Parameters:
dst- The data set to add the file to.dstInDataset- The path of the file in the data setlinkName- The name of the new link to createlinkTarget- The path of file/directory the new link should point to- Returns:
- The absolute path of the new link.
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getSearchService
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService getSearchService()Retrieve the search service for this transaction. If the user is available for this transaction, then the search service results will be filtered for this user.- Returns:
- The search service for this transaction.
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getSearchServiceUnfiltered
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService getSearchServiceUnfiltered()Retrieve the search service for this transaction. It returns the results unfiltered by the user, even if the user is available.- Returns:
- The search service for this transaction.
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getSearchServiceFilteredForUser
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService getSearchServiceFilteredForUser(String userId) Retrieve the search service for this transaction. The search service results will be filtered for the specified user.- Returns:
- The search service for this transaction.
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getAuthorizationService
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.authorization.IAuthorizationService getAuthorizationService()- Returns:
- A service which can be used to get authorization information about a user.
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getDatabaseQuery
net.lemnik.eodsql.DynamicTransactionQuery getDatabaseQuery(String dataSourceName) throws IllegalArgumentException Gets a database query object for the data source with the specified name.After the rest of the transaction is committed, the queries are committed. Failures in these secondary queries are not fatal, but they are caught and the clients of the transaction are notified.
- Parameters:
dataSourceName- The name of the data source to query against, as declared in the service.properties file.- Returns:
- The query.
- Throws:
IllegalArgumentException
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getRegistrationContext
ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationContext getRegistrationContext()Return a registration context object which can be used to store information that needs to be accessed through the registration process.It is important to use this registration context, and not global variables, for communication between code in different parts of the registration process. This is because the registration process is not guaranteed to run in a single process.
- Returns:
- The context, a hash-map-like object.
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getGlobalState
ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState getGlobalState()- Returns:
- Global state for this dropbox, including configuration properties specified by the user.
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getServerInformation
Returns information about the openBIS server. -
getIncoming
File getIncoming()Returns the file representing the logical incoming file. -
getUserId
String getUserId()Get the id of the user on whose behalf this registration transaction is performed.- Returns:
- A userId or null, if there is none.
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setUserId
Set the id of the user on whose behalf this registration transaction is performed.- Parameters:
userIdOrNull- The id of a user or null if this transaction should be performed as the system (etlserver).
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getExternalDataManagementSystem
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExternalDataManagementSystemImmutable getExternalDataManagementSystem(String externalDataManagementSystemCode) Get an external data management system from the openBIS AS. Returns null if the object does not exist.- Returns:
- external data management system or null
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getOpenBisServiceSessionToken
String getOpenBisServiceSessionToken()Returns the currently used session token by the openBIS service -
getLogger
IDSSRegistrationLogger getLogger()Returns the logger object that logs messages to openbis operation log and data store server registration logs.
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SearchService.getDataSet(String)