Interface IDataSetRegistrationTransactionV2

All Known Implementing Classes:
DataSetRegistrationTransaction, DataSetRegistrationTransactionV2Delegate

public interface IDataSetRegistrationTransactionV2
  • Method Details

    • createNewDataSet

      IDataSet createNewDataSet()
      Create a new data set for registration in openBIS.
    • createNewDataSet

      IDataSet createNewDataSet(String dataSetType)
      Create a new data set with the specified code.
    • createNewDataSet

      IDataSet createNewDataSet(String dataSetType, ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind datasetKindOrNull)
    • createNewDataSet

      IDataSet createNewDataSet(String dataSetType, String dataSetCode)
      Create a new data set with the specified type and code.
    • createNewDataSet

      IDataSet createNewDataSet(String dataSetType, String dataSetCode, ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind datasetKindOrNull)
    • getDataSet

      @Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable getDataSet(String dataSetCode)
      Get a data set from the openBIS AS. Returns null if the data set does not exist.
      Returns:
      A data set or null
    • getDataSetForUpdate

      IDataSetUpdatable getDataSetForUpdate(String dataSetCode)
      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
    • makeDataSetMutable

      IDataSetUpdatable makeDataSetMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable dataSet)
      Given an immutable data set, make it mutable.
      Returns:
      A data set
    • getSample

      @Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable getSample(String sampleIdentifierString)
      Get a sample from the openBIS AS. Returns null if the sample does not exist.
      Returns:
      A sample or null
    • getSampleForUpdate

      ISample getSampleForUpdate(String sampleIdentifierString)
      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
    • makeSampleMutable

      ISample makeSampleMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample)
      Given an immutable sample, make it mutable.
      Returns:
      A sample
    • createNewSample

      ISample createNewSample(String sampleIdentifierString, String sampleTypeCode)
      Create a new sample to register with the openBIS AS. The sample will have a permId.
      Parameters:
      sampleIdentifierString - The identifier for the new sample
      sampleTypeCode - The code of the type for the new sample
    • createNewSampleWithGeneratedCode

      ISample createNewSampleWithGeneratedCode(String spaceCode, String sampleTypeCode)
      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 sample
      sampleTypeCode - The code of the type for the new sample
    • createNewProjectSampleWithGeneratedCode

      ISample createNewProjectSampleWithGeneratedCode(String projectIdentifier, String sampleTypeCode)
      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 sample
      sampleTypeCode - The code of the type for the new sample
    • getExperiment

      @Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable getExperiment(String experimentIdentifierString)
      Get an experiment from the openBIS AS.
    • getExperimentForUpdate

      IExperimentUpdatable getExperimentForUpdate(String experimentIdentifierString)
      Get an experiment from the openBIS AS for the purpose of modifying it.
    • makeExperimentMutable

      IExperimentUpdatable makeExperimentMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment)
      Given an immutable experiment, make it mutable.
      Returns:
      An experiment
    • createNewExperiment

      IExperiment createNewExperiment(String experimentIdentifierString, String experimentTypeCode)
      Create a new experiment to register with the openBIS AS. The experiment will have a permId.
      Parameters:
      experimentIdentifierString - The identifier for the new experiment
      experimentTypeCode - The code of the type for the new experiment
    • createNewProject

      IProject createNewProject(String projectIdentifier)
      Create a new project to register with the openBIS AS.
      Parameters:
      projectIdentifier - .
    • getProject

      @Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable getProject(String projectIdentifier)
      Get a project from the openBIS AS. Returns null if the project does not exist.
      Returns:
      A project or null
    • getProjectForUpdate

      IProject getProjectForUpdate(String projectIdentifierString)
      Get an project from the openBIS AS for the purpose of modifying it.
    • makeProjectMutable

      IProject makeProjectMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project)
      Given an immutable project, make it mutable.
      Returns:
      A mutable project.
    • createNewSpace

      ISpace createNewSpace(String spaceCode, String spaceAdminUserIdOrNull)
      Create a new space to register with the openBIS AS.
      Parameters:
      spaceCode - the code of the space
      spaceAdminUserIdOrNull - the user id of the person, who will receive space admin priviliges.
    • getSpace

      @Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable getSpace(String spaceCode)
      Get a space from the openBIS AS. Returns null if the space does not exist.
      Returns:
      A space or null
    • 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
    • getMaterial

      @Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable getMaterial(String identifier)
      Get a material from the openBIS AS. Returns null if the material does not exist.
      Returns:
      A material or null
    • getMaterialForUpdate

      IMaterial getMaterialForUpdate(String materialCode, String materialType)
      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
    • getMaterialForUpdate

      IMaterial getMaterialForUpdate(String identifier)
      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
    • makeMaterialMutable

      IMaterial makeMaterialMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable material)
      Given an immutable material, make it mutable.
      Returns:
      A material
    • createNewMaterial

      IMaterial createNewMaterial(String materialCode, String materialType)
      Create a new material to register with the openBIS AS.
      Parameters:
      materialCode - the code of the material
      materialType - the type of the material
    • createNewMetaproject

      IMetaproject createNewMetaproject(String name, String description)
      Creates the new metaproject for the current user. Only allowed when there is a user available.
    • createNewMetaproject

      IMetaproject createNewMetaproject(String name, String description, String ownerId)
      Creates the new metaproject for the specified user. Only allowed when there is no user available.
    • getMetaproject

      IMetaproject getMetaproject(String name)
      Only allowed when the user is available.
      Returns:
      metaproject with given name for current user.
    • getMetaproject

      IMetaproject getMetaproject(String name, String ownerId)
      Only allowed when the user is not available.
      Returns:
      metaproject with given name for specified user.
    • getVocabulary

      @Deprecated ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IVocabularyImmutable getVocabulary(String code)
      Get the read-only vocabulary with given code
    • getVocabularyForUpdate

      IVocabulary getVocabularyForUpdate(String code)
      Get the vocabulary with given code
    • createNewVocabularyTerm

      IVocabularyTerm createNewVocabularyTerm()
      Creates a new vocabulary term, which has to be assigned to a IVocabulary.
    • moveFile

      String moveFile(String src, IDataSet dst)
      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.
    • moveFile

      String moveFile(String src, IDataSet dst, String dstInDataset)
      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.
    • createNewDirectory

      String createNewDirectory(IDataSet dst, String dirName)
      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.
    • createNewFile

      String createNewFile(IDataSet dst, String fileName)
      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.
    • createNewFile

      String createNewFile(IDataSet dst, String dstInDataset, String fileName)
      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 set
      fileName - The name of the new file to create. (Can be a simple file or directory.)
      Returns:
      The absolute path of the new file.
    • createNewLink

      String createNewLink(IDataSet dst, String dstInDataset, String linkName, String linkTarget)
      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 set
      linkName - The name of the new link to create
      linkTarget - The path of file/directory the new link should point to
      Returns:
      The absolute path of the new link.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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
    • 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.
    • getGlobalState

      ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState getGlobalState()
      Returns:
      Global state for this dropbox, including configuration properties specified by the user.
    • getServerInformation

      Map<String,String> 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.
    • setUserId

      void setUserId(String userIdOrNull)
      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).
    • 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
    • assignRoleToSpace

      void assignRoleToSpace(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.
    • revokeRoleFromSpace

      void revokeRoleFromSpace(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.
    • getAttachmentContent

      InputStream getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project, String fileName, Integer versionOrNull)
      Returns a project attachment content. If the version is not specified then the latest version of the attachment is returned. Returns null if the attachment does not exist.
    • getAttachmentContent

      InputStream getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment, String fileName, Integer versionOrNull)
      Returns an experiment attachment content. If the version is not specified then the latest version of the attachment is returned. Returns null if the attachment does not exist.
    • getAttachmentContent

      InputStream getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample, String fileName, Integer versionOrNull)
      Returns a sample attachment content. If the version is not specified then the latest version of the attachment is returned. Returns null if the attachment does not exist.
    • listAttachments

      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. Returns null if the project does not have any attachments.
    • listAttachments

      List<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. Returns null if the experiment does not have any attachments.
    • listAttachments

      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. Returns null if the sample does not have any attachments.
    • getOpenBisServiceSessionToken

      String getOpenBisServiceSessionToken()
      Returns the currently used session token by the openBIS service
    • getLogger

      Returns the logger object that logs messages to openbis operation log and data store server registration logs.