Interface IApplicationServerApi

  • All Superinterfaces:
    IRpcService

    public interface IApplicationServerApi
    extends IRpcService
    V3 application server API. Detailed documentation on how to use the API together code examples in both Java and Javascript can be found at "openBIS V3 API" openBIS WIKI page.

    The required access rights of the methods are the default ones. They can be configured with a capability-role map. For more details see "Installation and Administrator Guide of the openBIS Server" openBIS WIKI page.

    • Field Detail

      • SERVICE_NAME

        static final java.lang.String SERVICE_NAME
        Name of this service for which it is registered at the RPC name server.
        See Also:
        Constant Field Values
      • SERVICE_URL

        static final java.lang.String SERVICE_URL
        Application part of the URL to access this service remotely.
        See Also:
        Constant Field Values
    • Method Detail

      • login

        java.lang.String login​(java.lang.String userId,
                               java.lang.String password)
        Authenticates a user basing on the provided user id and password. If the authentication is successful, then returns a session token. Otherwise returns null.
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • loginAs

        java.lang.String loginAs​(java.lang.String userId,
                                 java.lang.String password,
                                 java.lang.String asUserId)
        Authenticates a user basing on the provided user id and password and makes the session look like as if it was a different user. If the authentication is successful, then returns a session token. Otherwise returns null. The provided user id and password must represent an INSTANCE_ADMIN account.
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • loginAsAnonymousUser

        java.lang.String loginAsAnonymousUser()
        Authenticates as an anonymous user who does not require a password.
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • logout

        void logout​(java.lang.String sessionToken)
        Terminates a user's session.
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getSessionInformation

        SessionInformation getSessionInformation​(java.lang.String sessionToken)
        Returns detailed information about a user's session.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • isSessionActive

        boolean isSessionActive​(java.lang.String sessionToken)
        Returns true if a user's session is active. Otherwise returns false.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • createSpaces

        java.util.List<SpacePermId> createSpaces​(java.lang.String sessionToken,
                                                 java.util.List<SpaceCreation> newSpaces)
        Creates spaces basing on the provided SpaceCreation objects. Returns ids of the newly created spaces where nth id corresponds to nth creation object.

        Required access rights: SPACE_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect SpaceCreation objects, insufficient access rights etc.
      • createProjects

        java.util.List<ProjectPermId> createProjects​(java.lang.String sessionToken,
                                                     java.util.List<ProjectCreation> newProjects)
        Creates projects basing on the provided ProjectCreation objects. Returns ids of the newly created projects where nth id corresponds to nth creation object.

        Required access rights: SPACE_POWER_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect ProjectCreation objects, insufficient access rights etc.
      • createExperiments

        java.util.List<ExperimentPermId> createExperiments​(java.lang.String sessionToken,
                                                           java.util.List<ExperimentCreation> newExperiments)
        Creates experiments basing on the provided ExperimentCreation objects. Returns ids of the newly created experiments where nth id corresponds to nth creation object.

        Required access rights: PROJECT_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect ExperimentCreation objects, insufficient access rights etc.
      • createExperimentTypes

        java.util.List<EntityTypePermId> createExperimentTypes​(java.lang.String sessionToken,
                                                               java.util.List<ExperimentTypeCreation> newExperimentTypes)
        Creates experiment types basing on the provided ExperimentTypeCreation objects. Returns ids of the newly created experiment types where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect ExperimentTypeCreation objects, insufficient access rights etc.
      • createSamples

        java.util.List<SamplePermId> createSamples​(java.lang.String sessionToken,
                                                   java.util.List<SampleCreation> newSamples)
        Creates samples basing on the provided SampleCreation objects. Returns ids of the newly created samples where nth id corresponds to nth creation object.

        Required access rights: PROJECT_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect SampleCreation objects, insufficient access rights etc.
      • createSampleTypes

        java.util.List<EntityTypePermId> createSampleTypes​(java.lang.String sessionToken,
                                                           java.util.List<SampleTypeCreation> newSampleTypes)
        Creates sample types basing on the provided SampleTypeCreation objects. Returns ids of the newly created sample types where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect SampleTypeCreation objects, insufficient access rights etc.
      • createDataSets

        java.util.List<DataSetPermId> createDataSets​(java.lang.String sessionToken,
                                                     java.util.List<DataSetCreation> newDataSets)
        Creates data sets basing on the provided DataSetCreation objects. Returns ids of the newly created data sets where nth id corresponds to nth creation object.

        Required access rights: SPACE_ETL_SERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect DataSetCreation objects, insufficient access rights etc.
      • createDataSetTypes

        java.util.List<EntityTypePermId> createDataSetTypes​(java.lang.String sessionToken,
                                                            java.util.List<DataSetTypeCreation> newDataSetTypes)
        Creates data set types basing on the provided DataSetTypeCreation objects. Returns ids of the newly created data set types where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect DataSetTypeCreation objects, insufficient access rights etc.
      • createMaterials

        java.util.List<MaterialPermId> createMaterials​(java.lang.String sessionToken,
                                                       java.util.List<MaterialCreation> newMaterials)
        Creates materials basing on the provided MaterialCreation objects. Returns ids of the newly created materials where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect MaterialCreation objects, insufficient access rights etc.
      • createMaterialTypes

        java.util.List<EntityTypePermId> createMaterialTypes​(java.lang.String sessionToken,
                                                             java.util.List<MaterialTypeCreation> newMaterialTypes)
        Creates material types basing on the provided MaterialTypeCreation objects. Returns ids of the newly created material types where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect MaterialTypeCreation objects, insufficient access rights etc.
      • createPropertyTypes

        java.util.List<PropertyTypePermId> createPropertyTypes​(java.lang.String sessionToken,
                                                               java.util.List<PropertyTypeCreation> newPropertyTypes)
        Creates property types basing on the provided PropertyTypeCreation objects. Returns ids of the newly created property types where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect PropertyTypeCreation objects, insufficient access rights etc.
      • createPlugins

        java.util.List<PluginPermId> createPlugins​(java.lang.String sessionToken,
                                                   java.util.List<PluginCreation> newPlugins)
        Creates plugins (i.e. dynamic property evaluators, managed property handlers, entity validators) basing on the provided PluginCreation objects. Returns ids of the newly created plugins where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect PluginCreation objects, insufficient access rights etc.
      • createVocabularies

        java.util.List<VocabularyPermId> createVocabularies​(java.lang.String sessionToken,
                                                            java.util.List<VocabularyCreation> newVocabularies)
        Creates vocabularies and vocabulary terms (optionally) basing on the provided VocabularyCreation objects. Returns ids of the newly created vocabularies where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect VocabularyCreation objects, insufficient access rights etc.
      • createVocabularyTerms

        java.util.List<VocabularyTermPermId> createVocabularyTerms​(java.lang.String sessionToken,
                                                                   java.util.List<VocabularyTermCreation> newVocabularyTerms)
        Creates vocabulary terms basing on the provided VocabularyTermCreation objects. Returns ids of the newly created vocabulary terms where nth id corresponds to nth creation object.
          Required access rights:
        • unofficial terms - PROJECT_USER or stronger
        • official terms - PROJECT_POWER_USER or stronger
        • internally managed - INSTANCE_ADMIN
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect VocabularyTermCreation objects, insufficient access rights etc.
      • createTags

        java.util.List<TagPermId> createTags​(java.lang.String sessionToken,
                                             java.util.List<TagCreation> newTags)
        Creates tags basing on the provided TagCreation objects. Returns ids of the newly created tags where nth id corresponds to nth creation object. Tags are only visible to a user who created them.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect TagCreation objects, insufficient access rights etc.
      • createAuthorizationGroups

        java.util.List<AuthorizationGroupPermId> createAuthorizationGroups​(java.lang.String sessionToken,
                                                                           java.util.List<AuthorizationGroupCreation> newAuthorizationGroups)
        Creates authorization groups basing on the provided AuthorizationGroupCreation objects. Returns ids of the newly created authorization groups where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect AuthorizationGroupCreation objects, insufficient access rights etc.
      • createRoleAssignments

        java.util.List<RoleAssignmentTechId> createRoleAssignments​(java.lang.String sessionToken,
                                                                   java.util.List<RoleAssignmentCreation> newRoleAssignments)
        Creates role assignments basing on the provided RoleAssignmentCreation objects. Returns ids of the newly created role assignments where nth id corresponds to nth creation object.
          Required access rights:
        • instance roles - INSTANCE_ADMIN
        • space roles - SPACE_ADMIN or stronger
        • project roles - PROJECT_ADMIN or stronger
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect RoleAssignmentCreation objects, insufficient access rights etc.
      • createPersons

        java.util.List<PersonPermId> createPersons​(java.lang.String sessionToken,
                                                   java.util.List<PersonCreation> newPersons)
        Creates persons basing on the provided PersonCreation objects. Returns ids of the newly created persons where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect PersonCreation objects, insufficient access rights etc.
      • createExternalDataManagementSystems

        java.util.List<ExternalDmsPermId> createExternalDataManagementSystems​(java.lang.String sessionToken,
                                                                              java.util.List<ExternalDmsCreation> newExternalDataManagementSystems)
        Creates external data management systems basing on the provided ExternalDmsCreation objects. Returns ids of the newly created external data management systems where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect ExternalDmsCreation objects, insufficient access rights etc.
      • createQueries

        java.util.List<QueryTechId> createQueries​(java.lang.String sessionToken,
                                                  java.util.List<QueryCreation> newQueries)
        Creates queries basing on the provided QueryCreation objects. Returns ids of the newly created queries where nth id corresponds to nth creation object.

        Required access rights: depends on a query database (more details at "Custom Database Queries" openBIS WIKI page)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect ExternalDmsCreation objects, insufficient access rights etc.
      • createSemanticAnnotations

        java.util.List<SemanticAnnotationPermId> createSemanticAnnotations​(java.lang.String sessionToken,
                                                                           java.util.List<SemanticAnnotationCreation> newAnnotations)
        Creates semantic annotations basing on the provided SemanticAnnotationCreation objects. Returns ids of the newly created semantic annotations where nth id corresponds to nth creation object.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect SemanticAnnotationCreation objects, insufficient access rights etc.
      • updateSpaces

        void updateSpaces​(java.lang.String sessionToken,
                          java.util.List<SpaceUpdate> spaceUpdates)
        Updates spaces basing on the provided SpaceUpdate objects.

        Required access rights: SPACE_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect SpaceUpdate objects, insufficient access rights etc.
      • updateProjects

        void updateProjects​(java.lang.String sessionToken,
                            java.util.List<ProjectUpdate> projectUpdates)
        Updates projects basing on the provided ProjectUpdate objects.

        Required access rights: SPACE_POWER_USER / PROJECT_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect ProjectUpdate objects, insufficient access rights etc.
      • updateExperiments

        void updateExperiments​(java.lang.String sessionToken,
                               java.util.List<ExperimentUpdate> experimentUpdates)
        Updates experiments basing on the provided ExperimentUpdate objects.

        Required access rights: PROJECT_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect ExperimentUpdate objects, insufficient access rights etc.
      • updateExperimentTypes

        void updateExperimentTypes​(java.lang.String sessionToken,
                                   java.util.List<ExperimentTypeUpdate> experimentTypeUpdates)
        Updates experiment types basing on the provided ExperimentTypeUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect ExperimentTypeUpdate objects, insufficient access rights etc.
      • updateSamples

        void updateSamples​(java.lang.String sessionToken,
                           java.util.List<SampleUpdate> sampleUpdates)
        Updates samples basing on the provided SampleUpdate objects.

        Required access rights: PROJECT_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect SampleUpdate objects, insufficient access rights etc.
      • updateSampleTypes

        void updateSampleTypes​(java.lang.String sessionToken,
                               java.util.List<SampleTypeUpdate> sampleTypeUpdates)
        Updates sample types basing on the provided SampleTypeUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect SampleTypeUpdate objects, insufficient access rights etc.
      • updateDataSets

        void updateDataSets​(java.lang.String sessionToken,
                            java.util.List<DataSetUpdate> dataSetUpdates)
        Updates data sets basing on the provided DataSetUpdate objects.

        Required access rights: PROJECT_POWER_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect DataSetUpdate objects, insufficient access rights etc.
      • updateDataSetTypes

        void updateDataSetTypes​(java.lang.String sessionToken,
                                java.util.List<DataSetTypeUpdate> dataSetTypeUpdates)
        Updates data set types basing on the provided DataSetTypeUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect DataSetTypeUpdate objects, insufficient access rights etc.
      • updateMaterials

        void updateMaterials​(java.lang.String sessionToken,
                             java.util.List<MaterialUpdate> materialUpdates)
        Updates materials basing on the provided MaterialUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect MaterialUpdate objects, insufficient access rights etc.
      • updateMaterialTypes

        void updateMaterialTypes​(java.lang.String sessionToken,
                                 java.util.List<MaterialTypeUpdate> materialTypeUpdates)
        Updates material types basing on the provided MaterialTypeUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect MaterialTypeUpdate objects, insufficient access rights etc.
      • updateExternalDataManagementSystems

        void updateExternalDataManagementSystems​(java.lang.String sessionToken,
                                                 java.util.List<ExternalDmsUpdate> externalDmsUpdates)
        Updates external data management systems basing on the provided ExternalDmsUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect ExternalDmsUpdate objects, insufficient access rights etc.
      • updatePropertyTypes

        void updatePropertyTypes​(java.lang.String sessionToken,
                                 java.util.List<PropertyTypeUpdate> propertyTypeUpdates)
        Updates property types basing on the provided PropertyTypeUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect PropertyTypeUpdate objects, insufficient access rights etc.
      • updatePlugins

        void updatePlugins​(java.lang.String sessionToken,
                           java.util.List<PluginUpdate> pluginUpdates)
        Updates plugins (i.e. dynamic property evaluators, managed property handlers, entity validators) basing on the provided PluginUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect PluginUpdate objects, insufficient access rights etc.
      • updateVocabularies

        void updateVocabularies​(java.lang.String sessionToken,
                                java.util.List<VocabularyUpdate> vocabularyUpdates)
        Updates vocabularies basing on the provided VocabularyUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect VocabularyUpdate objects, insufficient access rights etc.
      • updateVocabularyTerms

        void updateVocabularyTerms​(java.lang.String sessionToken,
                                   java.util.List<VocabularyTermUpdate> vocabularyTermUpdates)
        Updates vocabulary terms basing on the provided VocabularyTermUpdate objects.
          Required access rights:
        • unofficial terms - PROJECT_USER or stronger
        • official terms - PROJECT_POWER_USER or stronger
        • internally managed - INSTANCE_ADMIN
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect VocabularyTermUpdate objects, insufficient access rights etc.
      • updateTags

        void updateTags​(java.lang.String sessionToken,
                        java.util.List<TagUpdate> tagUpdates)
        Updates tags basing on the provided TagUpdate objects. A user can only update own tags (i.e. tags a user has created).

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect TagUpdate objects, insufficient access rights etc.
      • updateAuthorizationGroups

        void updateAuthorizationGroups​(java.lang.String sessionToken,
                                       java.util.List<AuthorizationGroupUpdate> authorizationGroupUpdates)
        Updates authorization groups basing on the provided AuthorizationGroupUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect AuthorizationGroupUpdate objects, insufficient access rights etc.
      • updatePersons

        void updatePersons​(java.lang.String sessionToken,
                           java.util.List<PersonUpdate> personUpdates)
        Updates persons basing on the provided PersonUpdate objects.
          Required access rights:
        • activate/deactivate - INSTANCE_ADMIN
        • home space - user himself/herself / SPACE_ADMIN or stronger
        • webapp settings - user himself/herself / INSTANCE_ADMIN
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect PersonUpdate objects, insufficient access rights etc.
      • updateOperationExecutions

        void updateOperationExecutions​(java.lang.String sessionToken,
                                       java.util.List<OperationExecutionUpdate> executionUpdates)
        Updates operation executions basing on the provided OperationExecutionUpdate objects.

        Required access rights: user who created the operation execution / INSTANCE_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect OperationExecutionUpdate objects, insufficient access rights etc.
      • updateSemanticAnnotations

        void updateSemanticAnnotations​(java.lang.String sessionToken,
                                       java.util.List<SemanticAnnotationUpdate> annotationUpdates)
        Updates semantic annotations basing on the provided SemanticAnnotationUpdate objects.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect SemanticAnnotationUpdate objects, insufficient access rights etc.
      • updateQueries

        void updateQueries​(java.lang.String sessionToken,
                           java.util.List<QueryUpdate> queryUpdates)
        Updates queries basing on the provided QueryUpdate objects.

        Required access rights: depends on a query and a query database (more details at "Custom Database Queries" openBIS WIKI page)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems, e.g. incorrect QueryUpdate objects, insufficient access rights etc.
      • getRights

        java.util.Map<IObjectId,​Rights> getRights​(java.lang.String sessionToken,
                                                        java.util.List<? extends IObjectId> ids,
                                                        RightsFetchOptions fetchOptions)
        Gets authorization rights for the provided IObjectId ids. A result map contains an entry for a given id only if an object for that id has been found and that object can be accessed by the user.
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getSpaces

        java.util.Map<ISpaceId,​Space> getSpaces​(java.lang.String sessionToken,
                                                      java.util.List<? extends ISpaceId> spaceIds,
                                                      SpaceFetchOptions fetchOptions)
        Gets spaces for the provided ISpaceId ids. A result map contains an entry for a given id only if a space for that id has been found and that space can be accessed by the user.

        By default the returned spaces contain only basic information. Any additional information to be fetched has to be explicitly requested via SpaceFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger (a project user can see a space if it has access to any of the projects in that space)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getProjects

        java.util.Map<IProjectId,​Project> getProjects​(java.lang.String sessionToken,
                                                            java.util.List<? extends IProjectId> projectIds,
                                                            ProjectFetchOptions fetchOptions)
        Gets projects for the provided IProjectId ids. A result map contains an entry for a given id only if a project for that id has been found and that project can be accessed by the user.

        By default the returned projects contain only basic information. Any additional information to be fetched has to be explicitly requested via ProjectFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getExperiments

        java.util.Map<IExperimentId,​Experiment> getExperiments​(java.lang.String sessionToken,
                                                                     java.util.List<? extends IExperimentId> experimentIds,
                                                                     ExperimentFetchOptions fetchOptions)
        Gets experiments for the provided IExperimentId ids. A result map contains an entry for a given id only if an experiment for that id has been found and that experiment can be accessed by the user.

        By default the returned experiments contain only basic information. Any additional information to be fetched has to be explicitly requested via ExperimentFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getExperimentTypes

        java.util.Map<IEntityTypeId,​ExperimentType> getExperimentTypes​(java.lang.String sessionToken,
                                                                             java.util.List<? extends IEntityTypeId> experimentTypeIds,
                                                                             ExperimentTypeFetchOptions fetchOptions)
        Gets experiment types for the provided IEntityTypeId ids. A result map contains an entry for a given id only if an experiment type for that id has been found and that experiment type can be accessed by the user.

        By default the returned experiment types contain only basic information. Any additional information to be fetched has to be explicitly requested via ExperimentTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getSamples

        java.util.Map<ISampleId,​Sample> getSamples​(java.lang.String sessionToken,
                                                         java.util.List<? extends ISampleId> sampleIds,
                                                         SampleFetchOptions fetchOptions)
        Gets samples for the provided ISampleId ids. A result map contains an entry for a given id only if a sample for that id has been found and that sample can be accessed by the user.

        By default the returned samples contain only basic information. Any additional information to be fetched has to be explicitly requested via SampleFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getSampleTypes

        java.util.Map<IEntityTypeId,​SampleType> getSampleTypes​(java.lang.String sessionToken,
                                                                     java.util.List<? extends IEntityTypeId> sampleTypeIds,
                                                                     SampleTypeFetchOptions fetchOptions)
        Gets sample types for the provided IEntityTypeId ids. A result map contains an entry for a given id only if an sample type for that id has been found and that sample type can be accessed by the user.

        By default the returned sample types contain only basic information. Any additional information to be fetched has to be explicitly requested via SampleTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getDataSets

        java.util.Map<IDataSetId,​DataSet> getDataSets​(java.lang.String sessionToken,
                                                            java.util.List<? extends IDataSetId> dataSetIds,
                                                            DataSetFetchOptions fetchOptions)
        Gets data sets for the provided IDataSetId ids. A result map contains an entry for a given id only if a data set for that id has been found and that data set can be accessed by the user.

        By default the returned data sets contain only basic information. Any additional information to be fetched has to be explicitly requested via DataSetFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getDataSetTypes

        java.util.Map<IEntityTypeId,​DataSetType> getDataSetTypes​(java.lang.String sessionToken,
                                                                       java.util.List<? extends IEntityTypeId> dataSetTypeIds,
                                                                       DataSetTypeFetchOptions fetchOptions)
        Gets data set types for the provided IEntityTypeId ids. A result map contains an entry for a given id only if a data set type for that id has been found and that data set type can be accessed by the user.

        By default the returned data set types contain only basic information. Any additional information to be fetched has to be explicitly requested via DataSetTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getMaterials

        java.util.Map<IMaterialId,​Material> getMaterials​(java.lang.String sessionToken,
                                                               java.util.List<? extends IMaterialId> materialIds,
                                                               MaterialFetchOptions fetchOptions)
        Gets materials for the provided IMaterialId ids. A result map contains an entry for a given id only if a material for that id has been found and that material can be accessed by the user.

        By default the returned materials contain only basic information. Any additional information to be fetched has to be explicitly requested via MaterialFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getMaterialTypes

        java.util.Map<IEntityTypeId,​MaterialType> getMaterialTypes​(java.lang.String sessionToken,
                                                                         java.util.List<? extends IEntityTypeId> materialTypeIds,
                                                                         MaterialTypeFetchOptions fetchOptions)
        Gets material types for the provided IEntityTypeId ids. A result map contains an entry for a given id only if a material type for that id has been found and that material type can be accessed by the user.

        By default the returned material types contain only basic information. Any additional information to be fetched has to be explicitly requested via MaterialTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getPropertyTypes

        java.util.Map<IPropertyTypeId,​PropertyType> getPropertyTypes​(java.lang.String sessionToken,
                                                                           java.util.List<? extends IPropertyTypeId> typeIds,
                                                                           PropertyTypeFetchOptions fetchOptions)
        Gets property types for the provided IPropertyTypeId ids. A result map contains an entry for a given id only if a property type for that id has been found and that property type can be accessed by the user.

        By default the returned property types contain only basic information. Any additional information to be fetched has to be explicitly requested via PropertyTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getPlugins

        java.util.Map<IPluginId,​Plugin> getPlugins​(java.lang.String sessionToken,
                                                         java.util.List<? extends IPluginId> pluginIds,
                                                         PluginFetchOptions fetchOptions)
        Gets plugins (i.e. dynamic property evaluators, managed property handlers, entity validators) for the provided IPluginId ids. A result map contains an entry for a given id only if a plugin for that id has been found and that plugin can be accessed by the user.

        By default the returned plugins contain only basic information. Any additional information to be fetched has to be explicitly requested via PluginFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getVocabularies

        java.util.Map<IVocabularyId,​Vocabulary> getVocabularies​(java.lang.String sessionToken,
                                                                      java.util.List<? extends IVocabularyId> vocabularyIds,
                                                                      VocabularyFetchOptions fetchOptions)
        Gets vocabularies for the provided IVocabularyId ids. A result map contains an entry for a given id only if a vocabulary for that id has been found and that vocabulary can be accessed by the user.

        By default the returned vocabularies contain only basic information. Any additional information to be fetched has to be explicitly requested via VocabularyFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getVocabularyTerms

        java.util.Map<IVocabularyTermId,​VocabularyTerm> getVocabularyTerms​(java.lang.String sessionToken,
                                                                                 java.util.List<? extends IVocabularyTermId> vocabularyTermIds,
                                                                                 VocabularyTermFetchOptions fetchOptions)
        Gets vocabulary terms for the provided IVocabularyTermId ids. A result map contains an entry for a given id only if a vocabulary term for that id has been found and that vocabulary term can be accessed by the user.

        By default the returned vocabulary terms contain only basic information. Any additional information to be fetched has to be explicitly requested via VocabularyTermFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getTags

        java.util.Map<ITagId,​Tag> getTags​(java.lang.String sessionToken,
                                                java.util.List<? extends ITagId> tagIds,
                                                TagFetchOptions fetchOptions)
        Gets tags for the provided ITagId ids. A result map contains an entry for a given id only if a tag for that id has been found and that tag can be accessed by the user. A user can get own tags only (i.e. tags a user has created).

        By default the returned tags contain only basic information. Any additional information to be fetched has to be explicitly requested via TagFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getAuthorizationGroups

        java.util.Map<IAuthorizationGroupId,​AuthorizationGroup> getAuthorizationGroups​(java.lang.String sessionToken,
                                                                                             java.util.List<? extends IAuthorizationGroupId> groupIds,
                                                                                             AuthorizationGroupFetchOptions fetchOptions)
        Gets authorization groups for the provided IAuthorizationGroupId ids. A result map contains an entry for a given id only if an authorization group for that id has been found and that authorization group can be accessed by the user.

        By default the returned authorization groups contain only basic information. Any additional information to be fetched has to be explicitly requested via AuthorizationGroupFetchOptions.

        Required access rights: PROJECT_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getRoleAssignments

        java.util.Map<IRoleAssignmentId,​RoleAssignment> getRoleAssignments​(java.lang.String sessionToken,
                                                                                 java.util.List<? extends IRoleAssignmentId> ids,
                                                                                 RoleAssignmentFetchOptions fetchOptions)
        Gets role assignments for the provided IRoleAssignmentId ids. A result map contains an entry for a given id only if a role assignment for that id has been found and that role assignment can be accessed by the user.

        By default the returned role assignments contain only basic information. Any additional information to be fetched has to be explicitly requested via RoleAssignmentFetchOptions.

        Required access rights: PROJECT_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getPersons

        java.util.Map<IPersonId,​Person> getPersons​(java.lang.String sessionToken,
                                                         java.util.List<? extends IPersonId> ids,
                                                         PersonFetchOptions fetchOptions)
        Gets persons for the provided IPersonId ids. A result map contains an entry for a given id only if a person for that id has been found and that person can be accessed by the user.

        By default the returned persons contain only basic information. Any additional information to be fetched has to be explicitly requested via PersonFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getExternalDataManagementSystems

        java.util.Map<IExternalDmsId,​ExternalDms> getExternalDataManagementSystems​(java.lang.String sessionToken,
                                                                                         java.util.List<? extends IExternalDmsId> externalDmsIds,
                                                                                         ExternalDmsFetchOptions fetchOptions)
        Gets external data management systems for the provided IExternalDmsId ids. A result map contains an entry for a given id only if an external data management system for that id has been found and that external data management system can be accessed by the user.

        By default the returned external data management systems contain only basic information. Any additional information to be fetched has to be explicitly requested via ExternalDmsFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getSemanticAnnotations

        java.util.Map<ISemanticAnnotationId,​SemanticAnnotation> getSemanticAnnotations​(java.lang.String sessionToken,
                                                                                             java.util.List<? extends ISemanticAnnotationId> annotationIds,
                                                                                             SemanticAnnotationFetchOptions fetchOptions)
        Gets semantic annotations for the provided ISemanticAnnotationId ids. A result map contains an entry for a given id only if a semantic annotation for that id has been found and that semantic annotation can be accessed by the user.

        By default the returned semantic annotations contain only basic information. Any additional information to be fetched has to be explicitly requested via SemanticAnnotationFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getOperationExecutions

        java.util.Map<IOperationExecutionId,​OperationExecution> getOperationExecutions​(java.lang.String sessionToken,
                                                                                             java.util.List<? extends IOperationExecutionId> executionIds,
                                                                                             OperationExecutionFetchOptions fetchOptions)
        Gets operation executions for the provided IOperationExecutionId ids. A result map contains an entry for a given id only if an operation execution for that id has been found and that operation execution can be accessed by the user.

        By default the returned operation executions contain only basic information. Any additional information to be fetched has to be explicitly requested via OperationExecutionFetchOptions.

        Required access rights: user who created the operation execution / INSTANCE_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getQueries

        java.util.Map<IQueryId,​Query> getQueries​(java.lang.String sessionToken,
                                                       java.util.List<? extends IQueryId> queryIds,
                                                       QueryFetchOptions fetchOptions)
        Gets queries for the provided IQueryId ids. A result map contains an entry for a given id only if a query for that id has been found and that query can be accessed by the user.

        By default the returned queries contain only basic information. Any additional information to be fetched has to be explicitly requested via QueryFetchOptions.

        Required access rights: depends on a query and a query database (more details at "Custom Database Queries" openBIS WIKI page)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getQueryDatabases

        java.util.Map<IQueryDatabaseId,​QueryDatabase> getQueryDatabases​(java.lang.String sessionToken,
                                                                              java.util.List<? extends IQueryDatabaseId> queryDatabaseIds,
                                                                              QueryDatabaseFetchOptions fetchOptions)
        Gets query databases for the provided IQueryDatabaseId ids. A result map contains an entry for a given id only if a query database for that id has been found and that query database can be accessed by the user.

        By default the returned query databases contain only basic information. Any additional information to be fetched has to be explicitly requested via QueryDatabaseFetchOptions.

        Required access rights: depends on a query database (more details at "Custom Database Queries" openBIS WIKI page)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchSpaces

        SearchResult<Space> searchSpaces​(java.lang.String sessionToken,
                                         SpaceSearchCriteria searchCriteria,
                                         SpaceFetchOptions fetchOptions)
        Searches for spaces basing on the provided SpaceSearchCriteria.

        By default the returned spaces contain only basic information. Any additional information to be fetched has to be explicitly requested via SpaceFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger (a project user can see a space if it has access to any of the projects in that space)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchProjects

        SearchResult<Project> searchProjects​(java.lang.String sessionToken,
                                             ProjectSearchCriteria searchCriteria,
                                             ProjectFetchOptions fetchOptions)
        Searches for projects basing on the provided ProjectSearchCriteria.

        By default the returned projects contain only basic information. Any additional information to be fetched has to be explicitly requested via ProjectFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchExperiments

        SearchResult<Experiment> searchExperiments​(java.lang.String sessionToken,
                                                   ExperimentSearchCriteria searchCriteria,
                                                   ExperimentFetchOptions fetchOptions)
        Searches for experiments basing on the provided ExperimentSearchCriteria.

        By default the returned experiments contain only basic information. Any additional information to be fetched has to be explicitly requested via ExperimentFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchExperimentTypes

        SearchResult<ExperimentType> searchExperimentTypes​(java.lang.String sessionToken,
                                                           ExperimentTypeSearchCriteria searchCriteria,
                                                           ExperimentTypeFetchOptions fetchOptions)
        Searches for experiment types basing on the provided ExperimentTypeSearchCriteria.

        By default the returned experiment types contain only basic information. Any additional information to be fetched has to be explicitly requested via ExperimentTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchSamples

        SearchResult<Sample> searchSamples​(java.lang.String sessionToken,
                                           SampleSearchCriteria searchCriteria,
                                           SampleFetchOptions fetchOptions)
        Searches for samples basing on the provided SampleSearchCriteria.

        By default the returned samples contain only basic information. Any additional information to be fetched has to be explicitly requested via SampleFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchSampleTypes

        SearchResult<SampleType> searchSampleTypes​(java.lang.String sessionToken,
                                                   SampleTypeSearchCriteria searchCriteria,
                                                   SampleTypeFetchOptions fetchOptions)
        Searches for sample types basing on the provided SampleTypeSearchCriteria.

        By default the returned sample types contain only basic information. Any additional information to be fetched has to be explicitly requested via SampleTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchDataSets

        SearchResult<DataSet> searchDataSets​(java.lang.String sessionToken,
                                             DataSetSearchCriteria searchCriteria,
                                             DataSetFetchOptions fetchOptions)
        Searches for data sets basing on the provided DataSetSearchCriteria.

        By default the returned data sets contain only basic information. Any additional information to be fetched has to be explicitly requested via DataSetFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchDataSetTypes

        SearchResult<DataSetType> searchDataSetTypes​(java.lang.String sessionToken,
                                                     DataSetTypeSearchCriteria searchCriteria,
                                                     DataSetTypeFetchOptions fetchOptions)
        Searches for data set types basing on the provided DataSetTypeSearchCriteria.

        By default the returned data set types contain only basic information. Any additional information to be fetched has to be explicitly requested via DataSetTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchMaterials

        SearchResult<Material> searchMaterials​(java.lang.String sessionToken,
                                               MaterialSearchCriteria searchCriteria,
                                               MaterialFetchOptions fetchOptions)
        Searches for materials basing on the provided MaterialSearchCriteria.

        By default the returned materials contain only basic information. Any additional information to be fetched has to be explicitly requested via MaterialFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchExternalDataManagementSystems

        SearchResult<ExternalDms> searchExternalDataManagementSystems​(java.lang.String sessionToken,
                                                                      ExternalDmsSearchCriteria searchCriteria,
                                                                      ExternalDmsFetchOptions fetchOptions)
        Searches for external data management systems basing on the provided ExternalDmsSearchCriteria.

        By default the returned external data management systems contain only basic information. Any additional information to be fetched has to be explicitly requested via ExternalDmsFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchMaterialTypes

        SearchResult<MaterialType> searchMaterialTypes​(java.lang.String sessionToken,
                                                       MaterialTypeSearchCriteria searchCriteria,
                                                       MaterialTypeFetchOptions fetchOptions)
        Searches for material types basing on the provided MaterialTypeSearchCriteria.

        By default the returned material types contain only basic information. Any additional information to be fetched has to be explicitly requested via MaterialTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchPlugins

        SearchResult<Plugin> searchPlugins​(java.lang.String sessionToken,
                                           PluginSearchCriteria searchCriteria,
                                           PluginFetchOptions fetchOptions)
        Searches for plugins (i.e. dynamic property evaluators, managed property handlers, entity validators) basing on the provided PluginSearchCriteria.

        By default the returned plugins contain only basic information. Any additional information to be fetched has to be explicitly requested via PluginFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchVocabularies

        SearchResult<Vocabulary> searchVocabularies​(java.lang.String sessionToken,
                                                    VocabularySearchCriteria searchCriteria,
                                                    VocabularyFetchOptions fetchOptions)
        Searches for vocabularies basing on the provided VocabularySearchCriteria.

        By default the returned vocabularies contain only basic information. Any additional information to be fetched has to be explicitly requested via VocabularyFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchVocabularyTerms

        SearchResult<VocabularyTerm> searchVocabularyTerms​(java.lang.String sessionToken,
                                                           VocabularyTermSearchCriteria searchCriteria,
                                                           VocabularyTermFetchOptions fetchOptions)
        Searches for vocabulary terms basing on the provided VocabularyTermSearchCriteria.

        By default the returned vocabulary terms contain only basic information. Any additional information to be fetched has to be explicitly requested via VocabularyTermFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchTags

        SearchResult<Tag> searchTags​(java.lang.String sessionToken,
                                     TagSearchCriteria searchCriteria,
                                     TagFetchOptions fetchOptions)
        Searches for tags basing on the provided TagSearchCriteria. A user can find own tags only (i.e. tags a user has created).

        By default the returned tags contain only basic information. Any additional information to be fetched has to be explicitly requested via TagFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchAuthorizationGroups

        SearchResult<AuthorizationGroup> searchAuthorizationGroups​(java.lang.String sessionToken,
                                                                   AuthorizationGroupSearchCriteria searchCriteria,
                                                                   AuthorizationGroupFetchOptions fetchOptions)
        Searches for authorization groups basing on the provided AuthorizationGroupSearchCriteria.

        By default the returned authorization groups contain only basic information. Any additional information to be fetched has to be explicitly requested via AuthorizationGroupFetchOptions.

        Required access rights: PROJECT_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchRoleAssignments

        SearchResult<RoleAssignment> searchRoleAssignments​(java.lang.String sessionToken,
                                                           RoleAssignmentSearchCriteria searchCriteria,
                                                           RoleAssignmentFetchOptions fetchOptions)
        Searches for role assignments basing on the provided RoleAssignmentSearchCriteria.

        By default the returned role assignments contain only basic information. Any additional information to be fetched has to be explicitly requested via RoleAssignmentFetchOptions.

        Required access rights: PROJECT_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchPersons

        SearchResult<Person> searchPersons​(java.lang.String sessionToken,
                                           PersonSearchCriteria searchCriteria,
                                           PersonFetchOptions fetchOptions)
        Searches for persons basing on the provided PersonSearchCriteria.

        By default the returned persons contain only basic information. Any additional information to be fetched has to be explicitly requested via PersonFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchCustomASServices

        SearchResult<CustomASService> searchCustomASServices​(java.lang.String sessionToken,
                                                             CustomASServiceSearchCriteria searchCriteria,
                                                             CustomASServiceFetchOptions fetchOptions)
        Searches for custom application server services basing on the provided CustomASServiceSearchCriteria. More details on the custom application server services can be found at "Custom Application Server Services" openBIS WIKI page.

        By default the returned custom application server services contain only basic information. Any additional information to be fetched has to be explicitly requested via CustomASServiceFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchSearchDomainServices

        SearchResult<SearchDomainService> searchSearchDomainServices​(java.lang.String sessionToken,
                                                                     SearchDomainServiceSearchCriteria searchCriteria,
                                                                     SearchDomainServiceFetchOptions fetchOptions)
        Searches for search domain services basing on the provided SearchDomainServiceSearchCriteria. More details on the search domain services can be found at "Search Domain Services" openBIS WIKI page.

        By default the returned search domain services contain only basic information. Any additional information to be fetched has to be explicitly requested via SearchDomainServiceFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchAggregationServices

        SearchResult<AggregationService> searchAggregationServices​(java.lang.String sessionToken,
                                                                   AggregationServiceSearchCriteria searchCriteria,
                                                                   AggregationServiceFetchOptions fetchOptions)
        Searches for aggregation services basing on the provided AggregationServiceSearchCriteria. More details on the aggregation services can be found at "Reporting Plugins" openBIS WIKI page (type: AGGREGATION_TABLE_MODEL).

        By default the returned aggregation services contain only basic information. Any additional information to be fetched has to be explicitly requested via AggregationServiceFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchReportingServices

        SearchResult<ReportingService> searchReportingServices​(java.lang.String sessionToken,
                                                               ReportingServiceSearchCriteria searchCriteria,
                                                               ReportingServiceFetchOptions fetchOptions)
        Searches for reporting services basing on the provided ReportingServiceSearchCriteria. More details on the reporting services can be found at "Reporting Plugins" openBIS WIKI page (type: TABLE_MODEL).

        By default the returned reporting services contain only basic information. Any additional information to be fetched has to be explicitly requested via ReportingServiceFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchProcessingServices

        SearchResult<ProcessingService> searchProcessingServices​(java.lang.String sessionToken,
                                                                 ProcessingServiceSearchCriteria searchCriteria,
                                                                 ProcessingServiceFetchOptions fetchOptions)
        Searches for processing services basing on the provided ProcessingServiceSearchCriteria. More details on the processing services can be found at "Processing Plugins" openBIS WIKI page.

        By default the returned processing services contain only basic information. Any additional information to be fetched has to be explicitly requested via ProcessingServiceFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchObjectKindModifications

        SearchResult<ObjectKindModification> searchObjectKindModifications​(java.lang.String sessionToken,
                                                                           ObjectKindModificationSearchCriteria searchCriteria,
                                                                           ObjectKindModificationFetchOptions fetchOptions)
        Searches for object kind modifications basing on the provided ObjectKindModificationSearchCriteria. An object kind modification contains information on when a given kind of operation was last performed for a given kind of object, e.g. when was the last sample update or when was the last property type creation etc.

        By default the returned object kind modifications contain only basic information. Any additional information to be fetched has to be explicitly requested via ObjectKindModificationFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchGlobally

        SearchResult<GlobalSearchObject> searchGlobally​(java.lang.String sessionToken,
                                                        GlobalSearchCriteria searchCriteria,
                                                        GlobalSearchObjectFetchOptions fetchOptions)
        Searches for experiments, samples, data sets and materials at once basing on the provided GlobalSearchCriteria.

        By default the returned objects contain only basic information. Any additional information to be fetched has to be explicitly requested via GlobalSearchObjectFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchOperationExecutions

        SearchResult<OperationExecution> searchOperationExecutions​(java.lang.String sessionToken,
                                                                   OperationExecutionSearchCriteria searchCriteria,
                                                                   OperationExecutionFetchOptions fetchOptions)
        Searches for operation executions basing on the provided OperationExecutionSearchCriteria.

        By default the returned operation executions contain only basic information. Any additional information to be fetched has to be explicitly requested via OperationExecutionFetchOptions.

        Required access rights: user who created the operation execution / INSTANCE_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchDataStores

        SearchResult<DataStore> searchDataStores​(java.lang.String sessionToken,
                                                 DataStoreSearchCriteria searchCriteria,
                                                 DataStoreFetchOptions fetchOptions)
        Searches for data stores basing on the provided DataStoreSearchCriteria.

        By default the returned data stores contain only basic information. Any additional information to be fetched has to be explicitly requested via DataStoreFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchSemanticAnnotations

        SearchResult<SemanticAnnotation> searchSemanticAnnotations​(java.lang.String sessionToken,
                                                                   SemanticAnnotationSearchCriteria searchCriteria,
                                                                   SemanticAnnotationFetchOptions fetchOptions)
        Searches for semantic annotations basing on the provided SemanticAnnotationSearchCriteria.

        By default the returned semantic annotations contain only basic information. Any additional information to be fetched has to be explicitly requested via SemanticAnnotationFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchPropertyTypes

        SearchResult<PropertyType> searchPropertyTypes​(java.lang.String sessionToken,
                                                       PropertyTypeSearchCriteria searchCriteria,
                                                       PropertyTypeFetchOptions fetchOptions)
        Searches for property types basing on the provided PropertyTypeSearchCriteria.

        By default the returned property types contain only basic information. Any additional information to be fetched has to be explicitly requested via PropertyTypeFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchPropertyAssignments

        SearchResult<PropertyAssignment> searchPropertyAssignments​(java.lang.String sessionToken,
                                                                   PropertyAssignmentSearchCriteria searchCriteria,
                                                                   PropertyAssignmentFetchOptions fetchOptions)
        Searches for property assignments basing on the provided PropertyAssignmentSearchCriteria.

        By default the returned property assignments contain only basic information. Any additional information to be fetched has to be explicitly requested via PropertyAssignmentFetchOptions.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchQueries

        SearchResult<Query> searchQueries​(java.lang.String sessionToken,
                                          QuerySearchCriteria searchCriteria,
                                          QueryFetchOptions fetchOptions)
        Searches for queries basing on the provided QuerySearchCriteria.

        By default the returned queries contain only basic information. Any additional information to be fetched has to be explicitly requested via QueryFetchOptions.

        Required access rights: depends on a query and a query database (more details at "Custom Database Queries" openBIS WIKI page)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchQueryDatabases

        SearchResult<QueryDatabase> searchQueryDatabases​(java.lang.String sessionToken,
                                                         QueryDatabaseSearchCriteria searchCriteria,
                                                         QueryDatabaseFetchOptions fetchOptions)
        Searches for query databases basing on the provided QueryDatabaseSearchCriteria.

        By default the returned query databases contain only basic information. Any additional information to be fetched has to be explicitly requested via QueryDatabaseFetchOptions.

        Required access rights: depends on a query database (more details at "Custom Database Queries" openBIS WIKI page)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteSpaces

        void deleteSpaces​(java.lang.String sessionToken,
                          java.util.List<? extends ISpaceId> spaceIds,
                          SpaceDeletionOptions deletionOptions)
        Permanently deletes spaces with the provided ISpaceId ids. Additional deletion options (e.g. deletion reason) can be set via SpaceDeletionOptions.

        Required access rights: SPACE_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteProjects

        void deleteProjects​(java.lang.String sessionToken,
                            java.util.List<? extends IProjectId> projectIds,
                            ProjectDeletionOptions deletionOptions)
        Permanently deletes projects with the provided IProjectId ids. Additional deletion options (e.g. deletion reason) can be set via ProjectDeletionOptions.

        Required access rights: SPACE_POWER_USER / PROJECT_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteExperiments

        IDeletionId deleteExperiments​(java.lang.String sessionToken,
                                      java.util.List<? extends IExperimentId> experimentIds,
                                      ExperimentDeletionOptions deletionOptions)
        Moves experiments with the provided IExperimentId ids to trash. Returns IDeletionId object which can be used either in confirmDeletions call to delete the experiments permanently or in revertDeletions call to bring the trashed experiments back to life. Additional deletion options (e.g. deletion reason) can be set via ExperimentDeletionOptions.

        Required access rights: PROJECT_POWER_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
        See Also:
        confirmDeletions(String, List), revertDeletions(String, List)
      • deleteSamples

        IDeletionId deleteSamples​(java.lang.String sessionToken,
                                  java.util.List<? extends ISampleId> sampleIds,
                                  SampleDeletionOptions deletionOptions)
        Moves samples with the provided ISampleId ids to trash. Returns IDeletionId object which can be used either in confirmDeletions call to delete the samples permanently or in revertDeletions call to bring the trashed samples back to life. Additional deletion options (e.g. deletion reason) can be set via SampleDeletionOptions.

        Required access rights: PROJECT_POWER_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
        See Also:
        confirmDeletions(String, List), revertDeletions(String, List)
      • deleteDataSets

        IDeletionId deleteDataSets​(java.lang.String sessionToken,
                                   java.util.List<? extends IDataSetId> dataSetIds,
                                   DataSetDeletionOptions deletionOptions)
        Moves data sets with the provided IDataSetId ids to trash. Returns IDeletionId object which can be used either in confirmDeletions call to delete the data sets permanently or in revertDeletions call to bring the trashed data sets back to life. Additional deletion options (e.g. deletion reason) can be set via DataSetDeletionOptions.

        Required access rights: PROJECT_POWER_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
        See Also:
        confirmDeletions(String, List), revertDeletions(String, List)
      • deleteMaterials

        void deleteMaterials​(java.lang.String sessionToken,
                             java.util.List<? extends IMaterialId> materialIds,
                             MaterialDeletionOptions deletionOptions)
        Permanently deletes materials with the provided IMaterialId ids. Additional deletion options (e.g. deletion reason) can be set via MaterialDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deletePlugins

        void deletePlugins​(java.lang.String sessionToken,
                           java.util.List<? extends IPluginId> pluginIds,
                           PluginDeletionOptions deletionOptions)
        Permanently deletes plugins (i.e. dynamic property evaluators, managed property handlers, entity validators) with the provided IPluginId ids. Additional deletion options (e.g. deletion reason) can be set via PluginDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deletePropertyTypes

        void deletePropertyTypes​(java.lang.String sessionToken,
                                 java.util.List<? extends IPropertyTypeId> propertyTypeIds,
                                 PropertyTypeDeletionOptions deletionOptions)
        Permanently deletes property types with the provided IPropertyTypeId ids. Additional deletion options (e.g. deletion reason) can be set via PropertyTypeDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteVocabularies

        void deleteVocabularies​(java.lang.String sessionToken,
                                java.util.List<? extends IVocabularyId> ids,
                                VocabularyDeletionOptions deletionOptions)
        Permanently deletes vocabularies with the provided IVocabularyId ids. Additional deletion options (e.g. deletion reason) can be set via VocabularyDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteVocabularyTerms

        void deleteVocabularyTerms​(java.lang.String sessionToken,
                                   java.util.List<? extends IVocabularyTermId> termIds,
                                   VocabularyTermDeletionOptions deletionOptions)
        Permanently deletes vocabulary terms with the provided IVocabularyTermId ids. Additional deletion options (e.g. deletion reason) can be set via VocabularyTermDeletionOptions.
          Required access rights:
        • unofficial and official terms - PROJECT_POWER_USER or stronger
        • internally managed - INSTANCE_ADMIN
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteExperimentTypes

        void deleteExperimentTypes​(java.lang.String sessionToken,
                                   java.util.List<? extends IEntityTypeId> experimentTypeIds,
                                   ExperimentTypeDeletionOptions deletionOptions)
        Permanently deletes experiment types with the provided IEntityTypeId ids. Additional deletion options (e.g. deletion reason) can be set via ExperimentTypeDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteSampleTypes

        void deleteSampleTypes​(java.lang.String sessionToken,
                               java.util.List<? extends IEntityTypeId> sampleTypeIds,
                               SampleTypeDeletionOptions deletionOptions)
        Permanently deletes sample types with the provided IEntityTypeId ids. Additional deletion options (e.g. deletion reason) can be set via SampleTypeDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteDataSetTypes

        void deleteDataSetTypes​(java.lang.String sessionToken,
                                java.util.List<? extends IEntityTypeId> dataSetTypeIds,
                                DataSetTypeDeletionOptions deletionOptions)
        Permanently deletes data set types with the provided IEntityTypeId ids. Additional deletion options (e.g. deletion reason) can be set via DataSetTypeDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteMaterialTypes

        void deleteMaterialTypes​(java.lang.String sessionToken,
                                 java.util.List<? extends IEntityTypeId> materialTypeIds,
                                 MaterialTypeDeletionOptions deletionOptions)
        Permanently deletes material types with the provided IEntityTypeId ids. Additional deletion options (e.g. deletion reason) can be set via MaterialTypeDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteExternalDataManagementSystems

        void deleteExternalDataManagementSystems​(java.lang.String sessionToken,
                                                 java.util.List<? extends IExternalDmsId> externalDmsIds,
                                                 ExternalDmsDeletionOptions deletionOptions)
        Permanently deletes external data management systems with the provided IExternalDmsId ids. Additional deletion options (e.g. deletion reason) can be set via ExternalDmsDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteTags

        void deleteTags​(java.lang.String sessionToken,
                        java.util.List<? extends ITagId> tagIds,
                        TagDeletionOptions deletionOptions)
        Permanently deletes tags with the provided ITagId ids. Additional deletion options (e.g. deletion reason) can be set via TagDeletionOptions. A user can only delete own tags (i.e. tags a user has created).

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteAuthorizationGroups

        void deleteAuthorizationGroups​(java.lang.String sessionToken,
                                       java.util.List<? extends IAuthorizationGroupId> groupIds,
                                       AuthorizationGroupDeletionOptions deletionOptions)
        Permanently deletes authorization groups with the provided IAuthorizationGroupId ids. Additional deletion options (e.g. deletion reason) can be set via AuthorizationGroupDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteRoleAssignments

        void deleteRoleAssignments​(java.lang.String sessionToken,
                                   java.util.List<? extends IRoleAssignmentId> assignmentIds,
                                   RoleAssignmentDeletionOptions deletionOptions)
        Permanently deletes role assignments with the provided IRoleAssignmentId ids. Additional deletion options (e.g. deletion reason) can be set via RoleAssignmentDeletionOptions.
          Required access rights:
        • instance roles - INSTANCE_ADMIN
        • space roles - SPACE_ADMIN or stronger
        • project roles - PROJECT_ADMIN or stronger
        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteOperationExecutions

        void deleteOperationExecutions​(java.lang.String sessionToken,
                                       java.util.List<? extends IOperationExecutionId> executionIds,
                                       OperationExecutionDeletionOptions deletionOptions)
        Permanently deletes operation executions with the provided IOperationExecutionId ids. Additional deletion options (e.g. deletion reason) can be set via OperationExecutionDeletionOptions.

        Required access rights: user who created the operation execution / INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteSemanticAnnotations

        void deleteSemanticAnnotations​(java.lang.String sessionToken,
                                       java.util.List<? extends ISemanticAnnotationId> annotationIds,
                                       SemanticAnnotationDeletionOptions deletionOptions)
        Permanently deletes semantic annotations with the provided ISemanticAnnotationId ids. Additional deletion options (e.g. deletion reason) can be set via SemanticAnnotationDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deleteQueries

        void deleteQueries​(java.lang.String sessionToken,
                           java.util.List<? extends IQueryId> queryIds,
                           QueryDeletionOptions deletionOptions)
        Permanently deletes queries with the provided IQueryId ids. Additional deletion options (e.g. deletion reason) can be set via QueryDeletionOptions.

        Required access rights: depends on a query and a query database (more details at "Custom Database Queries" openBIS WIKI page)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • deletePersons

        void deletePersons​(java.lang.String sessionToken,
                           java.util.List<? extends IPersonId> personIds,
                           PersonDeletionOptions deletionOptions)
        Permanently deletes persons with the provided IPersonId ids. Additional deletion options (e.g. deletion reason) can be set via PersonDeletionOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchDeletions

        SearchResult<Deletion> searchDeletions​(java.lang.String sessionToken,
                                               DeletionSearchCriteria searchCriteria,
                                               DeletionFetchOptions fetchOptions)
        Searches for deletions basing on the provided DeletionSearchCriteria.

        By default the returned deletions contain only basic information. Any additional information to be fetched has to be explicitly requested via DeletionFetchOptions.

        Required access rights: PROJECT_USER

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • searchEvents

        SearchResult<Event> searchEvents​(java.lang.String sessionToken,
                                         EventSearchCriteria searchCriteria,
                                         EventFetchOptions fetchOptions)
        Searches for events basing on the provided EventSearchCriteria.

        By default the returned events contain only basic information. Any additional information to be fetched has to be explicitly requested via EventFetchOptions.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • executeCustomASService

        java.lang.Object executeCustomASService​(java.lang.String sessionToken,
                                                ICustomASServiceId serviceId,
                                                CustomASServiceExecutionOptions options)
        Executes a custom application server service with the provided ICustomASServiceId id. Additional execution options (e.g. parameters) can be set via CustomASServiceExecutionOptions. More details on the custom application server services can be found at "Custom Application Server Services" openBIS WIKI page.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • executeSearchDomainService

        SearchResult<SearchDomainServiceExecutionResult> executeSearchDomainService​(java.lang.String sessionToken,
                                                                                    SearchDomainServiceExecutionOptions options)
        Executes a search domain service. Execution options (e.g. preferred search domain, search string, parameters) can be set via SearchDomainServiceExecutionOptions. More details on the search domain services can be found at "Search Domain Services" openBIS WIKI page.

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • executeAggregationService

        TableModel executeAggregationService​(java.lang.String sessionToken,
                                             IDssServiceId serviceId,
                                             AggregationServiceExecutionOptions options)
        Executes an aggregation service with the provided IDssServiceId id. Additional execution options (e.g. parameters) can be set via AggregationServiceExecutionOptions. More details on the aggregation services can be found at "Reporting Plugins" openBIS WIKI page (type: AGGREGATION_TABLE_MODEL).

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • executeReportingService

        TableModel executeReportingService​(java.lang.String sessionToken,
                                           IDssServiceId serviceId,
                                           ReportingServiceExecutionOptions options)
        Executes a reporting service with the provided IDssServiceId id. Additional execution options (e.g. data set codes) can be set via ReportingServiceExecutionOptions. More details on the reporting services can be found at "Reporting Plugins" openBIS WIKI page (type: TABLE_MODEL).

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • executeProcessingService

        void executeProcessingService​(java.lang.String sessionToken,
                                      IDssServiceId serviceId,
                                      ProcessingServiceExecutionOptions options)
        Executes a processing service with the provided IDssServiceId id. Additional execution options (e.g. data set codes, parameters) can be set via ProcessingServiceExecutionOptions. More details on the processing services can be found at "Processing Plugins" openBIS WIKI page.

        Required access rights: PROJECT_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • executeQuery

        TableModel executeQuery​(java.lang.String sessionToken,
                                IQueryId queryId,
                                QueryExecutionOptions options)
        Executes a query with the provided IQueryId id. Additional execution options (e.g. parameters) can be set via QueryExecutionOptions.

        Required access rights: depends on a query and a query database (more details at "Custom Database Queries" openBIS WIKI page)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • executeSql

        TableModel executeSql​(java.lang.String sessionToken,
                              java.lang.String sql,
                              SqlExecutionOptions options)
        Executes the provided SQL. Only SELECT statements are allowed. Additional execution options (e.g. databaseId, parameters) can be set via SqlExecutionOptions.

        Required access rights: depends on a database (more details at "Custom Database Queries" openBIS WIKI page)

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • evaluatePlugin

        PluginEvaluationResult evaluatePlugin​(java.lang.String sessionToken,
                                              PluginEvaluationOptions options)
        Evaluates the provided plugin (e.g. a dynamic property plugin or an entity validation plugin). Parameters to be passed to the plugin can be set via PluginEvaluationOptions subclasses. The method returns appropriate subclasses of PluginEvaluationResult depending on the plugin type.

        Required access rights: INSTANCE_ADMIN

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • archiveDataSets

        void archiveDataSets​(java.lang.String sessionToken,
                             java.util.List<? extends IDataSetId> dataSetIds,
                             DataSetArchiveOptions options)
        Archives data sets with the provided IDataSetId ids. Additional archiving options can be set via DataSetArchiveOptions.

        Required access rights: PROJECT_POWER_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • unarchiveDataSets

        void unarchiveDataSets​(java.lang.String sessionToken,
                               java.util.List<? extends IDataSetId> dataSetIds,
                               DataSetUnarchiveOptions options)
        Unarchives data sets with the provided IDataSetId ids. Additional unarchiving options can be set via DataSetUnarchiveOptions.

        Required access rights: PROJECT_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • lockDataSets

        void lockDataSets​(java.lang.String sessionToken,
                          java.util.List<? extends IDataSetId> dataSetIds,
                          DataSetLockOptions options)
        Locks data sets with the provided IDataSetId ids. Additional locking options can be set via DataSetLockOptions.

        Required access rights: PROJECT_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • unlockDataSets

        void unlockDataSets​(java.lang.String sessionToken,
                            java.util.List<? extends IDataSetId> dataSetIds,
                            DataSetUnlockOptions options)
        Unlocks data sets with the provided IDataSetId ids. Additional unlocking options can be set via DataSetUnlockOptions.

        Required access rights: PROJECT_ADMIN or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • getServerInformation

        java.util.Map<java.lang.String,​java.lang.String> getServerInformation​(java.lang.String sessionToken)
        Returns a map with additional server information:
        • api-version : major and minor version of the API (e.g. "3.4")
        • project-samples-enabled : true/false
        • archiving-configured : true/false
        • enabled-technologies : comma-separated list of enabled technologies (core-plugins modules)
        • authentication-service : currently used authenticated service (e.g. "ldap-authentication-service")

        Required access rights: PROJECT_OBSERVER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • createPermIdStrings

        java.util.List<java.lang.String> createPermIdStrings​(java.lang.String sessionToken,
                                                             int count)
        Generates globally unique identifiers that consist of a timestamp and a sequence generated number (e.g. "20180531170854641-944"). This method uses one global sequence.

        Required access rights: PROJECT_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems
      • createCodes

        java.util.List<java.lang.String> createCodes​(java.lang.String sessionToken,
                                                     java.lang.String prefix,
                                                     EntityKind entityKind,
                                                     int count)
        Generates identifiers that are unique for a given entity kind and consist of a prefix and a sequence generated number (e.g. "MY-PREFIX-147"); this method uses a dedicated sequence for each entity kind.

        Required access rights: PROJECT_USER or stronger

        Throws:
        ch.systemsx.cisd.common.exceptions.UserFailureException - in case of any problems