public interface ISimpleOpenbisServiceFacade
1. basic listing for the common openBIS entities kinds: projects, experiments, samples, and data sets. 2. uploading datasets to openBIS 3. downloading data sets from openBIS
Modifier and Type | Method and Description |
---|---|
void |
checkSession()
Checks whether the session is alive.
|
java.util.Map<java.lang.String,java.lang.String> |
extractMetadata(NewDataSetDTO newDataset,
java.io.File dataSetFile)
Extracts metadata from a file.
|
DataSet |
getDataSet(java.lang.String dataSetCode)
Return a
DataSet object for for the given code. |
java.util.List<DataSet> |
getDataSets(java.util.List<java.lang.String> dataSetCodes)
Return
DataSet objects for given a set of codes. |
java.util.List<Experiment> |
getExperiments(java.util.List<java.lang.String> experimentIdentifiers)
Return
Experiment objects for a set of given experiment identifiers. |
int |
getMinorVersionInformationService()
Returns the minor version of the general information service.
|
java.util.List<Sample> |
getSamples(java.util.List<java.lang.String> sampleIdentifiers)
Return
Sample objects for a set of given sample identifiers. |
java.util.List<Sample> |
getSamples(java.util.List<java.lang.String> sampleIdentifiers,
java.util.EnumSet<SampleFetchOption> fetchOptions)
Return
Sample objects for a set of given sample identifiers. |
java.util.List<SpaceWithProjectsAndRoleAssignments> |
getSpacesWithProjects()
Return all spaces enriched with their projects and role assignments.
|
java.util.List<DataSet> |
listDataSetsForExperiment(java.lang.String experimentPermId)
Returns all data sets of specified experiment.
|
java.util.List<DataSet> |
listDataSetsForExperiments(java.util.List<java.lang.String> experimentIdentifiers)
Return all data sets for a given list of experiments identifiers.
|
java.util.List<DataSet> |
listDataSetsForSample(java.lang.String samplePermId)
Returns all data sets of specified sample.
|
java.util.List<DataSet> |
listDataSetsForSamples(java.util.List<java.lang.String> sampleIdentifiers)
Return all data sets for a given list of sample identifiers.
|
java.util.List<DataSetType> |
listDataSetTypes()
Returns all data set types available in openBIS.
|
java.util.List<Experiment> |
listExperimentsForProjects(java.util.List<java.lang.String> projectIdentifiers)
Return all experiments for a given list of project identifiers.
|
java.util.List<Experiment> |
listExperimentsHavingDataSetsForProjects(java.util.List<java.lang.String> projectIdentifiers)
Return all experiments having data sets for a given list of project identifiers.
|
java.util.List<Experiment> |
listExperimentsHavingSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers)
Return all experiments having samples for a given list of project identifiers.
|
java.util.List<ExperimentType> |
listExperimentTypes()
Returns all experiment types available in openBIS.
|
java.util.List<Project> |
listProjects()
Returns all available projects.
|
java.util.List<Sample> |
listSamplesForExperimentAndSampleType(java.lang.String experimentPermId,
java.lang.String sampleType)
Returns all samples for specified experiment and of specified type.
|
java.util.List<Sample> |
listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers)
Return all samples for a given list of experiments identifiers.
|
java.util.List<Sample> |
listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers,
java.util.EnumSet<SampleFetchOption> fetchOptions)
Return all samples for a given list of experiments identifiers.
|
java.util.List<Sample> |
listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers)
Return all samples for a given list of project identifiers.
|
java.util.List<Sample> |
listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers,
java.util.EnumSet<SampleFetchOption> fetchOptions)
Return all samples for a given list of project identifiers.
|
java.util.List<Sample> |
listSamplesOfSample(java.lang.String samplePermId)
Returns all samples which are components or children of the specified sample.
|
java.util.List<SampleType> |
listSampleTypes()
Returns all sample types available in openBIS.
|
java.util.List<Vocabulary> |
listVocabularies()
Return all vocabularies available in openBIS together with the contained vocabulary terms.
|
void |
logout()
Logs out from openBIS and frees all associated resources on the server.
|
DataSet |
putDataSet(NewDataSetDTO newDataset,
java.io.File dataSetFile)
Upload a new data set to the DSS.
|
java.util.List<ValidationError> |
validateDataSet(NewDataSetDTO newDataset,
java.io.File dataSetFile)
Validates a data set.
|
int getMinorVersionInformationService()
java.util.List<Project> listProjects()
java.util.List<SpaceWithProjectsAndRoleAssignments> getSpacesWithProjects()
java.util.List<Experiment> getExperiments(java.util.List<java.lang.String> experimentIdentifiers)
Experiment
objects for a set of given experiment identifiers. If some of the
specified experiment identifiers does not exist in openBIS it will be silently ignored.java.util.List<Experiment> listExperimentsForProjects(java.util.List<java.lang.String> projectIdentifiers)
java.util.List<Experiment> listExperimentsHavingSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers)
java.util.List<Experiment> listExperimentsHavingDataSetsForProjects(java.util.List<java.lang.String> projectIdentifiers)
java.util.List<Sample> getSamples(java.util.List<java.lang.String> sampleIdentifiers)
Sample
objects for a set of given sample identifiers. If some of the specified
sample identifiers does not exist in openBIS it will be silently ignored.java.util.List<Sample> getSamples(java.util.List<java.lang.String> sampleIdentifiers, java.util.EnumSet<SampleFetchOption> fetchOptions)
Sample
objects for a set of given sample identifiers. If some of the specified
sample identifiers does not exist in openBIS it will be silently ignored.sampleIdentifiers
- sample identifiers for which samples should be retrievedfetchOptions
- Options that control which parts of the samples are fetched.java.util.List<Sample> listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers)
java.util.List<Sample> listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers, java.util.EnumSet<SampleFetchOption> fetchOptions)
experimentIdentifiers
- experiment identifiers for which samples should be retrievedfetchOptions
- Options that control which parts of the samples are fetched.java.util.List<Sample> listSamplesForExperimentAndSampleType(java.lang.String experimentPermId, java.lang.String sampleType)
java.util.List<Sample> listSamplesOfSample(java.lang.String samplePermId)
java.util.List<Sample> listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers)
java.util.List<Sample> listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers, java.util.EnumSet<SampleFetchOption> fetchOptions)
projectIdentifiers
- project identifiers for which samples should be retrievedfetchOptions
- Options that control which parts of the samples are fetched.DataSet getDataSet(java.lang.String dataSetCode)
DataSet
object for for the given code. If some of the specified data set
code does not exist in openBIS, null will be returned.java.util.List<DataSet> getDataSets(java.util.List<java.lang.String> dataSetCodes)
DataSet
objects for given a set of codes. If some of the specified data set
codes does not exist in openBIS it will be silently ignored.java.util.List<DataSet> listDataSetsForExperiments(java.util.List<java.lang.String> experimentIdentifiers)
java.util.List<DataSet> listDataSetsForExperiment(java.lang.String experimentPermId)
java.util.List<DataSet> listDataSetsForSamples(java.util.List<java.lang.String> sampleIdentifiers)
java.util.List<DataSet> listDataSetsForSample(java.lang.String samplePermId)
java.util.List<DataSetType> listDataSetTypes()
java.util.List<SampleType> listSampleTypes()
java.util.List<ExperimentType> listExperimentTypes()
java.util.List<Vocabulary> listVocabularies()
DataSet putDataSet(NewDataSetDTO newDataset, java.io.File dataSetFile)
newDataset
- The new data set that should be registereddataSetFile
- A file or folder containing the datajava.util.List<ValidationError> validateDataSet(NewDataSetDTO newDataset, java.io.File dataSetFile) throws java.lang.IllegalStateException, EnvironmentFailureException
newDataset
- The new data set that should be registereddataSetFile
- A file or folder containing the datajava.lang.IllegalStateException
- Thrown if the user has not yet been authenticated.EnvironmentFailureException
- Thrown in cases where it is not possible to connect to
the server.java.util.Map<java.lang.String,java.lang.String> extractMetadata(NewDataSetDTO newDataset, java.io.File dataSetFile) throws java.lang.IllegalStateException, EnvironmentFailureException
newDataset
- The new data set that should be registereddataSetFile
- A file or folder containing the datajava.lang.IllegalStateException
- Thrown if the user has not yet been authenticated.EnvironmentFailureException
- Thrown in cases where it is not possible to connect to
the server.void checkSession() throws InvalidSessionException
InvalidSessionException
- If the session is not alive.void logout()
IMPORTANT NOTE: If clients fail to call this method after finishing interaction with openBIS, then their session will be kept on the server until it expires. It is considered a security risk to leave openBIS sessions open.