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public interface ISimpleOpenbisServiceFacade
Provides a simplified view of an openBIS backend by allowing the following operations :
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
Method Summary | |
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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 dataSetCodes)
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. |
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> |
listDataSetsForExperiments(java.util.List<java.lang.String> experimentIdentifiers)
Return all data sets for a given list of experiments identifiers. |
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<Project> |
listProjects()
Returns all available projects. |
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<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. |
Method Detail |
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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> 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 dataSetCodes)
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> listDataSetsForSamples(java.util.List<java.lang.String> sampleIdentifiers)
java.util.List<DataSetType> listDataSetTypes()
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 data
java.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 data
java.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 data
java.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.
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