public class OpenbisServiceFacade extends java.lang.Object implements IOpenbisServiceFacade
IOpenbisServiceFacade.| Constructor and Description |
|---|
OpenbisServiceFacade(java.lang.String sessionToken,
IGeneralInformationService service,
IGeneralInformationChangingService changingService,
IDssComponent dssComponent) |
| Modifier and Type | Method and Description |
|---|---|
void |
addAdHocVocabularyTerm(java.lang.Long vocabularyId,
NewVocabularyTerm term)
Adds new ad-hoc terms to a vocabulary starting from specified ordinal + 1.
|
void |
addAdHocVocabularyTerm(ch.systemsx.cisd.openbis.generic.shared.basic.TechId vocabularyId,
java.lang.String code,
java.lang.String label,
java.lang.String description,
java.lang.Long previousTermOrdinal)
Adds new ad-hoc terms to a vocabulary starting from specified ordinal + 1.
|
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. |
IDataSetDss |
getDataSetDss(java.lang.String 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.HashMap<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary,java.util.List<ControlledVocabularyPropertyType.VocabularyTerm>> |
getVocabularyTermsMap()
Returns map of avaialable vocabulary terms.
|
WebAppSettings |
getWebAppSettings(java.lang.String webAppId)
Returns the persistent settings for a given custom web app.
|
java.util.List<DataSet> |
listDataSets(java.util.List<Sample> samples,
java.util.EnumSet<DataSet.Connections> connectionsToGet)
Return all data sets attached to the given samples with connections.
|
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<DataSet> |
searchForDataSets(SearchCriteria searchCriteria)
Return all data sets matching a specified search criteria.
|
java.util.List<Experiment> |
searchForExperiments(SearchCriteria searchCriteria)
Returns all experiments matching specified search criteria.
|
java.util.List<Sample> |
searchForSamples(SearchCriteria searchCriteria)
Return all samples that match the search criteria.
|
java.util.List<Sample> |
searchForSamples(SearchCriteria searchCriteria,
java.util.EnumSet<SampleFetchOption> fetchOptions)
Return all samples that match the search criteria.
|
void |
setWebAppSettings(WebAppSettings customDisplaySettings)
Sets the persistent settings for a given custom web app.
|
static IOpenbisServiceFacade |
tryCreate(java.lang.String sessionToken,
java.lang.String openbisUrl,
long timeoutInMillis) |
static IOpenbisServiceFacade |
tryCreate(java.lang.String username,
java.lang.String password,
java.lang.String openbisUrl,
long timeoutInMillis) |
java.util.List<ValidationError> |
validateDataSet(NewDataSetDTO newDataset,
java.io.File dataSetFile)
Validates a data set.
|
public OpenbisServiceFacade(java.lang.String sessionToken,
IGeneralInformationService service,
IGeneralInformationChangingService changingService,
IDssComponent dssComponent)
public static IOpenbisServiceFacade tryCreate(java.lang.String username, java.lang.String password, java.lang.String openbisUrl, long timeoutInMillis)
public static IOpenbisServiceFacade tryCreate(java.lang.String sessionToken, java.lang.String openbisUrl, long timeoutInMillis)
public java.util.List<Project> listProjects()
ISimpleOpenbisServiceFacadelistProjects in interface ISimpleOpenbisServiceFacadepublic java.util.List<SpaceWithProjectsAndRoleAssignments> getSpacesWithProjects() throws EnvironmentFailureException
ISimpleOpenbisServiceFacadegetSpacesWithProjects in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<Experiment> getExperiments(java.util.List<java.lang.String> experimentIdentifiers) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadeExperiment 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.getExperiments in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<Experiment> listExperimentsForProjects(java.util.List<java.lang.String> projectIdentifiers) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadelistExperimentsForProjects in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<Experiment> listExperimentsHavingSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadelistExperimentsHavingSamplesForProjects in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<Experiment> listExperimentsHavingDataSetsForProjects(java.util.List<java.lang.String> projectIdentifiers) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadelistExperimentsHavingDataSetsForProjects in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<Sample> getSamples(java.util.List<java.lang.String> sampleIdentifiers) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadeSample 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.getSamples in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<Sample> getSamples(java.util.List<java.lang.String> sampleIdentifiers, java.util.EnumSet<SampleFetchOption> fetchOptions)
ISimpleOpenbisServiceFacadeSample 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.getSamples in interface ISimpleOpenbisServiceFacadesampleIdentifiers - sample identifiers for which samples should be retrievedfetchOptions - Options that control which parts of the samples are fetched.public java.util.List<Sample> listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadelistSamplesForExperiments in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<Sample> listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers, java.util.EnumSet<SampleFetchOption> fetchOptions)
ISimpleOpenbisServiceFacadelistSamplesForExperiments in interface ISimpleOpenbisServiceFacadeexperimentIdentifiers - experiment identifiers for which samples should be retrievedfetchOptions - Options that control which parts of the samples are fetched.public java.util.List<Sample> listSamplesForExperimentAndSampleType(java.lang.String experimentPermId, java.lang.String sampleType)
ISimpleOpenbisServiceFacadelistSamplesForExperimentAndSampleType in interface ISimpleOpenbisServiceFacadepublic java.util.List<Sample> listSamplesOfSample(java.lang.String samplePermId)
ISimpleOpenbisServiceFacadelistSamplesOfSample in interface ISimpleOpenbisServiceFacadepublic java.util.List<Sample> listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers)
ISimpleOpenbisServiceFacadelistSamplesForProjects in interface ISimpleOpenbisServiceFacadepublic java.util.List<Sample> listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers, java.util.EnumSet<SampleFetchOption> fetchOptions)
ISimpleOpenbisServiceFacadelistSamplesForProjects in interface ISimpleOpenbisServiceFacadeprojectIdentifiers - project identifiers for which samples should be retrievedfetchOptions - Options that control which parts of the samples are fetched.public DataSet getDataSet(java.lang.String dataSetCode) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadeDataSet object for for the given code. If some of the specified data set
code does not exist in openBIS, null will be returned.getDataSet in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<DataSet> getDataSets(java.util.List<java.lang.String> dataSetCodes) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadeDataSet 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.getDataSets in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<DataSet> listDataSetsForExperiments(java.util.List<java.lang.String> experimentIdentifiers) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadelistDataSetsForExperiments in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<DataSet> listDataSetsForExperiment(java.lang.String experimentPermId)
ISimpleOpenbisServiceFacadelistDataSetsForExperiment in interface ISimpleOpenbisServiceFacadepublic java.util.List<DataSet> listDataSetsForSamples(java.util.List<java.lang.String> sampleIdentifiers) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadelistDataSetsForSamples in interface ISimpleOpenbisServiceFacadeEnvironmentFailureExceptionpublic java.util.List<DataSet> listDataSetsForSample(java.lang.String samplePermId)
ISimpleOpenbisServiceFacadelistDataSetsForSample in interface ISimpleOpenbisServiceFacadepublic java.util.List<DataSetType> listDataSetTypes()
ISimpleOpenbisServiceFacadelistDataSetTypes in interface ISimpleOpenbisServiceFacadepublic java.util.List<SampleType> listSampleTypes()
ISimpleOpenbisServiceFacadelistSampleTypes in interface ISimpleOpenbisServiceFacadepublic java.util.List<ExperimentType> listExperimentTypes()
ISimpleOpenbisServiceFacadelistExperimentTypes in interface ISimpleOpenbisServiceFacadepublic IDataSetDss getDataSetDss(java.lang.String code) throws EnvironmentFailureException
EnvironmentFailureExceptionpublic DataSet putDataSet(NewDataSetDTO newDataset, java.io.File dataSetFile) throws EnvironmentFailureException
ISimpleOpenbisServiceFacadeputDataSet in interface ISimpleOpenbisServiceFacadenewDataset - The new data set that should be registereddataSetFile - A file or folder containing the dataEnvironmentFailureExceptionpublic java.util.List<ValidationError> validateDataSet(NewDataSetDTO newDataset, java.io.File dataSetFile) throws java.lang.IllegalStateException, EnvironmentFailureException
ISimpleOpenbisServiceFacadevalidateDataSet in interface ISimpleOpenbisServiceFacadenewDataset - 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.public java.util.Map<java.lang.String,java.lang.String> extractMetadata(NewDataSetDTO newDataset, java.io.File dataSetFile) throws java.lang.IllegalStateException, EnvironmentFailureException
ISimpleOpenbisServiceFacadeextractMetadata in interface ISimpleOpenbisServiceFacadenewDataset - 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.public void checkSession()
throws InvalidSessionException
ISimpleOpenbisServiceFacadecheckSession in interface ISimpleOpenbisServiceFacadeInvalidSessionException - If the session is not alive.public void logout()
ISimpleOpenbisServiceFacadeIMPORTANT 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.
logout in interface ISimpleOpenbisServiceFacadepublic int getMinorVersionInformationService()
ISimpleOpenbisServiceFacadegetMinorVersionInformationService in interface ISimpleOpenbisServiceFacadepublic WebAppSettings getWebAppSettings(java.lang.String webAppId)
IOpenbisServiceFacadegetWebAppSettings in interface IOpenbisServiceFacadewebAppId - The id of the custom web app to get the display settings for.public void setWebAppSettings(WebAppSettings customDisplaySettings)
IOpenbisServiceFacadesetWebAppSettings in interface IOpenbisServiceFacadecustomDisplaySettings - The new display settingspublic java.util.List<Experiment> searchForExperiments(SearchCriteria searchCriteria)
IOpenbisServiceFacadesearchForExperiments in interface IOpenbisServiceFacadepublic java.util.List<Sample> searchForSamples(SearchCriteria searchCriteria)
IOpenbisServiceFacadesearchForSamples(searchCritera, EnumSet.of(SampleFetchOption.PROPERTIES))
searchForSamples in interface IOpenbisServiceFacadesearchCriteria - The sample metadata values to be matched against.public java.util.List<Sample> searchForSamples(SearchCriteria searchCriteria, java.util.EnumSet<SampleFetchOption> fetchOptions)
IOpenbisServiceFacadesearchForSamples in interface IOpenbisServiceFacadesearchCriteria - The sample metadata values to be matched against.fetchOptions - Describes the amount of information about the sample that is needed. For
more details see
IGeneralInformationService.searchForSamples(String, SearchCriteria, EnumSet)
.public java.util.List<DataSet> searchForDataSets(SearchCriteria searchCriteria)
IOpenbisServiceFacadesearchForDataSets in interface IOpenbisServiceFacadesearchCriteria - the criteria used for searching.public java.util.List<DataSet> listDataSets(java.util.List<Sample> samples, java.util.EnumSet<DataSet.Connections> connectionsToGet)
IOpenbisServiceFacadelistDataSets in interface IOpenbisServiceFacadesamples - The samples for which we return attached data sets.public void addAdHocVocabularyTerm(ch.systemsx.cisd.openbis.generic.shared.basic.TechId vocabularyId,
java.lang.String code,
java.lang.String label,
java.lang.String description,
java.lang.Long previousTermOrdinal)
IOpenbisServiceFacadeaddAdHocVocabularyTerm in interface IOpenbisServiceFacadevocabularyId - The id of vocabulary which should be extended.code - Code of new vocabulary term.label - Label of new vocabulary term.description - Free text describing new vocabulary term.previousTermOrdinal - new vocabulary term will be placed right after vocabulary term
with given ordinal number.public void addAdHocVocabularyTerm(java.lang.Long vocabularyId,
NewVocabularyTerm term)
IOpenbisServiceFacadeaddAdHocVocabularyTerm in interface IOpenbisServiceFacadevocabularyId - The id of vocabulary which should be extended.term - the vocabulary term to be added.public java.util.HashMap<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary,java.util.List<ControlledVocabularyPropertyType.VocabularyTerm>> getVocabularyTermsMap()
IOpenbisServiceFacadegetVocabularyTermsMap in interface IOpenbisServiceFacadepublic java.util.List<Vocabulary> listVocabularies()
ISimpleOpenbisServiceFacadelistVocabularies in interface ISimpleOpenbisServiceFacade