au.edu.archer.service.icat.impl
Class ICATServiceImpl

java.lang.Object
  au.edu.archer.service.icat.impl.ICATServiceImpl

All Implemented Interfaces:

ICATService

@Transactional
public class ICATServiceImpl
extends java.lang.Object
implements ICATService

ICATServiceImpl implements ICATService.

Constructor Summary

ICATServiceImpl()

Method Summary

au.edu.archer.domain.icat.api.DataSet	addDatasetToAnExpr(DatasetRequest request) Persist dataset.
au.edu.archer.domain.icat.api.Investigation	addExperimentToProject(ExperimentRequest request) Persist experiment.
au.edu.archer.domain.icat.api.Study	addProject(ProjectRequest request) Persist project.
au.edu.archer.domain.icat.api.Sample	addSampleToExperiment(SampleRequest request) Add sample to experiment.
au.edu.archer.domain.icat.api.DataSet	copyDataset(int datasetId, int experimentId, java.lang.String handle) Copy DataSet to another experiment.
void	deleteDataFile(int id) Delete DataFile by id.
void	deleteDataset(DatasetRequest request) Delete dataset.
void	deleteExperiment(ExperimentRequest request) Delete experiment.
void	deleteProject(ProjectRequest deleteRequest) Delete project.
void	deleteSample(SampleRequest request) Delete sample.
java.util.List<au.edu.archer.domain.icat.api.DataFileFormat>	getAllDataFileFormat() Get all existing DataFileFormats.
java.util.List<au.edu.archer.domain.icat.api.DataFile>	getAllDatasetFiles(int datasetId) Get all associated datafiles for a dataset.
java.util.List<au.edu.archer.domain.icat.api.DataSet>	getAllDatasetsByExpr(int experimentId) Get all associasted datasets.
java.util.List<au.edu.archer.domain.icat.api.DataSet>	getAllDatasetsBySampleId(int sampleId) Get all associasted datasets with a sample.
java.util.List<au.edu.archer.domain.icat.api.DataSetStatus>	getAllDatasetStatus() Get all available DataSet status.
java.util.List<au.edu.archer.domain.icat.api.DataSetType>	getAllDatasetType() Get all available Dataset Types.
java.util.List<au.edu.archer.domain.icat.api.Investigation>	getAllExperimentsByProjectId(int projId) Get all experiments by a project id.
java.util.List<au.edu.archer.domain.icat.api.InvestigationType>	getAllExperimentTypes() Get all available experiment types.
java.util.List<au.edu.archer.domain.icat.api.FacilityUser>	getAllFacilityUsers() Get list of all available facility users.
java.util.List<au.edu.archer.domain.icat.api.Keyword>	getAllKeywordsByExperimentId(int expId) Get all keywords by the experiment id.
java.util.List<au.edu.archer.domain.icat.api.DataSet>	getAllNonPackagedDatasetByExpId(int experimentId) Get all non-packaged datasets.
java.util.List<au.edu.archer.domain.icat.api.DataSetType>	getAllNonPackagedDatasetType() Get all non-package DataSet status.
java.util.List<au.edu.archer.domain.icat.api.Study>	getAllProjects() Get all projects.
java.util.List<au.edu.archer.domain.icat.api.StudyStatus>	getAllProjectStatus() Retrieve all available project status.
java.util.List<au.edu.archer.domain.icat.api.Sample>	getAllSamplesByExpId(SampleRequest request) Get all samples by experiment id.
java.util.List<au.edu.archer.domain.icat.api.Sample>	getAllSamplesByExpName(SampleRequest request) Get all samples by experiment name.
au.edu.archer.domain.icat.api.DataFile	getDataFile(int dfId) Get DataFile by id.
au.edu.archer.domain.icat.api.DataFile	getDataFile(java.lang.String projectName, java.lang.String experimentName, java.lang.String datasetName, java.lang.String datafileName) Get DataFile by name.
java.util.List<au.edu.archer.domain.icat.api.DataFileParameter>	getDataFileParametersById(DatafileRequest request) Retrieve datafile parameters.
java.util.Map<java.lang.String,DatafileSliceResponse>	getDatafileSliceByDatasetId(int datasetId) Get all datafile slices by a dataset id.
au.edu.archer.domain.icat.api.DataSet	getDataSetById(int datasetId) Get DataSet by Id.
au.edu.archer.domain.icat.api.DataSet	getDataSetByName(java.lang.String projectName, java.lang.String exprName, java.lang.String datasetName) Get Dataset by Name.
int	getDatasetIdByHandle(java.lang.String handleId) Get dataset id by dataset handle id.
java.util.List<au.edu.archer.domain.icat.api.DataSetParameter>	getDataSetParametersById(DatasetRequest request) Retrieve dataset parameters.
au.edu.archer.domain.icat.api.DataSetStatus	getDatasetStatusByName(java.lang.String datasetStatus) Get Dataset status by name.
au.edu.archer.domain.icat.api.DataSetType	getDatasetTypeByName(java.lang.String datasetType) Get Dataset type by name.
au.edu.archer.domain.icat.api.Investigation	getExperimentById(int expId) Get experiment by experiment id.
au.edu.archer.domain.icat.api.Investigation	getExperimentByName(java.lang.String invName, java.lang.String projectName) Retrieve a experiment by name.
au.edu.archer.domain.icat.api.InvestigationType	getExperimentTypeByName(java.lang.String type) Get the InvestigationType object by name.
au.edu.archer.domain.icat.api.FacilityUser	getFacilityUserById(int mgrId) Get facility user by Id.
java.util.List<au.edu.archer.domain.icat.api.DataSet>	getPackagedDatasetsByExpId(int experimentId) Get all packaged datasets.
au.edu.archer.domain.icat.api.Study	getProjectById(int projectId) Retrieve a project by id.
au.edu.archer.domain.icat.api.Study	getProjectByName(java.lang.String projectName) Retrieve a project by name.
au.edu.archer.domain.icat.api.StudyStatus	getProjectStatusByName(java.lang.String studyStatus) Get the StudyStatus object by name.
au.edu.archer.domain.icat.api.Sample	getSampleById(SampleRequest request) Get sample by sample id.
java.util.List<au.edu.archer.domain.icat.api.SampleParameter>	getSampleParametersById(SampleRequest request) Retrieve sample parameters.
au.edu.archer.domain.icat.api.Topic	getTopicById(int id) Get the Topic by Topic Id.
au.edu.archer.domain.icat.api.DataFile	insertMetadata(byte[] xmlMetadata, long fileSize, java.lang.String srbLocation, int datasetId) Insert the extracted meta data.
java.util.List<au.edu.archer.domain.icat.api.Investigator>	listAllInvestigatorsByExperimentId(int expid) List all investigators by experiment id.
java.util.List<au.edu.archer.domain.icat.api.TopicList>	listAllTopicListsByExperimentId(int expid) List all TopicLists by ExperimentId.
java.util.List<au.edu.archer.domain.icat.api.Topic>	listAllTopics() List of all Topics.
au.edu.archer.domain.icat.api.DataSet	moveDataset(int datasetId, int experimentId) Move DataSet to another experiment.
au.edu.archer.domain.icat.api.DataFile	retrieveMetadata(java.lang.String srbLocation) Retrieve Metadata information based on srbLocation.
void	setDatasetDao(au.edu.archer.dao.icat.api.DatasetDao datasetDao) Set DatasetDao.
void	setExperimentDao(au.edu.archer.dao.icat.api.ExperimentDao experimentDao) Set experimentDao.
void	setIcatDao(au.edu.archer.dao.icat.api.ICATDao icatDao) Set ICATDao.
void	setProjectDao(au.edu.archer.dao.icat.api.ProjectDao projectDao) Set ProjectDao.
void	setSampleDao(au.edu.archer.dao.icat.api.SampleDao sampleDao) Set sample dao.
au.edu.archer.domain.icat.impl.DataFileImpl	updateDataFile(au.edu.archer.domain.icat.api.DataFile df) Update Datafile object.
void	updateDatafileParameteres(DatafileRequest request) Add datafile parameteres.
au.edu.archer.domain.icat.api.DataSet	updateDataset(DatasetRequest request) Update dataset.
void	updateDatasetParameteres(DatasetRequest request) Update dataset parameters.Also referred as dataset variable metadata.
au.edu.archer.domain.icat.api.Investigation	updateExperiment(ExperimentRequest request) Update experiment.
au.edu.archer.domain.icat.api.Study	updateProject(ProjectRequest updateRequest) Update project.
au.edu.archer.domain.icat.api.Sample	updateSample(SampleRequest request) Update sample.
void	updateSampleParameters(SampleRequest request) Add sample parameteres.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ICATServiceImpl

public ICATServiceImpl()

Method Detail

getFacilityUserById

public au.edu.archer.domain.icat.api.FacilityUser getFacilityUserById(int mgrId)
                                                               throws ICATServiceException

Get facility user by Id.

Specified by:

getFacilityUserById in interface ICATService

Parameters:

mgrId - user id.

Returns:

FacilityUser object.

Throws:

ICATServiceException - if an error occurs while processing icat request.

getAllFacilityUsers

public java.util.List<au.edu.archer.domain.icat.api.FacilityUser> getAllFacilityUsers()
                                                                               throws ICATServiceException

Get list of all available facility users.

Specified by:

getAllFacilityUsers in interface ICATService

Returns:

list of FacilityUser object.

Throws:

ICATServiceException - if an error occurs while processing icat request.

getProjectStatusByName

public au.edu.archer.domain.icat.api.StudyStatus getProjectStatusByName(java.lang.String studyStatus)
                                                                 throws ICATServiceException

Get the StudyStatus object by name.

Specified by:

getProjectStatusByName in interface ICATService

Parameters:

studyStatus - study statuc name.

Returns:

StudyStatus object

Throws:

ICATServiceException - if an error occurs while processing icat request.

getAllProjectStatus

public java.util.List<au.edu.archer.domain.icat.api.StudyStatus> getAllProjectStatus()
                                                                              throws ICATServiceException

Retrieve all available project status.

Specified by:

getAllProjectStatus in interface ICATService

Returns:

Map of project status.

Throws:

ICATServiceException - if an error occurs while processing icat request.

getProjectById

public au.edu.archer.domain.icat.api.Study getProjectById(int projectId)
                                                   throws ICATServiceException

Retrieve a project by id.

Specified by:

getProjectById in interface ICATService

Parameters:

projectId - id.

Returns:

Study object.

Throws:

ICATServiceException - if an error occurs while processing icat request.

getProjectByName

public au.edu.archer.domain.icat.api.Study getProjectByName(java.lang.String projectName)
                                                     throws ICATServiceException

Retrieve a project by name.

Specified by:

getProjectByName in interface ICATService

Parameters:

projectName - name.

Returns:

Study object.

Throws:

ICATServiceException - if an error occurs while processing icat request.

addProject

public au.edu.archer.domain.icat.api.Study addProject(ProjectRequest request)
                                               throws InvalidICATRequestException,
                                                      ICATServiceException

Persist project.

Specified by:

addProject in interface ICATService

Parameters:

request - ProjectRequest object.

Returns:

newly created project object.

Throws:

InvalidICATRequestException - if invalid request received for processing.

ICATServiceException - if an error occurs while processing icat request.

updateProject

public au.edu.archer.domain.icat.api.Study updateProject(ProjectRequest updateRequest)
                                                  throws InvalidICATRequestException,
                                                         ICATServiceException

Update project.

Specified by:

updateProject in interface ICATService

Parameters:

updateRequest - ProjectRequest object.

Returns:

updated Project object.

Throws:

InvalidICATRequestException - if invalid request received for processing.

ICATServiceException - if an error occurs while processing icat request.

deleteProject

public void deleteProject(ProjectRequest deleteRequest)
                   throws InvalidICATRequestException,
                          ICATServiceException

Delete project.

Specified by:

deleteProject in interface ICATService

Parameters:

deleteRequest - ProjectRequest object.

Throws:

InvalidICATRequestException - if invalid request received for processing.

ICATServiceException - if an error occurs while processing icat request.

getDatasetIdByHandle

public int getDatasetIdByHandle(java.lang.String handleId)

Get dataset id by dataset handle id.

Specified by:

getDatasetIdByHandle in interface ICATService

Parameters:

handleId - dataset handle id.

Returns:

dataset id.

getAllDatasetType

public java.util.List<au.edu.archer.domain.icat.api.DataSetType> getAllDatasetType()
                                                                            throws ICATServiceException

Get all available Dataset Types.

Specified by:

getAllDatasetType in interface ICATService

Returns:

List of DataSetType obj.

Throws:

ICATServiceException - if an error occurs while processing icat request.

getDatasetTypeByName

public au.edu.archer.domain.icat.api.DataSetType getDatasetTypeByName(java.lang.String datasetType)
                                                               throws ICATServiceException

Get Dataset type by name.

Specified by:

getDatasetTypeByName in interface ICATService

Parameters:

datasetType - type

Returns:

DataSetType object.

Throws:

ICATServiceException - if an error occurs while processing icat request.

getAllNonPackagedDatasetType

public java.util.List<au.edu.archer.domain.icat.api.DataSetType> getAllNonPackagedDatasetType()
                                                                                       throws ICATServiceException

Get all non-package DataSet status.

Specified by:

getAllNonPackagedDatasetType in interface ICATService

Returns:

List of DataSetType

Throws:

ICATServiceException - if an error occurs while processing icat request.

getAllDatasetStatus

public java.util.List<au.edu.archer.domain.icat.api.DataSetStatus> getAllDatasetStatus()
                                                                                throws ICATServiceException

Get all available DataSet status.

Specified by:

getAllDatasetStatus in interface ICATService

Returns:

List of DataSetType

Throws:

ICATServiceException - if an error occurs while processing icat request.

getDatasetStatusByName

public au.edu.archer.domain.icat.api.DataSetStatus getDatasetStatusByName(java.lang.String datasetStatus)
                                                                   throws ICATServiceException

Get Dataset status by name.

Specified by:

getDatasetStatusByName in interface ICATService

Parameters:

datasetStatus - status name.

Returns:

DataSetStatus object.

Throws:

ICATServiceException - if an error occurs while processing icat request.

getDataSetById

public au.edu.archer.domain.icat.api.DataSet getDataSetById(int datasetId)
                                                     throws ICATServiceException

Get DataSet by Id.

Specified by:

getDataSetById in interface ICATService

Parameters:

datasetId - id.

Returns:

DataSet object.

Throws:

ICATServiceException - if an error occurs while processing icat request.

getDataSetByName

public au.edu.archer.domain.icat.api.DataSet getDataSetByName(java.lang.String projectName,
                                                              java.lang.String exprName,
                                                              java.lang.String datasetName)
                                                       throws InvalidICATRequestException,
                                                              ICATServiceException

Get Dataset by Name.

Specified by:

getDataSetByName in interface ICATService

Parameters:

projectName - project name.

exprName - experiment name.

datasetName - dataset name.

Returns:

DataSet object.

Throws:

InvalidICATRequestException - thrown when an invalid icat request is received.

ICATServiceException - if an error occurs while processing icat request.

getAllNonPackagedDatasetByExpId

public java.util.List<au.edu.archer.domain.icat.api.DataSet> getAllNonPackagedDatasetByExpId(int experimentId)
                                                                                      throws ICATServiceException

Get all non-packaged datasets.

Specified by:

getAllNonPackagedDatasetByExpId in interface ICATService

Parameters:

experimentId - id.

Returns:

List of DataSet objects.

Throws:

ICATServiceException

getPackagedDatasetsByExpId

public java.util.List<au.edu.archer.domain.icat.api.DataSet> getPackagedDatasetsByExpId(int experimentId)
                                                                                 throws ICATServiceException

Description copied from interface: ICATService

Get all packaged datasets.

Specified by:

getPackagedDatasetsByExpId in interface ICATService

Parameters:

experimentId - id.

Returns:

List of DataSet objects.

Throws:

ICATServiceException

getAllDatasetsByExpr

public java.util.List<au.edu.archer.domain.icat.api.DataSet> getAllDatasetsByExpr(int experimentId)

Get all associasted datasets.

Specified by:

getAllDatasetsByExpr in interface ICATService

Parameters:

experimentId - id.

Returns:

List of DataSet objects.

getAllDatasetsBySampleId

public java.util.List<au.edu.archer.domain.icat.api.DataSet> getAllDatasetsBySampleId(int sampleId)

Get all associasted datasets with a sample.

Specified by:

getAllDatasetsBySampleId in interface ICATService

Parameters:

sampleId - id.

Returns:

List of DataSet objects.

getAllDatasetFiles

public java.util.List<au.edu.archer.domain.icat.api.DataFile> getAllDatasetFiles(int datasetId)

Get all associated datafiles for a dataset.

Specified by:

getAllDatasetFiles in interface ICATService

Parameters:

datasetId - dataset id.

Returns:

List of DataFile DataFile object.

addDatasetToAnExpr

public au.edu.archer.domain.icat.api.DataSet addDatasetToAnExpr(DatasetRequest request)
                                                         throws InvalidICATRequestException,
                                                                ICATServiceException

Persist dataset.

Specified by:

addDatasetToAnExpr in interface ICATService

Parameters:

request - DatasetRequest object.

Returns:

newly persisted dataset object.

Throws:

InvalidICATRequestException - thrown when an invalid icat request is received.

ICATServiceException - if an error occurs while processing icat request.

updateDataset

public au.edu.archer.domain.icat.api.DataSet updateDataset(DatasetRequest request)
                                                    throws InvalidICATRequestException,
                                                           ICATServiceException

Update dataset.

Specified by:

updateDataset in interface ICATService

Parameters:

request - DatasetRequest object.

Returns:

updated dataset object.

Throws:

InvalidICATRequestException - thrown when an invalid icat request is received.

ICATServiceException - if an error occurs while processing icat request.

deleteDataset

public void deleteDataset(DatasetRequest request)
                   throws InvalidICATRequestException,
                          ICATServiceException

Delete dataset.

Specified by:

deleteDataset in interface ICATService

Parameters:

request - DatasetRequest object.

Throws:

InvalidICATRequestException - thrown when an invalid icat request is received.

ICATServiceException - if an error occurs while processing icat request.

updateDatasetParameteres

public void updateDatasetParameteres(DatasetRequest request)
                              throws InvalidICATRequestException,
                                     ICATServiceException

Update dataset parameters.Also referred as dataset variable metadata.

Specified by:

updateDatasetParameteres in interface ICATService

Parameters:

request - DatasetRequest object.

Throws:

InvalidICATRequestException - thrown when an invalid icat request is received.

ICATServiceException - if an error occurs while processing icat request.

getDataSetParametersById

public java.util.List<au.edu.archer.domain.icat.api.DataSetParameter> getDataSetParametersById(DatasetRequest request)

Retrieve dataset parameters. Also referred as dataset variable metadata.

Specified by:

getDataSetParametersById in interface ICATService

Parameters:

request - DatasetRequest object.

Returns:

List of DatasetParameter object.

insertMetadata

public au.edu.archer.domain.icat.api.DataFile insertMetadata(byte[] xmlMetadata,
                                                             long fileSize,
                                                             java.lang.String srbLocation,
                                                             int datasetId)
                                                      throws MetadataExtractionException,
                                                             InvalidICATRequestException,
                                                             ICATServiceException

Insert the extracted meta data.

Specified by:

insertMetadata in interface ICATService

Parameters:

xmlMetadata - meta data content in XML file.

fileSize - file content size.

srbLocation - String location of the file.

datasetId - dataset id.

Returns:

DataFile the DataFile persistent object saved.

Throws:

MetadataExtractionException - thrown when unable to extract the metadata.

InvalidICATRequestException - thrown when an invalid icat request is received.

ICATServiceException - if an error occurs while processing icat request.

retrieveMetadata

public au.edu.archer.domain.icat.api.DataFile retrieveMetadata(java.lang.String srbLocation)
                                                        throws InvalidICATRequestException

Retrieve Metadata information based on srbLocation.

Specified by:

retrieveMetadata in interface ICATService

Parameters:

srbLocation - String location used when inserting metadata.

Returns:

DataFile the DataFile object.

Throws:

InvalidICATRequestException - thrown when an invalid icat request is received.

getAllExperimentTypes

public java.util.List<au.edu.archer.domain.icat.api.InvestigationType> getAllExperimentTypes()

Get all available experiment types.

Specified by:

getAllExperimentTypes in interface ICATService

Returns:

List of Experiment types.

getExperimentTypeByName

public au.edu.archer.domain.icat.api.InvestigationType getExperimentTypeByName(java.lang.String type)

Get the InvestigationType object by name.

Specified by:

getExperimentTypeByName in interface ICATService

Parameters:

type - investigation type name.

Returns:

InvestigationType object.

getExperimentById

public au.edu.archer.domain.icat.api.Investigation getExperimentById(int expId)

Get experiment by experiment id.

Specified by:

getExperimentById in interface ICATService

Parameters:

expId - int experiment id.

Returns:

Investigation experiment object.

getAllExperimentsByProjectId

public java.util.List<au.edu.archer.domain.icat.api.Investigation> getAllExperimentsByProjectId(int projId)

Get all experiments by a project id.

Specified by:

getAllExperimentsByProjectId in interface ICATService

Parameters:

projId - The project id.

Returns:

A List of experiments.

getExperimentByName

public au.edu.archer.domain.icat.api.Investigation getExperimentByName(java.lang.String invName,
                                                                       java.lang.String projectName)

Retrieve a experiment by name.

Specified by:

getExperimentByName in interface ICATService

Parameters:

invName - String experiment name.

projectName - String project name.

Returns:

Investigation experiment object.

setProjectDao

public void setProjectDao(au.edu.archer.dao.icat.api.ProjectDao projectDao)

Set ProjectDao. Set by Spring framework.

Parameters:

projectDao - to set.

setDatasetDao

public void setDatasetDao(au.edu.archer.dao.icat.api.DatasetDao datasetDao)

Set DatasetDao. Set by Spring framework.

Parameters:

datasetDao - to set.

setIcatDao

public void setIcatDao(au.edu.archer.dao.icat.api.ICATDao icatDao)

Set ICATDao. Set by Spring framework.

Parameters:

icatDao - to set.

setExperimentDao

public void setExperimentDao(au.edu.archer.dao.icat.api.ExperimentDao experimentDao)

Set experimentDao.

Parameters:

experimentDao - ExperimentDao experiment dao.

addExperimentToProject

public au.edu.archer.domain.icat.api.Investigation addExperimentToProject(ExperimentRequest request)
                                                                   throws ICATServiceException,
                                                                          InvalidICATRequestException

Persist experiment.

Specified by:

addExperimentToProject in interface ICATService

Parameters:

request - ExperimentRequest request.

Returns:

Investigation experiment.

Throws:

ICATServiceException - if an error occurs while processing icat request.

InvalidICATRequestException - thrown when an invalid icat request is received.

updateExperiment

public au.edu.archer.domain.icat.api.Investigation updateExperiment(ExperimentRequest request)
                                                             throws ICATServiceException,
                                                                    InvalidICATRequestException

Update experiment.

Specified by:

updateExperiment in interface ICATService

Parameters:

request - ExperimentRequest request.

Returns:

Investigation updated investigation object.

Throws:

ICATServiceException - if an error occurs while processing icat request.

InvalidICATRequestException - if the request is invalid.

deleteExperiment

public void deleteExperiment(ExperimentRequest request)
                      throws ICATServiceException,
                             InvalidICATRequestException

Delete experiment.

Specified by:

deleteExperiment in interface ICATService

Parameters:

request - ExperimentRequest request.

Throws:

ICATServiceException - if an error occurs while processing icat request.

InvalidICATRequestException - if the request is invalid.

getAllSamplesByExpId

public java.util.List<au.edu.archer.domain.icat.api.Sample> getAllSamplesByExpId(SampleRequest request)

Get all samples by experiment id.

Specified by:

getAllSamplesByExpId in interface ICATService

Parameters:

request - SampleRequest request object.

Returns:

List<Sample> set of samples that belongs to the experiment.

addSampleToExperiment

public au.edu.archer.domain.icat.api.Sample addSampleToExperiment(SampleRequest request)
                                                           throws InvalidICATRequestException,
                                                                  ICATServiceException

Add sample to experiment.

Specified by:

addSampleToExperiment in interface ICATService

Parameters:

request - SampleRequest request.

Returns:

Sample sample object.

Throws:

InvalidICATRequestException - if the request is invalid.

ICATServiceException - if an error occurs while processing icat request.

updateSampleParameters

public void updateSampleParameters(SampleRequest request)
                            throws InvalidICATRequestException,
                                   ICATServiceException

Add sample parameteres. Also referred as sample variable metadata.

Specified by:

updateSampleParameters in interface ICATService

Parameters:

request - SampleRequest object.

Throws:

InvalidICATRequestException - if invalid request received for processing.

ICATServiceException - if an error occurs while processing icat request.

deleteSample

public void deleteSample(SampleRequest request)
                  throws InvalidICATRequestException,
                         ICATServiceException

Delete sample.

Specified by:

deleteSample in interface ICATService

Parameters:

request - SampleRequest request object.

Throws:

InvalidICATRequestException - if the request is invalid.

ICATServiceException - if an error occurs while processing icat request.

updateSample

public au.edu.archer.domain.icat.api.Sample updateSample(SampleRequest request)
                                                  throws InvalidICATRequestException,
                                                         ICATServiceException

Update sample.

Specified by:

updateSample in interface ICATService

Parameters:

request - SampleRequest request object.

Returns:

Sample sample object.

Throws:

InvalidICATRequestException - if the request is invalid.

ICATServiceException - if an error occurs while processing icat request.

getSampleById

public au.edu.archer.domain.icat.api.Sample getSampleById(SampleRequest request)
                                                   throws InvalidICATRequestException

Get sample by sample id.

Specified by:

getSampleById in interface ICATService

Parameters:

request - SampleRequest request object.

Returns:

Sample sample object.

Throws:

InvalidICATRequestException - if the request is invalid.

getAllSamplesByExpName

public java.util.List<au.edu.archer.domain.icat.api.Sample> getAllSamplesByExpName(SampleRequest request)

Get all samples by experiment name.

Specified by:

getAllSamplesByExpName in interface ICATService

Parameters:

request - SampleRequest request object.

Returns:

List<Sample> set of samples that belongs to the experiment.

getSampleParametersById

public java.util.List<au.edu.archer.domain.icat.api.SampleParameter> getSampleParametersById(SampleRequest request)

Retrieve sample parameters. Also referred as sample variable metadata.

Specified by:

getSampleParametersById in interface ICATService

Parameters:

request - SampleRequest object.

Returns:

List of SampleParameter object.

moveDataset

public au.edu.archer.domain.icat.api.DataSet moveDataset(int datasetId,
                                                         int experimentId)

Move DataSet to another experiment.

Specified by:

moveDataset in interface ICATService

Parameters:

datasetId - int id of the dataset to be moved.

experimentId - int id of the experiment that will hold the dataset.

Returns:

DataSet new DataSet object.

copyDataset

public au.edu.archer.domain.icat.api.DataSet copyDataset(int datasetId,
                                                         int experimentId,
                                                         java.lang.String handle)

Copy DataSet to another experiment.

Specified by:

copyDataset in interface ICATService

Parameters:

datasetId - int id of the dataset to be copied.

experimentId - int id of the experiment that will hold the dataset.

handle - handle

Returns:

DataSet new DataSet object.

getAllProjects

public java.util.List<au.edu.archer.domain.icat.api.Study> getAllProjects()

Get all projects.

Specified by:

getAllProjects in interface ICATService

Returns:

List<Study> list of projects.

getDataFile

public au.edu.archer.domain.icat.api.DataFile getDataFile(int dfId)

Get DataFile by id.

Specified by:

getDataFile in interface ICATService

Parameters:

dfId - int DataFile id.

Returns:

DataFile DataFile object to be returned.

getDataFile

public au.edu.archer.domain.icat.api.DataFile getDataFile(java.lang.String projectName,
                                                          java.lang.String experimentName,
                                                          java.lang.String datasetName,
                                                          java.lang.String datafileName)

Get DataFile by name.

Specified by:

getDataFile in interface ICATService

Parameters:

projectName - String project name.

experimentName - String experiment name.

datasetName - String dataset name.

datafileName - String datafile name.

Returns:

DataFile DataFile object to be returned.

deleteDataFile

public void deleteDataFile(int id)

Delete DataFile by id.

Specified by:

deleteDataFile in interface ICATService

Parameters:

id - int DataFile id.

updateDatafileParameteres

public void updateDatafileParameteres(DatafileRequest request)
                               throws InvalidICATRequestException,
                                      ICATServiceException

Add datafile parameteres. Also referred as datafile variable metadata.

Specified by:

updateDatafileParameteres in interface ICATService

Parameters:

request - DatafileRequest object.

Throws:

InvalidICATRequestException - if invalid request received for processing.

ICATServiceException - if an error occurs while processing icat request.

getDataFileParametersById

public java.util.List<au.edu.archer.domain.icat.api.DataFileParameter> getDataFileParametersById(DatafileRequest request)

Retrieve datafile parameters. Also referred as datafile variable metadata.

Specified by:

getDataFileParametersById in interface ICATService

Parameters:

request - DatafileRequest object.

Returns:

List of DataFileParameter object.

setSampleDao

public void setSampleDao(au.edu.archer.dao.icat.api.SampleDao sampleDao)

Set sample dao.

Parameters:

sampleDao - to set.

updateDataFile

public au.edu.archer.domain.icat.impl.DataFileImpl updateDataFile(au.edu.archer.domain.icat.api.DataFile df)

Update Datafile object.

Specified by:

updateDataFile in interface ICATService

Parameters:

df - DataFile datafile to be updated.

Returns:

DataFileImpl updated datafile object.

getAllDataFileFormat

public java.util.List<au.edu.archer.domain.icat.api.DataFileFormat> getAllDataFileFormat()

Get all existing DataFileFormats.

Specified by:

getAllDataFileFormat in interface ICATService

Returns:

List<DataFileFormat> list of DataFileFormats.

getDatafileSliceByDatasetId

public java.util.Map<java.lang.String,DatafileSliceResponse> getDatafileSliceByDatasetId(int datasetId)

Get all datafile slices by a dataset id.

Specified by:

getDatafileSliceByDatasetId in interface ICATService

Parameters:

datasetId - The dataset id.

Returns:

A Collection of DatafileSliceResponse.

getAllKeywordsByExperimentId

public java.util.List<au.edu.archer.domain.icat.api.Keyword> getAllKeywordsByExperimentId(int expId)

Get all keywords by the experiment id.

Specified by:

getAllKeywordsByExperimentId in interface ICATService

Parameters:

expId - The experiment id.

Returns:

A list of Keywords.

listAllInvestigatorsByExperimentId

public java.util.List<au.edu.archer.domain.icat.api.Investigator> listAllInvestigatorsByExperimentId(int expid)

List all investigators by experiment id.

Specified by:

listAllInvestigatorsByExperimentId in interface ICATService

Parameters:

expid - The experiment Id.

Returns:

A list of investigators.

listAllTopicListsByExperimentId

public java.util.List<au.edu.archer.domain.icat.api.TopicList> listAllTopicListsByExperimentId(int expid)

List all TopicLists by ExperimentId.

Specified by:

listAllTopicListsByExperimentId in interface ICATService

Parameters:

expid - The experiment Id.

Returns:

A list of TopicList of the this experiment.

listAllTopics

public java.util.List<au.edu.archer.domain.icat.api.Topic> listAllTopics()
                                                                  throws ICATServiceException

List of all Topics.

Specified by:

listAllTopics in interface ICATService

Returns:

A list of all Topics.

Throws:

ICATServiceException - if any errors occur.

getTopicById

public au.edu.archer.domain.icat.api.Topic getTopicById(int id)

Get the Topic by Topic Id.

Specified by:

getTopicById in interface ICATService

Parameters:

id - The Topic Id.

Returns:

A Topic.