au.edu.archer.services.icat.impl
Class ICATWsClientImpl

java.lang.Object
  au.edu.archer.services.icat.AbstractICATClient
      au.edu.archer.services.icat.impl.ICATWsClientImpl

All Implemented Interfaces:

ICAT, ICATHelpers, ICATTraversal, SearchService

public class ICATWsClientImpl
extends AbstractICATClient

Field Summary

protected org.apache.log4j.Logger

logger

Constructor Summary

ICATWsClientImpl(java.lang.String address)

ICATWsClientImpl(java.lang.String address, org.globus.gsi.GlobusCredential cred)

Method Summary

void	deleteDataFile(DataFile in)
void	deleteDataFileFormat(DataFileFormat in)
void	deleteDataFileParameter(DataFileParameter in)
void	deleteDataSet(DataSet in)
void	deleteDataSetParameter(DataSetParameter in)
void	deleteDataSetStatus(DataSetStatus in)
void	deleteDataSetType(DataSetType in)
void	deleteFacilityCycle(FacilityCycle in)
void	deleteFacilityUser(FacilityUser in)
void	deleteInstrument(Instrument in)
void	deleteInvestigation(Investigation in)
void	deleteInvestigationType(InvestigationType in)
void	deleteParameter(Parameter in)
void	deleteSample(Sample in)
void	deleteSampleParameter(SampleParameter in)
void	deleteStudy(Study in)
void	deleteStudyStatus(StudyStatus in)
java.util.List<DataFileFormat>	getAllDataFileFormats()
java.util.List<DataFileParameter>	getAllDataFileParameters(java.lang.Integer dataFileID)
java.util.List<DataFile>	getAllDataFilesByDataSetId(java.lang.Integer dataSetID)
java.util.List<DataSetParameter>	getAllDataSetParameters(java.lang.Integer in)
java.util.List<DataSet>	getAllDataSetsByInvestigationId(java.lang.Integer investigationID)
java.util.List<DataSetStatus>	getAllDataSetStatus()
java.util.List<DataSetType>	getAllDataSetTypes()
java.util.List<FacilityCycle>	getAllFacilityCycles()
java.util.List<FacilityUser>	getAllFacilityUsers()
java.util.List<Instrument>	getAllInstruments()
java.util.List<Investigation>	getAllInvestigationsByStudyId(java.lang.Integer in)
java.util.List<InvestigationType>	getAllInvestigationTypes()
java.util.List<Parameter>	getAllParameters()
java.util.List<Parameter>	getAllParametersByType(boolean isSampleParameter, boolean isDataSetParameter, boolean isDataFileParameter) Returns the parameters for which the boolean parameters are true.
java.util.List<SampleParameter>	getAllSampleParameters(java.lang.Integer in)
java.util.List<Sample>	getAllSamplesByInvestigationId(java.lang.Integer in)
java.util.List<Sample>	getAllSamplesByInvestigationName(java.lang.String studyName, java.lang.String investigationName)
java.util.List<Study>	getAllStudies()
java.util.List<StudyStatus>	getAllStudyStatus()
DataFile	getDataFileById(java.lang.Integer in)
DataFile	getDataFileByLocation(java.lang.String location) Get the Data file object associated with the given location URI.
DataFile	getDataFileByName(java.lang.String studyName, java.lang.String investigationName, java.lang.String datasetName, java.lang.String datafileName) Get the data file based on the names of it's path components in the icat structure.
DataFileFormat	getDataFileFormatById(java.lang.String name, java.lang.String version)
java.util.List<DataFileFormat>	getDataFileFormatByName(java.lang.String in)
DataFileParameter	getDataFileParameterById(java.lang.String name, java.lang.String units, java.lang.Integer dataFileID)
DataSet	getDataSetById(java.lang.Integer in)
DataSet	getDataSetByLocation(java.lang.String location)
DataSet	getDataSetByName(java.lang.String studyName, java.lang.String investigationName, java.lang.String datasetName) Lookup the dataset based on the path name components made up of study, investigation and dataset names.
java.lang.Integer	getDataSetIdByHandle(java.lang.String in)
DataSetParameter	getDataSetParameterById(java.lang.String name, java.lang.String units, java.lang.Integer dataSetID)
DataSetStatus	getDataSetStatusByName(java.lang.String in)
DataSetType	getDataSetTypeByName(java.lang.String in)
FacilityCycle	getFacilityCycleByName(java.lang.String in)
FacilityUser	getFacilityUserById(java.lang.String in)
Instrument	getInstrumentByName(java.lang.String in)
Investigation	getInvestigationById(java.lang.Integer in)
Investigation	getInvestigationByLocation(java.lang.String location)
Investigation	getInvestigationByName(java.lang.String studyName, java.lang.String investigationName) Lookup the Investigation based on the path components of study name and investigation name.
InvestigationType	getInvestigationTypeByName(java.lang.String in)
ICATObjectFactory	getObjectFactory()
Parameter	getParameterById(java.lang.Integer in)
Parameter	getParameterByName(java.lang.String name, java.lang.String units) Gets the parameter with this name-unit key
java.util.List<java.lang.String>	getResourceUrlPrefixes()
Sample	getSampleById(java.lang.Integer in)
Sample	getSampleByName(java.lang.String studyName, java.lang.String investigationName, java.lang.String sampleName)
SampleParameter	getSampleParameterById(java.lang.String name, java.lang.String units, java.lang.Integer sampleID)
Study	getStudyById(java.lang.Integer in)
Study	getStudyByLocation(java.lang.String location)
Study	getStudyByName(java.lang.String in)
StudyStatus	getStudyStatusByName(java.lang.String in)
java.util.List<DataFile>	searchDataFile(SearchRequestType search) Search datafiles.
java.util.List<DataSet>	searchDataSet(SearchRequestType search) Search datasets.
java.util.List<Investigation>	searchExperiment(SearchRequestType search) Search experiments.
java.util.List<Study>	searchProject(SearchRequestType search) Search project.
java.util.List<Sample>	searchSample(SearchRequestType search) Search samples.
java.lang.String	testCall(java.lang.String str1, java.lang.String str2)
void	triggerNotifications()
DataFile	updateDataFile(DataFile in) Save the datafile object.
DataFileFormat	updateDataFileFormat(DataFileFormat in) Save the datafile format object.
DataFileParameter	updateDataFileParameter(DataFileParameter in) Save the datafile parameter object.
DataSet	updateDataSet(DataSet in) Save the dataset object.
DataSetParameter	updateDataSetParameter(DataSetParameter in) Save the dataset parameter object.
DataSetStatus	updateDataSetStatus(DataSetStatus in) Save the dataset status object.
DataSetType	updateDataSetType(DataSetType in) Save the dataset type object.
FacilityCycle	updateFacilityCycle(FacilityCycle in) Save the facility cycle object.
FacilityUser	updateFacilityUser(FacilityUser in) Save the facility user object.
Instrument	updateInstrument(Instrument in) Save the instrument object.
Investigation	updateInvestigation(Investigation in) Save the investigation object.
InvestigationType	updateInvestigationType(InvestigationType in) Save the investigation type object.
Parameter	updateParameter(Parameter in) Save the parameter, updating or creating if id is null or 0.
Sample	updateSample(Sample in) Save the study object.
SampleParameter	updateSampleParameter(SampleParameter in) Save the sample parameter object.
Study	updateStudy(Study in) Save the study object.
StudyStatus	updateStudyStatus(StudyStatus in) Save the study status object.

Methods inherited from class au.edu.archer.services.icat.AbstractICATClient

getDataFileFormatById, getDataFileParameterById, getDataFilesFor, getDataSetFor, getDataSetParameterById, getDataSetsFor, getDataSetsFor, getInvestigationFor, getInvestigationFor, getInvestigationsFor, getSamplesFor, getStudyFor, normaliseLocation

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected org.apache.log4j.Logger logger

Constructor Detail

ICATWsClientImpl

public ICATWsClientImpl(java.lang.String address)

ICATWsClientImpl

public ICATWsClientImpl(java.lang.String address,
                        org.globus.gsi.GlobusCredential cred)
                 throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

testCall

public java.lang.String testCall(java.lang.String str1,
                                 java.lang.String str2)
                          throws ICATServiceException

Throws:

ICATServiceException

updateStudy

public Study updateStudy(Study in)
                  throws ICATServiceException

Save the study object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateStudyStatus

public StudyStatus updateStudyStatus(StudyStatus in)
                              throws ICATServiceException

Save the study status object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateInvestigation

public Investigation updateInvestigation(Investigation in)
                                  throws ICATServiceException

Save the investigation object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateInvestigationType

public InvestigationType updateInvestigationType(InvestigationType in)
                                          throws ICATServiceException

Save the investigation type object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateSample

public Sample updateSample(Sample in)
                    throws ICATServiceException

Save the study object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateDataSet

public DataSet updateDataSet(DataSet in)
                      throws ICATServiceException

Save the dataset object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateDataSetType

public DataSetType updateDataSetType(DataSetType in)
                              throws ICATServiceException

Save the dataset type object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateDataSetStatus

public DataSetStatus updateDataSetStatus(DataSetStatus in)
                                  throws ICATServiceException

Save the dataset status object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateDataFile

public DataFile updateDataFile(DataFile in)
                        throws ICATServiceException

Save the datafile object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateDataFileFormat

public DataFileFormat updateDataFileFormat(DataFileFormat in)
                                    throws ICATServiceException

Save the datafile format object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateDataFileParameter

public DataFileParameter updateDataFileParameter(DataFileParameter in)
                                          throws ICATServiceException

Save the datafile parameter object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateInstrument

public Instrument updateInstrument(Instrument in)
                            throws ICATServiceException

Save the instrument object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateFacilityCycle

public FacilityCycle updateFacilityCycle(FacilityCycle in)
                                  throws ICATServiceException

Save the facility cycle object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateFacilityUser

public FacilityUser updateFacilityUser(FacilityUser in)
                                throws ICATServiceException

Save the facility user object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

deleteStudy

public void deleteStudy(Study in)
                 throws ICATServiceException

Throws:

ICATServiceException

deleteStudyStatus

public void deleteStudyStatus(StudyStatus in)
                       throws ICATServiceException

Throws:

ICATServiceException

deleteInvestigation

public void deleteInvestigation(Investigation in)
                         throws ICATServiceException

Throws:

ICATServiceException

deleteInvestigationType

public void deleteInvestigationType(InvestigationType in)
                             throws ICATServiceException

Throws:

ICATServiceException

deleteSample

public void deleteSample(Sample in)
                  throws ICATServiceException

Throws:

ICATServiceException

deleteDataSet

public void deleteDataSet(DataSet in)
                   throws ICATServiceException

Throws:

ICATServiceException

deleteDataSetType

public void deleteDataSetType(DataSetType in)
                       throws ICATServiceException

Throws:

ICATServiceException

deleteDataSetStatus

public void deleteDataSetStatus(DataSetStatus in)
                         throws ICATServiceException

Throws:

ICATServiceException

deleteDataFile

public void deleteDataFile(DataFile in)
                    throws ICATServiceException

Throws:

ICATServiceException

deleteDataFileFormat

public void deleteDataFileFormat(DataFileFormat in)
                          throws ICATServiceException

Throws:

ICATServiceException

deleteDataFileParameter

public void deleteDataFileParameter(DataFileParameter in)
                             throws ICATServiceException

Throws:

ICATServiceException

deleteInstrument

public void deleteInstrument(Instrument in)
                      throws ICATServiceException

Throws:

ICATServiceException

deleteFacilityCycle

public void deleteFacilityCycle(FacilityCycle in)
                         throws ICATServiceException

Throws:

ICATServiceException

deleteFacilityUser

public void deleteFacilityUser(FacilityUser in)
                        throws ICATServiceException

Throws:

ICATServiceException

getAllStudies

public java.util.List<Study> getAllStudies()
                                    throws ICATServiceException

Throws:

ICATServiceException

getAllStudyStatus

public java.util.List<StudyStatus> getAllStudyStatus()
                                              throws ICATServiceException

Throws:

ICATServiceException

getAllInvestigationsByStudyId

public java.util.List<Investigation> getAllInvestigationsByStudyId(java.lang.Integer in)
                                                            throws ICATServiceException

Throws:

ICATServiceException

getAllInvestigationTypes

public java.util.List<InvestigationType> getAllInvestigationTypes()
                                                           throws ICATServiceException

Throws:

ICATServiceException

getAllSamplesByInvestigationId

public java.util.List<Sample> getAllSamplesByInvestigationId(java.lang.Integer in)
                                                      throws ICATServiceException

Throws:

ICATServiceException

getAllSamplesByInvestigationName

public java.util.List<Sample> getAllSamplesByInvestigationName(java.lang.String studyName,
                                                               java.lang.String investigationName)
                                                        throws ICATServiceException

Throws:

ICATServiceException

getAllDataSetsByInvestigationId

public java.util.List<DataSet> getAllDataSetsByInvestigationId(java.lang.Integer investigationID)
                                                        throws ICATServiceException

Throws:

ICATServiceException

getAllDataSetTypes

public java.util.List<DataSetType> getAllDataSetTypes()
                                               throws ICATServiceException

Throws:

ICATServiceException

getAllDataSetStatus

public java.util.List<DataSetStatus> getAllDataSetStatus()
                                                  throws ICATServiceException

Throws:

ICATServiceException

getAllDataFilesByDataSetId

public java.util.List<DataFile> getAllDataFilesByDataSetId(java.lang.Integer dataSetID)
                                                    throws ICATServiceException

Throws:

ICATServiceException

getAllDataFileFormats

public java.util.List<DataFileFormat> getAllDataFileFormats()
                                                     throws ICATServiceException

Throws:

ICATServiceException

getAllDataFileParameters

public java.util.List<DataFileParameter> getAllDataFileParameters(java.lang.Integer dataFileID)
                                                           throws ICATServiceException

Throws:

ICATServiceException

getAllInstruments

public java.util.List<Instrument> getAllInstruments()
                                             throws ICATServiceException

Throws:

ICATServiceException

getAllFacilityCycles

public java.util.List<FacilityCycle> getAllFacilityCycles()
                                                   throws ICATServiceException

Throws:

ICATServiceException

getAllFacilityUsers

public java.util.List<FacilityUser> getAllFacilityUsers()
                                                 throws ICATServiceException

Throws:

ICATServiceException

getStudyById

public Study getStudyById(java.lang.Integer in)
                   throws ICATServiceException

Throws:

ICATServiceException

getStudyByName

public Study getStudyByName(java.lang.String in)
                     throws ICATServiceException

Throws:

ICATServiceException

getStudyStatusByName

public StudyStatus getStudyStatusByName(java.lang.String in)
                                 throws ICATServiceException

Throws:

ICATServiceException

getInvestigationById

public Investigation getInvestigationById(java.lang.Integer in)
                                   throws ICATServiceException

Throws:

ICATServiceException

getInvestigationByName

public Investigation getInvestigationByName(java.lang.String studyName,
                                            java.lang.String investigationName)
                                     throws ICATServiceException

Lookup the Investigation based on the path components of study name and investigation name.

Returns:

Throws:

ICATServiceException

getInvestigationTypeByName

public InvestigationType getInvestigationTypeByName(java.lang.String in)
                                             throws ICATServiceException

Throws:

ICATServiceException

getSampleById

public Sample getSampleById(java.lang.Integer in)
                     throws ICATServiceException

Throws:

ICATServiceException

getSampleByName

public Sample getSampleByName(java.lang.String studyName,
                              java.lang.String investigationName,
                              java.lang.String sampleName)
                       throws ICATServiceException

Throws:

ICATServiceException

getDataSetById

public DataSet getDataSetById(java.lang.Integer in)
                       throws ICATServiceException

Throws:

ICATServiceException

getDataSetByName

public DataSet getDataSetByName(java.lang.String studyName,
                                java.lang.String investigationName,
                                java.lang.String datasetName)
                         throws ICATServiceException

Lookup the dataset based on the path name components made up of study, investigation and dataset names.

Returns:

Throws:

ICATServiceException

getDataSetIdByHandle

public java.lang.Integer getDataSetIdByHandle(java.lang.String in)
                                       throws ICATServiceException

Throws:

ICATServiceException

getDataSetStatusByName

public DataSetStatus getDataSetStatusByName(java.lang.String in)
                                     throws ICATServiceException

Throws:

ICATServiceException

getDataSetTypeByName

public DataSetType getDataSetTypeByName(java.lang.String in)
                                 throws ICATServiceException

Throws:

ICATServiceException

getDataFileById

public DataFile getDataFileById(java.lang.Integer in)
                         throws ICATServiceException

Throws:

ICATServiceException

getDataFileFormatById

public DataFileFormat getDataFileFormatById(java.lang.String name,
                                            java.lang.String version)
                                     throws ICATServiceException

Throws:

ICATServiceException

getDataFileFormatByName

public java.util.List<DataFileFormat> getDataFileFormatByName(java.lang.String in)
                                                       throws ICATServiceException

Throws:

ICATServiceException

getDataFileParameterById

public DataFileParameter getDataFileParameterById(java.lang.String name,
                                                  java.lang.String units,
                                                  java.lang.Integer dataFileID)
                                           throws ICATServiceException

Throws:

ICATServiceException

getInstrumentByName

public Instrument getInstrumentByName(java.lang.String in)
                               throws ICATServiceException

Throws:

ICATServiceException

getFacilityCycleByName

public FacilityCycle getFacilityCycleByName(java.lang.String in)
                                     throws ICATServiceException

Throws:

ICATServiceException

getFacilityUserById

public FacilityUser getFacilityUserById(java.lang.String in)
                                 throws ICATServiceException

Throws:

ICATServiceException

getObjectFactory

public ICATObjectFactory getObjectFactory()

getDataFileByName

public DataFile getDataFileByName(java.lang.String studyName,
                                  java.lang.String investigationName,
                                  java.lang.String datasetName,
                                  java.lang.String datafileName)
                           throws ICATServiceException

Get the data file based on the names of it's path components in the icat structure.

Returns:

Throws:

ICATServiceException

deleteDataSetParameter

public void deleteDataSetParameter(DataSetParameter in)
                            throws ICATServiceException

Throws:

ICATServiceException

deleteParameter

public void deleteParameter(Parameter in)
                     throws ICATServiceException

Throws:

ICATServiceException

deleteSampleParameter

public void deleteSampleParameter(SampleParameter in)
                           throws ICATServiceException

Throws:

ICATServiceException

getAllDataSetParameters

public java.util.List<DataSetParameter> getAllDataSetParameters(java.lang.Integer in)
                                                         throws ICATServiceException

Throws:

ICATServiceException

getAllParameters

public java.util.List<Parameter> getAllParameters()
                                           throws ICATServiceException

Throws:

ICATServiceException

getAllParametersByType

public java.util.List<Parameter> getAllParametersByType(boolean isSampleParameter,
                                                        boolean isDataSetParameter,
                                                        boolean isDataFileParameter)
                                                 throws ICATServiceException

Returns the parameters for which the boolean parameters are true. The parameters are ored together so getAllParametersByType(true, true, true) will return all the parameters

Returns:

Throws:

ICATServiceException

getAllSampleParameters

public java.util.List<SampleParameter> getAllSampleParameters(java.lang.Integer in)
                                                       throws ICATServiceException

Throws:

ICATServiceException

getDataSetParameterById

public DataSetParameter getDataSetParameterById(java.lang.String name,
                                                java.lang.String units,
                                                java.lang.Integer dataSetID)
                                         throws ICATServiceException

Throws:

ICATServiceException

getParameterById

public Parameter getParameterById(java.lang.Integer in)
                           throws ICATServiceException

Throws:

ICATServiceException

getParameterByName

public Parameter getParameterByName(java.lang.String name,
                                    java.lang.String units)
                             throws ICATServiceException

Gets the parameter with this name-unit key

Returns:

Throws:

ICATServiceException

getSampleParameterById

public SampleParameter getSampleParameterById(java.lang.String name,
                                              java.lang.String units,
                                              java.lang.Integer sampleID)
                                       throws ICATServiceException

Throws:

ICATServiceException

updateDataSetParameter

public DataSetParameter updateDataSetParameter(DataSetParameter in)
                                        throws ICATServiceException

Save the dataset parameter object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

updateParameter

public Parameter updateParameter(Parameter in)
                          throws ICATServiceException

Save the parameter, updating or creating if id is null or 0.

Returns:

Throws:

ICATServiceException

updateSampleParameter

public SampleParameter updateSampleParameter(SampleParameter in)
                                      throws ICATServiceException

Save the sample parameter object. First unflatten, then persist, then flatten and return.

Returns:

Throws:

ICATServiceException

getDataFileByLocation

public DataFile getDataFileByLocation(java.lang.String location)
                               throws ICATServiceException

Get the Data file object associated with the given location URI.

Returns:

Throws:

ICATServiceException

getDataSetByLocation

public DataSet getDataSetByLocation(java.lang.String location)
                             throws ICATServiceException

Throws:

ICATServiceException

getInvestigationByLocation

public Investigation getInvestigationByLocation(java.lang.String location)
                                         throws ICATServiceException

Throws:

ICATServiceException

getStudyByLocation

public Study getStudyByLocation(java.lang.String location)
                         throws ICATServiceException

Throws:

ICATServiceException

getResourceUrlPrefixes

public java.util.List<java.lang.String> getResourceUrlPrefixes()
                                                        throws ICATServiceException

Throws:

ICATServiceException

triggerNotifications

public void triggerNotifications()
                          throws ICATServiceException

Throws:

ICATServiceException

searchDataFile

public java.util.List<DataFile> searchDataFile(SearchRequestType search)
                                        throws ICATServiceException

Search datafiles.

Parameters:

search - SearchRequest search request.

Returns:

List<DataFile> list of data files.

Throws:

ICATServiceException

searchDataSet

public java.util.List<DataSet> searchDataSet(SearchRequestType search)
                                      throws ICATServiceException

Search datasets.

Parameters:

search - SearchRequest search request.

Returns:

List<DataSet> list of data sets.

Throws:

ICATServiceException

searchExperiment

public java.util.List<Investigation> searchExperiment(SearchRequestType search)
                                               throws ICATServiceException

Search experiments.

Parameters:

search - SearchRequest search request.

Returns:

List<Investigation> list of investigations.

Throws:

ICATServiceException

searchProject

public java.util.List<Study> searchProject(SearchRequestType search)
                                    throws ICATServiceException

Search project.

Parameters:

search - SearchRequest search request.

Returns:

List<Study> list of studies.

Throws:

ICATServiceException

searchSample

public java.util.List<Sample> searchSample(SearchRequestType search)
                                    throws ICATServiceException

Search samples.

Parameters:

search - SearchRequest search request.

Returns:

List<Sample> list of samples.

Throws:

ICATServiceException