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

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

All Implemented Interfaces:

ICAT, ICATHelpers, ICATLocationListener, ICATTraversal, SearchService, au.edu.jcu.hpc.srb.mcatext.notify.PathNotificationListener, java.util.EventListener, org.springframework.context.ApplicationListener

public class ICATHibernateImpl
extends AbstractICATClient
implements org.springframework.context.ApplicationListener, au.edu.jcu.hpc.srb.mcatext.notify.PathNotificationListener, ICATLocationListener

The implemention of the ICAT storage interface using JPA. Capable of receiving MCATExt notifications.

Author:

nigel

Constructor Summary

ICATHibernateImpl(javax.sql.DataSource dataSource, java.util.Map properties)

ICATHibernateImpl(org.hibernate.ejb.Ejb3Configuration ejb3Config)

Method Summary

void	collectionChanged(java.lang.String oldParentGroupName, java.lang.String oldDataGroupName, java.lang.String newParentGroupName, java.lang.String newDataGroupName)
void	collectionCreated(java.lang.String parentGroupName, java.lang.String dataGroupName)
void	collectionDeleted(java.lang.String parentGroupName, java.lang.String dataGroupName)
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)
protected DataFile	flattenDataFile(DataFile df)
protected DataFileParameter	flattenDataFileParameter(DataFileParameter dfp)
protected DataSet	flattenDataSet(DataSet ds, int levelsToPreserve)
protected DataSetParameter	flattenDataSetParameter(DataSetParameter dsp)
protected Investigation	flattenInvestigation(Investigation i, int levelsToPreserve) Convert study link to study ID, and cascade flattening dataset and samples, else clear.
protected Sample	flattenSample(Sample s)
protected SampleParameter	flattenSampleParameter(SampleParameter dfp)
protected Study	flattenStudy(Study s, int levelsToPreserve) Convert the references out of the study into ID references.
java.util.List<DataFileFormat>	getAllDataFileFormats()
java.util.List<java.lang.String>	getAllDataFileLocations() Get all the locations referenced in the iCAT.
java.util.List<DataFileParameter>	getAllDataFileParameters(java.lang.Integer dataFileID)
java.util.List<DataFile>	getAllDataFilesByDataSetId(java.lang.Integer dataSetID)
java.util.List<java.lang.String>	getAllDataSetLocations()
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()
java.util.List<ClientLocationPair>	getClients()
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)
javax.persistence.EntityManagerFactory	getEntityManagerFactory()
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)
ICATSecurityManager	getSecurityManager() Security manager getter.
Study	getStudyById(java.lang.Integer in)
Study	getStudyByLocation(java.lang.String location)
Study	getStudyByName(java.lang.String in)
StudyStatus	getStudyStatusByName(java.lang.String in)
void	locationAdded(java.lang.String location) Method to be called when a location is added to the ICAT.
void	locationChanged(java.lang.String oldLocation, java.lang.String newLocation) Method to be called when a location is changed in the the ICAT.
void	locationRemoved(java.lang.String location) Method to be called when a location is removed from the ICAT.
void	objectChanged(java.lang.String oldParentName, java.lang.String oldName, java.lang.String newParentName, java.lang.String newName)
void	objectCreated(java.lang.String parentName, java.lang.String name)
void	objectDeleted(java.lang.String parentName, java.lang.String name)
void	onApplicationEvent(org.springframework.context.ApplicationEvent event) When the context finishes loading we need to register our notification requirements.
java.util.List<DataFile>	searchDataFile(SearchRequestType search) SEARCH SERVICES
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.
void	setClients(java.util.List<ClientLocationPair> clients)
void	setSecurityManager(ICATSecurityManager securityManager) Used for setting the security manager used by this ICAT.
void	start()
void	stop()
java.lang.String	testCall(java.lang.String str1, java.lang.String str2)
void	triggerNotifications()
protected DataFile	unflattenDataFile(DataFile df, DataSet parentDS, javax.persistence.EntityManager em)
protected DataFileParameter	unflattenDataFileParameter(DataFileParameter dfp, DataFile parentDataFile, javax.persistence.EntityManager em)
protected DataSet	unflattenDataSet(DataSet ds, Investigation inv, javax.persistence.EntityManager em)
protected DataSetParameter	unflattenDataSetParameter(DataSetParameter dsp, DataSet parentDataSet, javax.persistence.EntityManager em)
protected Investigation	unflattenInvestigation(Investigation i, Study parentStudy, javax.persistence.EntityManager em) Convert parent ID link back into a reference, and unflattern any datasets or samples.
protected Sample	unflattenSample(Sample s, Investigation parentInv, javax.persistence.EntityManager em)
protected SampleParameter	unflattenSampleParameter(SampleParameter sp, Sample parent, javax.persistence.EntityManager em)
protected Study	unflattenStudy(Study s, javax.persistence.EntityManager em) Convert the references out of the Study from IDs to references.
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

Constructor Detail

ICATHibernateImpl

public ICATHibernateImpl(javax.sql.DataSource dataSource,
                         java.util.Map properties)

ICATHibernateImpl

public ICATHibernateImpl(org.hibernate.ejb.Ejb3Configuration ejb3Config)

Method Detail

getEntityManagerFactory

public javax.persistence.EntityManagerFactory getEntityManagerFactory()

flattenStudy

protected Study flattenStudy(Study s,
                             int levelsToPreserve)

Convert the references out of the study into ID references. Investigation -> InvestigationID

Parameters:

s -

levelsToPreserve - TODO

Returns:

dereferenced Study object

unflattenStudy

protected Study unflattenStudy(Study s,
                               javax.persistence.EntityManager em)
                        throws java.net.MalformedURLException

Convert the references out of the Study from IDs to references. InvestigationID -> Investigation

Parameters:

s -

em -

Returns:

Throws:

java.net.MalformedURLException

flattenInvestigation

protected Investigation flattenInvestigation(Investigation i,
                                             int levelsToPreserve)

Convert study link to study ID, and cascade flattening dataset and samples, else clear.

Parameters:

i -

levelsToPreserve -

Returns:

unflattenInvestigation

protected Investigation unflattenInvestigation(Investigation i,
                                               Study parentStudy,
                                               javax.persistence.EntityManager em)
                                        throws java.net.MalformedURLException

Convert parent ID link back into a reference, and unflattern any datasets or samples.

Parameters:

i -

parentStudy -

em -

Returns:

Throws:

java.net.MalformedURLException

flattenSample

protected Sample flattenSample(Sample s)

unflattenSample

protected Sample unflattenSample(Sample s,
                                 Investigation parentInv,
                                 javax.persistence.EntityManager em)

flattenDataSet

protected DataSet flattenDataSet(DataSet ds,
                                 int levelsToPreserve)

unflattenDataSet

protected DataSet unflattenDataSet(DataSet ds,
                                   Investigation inv,
                                   javax.persistence.EntityManager em)
                            throws java.net.MalformedURLException

Throws:

java.net.MalformedURLException

flattenDataFile

protected DataFile flattenDataFile(DataFile df)

unflattenDataFile

protected DataFile unflattenDataFile(DataFile df,
                                     DataSet parentDS,
                                     javax.persistence.EntityManager em)
                              throws java.net.MalformedURLException

Throws:

java.net.MalformedURLException

flattenDataFileParameter

protected DataFileParameter flattenDataFileParameter(DataFileParameter dfp)

unflattenDataFileParameter

protected DataFileParameter unflattenDataFileParameter(DataFileParameter dfp,
                                                       DataFile parentDataFile,
                                                       javax.persistence.EntityManager em)

flattenDataSetParameter

protected DataSetParameter flattenDataSetParameter(DataSetParameter dsp)

unflattenDataSetParameter

protected DataSetParameter unflattenDataSetParameter(DataSetParameter dsp,
                                                     DataSet parentDataSet,
                                                     javax.persistence.EntityManager em)

flattenSampleParameter

protected SampleParameter flattenSampleParameter(SampleParameter dfp)

unflattenSampleParameter

protected SampleParameter unflattenSampleParameter(SampleParameter sp,
                                                   Sample parent,
                                                   javax.persistence.EntityManager em)

testCall

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

Specified by:

testCall in interface ICAT

updateStudy

public Study updateStudy(Study in)
                  throws ICATServiceException

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

Specified by:

updateStudy in interface ICAT

Returns:

Throws:

ICATServiceException

updateStudyStatus

public StudyStatus updateStudyStatus(StudyStatus in)
                              throws ICATServiceException

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

Specified by:

updateStudyStatus in interface ICAT

Returns:

Throws:

ICATServiceException

updateInvestigation

public Investigation updateInvestigation(Investigation in)
                                  throws ICATServiceException

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

Specified by:

updateInvestigation in interface ICAT

Returns:

Throws:

ICATServiceException

updateInvestigationType

public InvestigationType updateInvestigationType(InvestigationType in)
                                          throws ICATServiceException

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

Specified by:

updateInvestigationType in interface ICAT

Returns:

Throws:

ICATServiceException

updateSample

public Sample updateSample(Sample in)
                    throws ICATServiceException

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

Specified by:

updateSample in interface ICAT

Returns:

Throws:

ICATServiceException

updateDataSet

public DataSet updateDataSet(DataSet in)
                      throws ICATServiceException

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

Specified by:

updateDataSet in interface ICAT

Returns:

Throws:

ICATServiceException

updateDataSetType

public DataSetType updateDataSetType(DataSetType in)
                              throws ICATServiceException

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

Specified by:

updateDataSetType in interface ICAT

Returns:

Throws:

ICATServiceException

updateDataSetStatus

public DataSetStatus updateDataSetStatus(DataSetStatus in)
                                  throws ICATServiceException

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

Specified by:

updateDataSetStatus in interface ICAT

Returns:

Throws:

ICATServiceException

updateDataFile

public DataFile updateDataFile(DataFile in)
                        throws ICATServiceException

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

Specified by:

updateDataFile in interface ICAT

Returns:

Throws:

ICATServiceException

updateDataFileFormat

public DataFileFormat updateDataFileFormat(DataFileFormat in)
                                    throws ICATServiceException

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

Specified by:

updateDataFileFormat in interface ICAT

Returns:

Throws:

ICATServiceException

updateDataFileParameter

public DataFileParameter updateDataFileParameter(DataFileParameter in)
                                          throws ICATServiceException

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

Specified by:

updateDataFileParameter in interface ICAT

Returns:

Throws:

ICATServiceException

updateInstrument

public Instrument updateInstrument(Instrument in)
                            throws ICATServiceException

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

Specified by:

updateInstrument in interface ICAT

Returns:

Throws:

ICATServiceException

updateFacilityCycle

public FacilityCycle updateFacilityCycle(FacilityCycle in)
                                  throws ICATServiceException

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

Specified by:

updateFacilityCycle in interface ICAT

Returns:

Throws:

ICATServiceException

updateFacilityUser

public FacilityUser updateFacilityUser(FacilityUser in)
                                throws ICATServiceException

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

Specified by:

updateFacilityUser in interface ICAT

Returns:

Throws:

ICATServiceException

deleteStudy

public void deleteStudy(Study in)
                 throws ICATServiceException

Specified by:

deleteStudy in interface ICAT

Throws:

ICATServiceException

deleteStudyStatus

public void deleteStudyStatus(StudyStatus in)
                       throws ICATServiceException

Specified by:

deleteStudyStatus in interface ICAT

Throws:

ICATServiceException

deleteInvestigation

public void deleteInvestigation(Investigation in)
                         throws ICATServiceException

Specified by:

deleteInvestigation in interface ICAT

Throws:

ICATServiceException

deleteInvestigationType

public void deleteInvestigationType(InvestigationType in)
                             throws ICATServiceException

Specified by:

deleteInvestigationType in interface ICAT

Throws:

ICATServiceException

deleteSample

public void deleteSample(Sample in)
                  throws ICATServiceException

Specified by:

deleteSample in interface ICAT

Throws:

ICATServiceException

deleteDataSet

public void deleteDataSet(DataSet in)
                   throws ICATServiceException

Specified by:

deleteDataSet in interface ICAT

Throws:

ICATServiceException

deleteDataSetType

public void deleteDataSetType(DataSetType in)
                       throws ICATServiceException

Specified by:

deleteDataSetType in interface ICAT

Throws:

ICATServiceException

deleteDataSetStatus

public void deleteDataSetStatus(DataSetStatus in)
                         throws ICATServiceException

Specified by:

deleteDataSetStatus in interface ICAT

Throws:

ICATServiceException

deleteDataFile

public void deleteDataFile(DataFile in)
                    throws ICATServiceException

Specified by:

deleteDataFile in interface ICAT

Throws:

ICATServiceException

deleteDataFileFormat

public void deleteDataFileFormat(DataFileFormat in)
                          throws ICATServiceException

Specified by:

deleteDataFileFormat in interface ICAT

Throws:

ICATServiceException

deleteDataFileParameter

public void deleteDataFileParameter(DataFileParameter in)
                             throws ICATServiceException

Specified by:

deleteDataFileParameter in interface ICAT

Throws:

ICATServiceException

deleteInstrument

public void deleteInstrument(Instrument in)
                      throws ICATServiceException

Specified by:

deleteInstrument in interface ICAT

Throws:

ICATServiceException

deleteFacilityCycle

public void deleteFacilityCycle(FacilityCycle in)
                         throws ICATServiceException

Specified by:

deleteFacilityCycle in interface ICAT

Throws:

ICATServiceException

deleteFacilityUser

public void deleteFacilityUser(FacilityUser in)
                        throws ICATServiceException

Specified by:

deleteFacilityUser in interface ICAT

Throws:

ICATServiceException

getAllStudies

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

Specified by:

getAllStudies in interface ICAT

Throws:

ICATServiceException

getAllStudyStatus

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

Specified by:

getAllStudyStatus in interface ICAT

Throws:

ICATServiceException

getAllInvestigationsByStudyId

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

Specified by:

getAllInvestigationsByStudyId in interface ICAT

Throws:

ICATServiceException

getAllInvestigationTypes

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

Specified by:

getAllInvestigationTypes in interface ICAT

Throws:

ICATServiceException

getAllSamplesByInvestigationId

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

Specified by:

getAllSamplesByInvestigationId in interface ICAT

Throws:

ICATServiceException

getAllSamplesByInvestigationName

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

Specified by:

getAllSamplesByInvestigationName in interface ICAT

Throws:

ICATServiceException

getAllDataSetsByInvestigationId

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

Specified by:

getAllDataSetsByInvestigationId in interface ICAT

Throws:

ICATServiceException

getAllDataSetTypes

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

Specified by:

getAllDataSetTypes in interface ICAT

Throws:

ICATServiceException

getAllDataSetStatus

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

Specified by:

getAllDataSetStatus in interface ICAT

Throws:

ICATServiceException

getAllDataFilesByDataSetId

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

Specified by:

getAllDataFilesByDataSetId in interface ICAT

Throws:

ICATServiceException

getAllDataFileFormats

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

Specified by:

getAllDataFileFormats in interface ICAT

Throws:

ICATServiceException

getAllDataFileParameters

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

Specified by:

getAllDataFileParameters in interface ICAT

Throws:

ICATServiceException

getAllInstruments

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

Specified by:

getAllInstruments in interface ICAT

Throws:

ICATServiceException

getAllFacilityCycles

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

Specified by:

getAllFacilityCycles in interface ICAT

Throws:

ICATServiceException

getAllFacilityUsers

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

Specified by:

getAllFacilityUsers in interface ICAT

Throws:

ICATServiceException

getStudyById

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

Specified by:

getStudyById in interface ICAT

Throws:

ICATServiceException

getStudyByName

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

Specified by:

getStudyByName in interface ICAT

Throws:

ICATServiceException

getStudyStatusByName

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

Specified by:

getStudyStatusByName in interface ICAT

Throws:

ICATServiceException

getInvestigationById

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

Specified by:

getInvestigationById in interface ICAT

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.

Specified by:

getInvestigationByName in interface ICAT

Returns:

Throws:

ICATServiceException

getInvestigationTypeByName

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

Specified by:

getInvestigationTypeByName in interface ICAT

Throws:

ICATServiceException

getSampleById

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

Specified by:

getSampleById in interface ICAT

Throws:

ICATServiceException

getSampleByName

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

Specified by:

getSampleByName in interface ICAT

Throws:

ICATServiceException

getDataSetById

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

Specified by:

getDataSetById in interface ICAT

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.

Specified by:

getDataSetByName in interface ICAT

Returns:

Throws:

ICATServiceException

getDataSetTypeByName

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

Specified by:

getDataSetTypeByName in interface ICAT

Throws:

ICATServiceException

getDataSetStatusByName

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

Specified by:

getDataSetStatusByName in interface ICAT

Throws:

ICATServiceException

getDataSetIdByHandle

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

Specified by:

getDataSetIdByHandle in interface ICAT

Throws:

ICATServiceException

getDataFileById

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

Specified by:

getDataFileById in interface ICAT

Throws:

ICATServiceException

getDataFileFormatById

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

Specified by:

getDataFileFormatById in interface ICAT

Throws:

ICATServiceException

getDataFileFormatByName

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

Specified by:

getDataFileFormatByName in interface ICAT

Throws:

ICATServiceException

getDataFileParameterById

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

Specified by:

getDataFileParameterById in interface ICAT

Throws:

ICATServiceException

getInstrumentByName

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

Specified by:

getInstrumentByName in interface ICAT

Throws:

ICATServiceException

getFacilityCycleByName

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

Specified by:

getFacilityCycleByName in interface ICAT

Throws:

ICATServiceException

getFacilityUserById

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

Specified by:

getFacilityUserById in interface ICAT

Throws:

ICATServiceException

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.

Specified by:

getDataFileByName in interface ICAT

Returns:

Throws:

ICATServiceException

deleteParameter

public void deleteParameter(Parameter in)
                     throws ICATServiceException

Specified by:

deleteParameter in interface ICAT

Throws:

ICATServiceException

deleteDataSetParameter

public void deleteDataSetParameter(DataSetParameter in)
                            throws ICATServiceException

Specified by:

deleteDataSetParameter in interface ICAT

Throws:

ICATServiceException

deleteSampleParameter

public void deleteSampleParameter(SampleParameter in)
                           throws ICATServiceException

Specified by:

deleteSampleParameter in interface ICAT

Throws:

ICATServiceException

getAllDataSetParameters

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

Specified by:

getAllDataSetParameters in interface ICAT

Throws:

ICATServiceException

getAllSampleParameters

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

Specified by:

getAllSampleParameters in interface ICAT

Throws:

ICATServiceException

getDataSetParameterById

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

Specified by:

getDataSetParameterById in interface ICAT

Throws:

ICATServiceException

getSampleParameterById

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

Specified by:

getSampleParameterById in interface ICAT

Throws:

ICATServiceException

updateDataSetParameter

public DataSetParameter updateDataSetParameter(DataSetParameter in)
                                        throws ICATServiceException

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

Specified by:

updateDataSetParameter in interface ICAT

Returns:

Throws:

ICATServiceException

updateSampleParameter

public SampleParameter updateSampleParameter(SampleParameter in)
                                      throws ICATServiceException

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

Specified by:

updateSampleParameter in interface ICAT

Returns:

Throws:

ICATServiceException

getAllParameters

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

Specified by:

getAllParameters in interface ICAT

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

Specified by:

getAllParametersByType in interface ICAT

Returns:

Throws:

ICATServiceException

getParameterById

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

Specified by:

getParameterById in interface ICAT

Throws:

ICATServiceException

getParameterByName

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

Gets the parameter with this name-unit key

Specified by:

getParameterByName in interface ICAT

Returns:

Throws:

ICATServiceException

updateParameter

public Parameter updateParameter(Parameter in)
                          throws ICATServiceException

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

Specified by:

updateParameter in interface ICAT

Returns:

Throws:

ICATServiceException

getAllDataFileLocations

public java.util.List<java.lang.String> getAllDataFileLocations()

Get all the locations referenced in the iCAT. TODO We need to find a more efficient way to do this.

Returns:

getAllDataSetLocations

public java.util.List<java.lang.String> getAllDataSetLocations()

getDataFileByLocation

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

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

Specified by:

getDataFileByLocation in interface ICAT

Returns:

Throws:

ICATServiceException

getDataSetByLocation

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

Specified by:

getDataSetByLocation in interface ICAT

Throws:

ICATServiceException

getInvestigationByLocation

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

Specified by:

getInvestigationByLocation in interface ICAT

Throws:

ICATServiceException

getStudyByLocation

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

Specified by:

getStudyByLocation in interface ICAT

Throws:

ICATServiceException

onApplicationEvent

public void onApplicationEvent(org.springframework.context.ApplicationEvent event)

When the context finishes loading we need to register our notification requirements.

Specified by:

onApplicationEvent in interface org.springframework.context.ApplicationListener

start

public void start()

stop

public void stop()

locationAdded

public void locationAdded(java.lang.String location)

Description copied from interface: ICATLocationListener

Method to be called when a location is added to the ICAT.

Specified by:

locationAdded in interface ICATLocationListener

Parameters:

location - the location that was added.

locationRemoved

public void locationRemoved(java.lang.String location)

Description copied from interface: ICATLocationListener

Method to be called when a location is removed from the ICAT.

Specified by:

locationRemoved in interface ICATLocationListener

Parameters:

location - the location that was removed.

locationChanged

public void locationChanged(java.lang.String oldLocation,
                            java.lang.String newLocation)

Description copied from interface: ICATLocationListener

Method to be called when a location is changed in the the ICAT.

Specified by:

locationChanged in interface ICATLocationListener

Parameters:

oldLocation - the old location.

newLocation - the new location.

collectionDeleted

public void collectionDeleted(java.lang.String parentGroupName,
                              java.lang.String dataGroupName)

Specified by:

collectionDeleted in interface au.edu.jcu.hpc.srb.mcatext.notify.PathNotificationListener

collectionCreated

public void collectionCreated(java.lang.String parentGroupName,
                              java.lang.String dataGroupName)

Specified by:

collectionCreated in interface au.edu.jcu.hpc.srb.mcatext.notify.PathNotificationListener

collectionChanged

public void collectionChanged(java.lang.String oldParentGroupName,
                              java.lang.String oldDataGroupName,
                              java.lang.String newParentGroupName,
                              java.lang.String newDataGroupName)

Specified by:

collectionChanged in interface au.edu.jcu.hpc.srb.mcatext.notify.PathNotificationListener

objectDeleted

public void objectDeleted(java.lang.String parentName,
                          java.lang.String name)

Specified by:

objectDeleted in interface au.edu.jcu.hpc.srb.mcatext.notify.PathNotificationListener

objectCreated

public void objectCreated(java.lang.String parentName,
                          java.lang.String name)

Specified by:

objectCreated in interface au.edu.jcu.hpc.srb.mcatext.notify.PathNotificationListener

objectChanged

public void objectChanged(java.lang.String oldParentName,
                          java.lang.String oldName,
                          java.lang.String newParentName,
                          java.lang.String newName)

Specified by:

objectChanged in interface au.edu.jcu.hpc.srb.mcatext.notify.PathNotificationListener

getObjectFactory

public ICATObjectFactory getObjectFactory()

Specified by:

getObjectFactory in interface ICAT

setClients

public void setClients(java.util.List<ClientLocationPair> clients)

getClients

public java.util.List<ClientLocationPair> getClients()

getResourceUrlPrefixes

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

Specified by:

getResourceUrlPrefixes in interface ICAT

triggerNotifications

public void triggerNotifications()

Specified by:

triggerNotifications in interface ICAT

setSecurityManager

public void setSecurityManager(ICATSecurityManager securityManager)

Used for setting the security manager used by this ICAT. This overrides the default security manager.

Parameters:

securityManager -

getSecurityManager

public ICATSecurityManager getSecurityManager()

Security manager getter. Returns a null security manager if none specified.

Returns:

searchDataFile

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

SEARCH SERVICES

Specified by:

searchDataFile in interface SearchService

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

Description copied from interface: SearchService

Search datasets.

Specified by:

searchDataSet in interface SearchService

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

Description copied from interface: SearchService

Search experiments.

Specified by:

searchExperiment in interface SearchService

Parameters:

search - SearchRequest search request.

Returns:

List<Investigation> list of investigations.

Throws:

ICATServiceException

searchProject

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

Description copied from interface: SearchService

Search project.

Specified by:

searchProject in interface SearchService

Parameters:

search - SearchRequest search request.

Returns:

List<Study> list of studies.

Throws:

ICATServiceException

searchSample

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

Description copied from interface: SearchService

Search samples.

Specified by:

searchSample in interface SearchService

Parameters:

search - SearchRequest search request.

Returns:

List<Sample> list of samples.

Throws:

ICATServiceException