eu.transformproject.provenance.ws

Class ProvenanceWS_QueryTool

java.lang.Object

eu.transformproject.provenance.representation.commonItInstantiation.CommonInstantiation

eu.transformproject.provenance.ws.ProvenanceWS_QueryTool

All Implemented Interfaces:

CommomInstantiationInterface, ProvenanceWS_QueryTool_Interface

public class ProvenanceWS_QueryTool
extends CommonInstantiation
implements ProvenanceWS_QueryTool_Interface

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	MIDDLEWARE_GRAPH_PROJECT_NAME_IN_QT
static java.lang.String	NO_QDT_QUERY
static java.lang.String	TEMPLATE_ID_PLACEHOLDER
static java.lang.String	TEMPLATE_INST_INDEX_PLACEHOLDER
static java.lang.String	TEMPLATE_INST_URI_PLACEHOLDER
static java.lang.String	TEMPLATE_INSTGROUP_INDEX_PLACEHOLDER
static java.lang.String	TEMPLATE_INSTGROUP_URI_PLACEHOLDER

Fields inherited from class eu.transformproject.provenance.representation.commonItInstantiation.CommonInstantiation

MIDDLEWARE_GRAPH_PROJECT_NAME, server

Constructor Summary

Constructors

Constructor and Description
ProvenanceWS_QueryTool()

Method Summary

Methods

Modifier and Type	Method and Description
void	agregateLocalQueryECResults(java.lang.String queryExecutionURI, int rowNumberResults, java.util.List firstRowResult, java.util.Date start) agregateLocalQueryECResults.
void	basicQueryEC(int rowNumberResults, java.util.List firstRowResult, java.util.Date start) queryEC.
java.lang.String	createDataExtraction(java.lang.Object dataToExtract, java.util.Date start) createDataExtraction.
java.lang.String	createEC(java.lang.Object eligCriteria, java.util.Date start) createEC.
java.lang.String	createNewQueryEC() createNewQueryEC.
java.lang.String	createProtocol(java.lang.Object protocol, java.util.Date start) createProtocol.
java.lang.String	createStudy(java.lang.String projectName, java.lang.Object clStudy, java.util.Date start) createStudy.
java.lang.String	editDataExtraction(java.lang.Object updatedDE, java.util.Date start) editDataExtraction.
java.lang.String	editDataExtractionFromURI(java.lang.String dataExtractionURI, java.lang.Object updatedDE, java.util.Date start) editDataExtractionFromURI.
java.lang.String	editEC(java.lang.Object updatedEC, java.util.Date start) Edits a EC.
java.lang.String	editECFromURI(java.lang.String uriEC, java.lang.Object updatedEC, java.util.Date start) Annotates the eligibility criteria edition process at the end of the process, using as previous version the object at URI.
java.lang.String	editProtocol(java.lang.Object updatedprotocol, java.util.Date start) Edits the protocol.
java.lang.String	editProtocolFromURI(java.lang.String uriProtocol, java.lang.Object updatedprotocol, java.util.Date start) editProtocolFromURI.
java.lang.String	editStudy(java.lang.Object updatedStudy, java.util.Date start) Edits a clinical study.
java.lang.String	editStudyFromURI(java.lang.String uriStudy, java.lang.Object updatedStudy, java.util.Date start) editStudyFromURI.
void	endsPackageData(java.lang.Object signedDetails, java.lang.Object encryptedPackage) Ends of the packaging process.
java.lang.String	localqueryEC(java.lang.String queryExecutionURI, java.lang.String localDBURL, java.lang.String query, int rowNumberResults, java.util.List firstRowResult, java.util.Date start) localqueryEC.
java.lang.String	receiveData(java.lang.String receptorQueueName, java.lang.Object encryptedReceivedData) Reception of an encrypted data.
java.lang.String	recoverDataExtractionQuery(java.lang.String submittedQueryA, java.lang.Object linkToExtractedData, java.util.Date start) recoverDataExtractionQuery.
java.lang.String	recoverFlaggedPatientSet(java.lang.String uriSubmittedQueryA, java.lang.Object flaggedPatientSetId, java.util.Date start) recoverFlaggedPatientSet.
void	recoverPatientCountQuery(java.lang.String uriSubmittedQueryA, long patientCount, java.util.Date start) recoverPatientCountQuery.
void	sendData(java.lang.String receptorQueueName, java.lang.String encryptedDataA) Send an encrypted data.
java.lang.String	startPackageData(java.lang.String uriDataToPackage, java.util.Date start) Starts of the packaging processing.
java.lang.String	submitDataExtractionQuery(java.lang.String dataExtractionUri, java.lang.String uriFlaggedPatientSet, java.lang.String DQT_uriQuery, java.lang.Object CDIMquery, java.util.Date start) submitDataExtractionQuery.
java.lang.String	submitFlaggedPatientSet(java.lang.String uriEC, java.lang.Object query, java.util.Date start) submitFlaggedPatientSet.
java.lang.String	submitPatientCountQuery(java.lang.String uriEC, java.lang.Object CDIMquery, java.util.Date start) submitPatientCountQuery.
java.lang.String	unpackageData(java.lang.String encryptedReceivedDataA, java.lang.String provenanceA, java.lang.Object decryptedDataA, java.util.Date start) Decryptation of an encrypted data.

Methods inherited from class eu.transformproject.provenance.representation.commonItInstantiation.CommonInstantiation

closeSession, createSession, finalize, getSyncDateTime, login, logout

Methods inherited from class java.lang.Object

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

Methods inherited from interface eu.transformproject.provenance.representation.commonItInstantiation.CommomInstantiationInterface

closeSession, createSession, getSyncDateTime, login, logout

Field Detail

TEMPLATE_ID_PLACEHOLDER

public static java.lang.String TEMPLATE_ID_PLACEHOLDER

TEMPLATE_INST_INDEX_PLACEHOLDER

public static java.lang.String TEMPLATE_INST_INDEX_PLACEHOLDER

TEMPLATE_INSTGROUP_INDEX_PLACEHOLDER

public static java.lang.String TEMPLATE_INSTGROUP_INDEX_PLACEHOLDER

TEMPLATE_INST_URI_PLACEHOLDER

public static java.lang.String TEMPLATE_INST_URI_PLACEHOLDER

TEMPLATE_INSTGROUP_URI_PLACEHOLDER

public static java.lang.String TEMPLATE_INSTGROUP_URI_PLACEHOLDER

NO_QDT_QUERY

public static java.lang.String NO_QDT_QUERY

MIDDLEWARE_GRAPH_PROJECT_NAME_IN_QT

public static java.lang.String MIDDLEWARE_GRAPH_PROJECT_NAME_IN_QT

Constructor Detail

ProvenanceWS_QueryTool

public ProvenanceWS_QueryTool()
                       throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

createStudy

public java.lang.String createStudy(java.lang.String projectName,
                           java.lang.Object clStudy,
                           java.util.Date start)
                             throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

createStudy. Annotates the clinical study creation at the end of the process.

Specified by:

createStudy in interface ProvenanceWS_QueryTool_Interface

Parameters:

projectName - the project name. It is assumed that the projectName is unique for all the annotated studies.

clStudy - the clinical study object. The value returned by toString() method of this object will be maintaIn the provenance db.

start - the start time of the clinical study creation process.

Throws:

java.lang.Exception - the exception

createProtocol

public java.lang.String createProtocol(java.lang.Object protocol,
                              java.util.Date start)
                                throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

createProtocol. Annotates the protocol creation at the end of the process.

Specified by:

createProtocol in interface ProvenanceWS_QueryTool_Interface

Parameters:

protocol - protocol associated to a clinical study. It is assumed that an study has been previously created/edited.

start - the start time of the create protocol process.

Throws:

java.lang.Exception - the exception

createEC

public java.lang.String createEC(java.lang.Object eligCriteria,
                        java.util.Date start)
                          throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

createEC. Annotates the eligibility criteria creation at the end of the process.

Specified by:

createEC in interface ProvenanceWS_QueryTool_Interface

Parameters:

eligCriteria - the created eligibility criteria object. The value returned by toString() method of this object will be maintaIn the provenance db.

start - the start time of the create protocol process.

Throws:

java.lang.Exception - the exception

editStudyFromURI

public java.lang.String editStudyFromURI(java.lang.String uriStudy,
                                java.lang.Object updatedStudy,
                                java.util.Date start)
                                  throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

editStudyFromURI. Annotates the clinical study edition process at the end of the process, using as previous version the object at URI.

Specified by:

editStudyFromURI in interface ProvenanceWS_QueryTool_Interface

Parameters:

uriStudy - the uri of a previously annotated clinical study.

updatedStudy - the new version of the clinical study.

start - the start time of the create protocol process.

Throws:

java.lang.Exception - the exception

editStudy

public java.lang.String editStudy(java.lang.Object updatedStudy,
                         java.util.Date start)
                           throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

Edits a clinical study.

Specified by:

editStudy in interface ProvenanceWS_QueryTool_Interface

Parameters:

updatedStudy - the new version of the previously created/edited clinical study.

start - the start time of the create protocol process.

Throws:

java.lang.Exception - the exception

editProtocolFromURI

public java.lang.String editProtocolFromURI(java.lang.String uriProtocol,
                                   java.lang.Object updatedprotocol,
                                   java.util.Date start)
                                     throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

editProtocolFromURI. Annotates the protocol edition process at the end of the process, using as previous version the object at URI.

Specified by:

editProtocolFromURI in interface ProvenanceWS_QueryTool_Interface

Parameters:

uriProtocol - the uri protocol

updatedprotocol - the updatedprotocol

start - the start time of the create protocol process.

Throws:

java.lang.Exception - the exception

editProtocol

public java.lang.String editProtocol(java.lang.Object updatedprotocol,
                            java.util.Date start)
                              throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

Edits the protocol.

Specified by:

editProtocol in interface ProvenanceWS_QueryTool_Interface

Parameters:

updatedprotocol - the new version of the previously created/edited protocol

start - the start time of the create protocol process.

Throws:

java.lang.Exception - the exception

editECFromURI

public java.lang.String editECFromURI(java.lang.String uriEC,
                             java.lang.Object updatedEC,
                             java.util.Date start)
                               throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

Annotates the eligibility criteria edition process at the end of the process, using as previous version the object at URI.

Specified by:

editECFromURI in interface ProvenanceWS_QueryTool_Interface

Parameters:

uriEC - the URI of an eligibility criteria.

updatedEC - the updated eligibility criteria.

start - the start time of the create protocol process.

Throws:

java.lang.Exception - the exception

editEC

public java.lang.String editEC(java.lang.Object updatedEC,
                      java.util.Date start)
                        throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

Edits a EC.

Specified by:

editEC in interface ProvenanceWS_QueryTool_Interface

Parameters:

updatedEC - the new version of the previously created/edited eligibility criteria.

start - the start time of the create protocol process.

Throws:

java.lang.Exception - the exception

basicQueryEC

public void basicQueryEC(int rowNumberResults,
                java.util.List firstRowResult,
                java.util.Date start)
                  throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

queryEC. Annotates a basic (considering only one default DB) eligibility criteria querying process at the end of the process. It is assumed that a eligibility criteria has been created/edited.

Specified by:

basicQueryEC in interface ProvenanceWS_QueryTool_Interface

Parameters:

rowNumberResults - the number of row of the result.

firstRowResult - the first row result.

start - the start time of the query process.

Throws:

java.lang.Exception - the exception

createNewQueryEC

public java.lang.String createNewQueryEC()
                                  throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

createNewQueryEC. Prepare the instantiator to maintain anew block of local queries and its aggregation. It is assumed that a eligibility criteria has been created/edited.

Specified by:

createNewQueryEC in interface ProvenanceWS_QueryTool_Interface

Throws:

java.lang.Exception

localqueryEC

public java.lang.String localqueryEC(java.lang.String queryExecutionURI,
                            java.lang.String localDBURL,
                            java.lang.String query,
                            int rowNumberResults,
                            java.util.List firstRowResult,
                            java.util.Date start)
                              throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

localqueryEC. Annotates the eligibility criteria querying process at the end of the process. It is assumed that a eligibility criteria has been created/edited.

Specified by:

localqueryEC in interface ProvenanceWS_QueryTool_Interface

Parameters:

queryExecutionURI - the URI returned by createNewGroupQueryEC() method.

localDBURL - the URL of the accessed DB.

query - the executed query.

firstRowResult - the first row result.

start - the start time of the local query process.

Returns:

URI of the provenance entity associated to the local query result.

Throws:

java.lang.Exception - the exception

agregateLocalQueryECResults

public void agregateLocalQueryECResults(java.lang.String queryExecutionURI,
                               int rowNumberResults,
                               java.util.List firstRowResult,
                               java.util.Date start)
                                 throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

agregateLocalQueryECResults. Annotates the eligibility criteria aggregation query answering process at the end of the process. It is assumed that a eligibility criteria has been created/edited.

Specified by:

agregateLocalQueryECResults in interface ProvenanceWS_QueryTool_Interface

Parameters:

queryExecutionURI - the URI returned by createNewGroupQueryEC() method.

firstRowResult - the first row result.

start - the start time of the local query process.

Throws:

java.lang.Exception - the exception

submitPatientCountQuery

public java.lang.String submitPatientCountQuery(java.lang.String uriEC,
                                       java.lang.Object CDIMquery,
                                       java.util.Date start)
                                         throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

submitPatientCountQuery. Annotates the patient count query process at the end of the process, given the provenance EC URI.

Specified by:

submitPatientCountQuery in interface ProvenanceWS_QueryTool_Interface

Parameters:

uriEC - the URI of the EC for which the count is processed.

CDIMquery - the CDIM query that express this request.

start - the start time of the process.

Returns:

the URI of the patient count process

Throws:

java.lang.Exception - the exception

recoverPatientCountQuery

public void recoverPatientCountQuery(java.lang.String uriSubmittedQueryA,
                            long patientCount,
                            java.util.Date start)
                              throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

recoverPatientCountQuery. Annotates the recovery patient count process at the end of the process, given the URI returned by submitPatientCountQuery() method.

Specified by:

recoverPatientCountQuery in interface ProvenanceWS_QueryTool_Interface

Parameters:

uriSubmittedQueryA - the URI of the patient count process, as returned by submitPatientCountQuery() method.

patientCount - the total number of patients for the selected EC.

start - the start time of the process.

Throws:

java.lang.Exception - the exception

submitFlaggedPatientSet

public java.lang.String submitFlaggedPatientSet(java.lang.String uriEC,
                                       java.lang.Object query,
                                       java.util.Date start)
                                         throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

submitFlaggedPatientSet. Annotates the patient flagging process at the end of the process, given the provenance EC URI.

Specified by:

submitFlaggedPatientSet in interface ProvenanceWS_QueryTool_Interface

Parameters:

uriEC - the URI of the EC for which the count is processed.

query - the query that express this data request.

start - the start time of the process.

Returns:

the URI of the flagging process

Throws:

java.lang.Exception - the exception

recoverFlaggedPatientSet

public java.lang.String recoverFlaggedPatientSet(java.lang.String uriSubmittedQueryA,
                                        java.lang.Object flaggedPatientSetId,
                                        java.util.Date start)
                                          throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

recoverFlaggedPatientSet. Annotates the details flagging recovery process at the end of the process, given the URI returned by submitFlaggedPatientSet() method.

Specified by:

recoverFlaggedPatientSet in interface ProvenanceWS_QueryTool_Interface

Parameters:

uriSubmittedQueryA - the URI of the flagging process, as returned by submitFlaggedPatientSet() method.

flaggedPatientSetId - the identifier of the flagged Patient set ID. The value returned by toString() method of this object will be maintaIn the provenance db.

start - the start time of the process.

Returns:

the URI of the provenance flagged Patient Set entity.

Throws:

java.lang.Exception - the exception

createDataExtraction

public java.lang.String createDataExtraction(java.lang.Object dataToExtract,
                                    java.util.Date start)
                                      throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

createDataExtraction. Annotates the data extraction creation at the end of the process.

Specified by:

createDataExtraction in interface ProvenanceWS_QueryTool_Interface

Parameters:

dataToExtract - the description of the data to extract. The value returned by toString() method of this object will be maintaIn the provenance db.

start - the start time of the process.

Returns:

the URI of the created Data Extraction provenance entity.

Throws:

java.lang.Exception - the exception

editDataExtraction

public java.lang.String editDataExtraction(java.lang.Object updatedDE,
                                  java.util.Date start)
                                    throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

editDataExtraction. Edits the data extraction process at the end of the process. It assumes a data extraction object has been previously created.

Specified by:

editDataExtraction in interface ProvenanceWS_QueryTool_Interface

Parameters:

updatedDE - the new version of the previously created/edited data extraction object.

start - the start time of the process.

Returns:

dataExtractionURI the URI of a data extraction provenance entity.

Throws:

java.lang.Exception - the exception

editDataExtractionFromURI

public java.lang.String editDataExtractionFromURI(java.lang.String dataExtractionURI,
                                         java.lang.Object updatedDE,
                                         java.util.Date start)
                                           throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

editDataExtractionFromURI. Annotates the data extraction edition process at the end of the process, using as previous version the object at an specific URI.

Specified by:

editDataExtractionFromURI in interface ProvenanceWS_QueryTool_Interface

Parameters:

dataExtractionURI - the URI of a data extraction provenance entity.

updatedDE - the updated data extraction object.

start - the start time of the process.

Throws:

java.lang.Exception - the exception

submitDataExtractionQuery

public java.lang.String submitDataExtractionQuery(java.lang.String dataExtractionUri,
                                         java.lang.String uriFlaggedPatientSet,
                                         java.lang.String DQT_uriQuery,
                                         java.lang.Object CDIMquery,
                                         java.util.Date start)
                                           throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

submitDataExtractionQuery. Annotates the data extraction query submission at the end of the process, using the provenance data extraction entity at an specific URI.

Specified by:

submitDataExtractionQuery in interface ProvenanceWS_QueryTool_Interface

Parameters:

dataExtractionUri - the URI of a data extraction provenance entity.

uriFlaggedPatientSet - the URI of the provenance flagged Patient Set entity,as returned by recoverFlaggedPatientSet() method.

DQT_uriQuery - the URI of the data quality query provenance entity, as the first element in the list returned by createAndAnswerQuery method in Data Quality Web service.

CDIMquery - the CDIM query that express this request.

start - the start time of the process.

Returns:

the URI of the data extraction query process provenance entity.

Throws:

java.lang.Exception - the exception

recoverDataExtractionQuery

public java.lang.String recoverDataExtractionQuery(java.lang.String submittedQueryA,
                                          java.lang.Object linkToExtractedData,
                                          java.util.Date start)
                                            throws java.lang.Exception

Description copied from interface: ProvenanceWS_QueryTool_Interface

recoverDataExtractionQuery. Annotates the data extraction query result recovery at the end of the process, using as previous version the object at an specific URI.

Specified by:

recoverDataExtractionQuery in interface ProvenanceWS_QueryTool_Interface

Parameters:

submittedQueryA - the URI of a data extraction process provenance entity.

linkToExtractedData - the link to the extracted data. The value returned by toString() method of this object will be maintaIn the provenance db.

start - the start time of the process.

Returns:

the URI of the link for the extracted data provenance entity.

Throws:

java.lang.Exception - the exception

startPackageData

public java.lang.String startPackageData(java.lang.String uriDataToPackage,
                                java.util.Date start)
                                  throws java.lang.Exception

Description copied from interface: CommomInstantiationInterface

Starts of the packaging processing. Annotates the start of the packaging, and returns an artifact identifier that needs to be added in the package to encrypt and/or transmit.

Specified by:

startPackageData in interface CommomInstantiationInterface

Overrides:

startPackageData in class CommonInstantiation

Parameters:

uriDataToPackage - the uri of the artifact associated to the object to be transmitted. This value needs to be obtained through any of the provenance server method.

start - the time in which the packaging process started.

Returns:

encryptedDataA artifact identifier to which the encrypted data will be associated.

Throws:

java.lang.Exception

endsPackageData

public void endsPackageData(java.lang.Object signedDetails,
                   java.lang.Object encryptedPackage)
                     throws java.lang.Exception

Description copied from interface: CommomInstantiationInterface

Ends of the packaging process. Annotates the packaging of a data at the time the packaging has finished.

Specified by:

endsPackageData in interface CommomInstantiationInterface

Overrides:

endsPackageData in class CommonInstantiation

Parameters:

signedDetails - sign object created during encryptation.

encryptedPackage - the encrypted object.

Throws:

java.lang.Exception

sendData

public void sendData(java.lang.String receptorQueueName,
            java.lang.String encryptedDataA)
              throws java.lang.Exception

Description copied from interface: CommomInstantiationInterface

Send an encrypted data. Annotates the sending encrypted process data at the time it was sent.

Specified by:

sendData in interface CommomInstantiationInterface

Overrides:

sendData in class CommonInstantiation

Parameters:

receptorQueueName - an string that identifies the queue that controls the sent data messages (e.g. "QW2MW", "MW2DC", etc.).

encryptedDataA - identifier of the encryptedData artifact, as returned by the packageData method.

Throws:

java.lang.Exception

receiveData

public java.lang.String receiveData(java.lang.String receptorQueueName,
                           java.lang.Object encryptedReceivedData)
                             throws java.lang.Exception

Description copied from interface: CommomInstantiationInterface

Reception of an encrypted data. Annotates an encrypted data reception process at the time it was received.

Specified by:

receiveData in interface CommomInstantiationInterface

Overrides:

receiveData in class CommonInstantiation

Parameters:

receptorQueueName - an string that identifies the queue that controls the reception of data messages (e.g. "QW2MW", "MW2DC", etc.).

encryptedReceivedData - an object describing the data recovered from the queue.

Returns:

encryptedReceivedDataA identifier of the generated encrypted received data artifact.

Throws:

java.lang.Exception

unpackageData

public java.lang.String unpackageData(java.lang.String encryptedReceivedDataA,
                             java.lang.String provenanceA,
                             java.lang.Object decryptedDataA,
                             java.util.Date start)
                               throws java.lang.Exception

Description copied from interface: CommomInstantiationInterface

Decryptation of an encrypted data. Annotates a decryptation data process at the time it finished.

Specified by:

unpackageData in interface CommomInstantiationInterface

Overrides:

unpackageData in class CommonInstantiation

Parameters:

encryptedReceivedDataA - identifier of the generated encrypted received data artifact, as returned by receiveData or packageData methods

provenanceA - identifier of the provenance artifact from which the encrypted received data comes from. This data needs to be extracted from the transmitted package, and should contain the artifact identifier of the transmitted data.

decryptedDataA - an object describing the data decrypted data.

start - the time when the unpackage process starts.

Returns:

decryptedDataA identifier of the generated decrypted data artifact.

Throws:

java.lang.Exception