eu.transformproject.provenance.ws

Interface ProvenanceWS_QueryTool_Interface

All Superinterfaces:

CommomInstantiationInterface

All Known Implementing Classes:

ProvenanceWS_QueryTool

public interface ProvenanceWS_QueryTool_Interface
extends CommomInstantiationInterface

The Interface ProvenanceWSQueryTool_Interface.

Method Summary

Methods

Modifier and Type	Method and Description
void	agregateLocalQueryECResults(java.lang.String groupQueryURI, 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.
java.lang.String	localqueryEC(java.lang.String groupQueryURI, java.lang.String localDBURL, java.lang.String query, int rowNumberResults, java.util.List firstRowResult, java.util.Date start) localqueryEC.
java.lang.String	recoverDataExtractionQuery(java.lang.String uriDataExtractionProcess, java.lang.Object linkToExtractedData, java.util.Date start) recoverDataExtractionQuery.
java.lang.String	recoverFlaggedPatientSet(java.lang.String uriFlaggedPatientSetProcess, java.lang.Object flaggedPatientSetId, java.util.Date start) recoverFlaggedPatientSet.
void	recoverPatientCountQuery(java.lang.String uriPatientCountProcess, long patientCount, java.util.Date start) recoverPatientCountQuery.
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.

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

closeSession, createSession, endsPackageData, getSyncDateTime, login, logout, receiveData, sendData, startPackageData, unpackageData

Method Detail

createStudy

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

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

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

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

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

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

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

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

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

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

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

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

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

Edits a clinical study.

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

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

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

Parameters:

uriProtocol - the uri protocol

updatedprotocol - the updatedprotocol

start - the start time of the create protocol process.

Throws:

java.lang.Exception - the exception

editProtocol

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

Edits the protocol.

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

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

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

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

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

Edits a EC.

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

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

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.

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

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

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.

Throws:

java.lang.Exception

localqueryEC

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

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

Parameters:

groupQueryURI - 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

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

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.

Parameters:

groupQueryURI - 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

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

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

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

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

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

Parameters:

uriPatientCountProcess - 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

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

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

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

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

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

Parameters:

uriFlaggedPatientSetProcess - 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Parameters:

uriDataExtractionProcess - 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