/**
* Gets an ArrayList of whole record annotations, QRS Duration & QRS Axis; which are found in the
* Magellan text output file.
*
* @param userId - Id of the user who owns this data.
* @param docId - Document ID
* @param createdBy - Either original file format identifier, algorithm identifier, or user ID in
* the case of manual annotations.
* @param bioportalOntologyID - Identifier of the Ontology, e.g. "ECGT"
*/
private List<AnnotationDTO> getMagellanRecordAnnotationList(
long userId, long docId, String createdBy, String bioportalOntologyID) {
// List<AnnotationDTO> retList= new ArrayList<AnnotationDTO>();
List<String> bioportalClassIdList = new ArrayList<String>();
bioportalClassIdList.add("ECGOntology:ECG_000000072"); // QRS Duration
bioportalClassIdList.add("ECGOntology:ECG_000000838"); // QRS Axis
List<AnnotationDTO> paramList_Rec = null;
try {
paramList_Rec =
ConnectionFactory.createConnection()
.getLeadAnnotationListConceptIDList(
userId, docId, null, createdBy, bioportalOntologyID, bioportalClassIdList);
} catch (DataStorageException e) {
e.printStackTrace();
}
// retList.add(0, paramList_Rec.get(0)); // qa_I
// *********************************************
return paramList_Rec;
}
/**
* Initialize the analysis thread group
*
* @param selectedNodes Selected documents to be analyzed
* @param userId Logged user ID
* @param selectedAlgorithms Selected algorithms
* @return
*/
public boolean performAnalysis(
List<DocumentDragVO> selectedNodes, long userId, AlgorithmDTO[] selectedAlgorithms) {
try {
Connection dbUtility = ConnectionFactory.createConnection();
Set<AnalysisThread> threadSet = new HashSet<AnalysisThread>();
ThreadGroup analysisGroup = ThreadController.createSubGroup("AnalysisGroup");
String[] args = {
String.valueOf(ResourceUtility.getCurrentGroupId()),
String.valueOf(ResourceUtility.getCurrentUserId()),
String.valueOf(ResourceUtility.getCurrentCompanyId())
};
FileStorer fileStorer =
FileStoreFactory.returnFileStore(ResourceUtility.getFileStorageType(), args);
for (DocumentDragVO node : selectedNodes) {
List<FileInfoDTO> files =
dbUtility.getAllFilesByDocumentRecordId(node.getDocumentRecord().getDocumentRecordId());
FSFile headerFile = fileStorer.getFile(files.get(0).getFileEntryId(), true);
FileType originalFileType = node.getDocumentRecord().getOriginalFormat();
long docId = node.getDocumentRecord().getDocumentRecordId();
String timeseriesId = node.getDocumentRecord().getTimeSeriesId();
String name = node.getDocumentRecord().getRecordName();
String age = node.getDocumentRecord().getAge().toString();
String sex = node.getDocumentRecord().getGender();
String channels = String.valueOf(node.getDocumentRecord().getLeadCount());
String scalingFactor = String.valueOf(node.getDocumentRecord().getAduGain());
String samplesPerChannel = String.valueOf(node.getDocumentRecord().getSamplesPerChannel());
String samplingRate = String.valueOf(node.getDocumentRecord().getSamplingRate());
ThreadGroup fileGroup = new ThreadGroup(analysisGroup, docId + "Group");
List<Long> analysisIds = new ArrayList<Long>();
for (AlgorithmDTO algorithm : selectedAlgorithms) {
Map<String, Object> parameterMap = new HashMap<String, Object>();
parameterMap.put("userID", String.valueOf(userId));
parameterMap.put("groupID", String.valueOf(ResourceUtility.getCurrentGroupId()));
parameterMap.put("folderID", String.valueOf(headerFile.getParentId()));
parameterMap.put("subjectID", node.getDocumentRecord().getSubjectId());
parameterMap.put("durationSec", node.getDocumentRecord().getDurationSec());
parameterMap.put("channels", channels);
parameterMap.put("leadNames", node.getDocumentRecord().getLeadNames());
parameterMap.put("scalingFactor", scalingFactor);
parameterMap.put("samplesPerChannel", samplesPerChannel);
parameterMap.put("samplingRate", samplingRate);
parameterMap.put("timeseriesId", timeseriesId);
LinkedHashMap<String, String> parameterlistMap = new LinkedHashMap<String, String>();
if ((originalFileType.getLabel().equals("Schiller"))
&& (algorithm.getDisplayShortName().contentEquals("QRS-Score"))) {
List<AnnotationDTO> magellanAnnot =
getMagellanLeadAnnotationList(userId, docId, "Schiller Upload", "ECGT");
List<AnnotationDTO> magellanRecAnnot =
getMagellanRecordAnnotationList(userId, docId, "Schiller Upload", "ECGT");
String qrsd = null, qrsax = null;
if (magellanRecAnnot.get(0) != null) {
qrsd = magellanRecAnnot.get(0).getValue();
}
if (magellanRecAnnot.get(1) != null) {
qrsax = magellanRecAnnot.get(1).getValue();
}
parameterlistMap =
buildQRS_ScoreParameterListMap(docId, name, age, sex, qrsd, qrsax, magellanAnnot);
}
parameterMap.put("parameterlist", parameterlistMap);
parameterMap.put("method", algorithm.getServiceMethod());
parameterMap.put("serviceName", algorithm.getServiceName());
parameterMap.put("URL", algorithm.getAnalysisServiceURL());
parameterMap.put("openTsdbHost", ResourceUtility.getOpenTsdbHost());
parameterMap.put("openTsdbStrategy", ResourceUtility.getOpenTsdStrategy());
AnalysisJobDTO analysisJobDTO =
dbUtility.storeAnalysisJob(
node.getFileNode().getDocumentRecordId(),
0,
0,
algorithm.getAnalysisServiceURL(),
algorithm.getServiceName(),
algorithm.getServiceMethod(),
new Date(),
ResourceUtility.getCurrentUserId());
String jobID = "job_" + analysisJobDTO.getAnalysisJobId();
parameterMap.put("jobID", jobID);
AnalysisThread t =
new AnalysisThread(
parameterMap,
node.getDocumentRecord(),
ResourceUtility.getCurrentUserId(),
dbUtility,
fileGroup,
fileStorer,
algorithm.getResultType());
threadSet.add(t);
analysisIds.add(analysisJobDTO.getAnalysisJobId());
}
AnalysisStatusDTO dto =
new AnalysisStatusDTO(
node.getDocumentRecord().getDocumentRecordId(),
node.getDocumentRecord().getRecordName(),
analysisIds.size(),
0,
0);
dto.setAnalysisIds(analysisIds);
this.addToBackgroundQueue(dto);
}
tController = new ThreadController(threadSet);
tController.start();
return true;
} catch (FSException e) {
e.printStackTrace();
} catch (DataStorageException e) {
e.printStackTrace();
}
return false;
}
/**
* Gets an ArrayList of lead annotations, on all the standard 12 leads for Q_Wave_Amplitude,
* Q_Wave_Duration, R_Wave_Amplitude, R_Wave_Duration, S_Wave_Amplitude; which are found in the
* Magellan text output file.
*
* @param userId - Id of the user who owns this data.
* @param docId - Document ID
* @param createdBy - Either original file format identifier, algorithm identifier, or user ID in
* the case of manual annotations.
* @param bioportalOntologyID - Identifier of the Ontology, e.g. "ECGT"
*/
private List<AnnotationDTO> getMagellanLeadAnnotationList(
long userId, long docId, String createdBy, String bioportalOntologyID) {
List<AnnotationDTO> retList = new ArrayList<AnnotationDTO>();
List<String> bioportalClassIdList = new ArrayList<String>();
bioportalClassIdList.add(
"http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_000000652"); // Q_Wave_Amplitude
// ECGOntology:ECG_000000652
bioportalClassIdList.add(
"http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_000000551"); // Q_Wave_Duration
// ECGOntology:ECG_000000551
bioportalClassIdList.add(
"http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_000000750"); // R_Wave_Amplitude
// ECGOntology:ECG_000000750
bioportalClassIdList.add(
"http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_000000597"); // R_Wave_Duration
// ECGOntology:ECG_000000597
bioportalClassIdList.add(
"http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_000000107"); // S_Wave_Amplitude
// ECGOntology:ECG_000000107
// bioportalClassIdList.add("ECGOntology:ECG_000000072"); // QRS_Wave_Duration
try {
Connection conn = ConnectionFactory.createConnection();
List<AnnotationDTO> paramList_I =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 0, createdBy, bioportalOntologyID, bioportalClassIdList);
List<AnnotationDTO> paramList_II =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 1, createdBy, bioportalOntologyID, bioportalClassIdList);
// List<AnnotationDTO> paramList_III = conn.getLeadAnnotationListConceptIDList(userId,
// docId, 2, createdBy, bioportalOntologyID, bioportalClassIdList);
// List<AnnotationDTO> paramList_aVR = conn.getLeadAnnotationListConceptIDList(userId,
// docId, 3, createdBy, bioportalOntologyID, bioportalClassIdList);
List<AnnotationDTO> paramList_aVL =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 4, createdBy, bioportalOntologyID, bioportalClassIdList);
List<AnnotationDTO> paramList_aVF =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 5, createdBy, bioportalOntologyID, bioportalClassIdList);
List<AnnotationDTO> paramList_V1 =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 6, createdBy, bioportalOntologyID, bioportalClassIdList);
List<AnnotationDTO> paramList_V2 =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 7, createdBy, bioportalOntologyID, bioportalClassIdList);
List<AnnotationDTO> paramList_V3 =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 8, createdBy, bioportalOntologyID, bioportalClassIdList);
List<AnnotationDTO> paramList_V4 =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 9, createdBy, bioportalOntologyID, bioportalClassIdList);
List<AnnotationDTO> paramList_V5 =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 10, createdBy, bioportalOntologyID, bioportalClassIdList);
List<AnnotationDTO> paramList_V6 =
conn.getLeadAnnotationListConceptIDList(
userId, docId, 11, createdBy, bioportalOntologyID, bioportalClassIdList);
int i = 0;
retList.add(i++, paramList_I.get(0)); // qa_I
// retList.add(i++, paramList_II.get(0)); // qa_II
// retList.add(2, paramList_III.get(0)); // qa_III
// retList.add(3, paramList_aVR.get(0)); // qa_aVR
retList.add(i++, paramList_aVL.get(0)); // qa_aVL
retList.add(i++, paramList_aVF.get(0)); // qa_aVF
retList.add(i++, paramList_V1.get(0)); // qa_V1
retList.add(i++, paramList_V2.get(0)); // qa_V2
retList.add(i++, paramList_V3.get(0)); // qa_V3
retList.add(i++, paramList_V4.get(0)); // qa_V4
retList.add(i++, paramList_V5.get(0)); // qa_V5
retList.add(i++, paramList_V6.get(0)); // qa_V6
// *********************************************
retList.add(i++, paramList_I.get(1)); // qd_I
retList.add(i++, paramList_II.get(1)); // qd_II
// retList.add(14, paramList_III.get(1)); // qd_III
// retList.add(15, paramList_aVR.get(1)); // qd_aVR
retList.add(i++, paramList_aVL.get(1)); // qd_aVL
retList.add(i++, paramList_aVF.get(1)); // qd_aVF
retList.add(i++, paramList_V1.get(1)); // qd_V1
retList.add(i++, paramList_V2.get(1)); // qd_V2
retList.add(i++, paramList_V3.get(1)); // qd_V3
retList.add(i++, paramList_V4.get(1)); // qd_V4
retList.add(i++, paramList_V5.get(1)); // qd_V5
retList.add(i++, paramList_V6.get(1)); // qd_V6
// *********************************************
retList.add(i++, paramList_I.get(2)); // ra_I
retList.add(i++, paramList_II.get(2)); // ra_II
// retList.add(26, paramList_III.get(2)); // ra_III
// retList.add(27, paramList_aVR.get(2)); // ra_aVR
retList.add(i++, paramList_aVL.get(2)); // ra_aVL
retList.add(i++, paramList_aVF.get(2)); // ra_aVF
retList.add(i++, paramList_V1.get(2)); // ra_V1
retList.add(i++, paramList_V2.get(2)); // ra_V2
retList.add(i++, paramList_V3.get(2)); // ra_V3
retList.add(i++, paramList_V4.get(2)); // ra_V4
retList.add(i++, paramList_V5.get(2)); // ra_V5
retList.add(i++, paramList_V6.get(2)); // ra_V6
// *********************************************
// retList.add(36, paramList_I.get(3)); // rd_I
// retList.add(37, paramList_II.get(3)); // rd_II
// retList.add(38, paramList_III.get(3)); // rd_III
// retList.add(39, paramList_aVR.get(3)); // rd_aVR
// retList.add(40, paramList_aVL.get(3)); // rd_aVL
// retList.add(41, paramList_aVF.get(3)); // rd_aVF
retList.add(i++, paramList_V1.get(3)); // rd_V1
retList.add(i++, paramList_V2.get(3)); // rd_V2
retList.add(i++, paramList_V3.get(3)); // rd_V3
// retList.add(45, paramList_V4.get(3)); // rd_V4
// retList.add(46, paramList_V5.get(3)); // rd_V5
// retList.add(47, paramList_V6.get(3)); // rd_V6
// *********************************************
retList.add(i++, paramList_I.get(4)); // sa_I
retList.add(i++, paramList_II.get(4)); // sa_II
// retList.add(50, paramList_III.get(4)); // sa_III
// retList.add(51, paramList_aVR.get(4)); // sa_aVR
retList.add(i++, paramList_aVL.get(4)); // sa_aVL
retList.add(i++, paramList_aVF.get(4)); // sa_aVF
retList.add(i++, paramList_V1.get(4)); // sa_V1
retList.add(i++, paramList_V2.get(4)); // sa_V2
retList.add(i++, paramList_V3.get(4)); // sa_V3
retList.add(i++, paramList_V4.get(4)); // sa_V4
retList.add(i++, paramList_V5.get(4)); // sa_V5
retList.add(i++, paramList_V6.get(4)); // sa_V6
// *********************************************
// un-needed code which substitutes value from R' and S' when R or S are zero.
// Turned out that this was not the correct thing to do here. (Mike Shipway - July 16, 2014)
// List <String> nameList = new ArrayList<String>();
// nameList.add("Q-_AMPL"); // dummy place keeper, since Schiller doesn't seem to have
// negative Q entries
// nameList.add("Q-_DUR"); // dummy place keeper, since Schiller doesn't seem to have
// negative Q entries
// nameList.add("R-_AMPL"); // Negative R_Wave_Amplitude ECGOntology:ECG_000000750
// nameList.add("R-_DUR"); // Negative R_Wave_Duration ECGOntology:ECG_000000597
// nameList.add("S-_AMPL"); // Negative S_Wave_Amplitude ECGOntology:ECG_000000107
//
// List<AnnotationDTO> negParamList_I =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 0,
// createdBy, nameList);
// List<AnnotationDTO> negParamList_II =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 1,
// createdBy, nameList);
// List<AnnotationDTO> negParamList_aVL =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 4,
// createdBy, nameList);
// List<AnnotationDTO> negParamList_aVF =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 5,
// createdBy, nameList);
// List<AnnotationDTO> negParamList_V1 =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 6,
// createdBy, nameList);
// List<AnnotationDTO> negParamList_V2 =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 7,
// createdBy, nameList);
// List<AnnotationDTO> negParamList_V3 =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 8,
// createdBy, nameList);
// List<AnnotationDTO> negParamList_V4 =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 9,
// createdBy, nameList);
// List<AnnotationDTO> negParamList_V5 =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 10,
// createdBy, nameList);
// List<AnnotationDTO> negParamList_V6 =
// ConnectionFactory.createConnection().getLeadAnnotationbyNameList(userId, docId, 11,
// createdBy, nameList);
//
// List<AnnotationDTO> negList= new ArrayList<AnnotationDTO>();
// int n=0;
// negList.add(n++, negParamList_I.get(0)); // qa_I
// negList.add(n++, negParamList_aVL.get(0)); // qa_aVL
// negList.add(n++, negParamList_aVF.get(0)); // qa_aVF
// negList.add(n++, negParamList_V1.get(0)); // qa_V1
// negList.add(n++, negParamList_V2.get(0)); // qa_V2
// negList.add(n++, negParamList_V3.get(0)); // qa_V3
// negList.add(n++, negParamList_V4.get(0)); // qa_V4
// negList.add(n++, negParamList_V5.get(0)); // qa_V5
// negList.add(n++, negParamList_V6.get(0)); // qa_V6
// //*********************************************
// negList.add(n++, negParamList_I.get(1)); // qd_I
// negList.add(n++, negParamList_II.get(1)); // qd_II
// negList.add(n++, negParamList_aVL.get(1)); // qd_aVL
// negList.add(n++, negParamList_aVF.get(1)); // qd_aVF
// negList.add(n++, negParamList_V1.get(1)); // qd_V1
// negList.add(n++, negParamList_V2.get(1)); // qd_V2
// negList.add(n++, negParamList_V3.get(1)); // qd_V3
// negList.add(n++, negParamList_V4.get(1)); // qd_V4
// negList.add(n++, negParamList_V5.get(1)); // qd_V5
// negList.add(n++, negParamList_V6.get(1)); // qd_V6
// //*********************************************
// negList.add(n++, negParamList_I.get(2)); // ra_I
// negList.add(n++, negParamList_II.get(2)); // ra_II
// negList.add(n++, negParamList_aVL.get(2)); // ra_aVL
// negList.add(n++, negParamList_aVF.get(2)); // ra_aVF
// negList.add(n++, negParamList_V1.get(2)); // ra_V1
// negList.add(n++, negParamList_V2.get(2)); // ra_V2
// negList.add(n++, negParamList_V3.get(2)); // ra_V3
// negList.add(n++, negParamList_V4.get(2)); // ra_V4
// negList.add(n++, negParamList_V5.get(2)); // ra_V5
// negList.add(n++, negParamList_V6.get(2)); // ra_V6
// //*********************************************
// negList.add(n++, negParamList_V1.get(3)); // rd_V1
// negList.add(n++, negParamList_V2.get(3)); // rd_V2
// negList.add(n++, negParamList_V3.get(3)); // rd_V3
// //*********************************************
// negList.add(n++, negParamList_I.get(4)); // sa_I
// negList.add(n++, negParamList_II.get(4)); // sa_II
// negList.add(n++, negParamList_aVL.get(4)); // sa_aVL
// negList.add(n++, negParamList_aVF.get(4)); // sa_aVF
// negList.add(n++, negParamList_V1.get(4)); // sa_V1
// negList.add(n++, negParamList_V2.get(4)); // sa_V2
// negList.add(n++, negParamList_V3.get(4)); // sa_V3
// negList.add(n++, negParamList_V4.get(4)); // sa_V4
// negList.add(n++, negParamList_V5.get(4)); // sa_V5
// negList.add(n++, negParamList_V6.get(4)); // sa_V6
// //*********************************************
//
// for(int c=0;c<retList.size();c++){
// if( (retList.get(c).getValue() == "0") && (negList.get(c) != null) ){
// retList.set(c, negList.get(c) );
// }
// }
} catch (DataStorageException e) {
e.printStackTrace();
}
return retList;
}