Java tutorial
/* * Copyright (c) 2006-2010 Massachusetts General Hospital * All rights reserved. This program and the accompanying materials * are made available under the terms of the i2b2 Software License v2.1 * which accompanies this distribution. * * Contributors: * * Wensong Pan * */ /** * Class: TimelineFactory * * A utility class for generating timeline ".lld" files based on the PDO; some methods here were * ported from DBLib class. * */ package edu.harvard.i2b2.explorer.dataModel; import java.io.File; import java.io.IOException; import java.io.RandomAccessFile; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Calendar; import java.util.Date; import java.util.List; import java.util.TimeZone; import javax.xml.bind.JAXBElement; import javax.xml.datatype.DatatypeConstants; import javax.xml.datatype.XMLGregorianCalendar; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.jdom.Element; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.BodyType; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ResponseMessageType; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.StatusType; import edu.harvard.i2b2.crcxmljaxb.datavo.pdo.query.PageType; import edu.harvard.i2b2.crcxmljaxb.datavo.pdo.query.PatientDataResponseType; import edu.harvard.i2b2.common.datavo.pdo.ObservationSet; import edu.harvard.i2b2.common.datavo.pdo.PatientSet; import edu.harvard.i2b2.common.datavo.pdo.PatientType; import edu.harvard.i2b2.common.datavo.pdo.ObservationType; import edu.harvard.i2b2.common.util.jaxb.JAXBUnWrapHelper; import edu.harvard.i2b2.common.util.jaxb.JAXBUtil; import edu.harvard.i2b2.explorer.datavo.ExplorerJAXBUtil; import edu.harvard.i2b2.explorer.ui.MainComposite; import edu.harvard.i2b2.smlib.Lib; public class TimelineFactory { public String newline = System.getProperty("line.separator"); private static final Log log = LogFactory.getLog(TimelineFactory.class); /** * */ public TimelineFactory() { } @SuppressWarnings("unchecked") public String generateTimelineData(String result, ArrayList<TimelineRow> rows, boolean writeFile, boolean displayAll, boolean displayDemographics, final MainComposite explorer) { try { PDOResponseMessageModel pdoresponsefactory = new PDOResponseMessageModel(); StatusType statusType = pdoresponsefactory.getStatusFromResponseXML(result); if (!statusType.getType().equalsIgnoreCase("DONE")) { return "error"; } JAXBUtil jaxbUtil = ExplorerJAXBUtil.getJAXBUtil(); JAXBElement jaxbElement = jaxbUtil.unMashallFromString(result); ResponseMessageType messageType = (ResponseMessageType) jaxbElement.getValue(); BodyType bodyType = messageType.getMessageBody(); PatientDataResponseType responseType = (PatientDataResponseType) new JAXBUnWrapHelper() .getObjectByClass(bodyType.getAny(), PatientDataResponseType.class); PageType pageType = responseType.getPage(); if (pageType != null) { final int returnLastIndex = pageType.getPagingByPatients().getPatientsReturned().getLastIndex() .intValue(); final int returnFirstIndex = pageType.getPagingByPatients().getPatientsReturned().getFirstIndex() .intValue(); final int requestLastIndex = pageType.getPagingByPatients().getPatientsRequested().getLastIndex() .intValue(); if (returnLastIndex < requestLastIndex) { // System.out.println("Can't return all the requested "+ // requestIndex+" patients, only "+returnIndex+" patients returned"); explorer.getDisplay().syncExec(new Runnable() { public void run() { // MessageBox mBox = new MessageBox(explorer // .getShell(), SWT.ICON_INFORMATION // | SWT.OK ); // mBox.setText("Please Note ..."); // mBox.setMessage("Only "+(returnLastIndex-returnFirstIndex+1)+" patients returned"); // mBox.open(); if (explorer.runMode() >= 0) { explorer.setIncrementNumber(returnLastIndex - returnFirstIndex + 1); } else if (explorer.runMode() == -1) { explorer.setDecreaseNumber(returnLastIndex - returnFirstIndex + 1); } } }); explorer.returnedNumber(returnLastIndex - returnFirstIndex + 1); } else { explorer.returnedNumber(-1); } } else { explorer.getDisplay().syncExec(new Runnable() { public void run() { // MessageBox mBox = new MessageBox(explorer // .getShell(), SWT.ICON_INFORMATION // | SWT.OK ); // mBox.setText("Please Note ..."); // mBox.setMessage("Only "+(returnLastIndex-returnFirstIndex+1)+" patients returned"); // mBox.open(); if (explorer.runMode() >= 0) { explorer.setIncrementNumber(-1); } else if (explorer.runMode() == -1) { explorer.setDecreaseNumber(-1); } } }); } StringBuilder resultFile = new StringBuilder(); resultFile.append(GetTimelineHeader()); PatientSet patientDimensionSet = pdoresponsefactory.getPatientSetFromResponseXML(result); if (patientDimensionSet != null) { log.debug("Total patient: " + patientDimensionSet.getPatient().size()); // for(int i=0; // i<patientDimensionSet.getPatientDimension().size();i++) { // PatientDimensionType patientType = // patientDimensionSet.getPatientDimension().get(i); // System.out.println("PatientNum: " + // patientType.getPatientNum()); // } } else { return "error"; } // / testing the visit set // PatientDataType.VisitDimensionSet visitSet = // pdoresponsefactory.getVisitSetFromResponseXML(result); // System.out.println("Total visits: "+visitSet.getVisitDimension(). // size()); List<ObservationSet> factSets = pdoresponsefactory.getFactSetsFromResponseXML(result); log.debug("\nGenerate lld:"); String curPNum = "-1"; for (int i = 0; i < patientDimensionSet.getPatient().size(); i++) { PatientType patientType = patientDimensionSet.getPatient().get(i); String pnum = patientType.getPatientId().getValue(); // Integer pnum = new Integer(snum); // log.debug("PatientNum: " + snum); //if(curPNum.equals("-1")) { curPNum = new String(pnum); //} if (displayDemographics) { resultFile.append(getTimelinePatientString(pnum.toString(), patientType)); } else { resultFile.append(getTimelinePatientString(pnum.toString())); } String path = null; TimelineRow currentRow = null; ObservationSet observationFactSet = null; for (int j = 0; j < rows.size(); j++) { TimelineRow row = rows.get(j); int total = 0; StringBuilder resultString = new StringBuilder(); XMLGregorianCalendar curStartDate = null; //int currentInstanceNum = 0; //String currentConcept = ""; ArrayList<ObservationType> facts = new ArrayList<ObservationType>(); ObservationType curFact = null; boolean recorded = false; String sStart_date = null; String sEnd_date = null; // loop thru all the pdo sets for this row here for (int s = 0; s < row.pdoItems.size(); s++) { PDOItem pset = row.pdoItems.get(s); observationFactSet = null; for (int m = 0; m < factSets.size(); m++) { ObservationSet tmpFactSet = factSets.get(m); if (tmpFactSet.getPanelName().equalsIgnoreCase(pset.panelName())) { observationFactSet = tmpFactSet; path = observationFactSet.getPanelName(); currentRow = row; break; } } if (observationFactSet == null) { continue; } for (int k = 0; k < observationFactSet.getObservation().size(); k++) { ObservationType obsFactType = observationFactSet.getObservation().get(k); //if(curFact == null) { //curFact = obsFactType; //} //facts.add(obsFactType); if (pnum.equals(obsFactType.getPatientId().getValue())) { /* * if ((curStartDate != null) && * (obsFactType.getStartDate().compare( * curStartDate) == DatatypeConstants.EQUAL)) { * continue; } */ if (curFact == null) { curFact = obsFactType; } if (curStartDate == null) { curStartDate = obsFactType.getStartDate(); } sStart_date = obsFactType.getStartDate().getMonth() + "-" + obsFactType.getStartDate().getDay() + "-" + obsFactType.getStartDate().getYear(); if (obsFactType.getEndDate() == null) { sEnd_date = sStart_date; } else { sEnd_date = obsFactType.getEndDate().getMonth() + "-" + obsFactType.getEndDate().getDay() + "-" + obsFactType.getEndDate().getYear(); } double nval = -1; if (obsFactType.getNvalNum().getValue() != null) { nval = obsFactType.getNvalNum().getValue().doubleValue(); } PDOValueModel valdp = null; boolean same = sameInstance(curFact, obsFactType); if (false) {//pset.hasValueDisplayProperty) { for (int n = 0; n < pset.valDisplayProperties.size(); n++) { PDOValueModel tmpvaldp = pset.valDisplayProperties.get(n); // if (tmpvaldp.inRange(nval)) { valdp = tmpvaldp; // break; // } } String sValue = getSValue(obsFactType.getConceptCd().getName(), obsFactType, true); if ((curStartDate != null) && (obsFactType.getStartDate() .compare(curStartDate) == DatatypeConstants.EQUAL)) { resultString.append(getTimelineDateStringHeight(sStart_date, sEnd_date, "slateblue", valdp.height, sValue)); } else { resultString.append(getTimelineDateStringHeight(sStart_date, sEnd_date, valdp.color, valdp.height, sValue)); } } else { ////////////////////// String sValue = ""; if (same && k != observationFactSet.getObservation().size() - 1) { //if(recorded) { facts.add(obsFactType); //recorded = false; continue; //} /*sValue = getSValueSame(obsFactType.getConceptCd().getName(), obsFactType, false); if ((curStartDate != null) && (obsFactType.getStartDate() .compare(curStartDate) == DatatypeConstants.EQUAL)) { resultString .append(getTimelineDateStringHeightSame( sStart_date, sEnd_date, "slateblue", pset.height, sValue)); } else { resultString .append(getTimelineDateStringHeightSame( sStart_date, sEnd_date, pset.color, pset.height, sValue)); }*/ } //else { if (facts.size() == 0) { facts.add(obsFactType); } sValue = getSValue(curFact.getConceptCd().getName(), facts, false); //} sStart_date = curFact.getStartDate().getMonth() + "-" + curFact.getStartDate().getDay() + "-" + curFact.getStartDate().getYear(); if (curFact.getEndDate() == null) { sEnd_date = sStart_date; } else { sEnd_date = curFact.getEndDate().getMonth() + "-" + curFact.getEndDate().getDay() + "-" + curFact.getEndDate().getYear(); } //if ((curStartDate != null) // && (obsFactType.getStartDate() // .compare(curStartDate) == DatatypeConstants.EQUAL)) { //resultString //.append(getTimelineDateStringHeight( //sStart_date, sEnd_date, //"slateblue", //pset.height, sValue)); //} else { resultString.append(getTimelineDateStringHeight(sStart_date, sEnd_date, pset.color, pset.height, sValue)); //} } total++; recorded = false; facts.clear(); facts.add(obsFactType); curStartDate = obsFactType.getStartDate(); curFact = obsFactType; ///// if (!same && k == observationFactSet.getObservation().size() - 1) { String sValue = ""; sValue = getSValue(obsFactType.getConceptCd().getName(), facts, false); //} sStart_date = obsFactType.getStartDate().getMonth() + "-" + obsFactType.getStartDate().getDay() + "-" + obsFactType.getStartDate().getYear(); if (obsFactType.getEndDate() == null) { sEnd_date = sStart_date; } else { sEnd_date = obsFactType.getEndDate().getMonth() + "-" + obsFactType.getEndDate().getDay() + "-" + obsFactType.getEndDate().getYear(); } //if ((curStartDate != null) // && (obsFactType.getStartDate() // .compare(curStartDate) == DatatypeConstants.EQUAL)) { //resultString //.append(getTimelineDateStringHeight( //sStart_date, sEnd_date, //"slateblue", //pset.height, sValue)); //} else { resultString.append(getTimelineDateStringHeight(sStart_date, sEnd_date, pset.color, pset.height, sValue)); //} total++; } //// } else { if (recorded || facts.size() == 0) { curPNum = new String(pnum); continue; } sStart_date = curStartDate.getMonth() + "-" + curStartDate.getDay() + "-" + curStartDate.getYear(); //if (obsFactType.getEndDate() == null) { //sEnd_date = sStart_date; //} else { sEnd_date = curStartDate.getMonth() + "-" + curStartDate.getDay() + "-" + curStartDate.getYear() + " 12:00"; //} //curFact = null; String sValue = getSValue(curFact.getConceptCd().getName(), facts, false); //if ((curStartDate != null) //&& (obsFactType.getStartDate() //.compare(curStartDate) == DatatypeConstants.EQUAL)) { //resultString //.append(getTimelineDateStringHeight( //sStart_date, sEnd_date, //"slateblue", //pset.height, sValue)); //} else { resultString.append(getTimelineDateStringHeight(sStart_date, sEnd_date, pset.color, pset.height, sValue)); //} total++; recorded = true; facts.clear(); curStartDate = null;//obsFactType.getStartDate(); curFact = null;//obsFactType; curPNum = new String(pnum); } } } if (total > 0) { // log.debug("-- "+path+" has "+total+" events"); resultFile.append(getTimelineConceptString(row.displayName, total)); // log.debug(resultString.toString()); resultFile.append(resultString); total = 0; recorded = true; } else { // display all if (displayAll) { // log.debug("-- "+path+" has "+total+" events"); resultFile.append(getTimelineConceptString(row.displayName, 1)); // log.debug(getTimelineEmptyDateString()); resultFile.append(getTimelineEmptyDateString()); } } if (recorded || facts.size() == 0) { curPNum = new String(pnum); continue; } sStart_date = curStartDate.getMonth() + "-" + curStartDate.getDay() + "-" + curStartDate.getYear(); //if (obsFactType.getEndDate() == null) { //sEnd_date = sStart_date; //} else { sEnd_date = curStartDate.getMonth() + "-" + curStartDate.getDay() + "-" + curStartDate.getYear(); //} //curFact = null; String sValue = getSValue(curFact.getConceptCd().getName(), facts, false); resultString .append(getTimelineDateStringHeight(sStart_date, sEnd_date, "navyblue", "p10", sValue)); total++; recorded = true; facts.clear(); //curStartDate = obsFactType.getStartDate(); //curFact = obsFactType; curPNum = new String(pnum); if (total > 0) { // log.debug("-- "+path+" has "+total+" events"); resultFile.append(getTimelineConceptString(row.displayName, total)); // log.debug(resultString.toString()); resultFile.append(resultString); } } } resultFile.append(GetTimelineFooter()); if (writeFile) { String i2b2File = System.getProperty("user.dir") + "/temp/" + "i2b2xml.lld"; File oDelete = new File(i2b2File); if (oDelete != null) oDelete.delete(); RandomAccessFile f = new RandomAccessFile(i2b2File, "rw"); append(f, resultFile.toString()); f.close(); } // log.debug("\nThe lld file: \n"+resultFile.toString()); return resultFile.toString(); } catch (org.apache.axis2.AxisFault e) { e.printStackTrace(); log.error(e.getMessage()); return null; } catch (Exception e) { log.error(e.getMessage()); e.printStackTrace(); return "error"; } } public static void append(RandomAccessFile f, String outString) throws IOException { try { f.seek(f.length()); f.writeBytes(outString); } catch (IOException e) { throw new IOException("trouble writing to random access file."); } return; } public String createlld(int minPatientNum, int maxPatientNum, boolean bDisplayAll, boolean writeFile, boolean displayDemographics) { ArrayList conceptOrder = new ArrayList(); int maxLineCount = 0; // zero turns off check for maximum count of lines StringBuilder resultFile = new StringBuilder(); ArrayList<PatientDemographics> demographicsArray = new ArrayList<PatientDemographics>(); try { // get the root Element root = null;// doc.getRootElement(); // get the children from the i2b2 document java.util.List allChildren = root.getChildren(); int iNumberOfChildren = allChildren.size(); // set up the variables for the loop String sPatient_num = null; String sConcept_cd = null; String sOldPatient_num = "start"; String sOldConcept_cd = null; String sStart_date = null; String sOldStart_date = null; String sEnd_date = null; String sInout_cd = null; String sDeath_date = null; String sColor = null; String sHeight = null; String sValue = null; String sTablename = null; int patientNum = 0; Date oDate; resultFile.append(GetTimelineHeader()); boolean bOverMax = false; int conceptCount = 0; int patientCount = minPatientNum; StringBuilder patientRecord = new StringBuilder(); String currentPatientNum = null; int indexPos = 0; for (int p = 0; p < demographicsArray.size(); p++) { PatientDemographics record = demographicsArray.get(p); currentPatientNum = record.patientNumber(); if (displayDemographics) { patientRecord.append(getTimelinePatientString(currentPatientNum, record)); } else { patientRecord.append(getTimelinePatientString(currentPatientNum)); } resultFile.append(patientRecord.toString()); patientRecord = new StringBuilder(); patientCount++; conceptCount = 0; sOldConcept_cd = null; sOldStart_date = null; sOldPatient_num = ""; if ((indexPos == iNumberOfChildren) && bDisplayAll) { conceptCount = 0; while ((conceptOrder != null) && (conceptCount < conceptOrder.size())) { patientRecord.append(getTimelineConceptString((String) conceptOrder.get(conceptCount), 1)); patientRecord.append(getTimelineEmptyDateString()); conceptCount++; } resultFile.append(patientRecord.toString()); patientRecord = new StringBuilder(); } for (int i = indexPos; i < iNumberOfChildren; i++) { if ((maxLineCount > 0) && (i > maxLineCount)) { bOverMax = true; break; } Element oChild = (Element) allChildren.get(i); sPatient_num = "";// oChild.getChild(ss_patient_num).getText( // ); if (!sPatient_num.equals(currentPatientNum) && (sOldPatient_num.equals("start")) /* * && * !sOldPatient_num * .equals( * sPatient_num * ) */) { if (bDisplayAll) { try { patientNum = Integer.parseInt(sPatient_num); conceptCount = 0; while ((conceptOrder != null) && (conceptCount < conceptOrder.size())) { patientRecord.append( getTimelineConceptString((String) conceptOrder.get(conceptCount), 1)); patientRecord.append(getTimelineEmptyDateString()); conceptCount++; } resultFile.append(patientRecord.toString()); patientRecord = new StringBuilder(); // patientCount++; } catch (java.lang.OutOfMemoryError e) { log.error("In resultset builder 5: " + e.getMessage()); // closeConnection(oConnection); return "memory error"; } catch (Exception e) { log.error(e.getMessage()); // closeConnection(oConnection); return "error"; } conceptCount = 0; sOldConcept_cd = null; sOldStart_date = null; } break; } else if (!sPatient_num.equals(currentPatientNum) && !(sOldPatient_num.equals("start")) /* * &&! * sOldPatient_num * .equals( * sPatient_num * ) */) { if ((bDisplayAll) && (conceptCount < (conceptOrder.size()))) { while ((conceptOrder != null) && (conceptCount < conceptOrder.size())) { patientRecord.append( getTimelineConceptString((String) conceptOrder.get(conceptCount), 1)); patientRecord.append(getTimelineEmptyDateString()); conceptCount++; } } resultFile.append(patientRecord.toString()); patientRecord = new StringBuilder(); patientCount++; conceptCount = 0; sOldConcept_cd = null; sOldStart_date = null; break; } else if (sPatient_num.equals(currentPatientNum)) { indexPos = i + 1; sOldPatient_num = sPatient_num; // if (bUseConcept) { // sConcept_cd = // oChild.getChild(ss_concept_cd).getText(); // } // else { // sConcept_cd = // oChild.getAttributeValue(ss_q_name_char); // } if (!sConcept_cd.equals(sOldConcept_cd)) { // conceptCount++; if (bDisplayAll) { for (int j = conceptCount; j < conceptOrder.size(); j++) { if (sConcept_cd.equals(conceptOrder.get(j))) { break; } else { patientRecord .append(getTimelineConceptString((String) conceptOrder.get(j), 1)); patientRecord.append(getTimelineEmptyDateString()); conceptCount++; } } } // int iNumConceptObservations = // getNumConceptObservationsRollingupStartDate // (allChildren,i); // patientRecord.append(getTimelineConceptString( // sConcept_cd,iNumConceptObservations)); conceptCount++; sOldStart_date = null; } sOldConcept_cd = sConcept_cd; // sStart_date = // oChild.getChild(ss_start_date).getText(); // if (!sStart_date.equals(sOldStart_date)) { // if (!sStart_date.equals(null)) { if ((!sStart_date.equals(null)) && ((sOldStart_date == null) || (!sStart_date.equals(sOldStart_date)))) { // sEnd_date = // oChild.getChild(ss_end_date).getText(); if ((sEnd_date == null) || (sEnd_date.trim().length() == 0)) sEnd_date = sStart_date; // sInout_cd = // oChild.getChild(ss_inout_cd).getText(); sInout_cd = ""; // sColor = oChild.getChild(ss_color_cd).getText(); // sHeight = // oChild.getChild(ss_height_cd).getText(); // sValue = oChild.getChild(ss_value_cd).getText(); // sTablename = // oChild.getChild(ss_table_name).getText(); String prefix = "C"; if (sTablename.equalsIgnoreCase("visit_dimension")) { prefix = "E"; } else if (sTablename.equalsIgnoreCase("provider_dimension")) { prefix = "P"; } // if ((sValue==null)||(sValue.length()==0)) { // sValue = prefix+" = ::"+sConcept_cd+"::"+ // "$$"+oChild.getChild(ss_patient_num).getText()+ // "$$"+oChild.getChild(ss_concept_cd).getText() + // "$$"+ChangeRsDateFull(sStart_date) ;//+"::"; } else { // sValue = prefix+" Value = " + // "::"+sConcept_cd+": "+sValue+"::"+ // "$$"+oChild.getChild(ss_patient_num).getText()+ // "$$"+oChild.getChild(ss_concept_cd).getText() + // "$$"+ChangeRsDateFull(sStart_date) ;//+"::"; } // log.debug(" "+ ChangeRsDate(sStart_date) + " -> " + // ChangeRsDate(sEnd_date)); // System.out.print(getTimelineDateString(ChangeRsDate( // sStart_date),ChangeRsDate(sEnd_date))); // System.out.print(getTimelineDateString(ChangeRsDate( // sStart_date),ChangeRsDate(sEnd_date),sConcept_cd)); if (sInout_cd.equalsIgnoreCase("I")) { if (sColor != null) patientRecord.append(getTimelineDateStringSpecial(ChangeRsDate(sStart_date), ChangeRsDate(sEnd_date), sColor)); else patientRecord.append(getTimelineDateStringSpecial(ChangeRsDate(sStart_date), ChangeRsDate(sEnd_date))); } else if (sInout_cd.equalsIgnoreCase("E")) { if (sColor != null) patientRecord.append(getTimelineDateStringEncounter(ChangeRsDate(sStart_date), ChangeRsDate(sEnd_date), sColor)); else patientRecord.append(getTimelineDateStringEncounter(ChangeRsDate(sStart_date), ChangeRsDate(sEnd_date))); } else if (sInout_cd.equalsIgnoreCase("D")) { if (sStart_date.length() == 0) { if (sColor != null) patientRecord.append(getTimelineDateStringEncounter("today", "today", sColor)); else patientRecord.append(getTimelineDateStringEncounter("today", "today")); } else { if (sColor != null) patientRecord.append( getTimelineDateStringDeath(ChangeRsDate(sStart_date), "today", sColor)); else patientRecord.append( getTimelineDateStringDeath(ChangeRsDate(sStart_date), "today", sColor)); } } else { if (sConcept_cd.equals("Death")) { if (sStart_date.length() == 0) { sStart_date = "today"; sColor = "lightbrown"; } sEnd_date = "today"; } if (sColor != null) { if (sConcept_cd.equalsIgnoreCase("EGFR")) patientRecord.append(getTimelineDateString(ChangeRsDate(sStart_date), ChangeRsDate(sEnd_date), sColor, "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=1956")); else patientRecord.append(getTimelineDateStringHeight(ChangeRsDate(sStart_date), ChangeRsDate(sEnd_date), sColor, sHeight, sValue)); } else patientRecord.append(getTimelineDateStringHeight(ChangeRsDate(sStart_date), ChangeRsDate(sEnd_date), sHeight)); } } sOldStart_date = sStart_date; if (!bOverMax) { if (bDisplayAll && (indexPos == iNumberOfChildren)) { while ((conceptOrder != null) && (conceptCount < conceptOrder.size())) { patientRecord.append( getTimelineConceptString((String) conceptOrder.get(conceptCount), 1)); patientRecord.append(getTimelineEmptyDateString()); conceptCount++; } } resultFile.append(patientRecord.toString()); patientRecord = new StringBuilder(); patientCount++; } } } if ((!bOverMax) && bDisplayAll) { while ((conceptOrder != null) && (conceptCount < conceptOrder.size())) { patientRecord.append(getTimelineConceptString((String) conceptOrder.get(conceptCount), 1)); patientRecord.append(getTimelineEmptyDateString()); conceptCount++; } resultFile.append(patientRecord.toString()); } resultFile.append(GetTimelineFooter()); log.debug(" Total Count " + iNumberOfChildren); if (writeFile) { String i2b2File = System.getProperty("user.dir") + '/' + "i2b2xml.lld"; File oDelete = new File(i2b2File); if (oDelete != null) oDelete.delete(); RandomAccessFile f = new RandomAccessFile(i2b2File, "rw"); Lib.append(f, resultFile.toString()); f.close(); } if (bOverMax) { log.debug("reached maximum at " + new Date()); return "overmaximum"; } } catch (java.lang.OutOfMemoryError e) { log.error("In resultset builder 6: " + e.getMessage()); // closeConnection(oConnection); return "memory error"; } catch (Exception e) { log.error(e.getMessage()); // closeConnection(oConnection); return "error"; } log.debug("done at " + new Date()); return resultFile.toString(); } public static String ChangeRsDateFull(String sInputDate) { try { /* * sInputDate = Lib.StrFindAndReplace("Sunday, ","",sInputDate); * sInputDate = Lib.StrFindAndReplace("Monday, ","",sInputDate); * sInputDate = Lib.StrFindAndReplace("Tuesday, ","",sInputDate); * sInputDate = Lib.StrFindAndReplace("Wednesday, ","",sInputDate); * sInputDate = Lib.StrFindAndReplace("Thursday, ","",sInputDate); * sInputDate = Lib.StrFindAndReplace("Friday, ","",sInputDate); * sInputDate = Lib.StrFindAndReplace("Saturday, ","",sInputDate); * sInputDate = Lib.StrFindAndReplace(" EDT","",sInputDate); Date * oDate = java.text.DateFormat.getDateInstance().parse(sInputDate); */ SimpleDateFormat iFormat = new SimpleDateFormat("d-MMM-yyyy hh:mm:ss a"); Date oDate = iFormat.parse(sInputDate); // sInputDate = // DateFormat.getDateInstance(DateFormat.MEDIUM).format(oDate); SimpleDateFormat oFormat = new SimpleDateFormat("yyyy-M-d hh:mm:ss a"); sInputDate = oFormat.format(oDate); return sInputDate; } catch (Exception e) { return ""; } } /** * returns %facet,PERSON_#1...............,white,yes %c,comment %agg, * normal,1, no %-,2-15-1999,today,white,p1,.,chiempty.html,"" */ public String getTimelinePatientString(String sPatient_num) { String sFinished = newline + "%facet,Person_#" + sPatient_num + "................,white,yes" + newline + " %c,comment" + newline + " %agg, normal,1, no" + newline + " %-,2-15-1999 12:00,today,white,p1,.,chiempty.html,\"\"" + newline; return sFinished; } public String getTimelinePatientString(String sPatient_num, PatientDemographics record, String startDate) { String sFinished; sFinished = newline + "%facet,"; if (!System.getProperty("applicationName").equals("BIRN")) { sFinished += "Person_#"; } sFinished += sPatient_num + ",white,yes" + newline + " %c,comment" + newline + " %agg, normal,1, no" + newline + " %-," + ChangeRsDate(startDate) + ",today,white,p1,.,chiempty.html,\"\"" + newline; return sFinished; } /** * returns %facet,PERSON_#1 gender: age: race: vital-status: ,white,yes * %c,comment %agg, normal,1, no * %-,2-15-1999,today,white,p1,.,chiempty.html,"" */ public String getTimelinePatientString(String sPatient_num, PatientType record) { String sFinished = newline + "%facet,Person_#" + sPatient_num + ",white,yes" + newline + " %c,comment" + newline + " %agg, normal,1, no" + newline + " %-,2-15-1999 12:00,today,white,p1,.,chiempty.html,\"\"" + newline; PatientDemographics patientDemographics = new PatientDemographics(); patientDemographics.setParamData(record.getParam()); String age = patientDemographics.age() + "yrold"; String gender = ""; String race = ""; if (patientDemographics.vitalStatus().equalsIgnoreCase("Y")) { age = "Dead"; } if (patientDemographics.gender().toUpperCase().startsWith("M")) { gender = "Male"; } else if (patientDemographics.gender().toUpperCase().startsWith("F")) { gender = "Female"; } if (patientDemographics.race().equalsIgnoreCase("")) { race = "Unknown"; } else { if (patientDemographics.race().toUpperCase().startsWith("W")) { race = "White"; } else if (patientDemographics.race().toUpperCase().startsWith("B")) { race = "Black"; } else if (patientDemographics.race().toUpperCase().startsWith("A")) { race = "Asian"; } else if (patientDemographics.race().toUpperCase().startsWith("H")) { race = "Hispanic"; } else if (patientDemographics.race().toUpperCase().startsWith("O")) { if (patientDemographics.race().toUpperCase().indexOf("OR") >= 0) { race = "Oriental"; } else { race = "Other"; } } else { race = "Unknown"; } } sFinished = newline + "%facet,Person_#" + sPatient_num + "__" + gender + "__" + age + "__" + race + ",white,yes" + newline + " %c,comment" + newline + " %agg, normal,1, no" + newline + " %-,2-15-1999 12:00,today,white,p1,.,chiempty.html,\"\"" + newline; return sFinished; } /** * returns %facet,PERSON_#1 gender: age: race: vital-status: ,white,yes * %c,comment %agg, normal,1, no * %-,2-15-1999,today,white,p1,.,chiempty.html,"" */ public String getTimelinePatientString(String sPatient_num, PatientDemographics record) { String sFinished; if (record.age().equals("")) { sFinished = newline + "%facet,Person_#" + sPatient_num + ",white,yes" + newline + " %c,comment" + newline + " %agg, normal,1, no" + newline + " %-,2-15-1999 12:00,today,white,p1,.,chiempty.html,\"\"" + newline; return sFinished; } String age = record.age() + "yrold"; String gender = null; String race = null; if (record.vitalStatus().equalsIgnoreCase("Y")) { age = "Dead"; } if (record.gender().toUpperCase().startsWith("M")) { gender = "Male"; } else if (record.gender().toUpperCase().startsWith("F")) { gender = "Female"; } if (record.race().toUpperCase().startsWith("W")) { race = "White"; } else if (record.race().toUpperCase().startsWith("B")) { race = "Black"; } else if (record.race().toUpperCase().startsWith("A")) { race = "Asian"; } else if (record.race().toUpperCase().startsWith("H")) { race = "Hispanic"; } else if (record.race().toUpperCase().startsWith("O")) { if (record.race().toUpperCase().indexOf("OR") >= 0) { race = "Oriental"; } else { race = "Other"; } } else { race = "Unknown"; } sFinished = newline + "%facet,Person_#" + sPatient_num + "__" + gender + "__" + age + "__" + race + ",white,yes" + newline + " %c,comment" + newline + " %agg, normal,1, no" + newline + " %-,2-15-1999 12:00,today,white,p1,.,chiempty.html,\"\"" + newline; return sFinished; } /** * returns %facet,Diagnosis,lightbrown,yes %c,comment %agg, normal,6, no * %-,6-27-1999,today,slateblue,p5,ICH,blank.htm,"" * %-,6-26-1999,6-30-1999,slateblue,p10, ,blank.htm,"" */ public String getTimelineConceptString(String sConcept_cd, int iNumConceptObservations) { String sNewConcept = sConcept_cd.replaceAll(" ", "_").replaceAll(",", "_"); sNewConcept = sNewConcept.replaceAll("__", "_"); sNewConcept = sNewConcept.replaceAll(">", "_"); sNewConcept = sNewConcept.replaceAll("<", "_"); sNewConcept = sNewConcept.replaceAll("zz", ""); sNewConcept = sNewConcept.trim(); //if (sNewConcept.length() > 15) { //sNewConcept = sNewConcept.substring(0, 15) + "..."; //} return newline + "%facet," + sNewConcept + ",lightbrown," + "yes" + newline + " %c,comment" + newline + " %agg, normal," + Integer.toString(iNumConceptObservations) + ", no" + newline; } public String getTimelineDateString(String sStart_date, String sEnd_date) { String sFinished = " %-," + sStart_date + "," + sEnd_date + ",slateblue,p5, ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineDateStringHeight(String sStart_date, String sEnd_date, String height) { String pixel = "p10"; if (height.equalsIgnoreCase("Very Low")) { pixel = "p4"; } else if (height.equalsIgnoreCase("Very Tall")) { pixel = "p18"; } else if (height.equalsIgnoreCase("Tall")) { pixel = "p12"; } else if (height.equalsIgnoreCase("Low")) { pixel = "p8"; } String sFinished = " %-," + sStart_date + "," + sEnd_date + ",slateblue," + pixel + ", ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineEmptyDateString() { String sFinished = " %-,2-15-1999 12:00,2-15-1999 12:00" + ",lightbrown,p5, ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineDateString(String sStart_date, String sEnd_date, String colorName) { String sFinished = " %-," + sStart_date + "," + sEnd_date + "," + colorName + ",p5, ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineDateStringHeight(String sStart_date, String sEnd_date, String colorName, String height, String sValue) { String pixel = "p10"; if (height.equalsIgnoreCase("Very Low")) { pixel = "p4"; } else if (height.equalsIgnoreCase("Very Tall")) { pixel = "p18"; } else if (height.equalsIgnoreCase("Tall")) { pixel = "p12"; } else if (height.equalsIgnoreCase("Low")) { pixel = "p8"; } /* * if ((sValue==null)||(sValue.trim().length()==0)) sValue = ""; else * sValue = "Value = " + sValue; */ String sFinished = " %-," + sStart_date + "," + sEnd_date + "," + colorName + "," + pixel + ", ,blank.htm,\"" + sValue.replaceAll(",", "-") + "\"" + newline; return sFinished; } public String getTimelineDateStringHeightSame(String sStart_date, String sEnd_date, String colorName, String height, String sValue) { String pixel = "p10"; if (height.equalsIgnoreCase("Very Low")) { pixel = "p4"; } else if (height.equalsIgnoreCase("Very Tall")) { pixel = "p18"; } else if (height.equalsIgnoreCase("Tall")) { pixel = "p12"; } else if (height.equalsIgnoreCase("Low")) { pixel = "p8"; } /* * if ((sValue==null)||(sValue.trim().length()==0)) sValue = ""; else * sValue = "Value = " + sValue; */ String sFinished = " %-," + sStart_date + "," + sEnd_date + "," + colorName + "," + pixel + ", ,blank.htm,\"" + sValue.replaceAll(",", "-") + "\"" + newline; return sFinished; } public String getTimelineDateStringHeight(String sStart_date, String sEnd_date, String colorName, String height) { String pixel = "p10"; if (height.equalsIgnoreCase("Very Low")) { pixel = "p4"; } else if (height.equalsIgnoreCase("Very Tall")) { pixel = "p18"; } else if (height.equalsIgnoreCase("Tall")) { pixel = "p12"; } else if (height.equalsIgnoreCase("Low")) { pixel = "p8"; } String sFinished = " %-," + sStart_date + "," + sEnd_date + "," + colorName + "," + pixel + ", ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineDateString(String sStart_date, String sEnd_date, String colorName, String url) { String sFinished = " %-," + sStart_date + "," + sEnd_date + "," + colorName + ",p5, ," + url + ",\"\"" + newline; return sFinished; } public String getTimelineDateStringSpecial(String sStart_date, String sEnd_date) { String sFinished = " %-," + sStart_date + "," + sEnd_date + ",tomato,p10, ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineDateStringSpecial(String sStart_date, String sEnd_date, String colorName) { String sFinished = " %-," + sStart_date + "," + sEnd_date + "," + colorName + ",p10, ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineDateStringEncounter(String sStart_date, String sEnd_date) { String sFinished = " %-," + sStart_date + "," + sEnd_date + ",yellowgreen,p2, ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineDateStringEncounter(String sStart_date, String sEnd_date, String colorName) { String sFinished = " %-," + sStart_date + "," + sEnd_date + "," + colorName + ",p2, ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineDateStringDeath(String sStart_date, String sEnd_date) { String sFinished = " %-," + sStart_date + "," + sEnd_date + ",black,p5, ,blank.htm,\"\"" + newline; return sFinished; } public String getTimelineDateStringDeath(String sStart_date, String sEnd_date, String colorName) { String sFinished = " %-," + sStart_date + "," + sEnd_date + "," + colorName + ",p5, ,blank.htm,\"\"" + newline; return sFinished; } /* * public String getTimelineDateString(String sStart_date,String * sEnd_date, String concept_cd){ String sFinished = " %-," + sStart_date + * "," + sEnd_date + ",slateblue,p5," + concept_cd + ",blank.htm,\"\"" + * newline; return sFinished; } */ public String GetTimelineHeader() { Calendar cldr = Calendar.getInstance(TimeZone.getDefault()); cldr.setTimeInMillis(System.currentTimeMillis()); String todayStr = (cldr.get(Calendar.MONTH) + 1) + "-" + cldr.get(Calendar.DAY_OF_MONTH) + "-" + cldr.get(Calendar.YEAR); return "%beforeSeptember1997" + newline + "%today," + /* 5-02-2006 */todayStr + " 12:00" + newline + newline + "%c, Available colors:" + newline + "%c, " + newline + "%c, (\"seagreen\", \"2e8b57\");" + newline + "%c, (\"seashell\", \"fff5ee\");" + newline + "%c, (\"sienna\", \"a0522d\");" + newline + "%c, (\"skyblue\", \"87ceeb\");" + newline + "%c, (\"slateblue\", \"6a5acd\");" + newline + "%c, (\"slategray\", \"708090\");" + newline + "%c, (\"slategrey\", \"708090\");" + newline + "%c, (\"snow\", \"fffafa\");" + newline + "%c, (\"springgreen\", \"00ff7f\");" + newline + "%c, (\"steelblue\", \"4682b4\");" + newline + "%c, (\"tan\", \"d2b48c\");" + newline + "%c, (\"thistle\", \"d8bfd8\");" + newline + "%c, (\"tomato\", \"ff6347\");" + newline + "%c, (\"turquoise\", \"40e0d0\");" + newline + "%c, (\"violet\", \"ee82ee\");" + newline + "%c, (\"violetred\", \"d02090\");" + newline + "%c, (\"wheat\", \"f5deb3\");" + newline + "%c, (\"white\", \"ffffff\");" + newline + "%c, (\"whitesmoke\", \"f5f5f5\");" + newline + "%c, (\"yellow\", \"ffff00\");" + newline + "%c, (\"yellowgreen\", \"9acd32\");" + newline + "%c, (\"lightbrown\", \"fff5c8\");" + newline + "%c, (\"darkbrown\", \"ffecaf\");" + newline + newline + "%person,i2b2 Timeline Application,.," + cldr.get(Calendar.YEAR)/* 2007 */ + ",.,images/cath.gif" + newline + newline + "%c,PERSON 1" + newline; } public String GetTimelineFooter() { return newline + "%end" + newline; } public String ChangeRsDate(String sInputDate) { try { SimpleDateFormat iFormat = new SimpleDateFormat("d-MMM-yyyy hh:mm:ss a"); Date oDate = iFormat.parse(sInputDate); SimpleDateFormat oFormat = new SimpleDateFormat("M-d-yyyy HH:mm"); sInputDate = oFormat.format(oDate); return sInputDate; } catch (Exception e) { if (System.getProperty("applicationName").equals("BIRN")) { try { SimpleDateFormat iFormat = new SimpleDateFormat("EEEEEEEE, MMMMMM dd, yyyy hh:mm:ss a z"); Date oDate = iFormat.parse(sInputDate); SimpleDateFormat oFormat = new SimpleDateFormat("M-d-yyyy HH:mm"); sInputDate = oFormat.format(oDate); return sInputDate; } catch (Exception eee) { return sInputDate; } } else { try { SimpleDateFormat iFormat = new SimpleDateFormat("EEEEEEEE, MMMMMM dd, yyyy"); Date oDate = iFormat.parse(sInputDate); SimpleDateFormat oFormat = new SimpleDateFormat("M-d-yyyy 12:00"); sInputDate = oFormat.format(oDate); return sInputDate; } catch (Exception eee) { return sInputDate; } } } } private boolean sameInstance(ObservationType curFact, ObservationType obsFactType) { boolean same = false; //if(obsFactType.getInstanceNum() == null) { //return same; //} if (obsFactType.getStartDate().compare(curFact.getStartDate()) == DatatypeConstants.EQUAL && obsFactType.getConceptCd().getValue().equals(curFact.getConceptCd().getValue()) && ((obsFactType.getInstanceNum() == null) || obsFactType.getInstanceNum().getValue().equals(curFact.getInstanceNum().getValue()))) { same = true; } return same; } private String getSValue(String sConcept_cd, ObservationType obsFactType, boolean hasValue) { String prefix = "C"; String sValue = null; if (hasValue && obsFactType.getNvalNum().getValue() != null) { sValue = obsFactType.getNvalNum().getValue().toString(); } // if(sTablename.equalsIgnoreCase("visit_dimension")) { // prefix = "E"; // } // else if(sTablename.equalsIgnoreCase("provider_dimension")) { // prefix = "P"; // } if (!hasValue) { sValue = prefix + " = ::" + sConcept_cd + "::" + "$$" + obsFactType.getPatientId().getValue() + "$$" + obsFactType.getConceptCd().getValue() + "$$" + obsFactType.getEventId().getValue() + "$$" + obsFactType.getObserverCd().getValue() + "$$" + obsFactType.getModifierCd().getValue() + " " + (obsFactType.getValuetypeCd().equals("T") ? obsFactType.getTvalChar() : (obsFactType.getNvalNum().getValue() + obsFactType.getUnitsCd())) + "$$"; } else { sValue = prefix + " Value = " + "::" + sConcept_cd + ": " + sValue + "::" + "$$" + obsFactType.getPatientId().getValue() + "$$" + obsFactType.getConceptCd().getValue() + "$$" + obsFactType.getEventId().getValue() + "$$" + obsFactType.getModifierCd().getValue() + " " + (obsFactType.getValuetypeCd().equals("T") ? obsFactType.getTvalChar() : (obsFactType.getNvalNum().getValue() + obsFactType.getUnitsCd())) + "$$"; } return sValue; } private String getSValueSame(String sConcept_cd, ObservationType obsFactType, boolean hasValue) { String prefix = "C"; String sValue = null; if (hasValue && obsFactType.getNvalNum().getValue() != null) { sValue = obsFactType.getNvalNum().getValue().toString(); } // if(sTablename.equalsIgnoreCase("visit_dimension")) { // prefix = "E"; // } // else if(sTablename.equalsIgnoreCase("provider_dimension")) { // prefix = "P"; // } if (!hasValue) { sValue = prefix + " = ::" + sConcept_cd + "::" + "$$" + obsFactType.getPatientId().getValue() + "$$" + obsFactType.getConceptCd().getValue() + "$$" + obsFactType.getEventId().getValue() + "$$" + obsFactType.getObserverCd().getValue() + "$$" + obsFactType.getModifierCd().getValue() + " " + (obsFactType.getValuetypeCd().equals("T") ? obsFactType.getTvalChar() : (obsFactType.getNvalNum().getValue() + obsFactType.getUnitsCd())) + "$$"; } else { sValue = prefix + " Value = " + "::" + sConcept_cd + ": " + sValue + "::" + "$$" + obsFactType.getPatientId().getValue() + "$$" + obsFactType.getConceptCd().getValue() + "$$" + obsFactType.getEventId().getValue() + "$$" + obsFactType.getModifierCd().getValue() + " " + (obsFactType.getValuetypeCd().equals("T") ? obsFactType.getTvalChar() : (obsFactType.getNvalNum().getValue() + obsFactType.getUnitsCd())) + "$$"; } return sValue; } private String getSValue(String sConcept_cd, ArrayList<ObservationType> obsFactTypes, boolean hasValue) { String prefix = "C"; String sValue = null; //if (hasValue && obsFactType.getNvalNum().getValue() != null) { //sValue = obsFactType.getNvalNum().getValue().toString(); //} // if(sTablename.equalsIgnoreCase("visit_dimension")) { // prefix = "E"; // } // else if(sTablename.equalsIgnoreCase("provider_dimension")) { // prefix = "P"; // } String mds = new String("$$"); for (int i = 0; i < obsFactTypes.size(); i++) { if (obsFactTypes.get(i).getValuetypeCd() != null) { mds += obsFactTypes.get(i).getModifierCd().getValue() + " " + (obsFactTypes.get(i).getValuetypeCd().equals("T") ? obsFactTypes.get(i).getTvalChar() : (obsFactTypes.get(i).getNvalNum().getValue() + obsFactTypes.get(i).getUnitsCd())) + "@2@"; } else { mds += obsFactTypes.get(i).getModifierCd().getValue() + "@2@"; } } if (!hasValue) { sValue = prefix + " = ::" + sConcept_cd + "::" + "$$" + obsFactTypes.get(0).getPatientId().getValue() + "$$" + obsFactTypes.get(0).getConceptCd().getValue() + "$$" + obsFactTypes.get(0).getEventId().getValue() + "$$" + obsFactTypes.get(0).getObserverCd().getValue() //+ "$$" /*+ obsFactTypes.get(0).getModifierCd().getValue() + " " + (obsFactTypes.get(0).getValuetypeCd().equals("T")?obsFactTypes.get(0).getTvalChar() :(obsFactTypes.get(0).getNvalNum().getValue()+obsFactTypes.get(0).getUnitsCd()))*/ + mds + "$$"; } else { sValue = prefix + " Value = " + "::" + sConcept_cd + ": " + sValue + "::" + "$$" + obsFactTypes.get(0).getPatientId().getValue() + "$$" + obsFactTypes.get(0).getConceptCd().getValue() + "$$" + obsFactTypes.get(0).getEventId().getValue() //+ "$$" /*+ obsFactTypes.get(0).getModifierCd().getValue() + " " + (obsFactTypes.get(0).getValuetypeCd().equals("T")?obsFactTypes.get(0).getTvalChar() :(obsFactTypes.get(0).getNvalNum().getValue()+obsFactTypes.get(0).getUnitsCd()))*/ + mds + "$$"; } return sValue; } }