/*
* OpenClinica is distributed under the
* GNU Lesser General Public License (GNU LGPL).
* For details see: http://www.openclinica.org/license
* copyright 2003-2005 Akaza Research
*/
package org.akaza.openclinica.logic.score;
/**
* The ScoreCalculator acts as the Controller for scoring. Tasks performed as
* following:
*
* 1) Find out all items with "calculation" control type. 2) Parse the actual
* formula using the <code>Parser</code>. 3) According to the parser, picks
* the right function and instantiate this function. 4) Performs the actual
* calculation using the function.
*
*
* @author Hailong Wang, Ph.D
* @version 1.0 08/25/2006
*
* @author ywang <br>
* <p>
* Modified for OpenClinica version 2.2 to enable scoring for group
* items. For this purpose, class structure has been modified. (ywang,
* Jan. 2008)
*
*/
import org.akaza.openclinica.bean.core.ItemDataType;
import org.akaza.openclinica.bean.core.ResponseType;
import org.akaza.openclinica.bean.core.Status;
import org.akaza.openclinica.bean.login.UserAccountBean;
import org.akaza.openclinica.bean.submit.DisplayItemBean;
import org.akaza.openclinica.bean.submit.EventCRFBean;
import org.akaza.openclinica.bean.submit.ItemBean;
import org.akaza.openclinica.bean.submit.ItemDataBean;
import org.akaza.openclinica.bean.submit.ItemFormMetadataBean;
import org.akaza.openclinica.bean.submit.ResponseOptionBean;
import org.akaza.openclinica.core.SessionManager;
import org.akaza.openclinica.dao.submit.ItemDAO;
import org.akaza.openclinica.dao.submit.ItemDataDAO;
import org.akaza.openclinica.dao.submit.ItemFormMetadataDAO;
import org.akaza.openclinica.exception.OpenClinicaException;
import org.akaza.openclinica.exception.ScoreException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.math.BigDecimal;
import java.math.MathContext;
import java.math.RoundingMode;
import java.text.NumberFormat;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.TreeSet;
public class ScoreCalculator {
private final Logger logger = LoggerFactory.getLogger(getClass().getName());
private final SessionManager sm;
private final EventCRFBean ecb;
private final UserAccountBean ub;
private final ArrayList<String> errors = new ArrayList<String>();
private static int DEFAULT_DECIMAL = 4;
public ScoreCalculator(SessionManager sm, EventCRFBean ecb, UserAccountBean ub) {
this.sm = sm;
this.ecb = ecb;
this.ub = ub;
}
/*
* Perform all calculations in a CRFVersion. The parameter 'itemdata' might
* be overwritten.
*
* @param calcItemGroupSizes @param items @param itemdata @param
* itemGroupSizes @param databaseErrors @return ArrayList<String> which
* records left_item_text of items who failed to be updated into database.
*
*
* //this method has not been fully tested yet
*
*
* public ArrayList<String> doCalculations( HashMap<String,ItemBean>
* items, HashMap<String,String> itemdata, HashMap<Integer,TreeSet<Integer>>
* itemOrdinals) { ArrayList<String> updateFailedItems = new ArrayList<String>();
* if(itemdata==null) { //here, actually only record errors but doesn't
* return errors. logger.error("In scoreCalculator doCalculations(), items
* are empty!"); errors.add("Calculation cannot be started because needed
* items are empty!"); return updateFailedItems; } ItemFormMetadataDAO
* ifmdao = new ItemFormMetadataDAO(sm.getDataSource()); ItemDAO idao = new
* ItemDAO(sm.getDataSource()); ItemDataDAO iddao = new
* ItemDataDAO(sm.getDataSource());
*
* NumberFormat nf = NumberFormat.getInstance(); Parser parser = new
* Parser(items,itemdata); try { //for calculation type List<ItemFormMetadataBean>
* derivedItemList = ifmdao.findAllByCRFVersionIdAndResponseTypeId(
* ecb.getCRFVersionId(), ResponseType.CALCULATION.getId());
* if(derivedItemList.size()>0) { Collections.sort(derivedItemList); for
* (ItemFormMetadataBean ifmb: derivedItemList) { ItemBean ib =
* (ItemBean)idao.findByPK(ifmb.getItemId()); ResponseOptionBean rob =
* (ResponseOptionBean)ifmb.getResponseSet().getOptions().get(0); //YW,
* 1-16-2008, << enable: 1. evaluate combination of expression and
* functions 2. scoring for group items. //int groupsize =
* iddao.getMaxOrdinalForGroup(ecb,
* (SectionBean)sdao.findByPK(ifmb.getSectionId()), //
* (ItemGroupBean)igdao.findByName(ifmb.getGroupLabel())); int groupsize =
* 1; if(itemOrdinals.containsKey(ib.getId())) { groupsize =
* (itemOrdinals.get(ib.getId())).size(); } String value = ""; String
* parsedExp = ""; for(int i=0; i<groupsize; ++i) { ItemDataBean idb =
* (ItemDataBean)iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb
* .getItemId(), ecb.getId(), i+1); StringBuffer err = new StringBuffer();
* parsedExp = parser.parse(rob.getValue(), i+1);
* if(parser.getErrors().length()>0) { err.append(parser.getErrors());
* parser.setErrors(new StringBuffer()); } else { value =
* ScoreUtil.eval(parsedExp, err); //YW >> String exp = rob.getValue(); exp =
* exp.replace("##", ","); if(writeToDB(ib,idb,exp,value,err)) {
* itemdata.put(ib.getId()+"_"+(i+1), idb.getValue()); }else { String key =
* (i+1)>1 ? ifmb.getLeftItemText()+"_"+(i+1) : ifmb.getLeftItemText();
* updateFailedItems.add(key); } } if(err.length()>0) { String key = (i+1)>1 ?
* ifmb.getLeftItemText()+"_"+(i+1) : ifmb.getLeftItemText();
* errors.add("Item " + key + " contains calculation errors: " +
* err.toString()); } } } }
*
* //YW, 1-16-2008, for group-calculation type. Current restrictions: //1.
* an item with group-calculation type is not repeatable. //2. only
* calculate sum(), avg(), min(), max(), median(), stdev() //3. formula
* arguments only contain item beans //4. only one item bean per argument
* List<ItemFormMetadataBean> itemList =
* ifmdao.findAllByCRFVersionIdAndResponseTypeId( ecb.getCRFVersionId(),
* ResponseType.GROUP_CALCULATION.getId()); if(itemList.size()>0) {
* Collections.sort(itemList); for (ItemFormMetadataBean ifmb: itemList) {
* ItemBean ib = (ItemBean)idao.findByPK(ifmb.getItemId());
* ResponseOptionBean rob =
* (ResponseOptionBean)ifmb.getResponseSet().getOptions().get(0);
* StringBuffer err = new StringBuffer(); parser.setErrors(err); String
* parsedExp = parser.parse(rob.getValue(),itemOrdinals); String value = "";
* if(parser.getErrors().length()>0) { err.append(parser.getErrors()); }else {
* value = ScoreUtil.eval(parsedExp,err);
*
* ItemDataBean idb =
* (ItemDataBean)iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb
* .getItemId(), ecb.getId(), 1); String exp = rob.getValue(); exp =
* exp.replace("##", ","); if(writeToDB(ib,idb,exp,value,err)) {
* itemdata.put(ib.getId()+"_"+idb.getOrdinal(), idb.getValue()); } else {
* updateFailedItems.add(ifmb.getLeftItemText()); } }
*
* if(err.length()>0) { errors.add("Item " + ifmb.getLeftItemText() + "
* contains calculation errors: " + err.toString()); } } } } catch
* (OpenClinicaException e) { logger.error(e.getMessage()); }
* //ecb.setNeedsRecalc(false); //EventCRFDAO ecdao = new
* EventCRFDAO(sm.getDataSource()); //ecb = ecdao.update(ecb);
*
* return updateFailedItems; }
*/
/**
* Performs calculation. <br>
* Notice: both parameter 'itemdata' and parameter 'errs' might be updated
* in this method.
*
* @param displayItems
* @param items
* @param itemdata
* @param errs
* @return
*
* @author ywang (Jan. 2008)
*/
public String doCalculation(DisplayItemBean displayItem, HashMap<String, ItemBean> items, HashMap<String, String> itemdata,
HashMap<Integer, TreeSet<Integer>> itemOrdinals, StringBuffer errs, int ordinal) {
if (itemdata == null) {
logger.error("In DataEntryServlet doCalculation(), itemdata map is empty!");
errs.append("Calculation cannot be started because needed items are empty" + "; ");
return "";
}
String value = "";
NumberFormat nf = NumberFormat.getInstance();
Parser parser = new Parser(items, itemdata);
ItemBean ib = displayItem.getItem();
ItemFormMetadataBean ifm = displayItem.getMetadata();
ResponseOptionBean rob = (ResponseOptionBean) ifm.getResponseSet().getOptions().get(0);
ArrayList<ScoreToken> parsedExp = new ArrayList<ScoreToken>();
int type = ifm.getResponseSet().getResponseTypeId();
if (type == 8) {
parsedExp = parser.assignVariables(parser.parseScoreTokens(rob.getValue()), ordinal);
} else if (type == 9) {
// YW, 1-16-2008, for group-calculation type. Current restrictions:
// 1. only calculate sum(), avg(), min(), max(), median(), stdev()
// 2. formula arguments only contain item beans
// 3. only one item bean per argument
parsedExp = parser.assignVariables(parser.parseScoreTokens(rob.getValue()), itemOrdinals);
}
if (parser.getErrors().length() > 0) {
errs.append(parser.getErrors());
} else {
try {
value = ScoreUtil.eval(parsedExp);
} catch (ScoreException se) {
logger.error(se.getMessage());
}
ItemDataType idt = ib.getDataType();
if (value == null || value.length() == 0) {
value = "";
String exp = rob.getValue();
exp = exp.replace("##", ",");
errs.append("Result is empty in" + " " + exp + "; ");
// errors.append(resexception.getString("result_is_empty_in") +
// " " + exp + "; ");
} else {
value = this.getMathContextValue(value, ifm, idt, errs);
}
// idb.setStatus(Status.UNAVAILABLE);
itemdata.put(ib.getId() + "_" + ordinal, value);
}
return value;
}
/**
* Re-do calculations if funcs include changed item(s) and funcs are not
* included in the current section. If calculation can not sucessfully redo,
* old value will be erased and "<erased>" will be saved in database. <br>
* The parameter 'itemdata' might be overwritten.
*
* @param itemGroupSizes
* @param items
* @param itemdata
* @param oldItemdata
* @param updatedData
* @param sectionId
* @return ArrayList<String> which records left_item_text of items who
* failed to be updated into database.
*/
public ArrayList<String> redoCalculations(HashMap<String, ItemBean> items, HashMap<String, String> itemdata, TreeSet<String> changedItems,
HashMap<Integer, TreeSet<Integer>> itemOrdinals, int sectionId) {
ArrayList<String> updateFailedItems = new ArrayList<String>();
if (itemdata == null) {
logger.error("In ScoreCalculator redoCalculations(), itemdata is empty!");
errors.add("In ScoreCalculator redoCalculations(), 'itemdata' map is empty!");
return updateFailedItems;
}
if (changedItems == null) {
logger.error("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
errors.add("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
return updateFailedItems;
}
ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
ItemDAO idao = new ItemDAO(sm.getDataSource());
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
NumberFormat nf = NumberFormat.getInstance();
Parser parser = new Parser(items, itemdata);
try {
// for calculation type
List<ItemFormMetadataBean> derivedItemList = ifmdao.findAllByCRFVersionIdAndResponseTypeId(ecb.getCRFVersionId(), ResponseType.CALCULATION.getId());
if (derivedItemList.size() > 0) {
Collections.sort(derivedItemList);
for (ItemFormMetadataBean ifmb : derivedItemList) {
if (ifmb.getSectionId() != sectionId) {
ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
int groupsize = 1;
if (itemOrdinals.containsKey(ib.getId())) {
groupsize = itemOrdinals.get(ib.getId()).size();
}
String value = "";
ArrayList<ScoreToken> parsedExp = new ArrayList<ScoreToken>();
for (int i = 0; i < groupsize; ++i) {
ItemDataBean idb = iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), i + 1);
// is there any changed item
Parser p = new Parser(items, itemdata);
parsedExp = parser.parseScoreTokens(rob.getValue());
if (p.isChanged(changedItems, parsedExp)) {
StringBuffer err = new StringBuffer();
parsedExp = parser.assignVariables(parsedExp, i + 1);
// if parser has error and has been calculated
// before, set "<erased>"
if (parser.getErrors().length() > 0) {
err.append(parser.getErrors());
if (idb.isActive()) {
idb.setValue("<erased>");
idb.setStatus(Status.UNAVAILABLE);
idb = (ItemDataBean) iddao.update(idb);
if (!idb.isActive()) {
String key = i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
updateFailedItems.add(key);
}
}
parser.setErrors(new StringBuffer());
}
// otherwise do calculation
else {
try {
value = ScoreUtil.eval(parsedExp);
} catch (ScoreException se) {
logger.error(se.getMessage());
}
String exp = rob.getValue();
exp = exp.replace("##", ",");
if (writeToDB(ib, ifmb, idb, exp, value, err)) {
changedItems.add(ib.getName());
itemdata.put(ib.getId() + "_" + (i + 1), idb.getValue());
} else {
String key = i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
updateFailedItems.add(key);
}
}
if (err.length() > 0) {
String key = i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
errors.add("Item " + key + " contains calculation errors: " + err.toString());
}
}
}
}
}
}
List<ItemFormMetadataBean> itemList = ifmdao.findAllByCRFVersionIdAndResponseTypeId(ecb.getCRFVersionId(), ResponseType.GROUP_CALCULATION.getId());
if (itemList.size() > 0) {
Collections.sort(itemList);
for (ItemFormMetadataBean ifmb : itemList) {
if (ifmb.getSectionId() != sectionId) {
ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
String value = "";
Parser p = new Parser(items, itemdata);
ArrayList<ScoreToken> parsedExp = parser.parseScoreTokens(rob.getValue());
if (p.isChanged(changedItems, parsedExp)) {
StringBuffer err = new StringBuffer();
parser.setErrors(err);
parsedExp = parser.assignVariables(parsedExp, itemOrdinals);
ItemDataBean idb = iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), 1);
if (parser.getErrors().length() > 0) {
err.append(parser.getErrors());
if (idb.isActive()) {
idb.setValue("<erased>");
idb.setStatus(Status.UNAVAILABLE);
idb = (ItemDataBean) iddao.update(idb);
if (!idb.isActive()) {
updateFailedItems.add(ifmb.getLeftItemText());
}
}
} else {
try {
value = ScoreUtil.eval(parsedExp);
} catch (ScoreException se) {
logger.error(se.getMessage());
}
String exp = rob.getValue();
exp = exp.replace("##", ",");
if (writeToDB(ib, ifmb, idb, exp, value, err)) {
changedItems.add(ib.getName());
itemdata.put(ib.getId() + "_" + idb.getOrdinal(), idb.getValue());
} else {
updateFailedItems.add(ifmb.getLeftItemText());
}
}
if (err.length() > 0) {
errors.add("Item " + ifmb.getLeftItemText() + " contains calculation errors: " + err.toString());
}
}
}
}
}
} catch (OpenClinicaException e) {
logger.error(e.getMessage());
}
return updateFailedItems;
}
protected boolean writeToDB(ItemBean ib, ItemFormMetadataBean ifm, ItemDataBean idb, String exp, String value, StringBuffer err) {
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
NumberFormat nf = NumberFormat.getInstance();
if (idb == null) {
idb = new ItemDataBean();
}
ItemDataType idt = ib.getDataType();
if (value == null || value.length() == 0) {
if (idb.isActive() && !"".equals(idb.getValue())) {
idb.setValue("<erased>");
} else {
idb.setValue("");
}
err.append("Result is empty in" + " " + exp + "; ");
} else {
idb.setValue(this.getMathContextValue(value, ifm, idt, err));
}
idb.setStatus(Status.UNAVAILABLE);
// idb.setNeedsRecalc(false);
if (!idb.isActive()) {
// will this need to change for double data entry?
idb.setCreatedDate(new Date());
idb.setOwner(ub);
idb.setItemId(ib.getId());
idb.setEventCRFId(ecb.getId());
idb = (ItemDataBean) iddao.create(idb);
} else {
idb = (ItemDataBean) iddao.update(idb);
}
return idb.isActive();
}
public int parseWidth(String widthDecimal) {
String w = "";
widthDecimal = widthDecimal.trim();
if (widthDecimal.startsWith("(")) {
} else if (widthDecimal.contains("(")) {
w = widthDecimal.split("\\(")[0];
} else {
w = widthDecimal;
}
if (w.length() > 0) {
return "w".equalsIgnoreCase(w) ? 0 : Integer.parseInt(w);
}
return 0;
}
public int parseDecimal(String widthDecimal) {
String d = "";
widthDecimal = widthDecimal.trim();
if (widthDecimal.startsWith("(")) {
d = widthDecimal.substring(1, widthDecimal.length() - 1);
} else if (widthDecimal.contains("(")) {
d = widthDecimal.split("\\(")[1].trim();
d = d.substring(0, d.length() - 1);
}
if (d.length() > 0) {
return "d".equalsIgnoreCase(d) ? 0 : Integer.parseInt(d);
}
return 0;
}
protected String getMathContextValue(String value, ItemFormMetadataBean ifm, ItemDataType idt, StringBuffer errorMessage) {
ResponseOptionBean rob = (ResponseOptionBean) ifm.getResponseSet().getOptions().get(0);
String widthDecimal = ifm.getWidthDecimal();
int width = parseWidth(widthDecimal);
int decimal = parseDecimal(widthDecimal);
NumberFormat nf = NumberFormat.getInstance(Locale.ENGLISH);
if (idt.equals(ItemDataType.INTEGER)) {
try {
Double d = nf.parse(value).doubleValue();
int p = 0;
if (width > 0) {
p = d >= 0 ? width : width - 1;
} else {
p = BigDecimal.valueOf(d).precision();
}
MathContext mc = new MathContext(p, RoundingMode.valueOf(BigDecimal.ROUND_HALF_UP));
value = (new BigDecimal(d, mc)).setScale(0, BigDecimal.ROUND_HALF_UP).toPlainString();
} catch (ParseException e) {
logger.error("Number was expected in " + rob.getValue() + " : " + value);
String exp = rob.getValue();
exp = exp.replace("##", ",");
errorMessage.append("Number was expected in" + " " + exp + " : " + value + "; ");
// errors.append(resexception.getString("number_expected_in")
// + " " + exp + ": " + value + "; ");
value = "";
}
} else if (idt.equals(ItemDataType.REAL)) {
try {
Double d = nf.parse(value).doubleValue();
// there should be no width specify for calculation item
int p = BigDecimal.valueOf(d).precision();
// set default scale as 4
int scale = decimal > 0 ? decimal : DEFAULT_DECIMAL;
MathContext mc = new MathContext(p, RoundingMode.valueOf(BigDecimal.ROUND_HALF_UP));
value = (new BigDecimal(d, mc)).setScale(scale, BigDecimal.ROUND_HALF_UP).toPlainString();
} catch (Exception ee) {
String exp = rob.getValue();
exp = exp.replace("##", ",");
logger.error("Number was expected in " + exp + " : " + value);
errorMessage.append("Number was expected in" + " " + exp + " : " + value + "; ");
// errors.append(resexception.getString("number_expected_in")
// + " " + exp + ": " + value + "; ");
value = "";
}
}
return value;
}
}