public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int itemId = fp.getInt(ITEM_ID);
ItemDAO idao = new ItemDAO(sm.getDataSource());
ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
if (itemId == 0) {
addPageMessage("Please choose an item first.");
forwardPage(Page.ITEM_DETAIL);
return;
}
ItemBean item = (ItemBean) idao.findByPK(itemId);
ArrayList versions = idao.findAllVersionsByItemId(item.getId());
ArrayList versionItems = new ArrayList();
// finds each item metadata for each version
for (int i = 0; i < versions.size(); i++) {
Integer versionId = (Integer) versions.get(i);
CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId.intValue());
if (versionId != null && versionId.intValue() > 0) {
ItemFormMetadataBean imfBean =
ifmdao.findByItemIdAndCRFVersionId(item.getId(), versionId.intValue());
imfBean.setCrfVersionName(version.getName());
CRFBean crf = (CRFBean) cdao.findByPK(version.getCrfId());
imfBean.setCrfName(crf.getName());
versionItems.add(imfBean);
}
}
request.setAttribute(VERSION_ITEMS, versionItems);
request.setAttribute(ITEM_BEAN, item);
forwardPage(Page.ITEM_DETAIL);
}
/**
* 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;
}
public EntityBean update(EntityBean eb) {
ItemBean ib = (ItemBean) eb;
HashMap variables = new HashMap();
variables.put(new Integer(1), ib.getName());
variables.put(new Integer(2), ib.getDescription());
variables.put(new Integer(3), ib.getUnits());
variables.put(new Integer(4), new Boolean(ib.isPhiStatus()));
variables.put(new Integer(5), new Integer(ib.getItemDataTypeId()));
variables.put(new Integer(6), new Integer(ib.getItemReferenceTypeId()));
variables.put(new Integer(7), new Integer(ib.getStatus().getId()));
variables.put(new Integer(8), new Integer(ib.getUpdaterId()));
variables.put(new Integer(9), new Integer(ib.getId()));
this.execute(digester.getQuery("update"), variables);
return eb;
}
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();
}
/**
* createSPSSFile, added by tbh, 01/2009
*
* @param db
* @param eb
* @param currentstudyid
* @param parentstudy
* @return
*/
public HashMap<String, Integer> createSPSSFile(
DatasetBean db,
ExtractBean eb2,
StudyBean currentStudy,
StudyBean parentStudy,
long sysTimeBegin,
String generalFileDir,
SPSSReportBean answer,
String generalFileDirCopy) {
setUpResourceBundles();
String SPSSFileName = db.getName() + "_data_spss.dat";
String DDLFileName = db.getName() + "_ddl_spss.sps";
String ZIPFileName = db.getName() + "_spss";
SPSSVariableNameValidationBean svnvbean = new SPSSVariableNameValidationBean();
answer.setDatFileName(SPSSFileName);
// DatasetDAO dsdao = new DatasetDAO(ds);
// create the extract bean here, tbh
// ExtractBean eb = this.generateExtractBean(db, currentStudy,
// parentStudy);
// eb = dsdao.getDatasetData(eb, currentStudy.getId(),
// parentStudy.getId());
// eb.getMetadata();
// eb.computeReport(answer);
answer.setItems(eb2.getItemNames()); // set up items here to get
// itemMetadata
// set up response sets for each item here
ItemDAO itemdao = new ItemDAO(ds);
ItemFormMetadataDAO imfdao = new ItemFormMetadataDAO(ds);
ArrayList items = answer.getItems();
for (int i = 0; i < items.size(); i++) {
DisplayItemHeaderBean dih = (DisplayItemHeaderBean) items.get(i);
ItemBean item = dih.getItem();
ArrayList metas = imfdao.findAllByItemId(item.getId());
// for (int h = 0; h < metas.size(); h++) {
// ItemFormMetadataBean ifmb = (ItemFormMetadataBean)
// metas.get(h);
// logger.info("group name found:
// "+ifmb.getGroupLabel());
// }
// logger.info("crf versionname" +
// meta.getCrfVersionName());
item.setItemMetas(metas);
}
HashMap eventDescs = new HashMap<String, String>();
eventDescs = eb2.getEventDescriptions();
eventDescs.put("SubjID", resword.getString("study_subject_ID"));
eventDescs.put("ProtocolID", resword.getString("protocol_ID_site_ID"));
eventDescs.put("DOB", resword.getString("date_of_birth"));
eventDescs.put("YOB", resword.getString("year_of_birth"));
eventDescs.put("Gender", resword.getString("gender"));
answer.setDescriptions(eventDescs);
ArrayList generatedReports = new ArrayList<String>();
try {
// YW <<
generatedReports.add(answer.getMetadataFile(svnvbean, eb2).toString());
generatedReports.add(answer.getDataFile().toString());
// YW >>
} catch (IndexOutOfBoundsException i) {
generatedReports.add(answer.getMetadataFile(svnvbean, eb2).toString());
logger.debug("throw the error here");
}
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
ArrayList titles = new ArrayList();
// YW <<
titles.add(DDLFileName);
titles.add(SPSSFileName);
// YW >>
// create new createFile method that accepts array lists to
// put into zip files
int fId =
this.createFile(
ZIPFileName,
titles,
generalFileDir,
generatedReports,
db,
sysTimeEnd,
ExportFormatBean.TXTFILE,
true);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFile(
ZIPFileName,
titles,
generalFileDirCopy,
generatedReports,
db,
sysTimeEnd,
ExportFormatBean.TXTFILE,
false);
}
// return DDLFileName;
HashMap answerMap = new HashMap<String, Integer>();
answerMap.put(DDLFileName, new Integer(fId));
return answerMap;
}
/**
* 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;
}